Bio Linking Questions

Biology for the IB Diploma – Answers
Linking questions
The linking questions at the end of each chapter encourage you to apply broad, integrated and discipline-
specific concepts from one topic to another, ideally networking your knowledge. This document is designed
to help you build and check your answers. At the start of each answer is a linking table, which suggests from
where across the syllabus you could draw connections for your answer. If you need help with answering a
linking question, look at the table first for ideas and then try writing your answer. After, read the sample
answer and see how concepts and themes have been linked together. Perhaps there were links you did not at
first consider. Then re-read the answer you wrote. How could you improve it?
(HL-only content in the linking question answers is in blue)
Theme A Unity and diversity

A1.1 Water
Page 13
1 How do the various intermolecular forces of attraction affect biological systems?
This answer links material from:
Theme Chapter
A A1.1 Water
A1.2 Nucleic acids
B B1.2 Proteins
B3.2 Transport
B4.1 Adaptation to environment
C C1.1 Enzymes and metabolism
C1.2 Cell respiration
C1.3 Photosynthesis
C3.1 Integration of body systems
D D1.1 DNA replication
D1.2 Protein synthesis

Intermolecular forces refer to forces between molecules. This contrasts with intramolecular forces that exist within
a molecule, such as covalent bonding – where pairs of electrons are shared between atoms within a molecule.
Hydrogen bonds are a type of intermolecular force and play an important role in forming the three-dimensional
shape of folded proteins, the double helix of DNA and the shapes of polysaccharide molecules, such as cellulose.
Hydrogen bonding also occurs between mRNA and tRNA during translation.
Biological systems have a unique ability to connect complex molecular interactions to catalytic functions.
Intermolecular forces control formation of covalent bonds. This occurs in DNA and RNA polymerases, and in the
ribosome. Hydrogen bonding directs catalytic function during translation (protein synthesis).
Intermolecular electron transfer in biochemical reactions is common and occurs between sites on different
proteins. This leads to electron transport chains that function as a series of consecutive electron-transfer reactions
Biology for the IB Diploma 3rd edition © Hodder & Stoughton Limited 2023 1
between metal sites within a protein or group of proteins. Electron transport chains are important in
photosynthesis and respiration.
Denaturation occurs when the ionic interactions, hydrogen bonds and other weak intermolecular forces within the
globular protein, formed between different amino acid residues, break, thus changing the shape of the protein,
including the active site in enzymes. Both temperature and pH changes can lead to denaturation of enzymes.
Exposure to heat causes atoms to vibrate violently and this disrupts weak intermolecular forces within proteins.
Protein molecules change physical and chemical characteristics. Changes to pH, away from the optimum for an
enzyme, can also break hydrogen bonds and lead to denaturation. This effect of pH occurs because the structure of
a protein is maintained by various bonds and weaker intermolecular forces within the three-dimensional structure
of the protein. A change in pH from the optimum value alters the bonding patterns, progressively changing the
three-dimensional shape of the molecule. The active site may be quickly rendered inactive. However, unlike the
effects of temperature changes, the effects of pH on the active site are normally reversible – provided, that is, the
change in surrounding acidity or alkalinity is not too extreme. As the pH reverts to the optimum for the enzyme,
the active site may reform.
Changes to the hydrogen bonding in the cell wall of plants is utilized to move a plant towards a stimulus, such as
light (phototropism). Auxin promotes hydrogen ion secretion into the apoplast pathway, acidifying the cell wall.
Proteins called expansins, activated by H+ ions, alter the pattern of hydrogen bonding between the polysaccharides
in the cell wall, allowing these macromolecules to slip past each other, loosening cross-links between cellulose
molecules and facilitating the stretching of the cell wall and therefore cell elongation. Concentration gradients of
auxin cause the differences in growth rate needed for phototropism.
Cohesion is the force by which individual molecules of the same type attract and associate (stick together). Water
molecules stick together because of hydrogen bonding. These intermolecular forces are weak bonds compared to
covalent bonds, yet they are strong enough to hold water molecules together and to attract water molecules to
charged particles or to a charged surface. These bonds continually break and reform with surrounding water
molecules, although at any one moment a large number are held together by their hydrogen bonds. Cohesive
forces allow water molecules to be drawn up xylem vessels in plants, drawn by evaporative loss of water in the
leaves. Compared with other liquids, water has extremely strong cohesive properties that prevent it ‘breaking’
under tension.
Hydrogen bonding at the surface of water results in surface tension. The surface tension of water is exploited by
insects that ‘surface skate’. The insect’s waxy cuticle prevents the wetting of its body, and the mass of the insect
is not great enough to break the surface tension. This allows small animals to live on the surface of water and
provides a novel habitat, one that is not available to larger animals.
The physical properties of water depend on the hydrogen bonding between water molecules. A relatively large
amount of energy is required to raise the temperature of water, because a lot of energy is needed to break the large
number of hydrogen bonds that restrict the movement of water molecules. This property of water is its specific
heat capacity. Consequently, aquatic environments (rivers, ponds, lakes and seas) are very slow to change
temperature when the surrounding air temperature changes. The relatively stable sea temperatures enable seals to
live and feed throughout the year. Water, unlike many other substances, floats when it freezes because the density
of ice is lower than that of liquid water. This is due to the behaviour of hydrogen bonds and how they make water
molecules interact. Ice forms a platform on which seals can live. Ringed seals have claws to dig through ice to
produce holes so that they can emerge from their aquatic habitat to breathe. This enables them to live under and
on the ice throughout the year.
2 Which biological processes only happen at or near surfaces?

Theme Chapter
A A1.1 Water
A2.3 Viruses (HL only)
B B2.1 Membranes and membrane transport
B2.3 Cell specialization
B3.1 Gas exchange
B3.2 Transport
C C2.2 Neural signalling
C3.2 Defence against disease
D4.2 Stability and change

Adhesion is the attraction of water molecules to a surface. Soil contains many capillary tubes, in which plant
roots are located. When water enters capillary tubes, adhesion between the water molecules and the wall of
the capillary draws water up the small tube: this is called capillary action. Water adheres strongly to most
surfaces and can be drawn up long columns, such as through narrow tubes like the xylem vessels of plant
stems.
At the surface of water, hydrogen bonding between water molecules forms a surface tension. This enables
insects and other animals to move across the surface of water, hunting for prey or reproductive mates.
In plants, water evaporates from the spongy mesophyll in the interior of the leaf and diffuses through stomata
at the surface of the leaf, in a process known as transpiration.
The plasma membrane of animal cells can be regarded as the surface of the cell, separating it from its outside
environment of tissue fluid. Membrane transport, both passive (for example diffusion of gases in solution)
and active (for example endo/exocytosis), happens on and within the plasma membrane which forms the cell
surface.
Cell surface membranes can also be highly specialized, for example epithelial cells in the small intestine, for
the absorption of nutrients through microvilli, or the axon of a neuron, for the active pumping of sodium ions
via sodium–potassium ATPase.
Viruses can fuse either directly to the plasma membrane (receptor-mediated fusion) or after being taken into
an endosome (vesicle) by endocytosis. The route followed depends on the type of virus. Antiviral drugs have
been developed to prevent the entry of certain viruses into cells.
Bacterial cells often develop antibiotic resistance via the presence of efflux pumps (a type of active
transport) that removes antibiotics and enzymes (extrinsic membrane proteins) that modify or degrade them.
A1.2 Nucleic acids

Page 33
1 What makes RNA more likely to have been the first genetic material, rather than DNA?
Theme Chapter
A A2.1 Origins of cells (HL only)
The RNA world hypothesis suggests that around 4 billion years ago, RNA was the first replicating molecule
due to RNA’s unique ability to carry genetic information (in its base sequence) and show catalytic behaviour
as a ribozyme. RNA can be converted to DNA by reverse transcription, which supports the idea that the
RNA world could have been the initial evolutionary pathway to cells. The ribosome is composed of both
RNA and protein; the processes involved in translation are not catalysed by protein, but by rRNA, indicating
that early protocells may have used RNA to catalyse chemical reactions before they used proteins.
2 How can polymerization result in emergent properties?

Theme Chapter
A A1.2 Nucleic acids
A2.1 Origins of cells (HL only)
B B1.1 Carbohydrates and lipids
B1.2 Proteins
C C2.1 Chemical signalling (HL only)
D D1.2 Protein synthesis

Emergent properties are the characteristics gained when an entity at any biological level (from molecular,
cellular, tissue, and so on, to population) plays a role in an organized biological system. For example, when
carbon, hydrogen and oxygen atoms chemically bond in a particular structure, lipids are formed. Lipids are
capable of spontaneously forming cell membranes that separate living cells from the environment.
Membrane formation is an emergent property not found in the molecules that form them.
Polymers are long molecules built from repeating units of monomers. Biological polymers include RNA,
DNA, proteins and polysaccharides, for example cellulose and starch. Depending on the sequence of amino
acids that are polymerized to form a protein, different properties emerge, including enzyme action and
chemical signalling.
RNA is an example showing how a polymer can have very different properties from the monomers that it is
made from (ribonucleotides). The bases in an RNA sequence give rise to the first emergent property of RNA:
three-dimensional folding. Most types of RNA molecules show extensive intramolecular base pairing
between complementary sequences within the RNA strand, causing folding of the molecule and creating
predictable three-dimensional structures that are essential for their function. tRNA, for example, has short
(70–90 nucleotides) stable lengths of RNA with extensive intramolecular base pairing, which contain an
amino acid binding site and an mRNA binding site. The attraction of complementary bases within an mRNA
molecule can also cause it to fold up into a fixed and precise three-dimensional shape, with mRNA folding
likely to affect aspects of translation. mRNA is clearly a simpler molecule than DNA (it is single stranded
rather than double stranded), and hydrogen bonds can occur between nucleotides in the same chain, causing
RNA to fold up in a unique way, determined by its nucleotide sequence. This folding can confer enzymatic
properties on the RNA – a property that would have been needed in the earliest forms of life. This is known
as the RNA world hypothesis.

Page 48
1 For what reasons is heredity an essential feature of living things?
Theme Chapter
A4.1 Evolution and speciation
D2.1 Cell and nuclear division
D4.1 Natural selection

DNA encodes an organism’s entire hereditary information and controls the growth and division of cells. In
most organisms, the genetic information stored in DNA is transcribed into RNA. This information can then
be translated for the synthesis of all the proteins needed for cellular structure and function. Genes are a
hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome, which
encodes a particular protein product, and determines a particular characteristic in an organism. Heredity is an
essential feature of the origin of life since the first replicating molecules (RNA world) and later protocells
would have to pass on their essential characteristics – otherwise the process ends immediately there. This
indicates that heredity is completely central to life.
Evolution is the development of new types of living organism from pre-existing types by the accumulation of
genetic differences over many generations through the process of natural selection of chance variations.
Evolution is the process of cumulative change in the heritable characteristics of a population and is an
organizing principle of modern biology. DNA, as the biological molecule of heredity, shows how genetics
underpins the mechanism by which evolution takes place. It confirms Darwin’s theory of evolution by
natural selection, where variation in populations plays a key role. Variation is caused by random mutations in
DNA, leading to alterations in the genetic makeup of members of a species (new alleles) that may confer a
selective advantage. If modification of DNA code occurs in reproductive cells, these changes can be passed
on to the next generation. Favourable characteristics in changing environments allow some individuals to
survive, whereas others which do not inherit this selective advantage do not survive to pass on their DNA
(survival of the fittest). If populations become isolated, speciation occurs.
Heredity is therefore essential to both the ongoing generation of new life and the evolution of biodiversity on
Earth.
2 What is needed for structures to be able to evolve by natural selection?

Theme Chapter
A A4.1 Evolution and speciation
C C3.2 Defence against disease
D1.3 Mutation and gene editing
D3.1 Reproduction
D4.3 Climate change

Evolution occurs when the heritable characteristics of a species change. Evolution by ‘natural selection’ is
the explanation for how these changes occur – a theory first proposed by Charles Darwin in the 1800s.
Natural selection is the mechanism that explains how evolution occurs: it is the process by which genetic
variation in a population of a species leads to some individuals being better adapted to their environment
than others. These individuals are more likely to survive and pass on the adaptive genes to subsequent
generations when the individual reproduces. Over time, the genotype of the population changes, leading to
new species. Natural selection therefore requires heritable variation and a changing environment for the
selection process to take place. Natural selection operates continuously, over billions of years, resulting in
the biodiversity of life found on Earth. It can also happen over much more rapid timescales, such as in the
evolution of viruses and antibiotic-resistant bacteria.
Gene mutation is a change in the chemical structure (base sequence) of a gene that may result in change in
the characteristics of an organism or individual cell. Different versions of a gene (alleles) are produced by
mutation, which results in variation in a population. Mutations change the genetic code through insertion,
deletion or substitution. As a result of mutations, changes to the proteome of an organism can occur, which
can give some individuals a selective advantage if the environment of a species changes. Those best adapted
to the environment survive and pass on the alleles, conferring this advantage to their offspring, which, over
time, can result in the evolution of new species.
Variation also arises via random assortment of paternal and maternal chromosomes in meiosis (in the process
of gamete formation), crossing over of segments of individual maternal and paternal homologous
chromosomes (resulting in new combinations of genes on the chromosomes of the haploid gametes produced
by meiosis), and the random fusion of male and female gametes during fertilization. These processes operate
each time meiosis occurs and is followed by fertilization. The results are new combinations of existing
characteristics that may favour individuals in their lifetime – they may affect survival and opportunities to
reproduce. If so, a particular individual’s success in reproduction will result in certain alleles being passed on
to the next generation in greater proportions than other alleles. Such variation allows structures to be able to
evolve by natural selection.
The body structures of some organisms appear fundamentally similar. For example, the limbs of vertebrates
seem to conform to a common plan – called the pentadactyl limb (meaning ‘five fingered’). Scientists
describe these limbs as homologous structures as they occupy similar positions in an organism and have a
common underlying basic structure, but may have evolved different functions. The fact that limbs of
vertebrates conform but show modification suggests these organisms share a common ancestry. From this
common origin, the tetrapod vertebrates have diverged, through adaptive radiation, over a long period of
time.
As discussed above, changes in the environment can lead to changes in the selective pressure on a
population, ultimately resulting in the evolution of new species. For example, during the Industrial
Revolution in Britain, in the early part of the nineteenth century, air pollution by gases (such as sulfur
dioxide) and solid matter (mainly soot) was distributed over the industrial towns, cities and surrounding
countryside. Brickwork and tree trunk surfaces turned black. The numbers of dark varieties of some 80 moth
species increased during this period. The dark-coloured moth was effectively camouflaged from predation by
insectivorous birds and became the dominant species. Evidence suggests that tawny owls in southern Finland
are evolving because of milder winters over many decades. The milder winters have resulted in less snow,
and so birds with lighter feathers are at a selective disadvantage, as they are more visible to their prey and
thus catch less food. Research has shown there has been an increase in dark brown tawny owls in a
population that also is usually dominated by pale grey owls. Darker coloured brown owls, which used to
form 30% of the tawny owl population in Finland, now make up 50%. In years when winter weather is more
severe, there is a higher mortality rate in the brown owl population. This could be because brown owls are
more visible to predators when there is thick snow cover. This research has provided the first evidence for a
population evolving in response to climate change.
A2.2 Cell structure

Page 87
1 What explains the use of certain molecular building blocks in all living cells?
Theme Chapter
A A1.1 Water
A1.2 Nucleic acids
A2.2 Cell structure
B1.2 Proteins
B2.1 Membranes and membrane transport
C2.2 Neural signalling
D D4.1 Natural selection

Although the detailed cellular biochemistry of prokaryotes and eukaryotes is different, the types of chemicals
present, and the factors affecting their location, are similar: lipids are found in membranes, and polar
molecules, such as sugars and amino acids, are found in aqueous solutions.
The biochemical reactions within cells are known collectively as metabolism and these organic compounds
are known as metabolites. Some of these small organic metabolites are used as the chemical ‘building
blocks’ (monomers) of biological polymers used by cells. Figure A2.2.1 below shows the synthesis of
biological macromolecules from smaller monomers.
Figure A2.2.1 The synthesis of biological macromolecules from monomers
These polymers include proteins synthesized from amino acids (20 amino acids are encoded by the genetic
code), and nucleic acids (RNA and DNA), which are derived from pentose sugars and phosphate ions in
chemical combination with another class of organic compound, the bases found in DNA and RNA (purines
and pyrimidines).
Fatty acids and glycerol are the chemical ‘building blocks’ for the synthesis of simple lipids, and D-glucose
is the monomer and ‘building block’ for the synthesis of cellulose, starch and glycogen. Derivatives of
sugars, for example amino sugars, are also used as monomers, for example in the synthesis of sialic acids,
which play an important role in neural transmission and formation of synapses.
The use of certain common metabolites, for example amino acids and nucleotides, in anabolic pathways
within all cells is explained by evolution by natural selection (descent) from a common ancestor.
There are other shared features in cells, such as similar metabolism, ribosomes and the genetic code, but
these are not ‘building blocks’. The chemicals present in cells appear to have been selected by the process of
natural selection for their chemical utility (usefulness).
2 What are the features of a compelling theory?

Theme Chapter
A A2.2 Cell structure

There are many features associated with compelling scientific theories from the natural sciences. A
compelling theory:
• exhibits rationality and is expressed, especially in physics, in a general mathematical abstraction that
can be applied in other situations (deduction)
• is law-giving and accounts for the data that scientists have collected, analysed and evaluated, but also
tells us something fundamental about the universe
• exhibits consilience and is one that accounts for many phenomena of different kinds – for example, a
universal law of gravitation that explains the motion of planets, falling bodies on Earth and moving
vehicles on the road. The second law of thermodynamics is another example of consilience, which helps
to explain the direction of all physical processes and chemical reactions
• goes beyond description of phenomena to also give a mechanistic explanation. If there is no mechanism
then it is not a good theory; for example, continental drift was rejected until a plausible mechanism
(mantle convection) for tectonic plate movement was proposed.
Some examples of compelling theories:

1 Karl Popper’s falsification principle would imply that a compelling theory is a theory that has not been
contradicted by any of the current scientific data and is unlikely to by future scientific data.
2 Cell theory states that: cells can only arise from pre-existing cells; living organisms are composed of
cells, which are the smallest unit of life; organisms consisting of only one cell carry out all functions of
life in that cell; and that cells perform life functions at some point in their existence. Based on cell
theory, a newly discovered organism can be predicted to consist of one or more cells. Even though it is a
compelling theory, in that it is correct for most cellular organisms, there are exceptions, such as
multinucleate cells (see page 78 of the Student’s book.
3 Evolutionary theory (Chapters A4.1 and D4.1) explains the change in the heritable characteristics of a
population through time. The explanation of evolution by natural selection developed by Charles Darwin
and Alfred Russel Wallace has stood the test of time, and is still the accepted theory today. Darwin and
Wallace did not know about genetics or the biochemical basis of evolution, and yet still developed a
theory that is both compelling and supported by a wide range of evidence from all fields of biology (see
page 140 of the Student’s book).
4 Empiricism is a theory of knowledge emphasizing the role of sense perception, suggesting that a
compelling theory is built on a wide range of empirical observations and data collected from
experiments, and can explain many examples of a phenomenon.

Page 101
1 What mechanisms contribute to convergent evolution?
Theme Chapter
B B4.1 Adaptation to environment
B4.2 Ecological niches

Convergent evolution occurs when different species evolve similar biological adaptations in response to
similar pressures from natural selection. Convergent evolution can be observed at both the phenotypic and
molecular levels (amino acid and DNA sequences). Mutation, meiosis and fertilization all contribute to
variation within a population, which result in changes to the genome of a population, which in turn affects
the proteome. It is now thought that morphology and physiology often converge owing to the evolution of
similar molecular mechanisms in independent lineages.
Convergent evolution contrasts with evolution from a common ancestor, which is known as divergent
evolution. The vertebrates and invertebrates, for example, share a common ancestor (Figure A4.1.7, page
146 of the Student’s book). Analogous features, as discussed above, are features that have similar functions
in different organisms but have different evolutionary origins. The similarity of function makes them look
similar, such as bird and insect wings or the fins in dolphins and sharks, but they are not similar either in
terms of anatomy or origin.
Most mammals have a placenta, which supports the offspring until birth. A separate group of mammals, the
marsupials, do not have a placenta and so give birth to undeveloped offspring which they then need to
support outside the body. Today, the marsupials are largely found in Australia. The placental mammals and
Australian marsupials show many examples of convergent evolution. Animals with comparable appearances
occur in both groups, due to similar selection pressures.
Biomes are groups of ecosystems that share similar abiotic conditions, and so develop similar communities
through convergent evolution. For any given temperature and rainfall pattern, one natural ecosystem type is
likely to develop. A rainforest, for example, is maintained by year-round insolation, plentiful rainfall and
warm temperatures that maximize growth and productivity. Given similar environments, similar selective
pressures are likely to exist resulting in similar fundamental and realized niches, where a fundamental niche
is the potential of a species based on adaptations and tolerance limits and the realized niche is the actual
extent of a species niche when in competition with other species. Similar environments will therefore select
for similar traits in any species occupying the same type of ecosystem. This is highlighted by convergent
evolution of marsupials in Australian biomes which are morphologically and functionally similar to placental
mammals in similar biomes elsewhere on Earth.
2 To what extent is the history of life characterized by increasing complexity or simplicity?

Theme Chapter
B B3.2 Transport
D D3.1 Reproduction

There is a widespread belief that life has increased in its complexity throughout evolutionary history,
although it is difficult to define and measure biological complexity. It could be argued that there are a
number of major evolutions in transition that have resulted in an increase in complexity, for example the
emergence of replicating RNA molecules (RNA world), endosymbiosis and the evolution of sex and
multicellularity.
Some biologists avoid discussing the idea of increasing complexity or reject it. However, an increase in
biological complexity can be observed in the evolution of the heart. In bony fish the chambers are arranged
sequentially. In mammals the heart developed into a true four-chambered heart, making possible the
separation of deoxygenated blood for the lungs and oxygenated blood to the rest of the body, and thus
making a more efficient circulatory system.
This evolutionary change meant an increase of the number of components and of the amount of
differentiation and, hence, specialization among cells and tissues of the heart, resulting in an increasing level
of complexity. The changes are driven by their reproductive advantage, in this case making possible the
colonization of land.
However, if natural selection has forced complexity to increase, how then to explain the fact that the oldest
organisms, i.e. bacteria and archaea, those having been exposed to natural selection for the longest time, are
the most ‘primitive’? In answer to this question, it can be argued that these organisms are not ‘primitive’ per
se: 3 billion years ago, the Earth was more uniform in habitats and thus so were the organisms found there.
As the Earth developed as a planet, with more complex biomes and habitats, organisms evolved to become
more complicated in order to survive in these habitats. As Earth conditions changed, then so could the
complexity level of organisms.
Not all evolutionary processes have resulted in increased complexity. It is likely that some groups of viruses
evolved from complex ancestral cells into viruses, with lower complexity in their structure and genome.
A3.1 Diversity of organisms

Page 124
1 What might cause a species to persist or go extinct?
Theme Chapter
A4.2 Conservation of biodiversity

The fossil record shows five mass extinction events. The sequence of mass extinctions, obtained by plotting
the rate that genera have died out in a geological period, is shown in Figure A3.1.1 below, which highlights
Earth’s five mass extinction events.
Figure A3.1.1 Earth’s mass extinction

events
The most well-known extinction event

is the extinction of the dinosaurs about
65 million years ago; this was also
accompanied by the extinction of half
the genera of marine non-vertebrates.
In the Cretaceous–Tertiary mass

extinction, researchers have found that
ecologically specialist species were
more vulnerable to extinction than
ecologically generalist species. For
example, specialist insects feed on only
one plant species whereas generalists
feed on several plant species.
After the dinosaurs became extinct at the end of the Cretaceous period, the mammals (which had appeared in
the early Tertiary period) underwent rapid adaptive radiation and filled the ecological niches for large land
vertebrates formerly occupied by dinosaurs (see more about adaptive radiation in Chapter A4.1, page 152 of
the Student’s book). This is an example of evolutionary replacement in which one taxonomic group comes to
occupy the ecological space formerly occupied by another taxonomic group.
The Red Queen hypothesis is a biological theory about the cause of extinctions (see Chapter A4.1, page 149
of the Student’s book). It suggests that species go extinct when they are outcompeted by other species that
have made evolutionary advances. Asteroid impacts and other changes in the physical environment, such as
changes in sea levels and climate (due to plate tectonics), are a non-biological explanation for mass
extinction events.
Some ancient organisms have persisted to modern times without evolving further morphologically, for
example opossums, alligators, sturgeon (a freshwater fish), lungfish, horseshoe crabs (a member of the
arachnid family) and gingko trees.
The theory of punctuated equilibrium postulates that stasis (no change) is the normal condition within a
species. Stasis breaks down only when speciation occurs.
Occasionally biologists discover species remarkably similar to organisms believed to have become extinct
many years ago (‘living fossils’ or Lazarus species). For example, coelacanths are lobe-finned fishes related
to those which evolved into terrestrial vertebrates about 200 million years ago. Although the fossil record of
coelacanths seemed to have begun in the Devonian period (about 380 million years ago) and ended 80–100
million years ago, fishermen have found live coelacanths (Latimeria chalumnae) in deep waters off the
eastern coast of South Africa.
Some ‘living fossil’ species live in relatively isolated habitats, with no apparent competitors. If their habitats
have been stable, there will have been no selective pressure for them to change. Their stasis may be
explained by stabilizing selection (which favours the average individuals in a population).
Today, organisms are facing a sixth mass extinction event (see Chapter A4.2, page 162 of the Student’s
book), not caused by natural phenomena but by the actions of humans. Habitat loss, conversion of land to
agriculture, overhunting and overharvesting, pollution and the spread of invasive species have all led to the
mass extinction of species. Not all species are equally vulnerable to extinction. Certain animals and plants,
through their ecology or behaviour, are more at risk. Factors include:
• small population size, which leads to a reduced gene pool and, therefore, the species is more prone to
disease and inbreeding, and susceptible to environmental change (for example Asiatic cheetah)
• limited distribution (for example golden lion tamarin monkey in Brazil)
• high degree of specialization in, for example, dietary needs (for example giant panda, which mainly eats
bamboo)
• slow reproductive rate, i.e. species with a small number of young (for example western lowland gorilla)
• low reproductive potential (for example Bicknell’s thrush in Canada only has 2000–5000 breeding
pairs)
• non-competitive/altruistic behaviour (for example the dodo, extinct since the late seventeenth century)
• high trophic level, such as a top carnivore, which can accumulate toxins (for example Hawaiian monk
seal)
• long migration routes (for example Siberian crane)

• complex migration routes (for example southern bluefin tuna)
• habitat under threat (for example Sumatran tiger)
• human pressure from hunting, collecting, trade, and so on (for example Sumatran rhino).
2 How do species exemplify both continuous and discontinuous patterns of variation?

Theme Chapter
A A3.1 Diversity of organisms
D D3.2 Inheritance

Variation between organisms within a species is a defining feature of life, and no two individuals are
identical in all their traits. Mutation and sexual reproduction generate the variation on which natural selection
acts, with mutations generating new alleles and sexual reproduction generating new combinations of alleles.
All species show variation. Some of this variation, for example height in humans, can be at any value for a
specific characteristic, and is called continuous variation. Many features of humans are controlled by
polygenes (i.e. several different genes), including body weight and height.
Some variation in species is not continuous but discrete, such as blood type, and so is known as
discontinuous variation. Discontinuous variation is variation that has distinct groups which organisms belong
to – there is no intermediate form and no overlap between the phenotypes. Characteristics that demonstrate
discontinuous variation are controlled by a single gene, usually with two alleles (the human blood group
system has three alleles). Discontinuous variation is not subject to environmental factors and is determined
solely by the genotype (genetic composition) of the species. In this way, species can exemplify both
continuous and discontinuous patterns of variation.
Another factor that may affect the appearance of the phenotype and produce variation between organisms is
the effect of environmental conditions. This can affect the continuous variation of a species by altering the
physiology of individuals. For example, a tall plant may appear almost dwarf if it has been consistently
deprived of adequate essential mineral ions. Similarly, the physique of humans may be greatly affected by
the levels of nourishment received, particularly as children. So, the phenotype of an organism is the product
of both its genotype and the influences of the environment.
A3.2 Classification and cladistics (HL only)

Page 137
1 How can similarities between distantly related organisms be explained?
Theme Chapter

Coevolution of analogous structures can explain how distantly related organisms can show similarities.
Species evolve through the process of natural selection, with those best adapted to the environment surviving
and passing on advantageous alleles to offspring and subsequent generations. Organisms that have evolved
in similar environments can be expected to have similar adaptations.
Convergent evolution can be observed at both the phenotypic and molecular levels (amino acid and DNA
sequences). It is now thought that morphology and physiology often converge owing to the evolution of
similar molecular mechanisms in independent lineages (see page 145 of the Student’s book). Most mammals
have a placenta, which supports the offspring until birth. A separate group of mammals, the marsupials, do
not have a placenta and so give birth to undeveloped offspring which they then need to support outside the
body. Today, the marsupials are largely found in Australia. The placental mammals and Australian
marsupials show many examples of convergent evolution. Animals with comparable appearances occur in
both groups, due to similar selection pressures. For example, there are marsupial mice occupying a very
similar niche to placental mice.
2 What are some examples of ideas over which biologists disagree?

Theme Chapter
A A1.1 Water
B B3.2 Transport
D D3.1 Reproduction
The Earth formed approximately 4.5 billion years ago, in an environment at too high a temperature for water
to condense into liquid. This means that the Earth’s water must have an extraplanetary origin. Scientists
disagree over the origin of water, and there are many hypotheses for how water first arrived on the Earth,
including being carried on icy comets and the creation of water beneath the planet’s surface itself.
Researchers examining the composition of asteroids, and the meteorites that form by breaking off from them,
have hypothesized that asteroids are most likely to be the source of Earth’s water. Disagreements arise when
there are several alternative hypotheses, each of which is supported by evidence. Scientists must assess each
hypothesis and decide which is more likely to explain a phenomenon.
The origin and the evolution of the earliest cells are among the most intriguing topics being debated in the
scientific community. Traditionally, two approaches have been used to understand how life on the Earth
originated. The bottom-up approach is favoured by chemists; Miller’s experiment, for example, attempts to
reconstruct the conditions of the primitive Earth. The top-down approach is favoured by biologists, who
study modern organisms to find the relics of their ancestors to reconstruct ancient metabolic pathways and
molecular processes.
However, knowledge about evolutionary history is not restricted to perfectly replicating a point in the
geological past or finding fossils. Biologists interested in chemical evolution or the emergence of the first
protocell can carry out experiments to test the mechanisms upon which a theory rests – and they can do so in
laboratory conditions that match what scientists do know about the conditions that are likely to have existed
somewhere on the pre-biotic Earth. However, one of the problems of testing hypotheses in this way is that
the exact conditions on the pre-biotic Earth cannot be replicated. This approach can be illustrated for the
three main competing theories for the origin of life:
• Protocell-first: a cell-like compartment that had a basic metabolism, but lacked a fully developed
genetic system, arose spontaneously with the ability to grow and then divide into daughters that tended
to resemble the mother cell. These protocells evolved adaptively until they eventually acquired a genetic
system (probably RNA, then later DNA).
• Gene-first: a genetic molecule (thought to be RNA), or a small set of genetic molecules, capable of
replication arose spontaneously. The replicators evolved adaptively by natural selection forming genetic
variants that could assemble a cell membrane and start metabolizing.
• Metabolism-first: a self-sustaining system of simple reactions, capable of feeding on nutrients and
energy, arose spontaneously, perhaps adsorbed onto a mineral surface. The chemical mixture evolved
adaptively, eventually evolving cells (perhaps via selection for dispersal) and genetic systems (perhaps
via selection for catalysis of metabolic reactions).
Competing theories exist for how each of these processes evolved and in what sequence, although many
biologists favour the metabolism-first theory because rapid growth, replication and division, which are
essential processes for evolution of the protocells, all require significant amounts of energy. Although there
is a scientific consensus that organic molecules came first via chemical evolution, views differ between
scientists over whether metabolism, polymerized molecules (nucleic acids and proteins) or membranes then
evolved.
The definition of ‘species’ is fundamentally important in biology, although several different definitions exist
and biologists disagree on which is the most appropriate. The chosen definition may depend on a biologist’s
own interests. The most widely used definition of species is the biological species concept, where a species
is a group of organisms that can breed and produce fertile offspring. An alternative to the original
morphological species concept is the ecological species concept. Each species has a particular role in the
environment, known as its ‘niche’. The niche of a species is everything about where and how it lives – what
it eats, how it reproduces, its habitat, and so on. Each species has therefore, by definition, a unique niche.
The ecological species concept defines a species in terms of its ecological niche, i.e. the sum of how
members of the species interact with the non-living (abiotic) and living (biotic) aspects of their environment.
For example, two species of finches on the Galápagos Islands may be similar in appearance but
distinguishable based on what they feed on. Today, genetic techniques allow scientists to study genetic
sequences from different organisms to compare similarities and potential ancestry. These techniques have
allowed the evolutionary species concept to be developed, which gives scientists a detailed overview not
only of what defines a species, but also the interrelationship between species over geological time.
The number of species on Earth is difficult to quantify, as many parts of the Earth have not been fully
explored, for example, the deep ocean and the canopies of tropical rainforests. It is known that there are 1.8
million described species, although predications between biologists of the total number of species on Earth
vary widely. Classification is an example of pattern recognition, but the same observations can be classified
in different ways. Taxonomists can be divided into ‘splitters’ or ‘lumpers’: ‘splitters’ recognize more species
than ‘lumpers’ in a taxonomic group. Splitters split off subgroups within species into new species, whereas
lumpers tend to lump similar organisms together into the same species. Molecular biology can be used to
clarify the number of species within a sample, with similarity in genetic code being used to distinguish
between individuals of the same species and those of different species.
Disagreements between biologists can also result from apparent correlation in data. Correlations may be
based on a causal relationship, but correlation does not prove causation. Even strong correlations, such as
that between saturated fat intake and coronary heart disease (CHD), do not prove a causal link, but this
correlation has led to disagreements between scientists about the origin of CHD. Health claims about the
incidence of CHD need to be assessed in context. The issues continue to present complex challenges for
dieticians and politicians in all societies. Similarly, in early epidemiological studies, it was argued that
women undergoing hormone replacement therapy (HRT) had reduced incidence of CHD and this was
deemed to be a cause-and-effect relationship. Later randomized controlled trials showed that use of HRT led
to a small increase in the risk of CHD. The correlation between HRT and decreased incidence of CHD is
therefore not actually a cause-and-effect relationship. HRT patients have a higher socioeconomic status
(SES), and this status has a causal relationship with lower risk of CHD. The link between higher household
income and uptake of HRT is uncertain, although one hypothesis is that women with high SES use health
services more comprehensively and regularly than those from lower-income families, and so are more likely
to take up preventative health measures such as HRT.

Page 155
1 How does the theory of evolution by natural selection predict and explain the unity and diversity of life
on Earth?
Theme Chapter
A2.2 Cell structure
C C1.2 Cell respiration

Biological evolution by natural selection explains both the unity and diversity of all species (living and
extinct) on the Earth, but the diversity lies on a base of underlying unity. All organisms are cellular and have
some shared structural features, such as cell membranes and ribosomes, and similar biochemistry, for
example ATP and glycolysis. It is believed that all living cells are descended from a common ancestral cell
known as LUCA. Biological evolution is supported by extensive scientific evidence including the fossil
record, artificial selection and studies of natural selection in the field or laboratory. Evolution occurs when
natural selection acts on the genetic variation in a population and changes the frequency of traits in that
population over many generations. Traits that provide an individual with an advantage to reproduce are
selected to be passed on to the next generation. Over a large number of generations, this can lead to
speciation. Evolution by natural selection can therefore explain the similarities and difference across all the
species of organisms.
2 What counts as strong evidence in biology?

Theme Chapter
C4.1 Populations and communities

Darwin’s theory of evolution by natural selection is supported by a range of different evidence, from the
fossil record to molecular information. Theories and hypotheses in science need to be supported by strong
evidence if they are to stand the test of time. But what is meant by ‘strong evidence’?
Evidence must involve an explainable mechanism of action that fits with known processes. For example,
knowledge of the cell membrane was based on freeze-fracture techniques (see page 62 of the Student’s
book), which indicated a structure of the membrane that matched scientists’ understanding of its component
parts and the way in which the membrane was known to function.
Data must be repeatable and be produced using the scientific method. For example, when measuring the
effect of temperature on enzyme action, other variables (such as pH, substrate concentration and enzyme
concentration) must be controlled (i.e. kept the same) so that there is only one independent variable
(temperature) that affects the dependent variable (rate of reaction).
Statistics provides a technique for checking whether results are significant or just due to chance. Statistical
analysis is especially useful when data and associations between variables are complex. For example, in
ecological studies, statistics are used to assess the strength of evidence by testing correlations or associations
between data (see page 572 of the Student’s book).
Ultimately, peer review determines which evidence is published and becomes widely accepted within the
scientific community. Other scientists who are experts in the same field of research as the submitted research
judge whether the data, analysis and conclusions are strong enough to warrant publication.

Page 180
1 In what ways is diversity a property of life at all levels of biological organization?
Theme Chapter
A A3.1 Diversity of organisms
C C3.1 Integration of body systems
D D3.1 Reproduction

Diversity can be measured at each level of biological organization. At the molecular level, genetic diversity
is a measure of the variety of alleles within a gene pool of a species. Within an organism, different tissues
work together to make functioning organs, and the whole organism relies on several different organ systems
to support life (for example, nervous, endocrine, circulatory, reproduction and excretory systems). At the
population level, species diversity is a measure of the abundance and range of species found in a particular
area, and ecosystem diversity is a measure of the variety of different habitats, communities and ecological
processes. In this way, diversity ranges across all levels of organization, from the molecular to whole
ecosystems.
2 How does variation contribute to the stability of ecological communities?

Theme Chapter
C C4.2 Transfers of energy and matter
D D4.2 Stability and change

Complex ecosystems such as rainforests have complex food webs, which allow animals and plants many
ways to respond to disturbance of the ecosystem and thus maintain stability.
An ecosystem’s capacity to survive change depends on diversity, which itself depends on the variety of
species found in the ecosystem. A stable ecosystem is able to maintain its structure, ecological functions and
processes. For example, the tall grass prairie ecosystem in the USA has higher diversity and greater stability
than a monoculture (i.e. one species with no variety) such as that created by wheat farming. The greater
diversity of the tall grass prairie creates a more complex food web that has an increased resistance to change,
and therefore provides a more stable ecosystem.
In complex, diverse ecosystems, certain species perform essential functions. Bird predation, for example, can
maintain low numbers of insects, reducing levels of insect herbivory and therefore increasing productivity.
Pollinators are also important for the functioning of ecosystems and without them many plant species would
not be able to reproduce.
Each ecosystem has its own keystone species: often but not always top predators, they are necessary to
maintain a healthy balance of species and interactions. In the USA, beavers are the keystone species in a
wetland ecosystem, prairie dogs are the keystone species in a grassland ecosystem and grey wolves are the
keystone species in the Yellowstone ecosystem.
The agouti is a small rodent that is found in tropical South and Central America (see Figure D4.2.8 in the
Student’s book, page 805), which feeds on the nuts of the Brazil nut tree. The Brazil nut tree (Bertholletia
excelsa) is a hardwood species that is found from eastern Peru and northern Bolivia across the Brazilian
Amazon, and some specimens are among the oldest and tallest trees (they grow up to 50 m high) in the
Amazon.
The agouti is the only animal with teeth strong enough to open the Brazil nut tree’s tough seed pods, to
access the nuts inside. The agouti does not immediately eat all the nuts within the seed pod but buries many
of them around the forest floor for times when the Brazil nuts are less abundant. Inevitably, the agouti does
not remember to dig up and feed on all these buried seeds, and the remaining ones are able to germinate and
grow into adult plants. Without the agouti, the Brazil nut tree would not be able to distribute its seeds and the
species would eventually die out. Without the Brazil nut tree, other animals and plants that depend on it
would be affected, such as harpy eagles that use them for nesting sites. Brazil nuts are one of the most
valuable non-timber products found in the Amazon: they are a protein-rich food source, and their extracted
oils are a popular ingredient in many cosmetic products. The sale of Brazil nuts provides an important source
of income for many local communities. The agouti is the keystone species of the Brazilian Amazon
ecosystem.
Theme B Form and function

B1.1 Carbohydrates and lipids
Page 204
1 How can compounds synthesized by living organisms accumulate and become carbon sinks?
Theme Chapter
B1.2 Proteins
C1.3 Photosynthesis
C4.2 Transfers of energy and matter
D D4.3 Climate change

Organic compounds containing carbon include amino acids (which form proteins), fatty acids and glycerol
(which form lipids), carbohydrates such as glucose and starch, and nucleic acids (DNA and RNA).
Proteins differ from carbohydrates and lipids in that they contain the element nitrogen and sometimes the
element sulfur, as well as carbon, hydrogen and oxygen. Nucleic acids contain phosphate in addition to
carbon, hydrogen, oxygen and nitrogen. All carbon compounds fit into a relatively small number of
‘families’ of compounds, with the families identified by their functional group, which gives them their
characteristic chemical properties. Green plants and other photosynthetic organisms use the energy of
sunlight to produce glucose from the inorganic raw materials carbon dioxide and water, through the process
of photosynthesis. Glucose formed in photosynthesis may temporarily be stored as starch but, sooner or later,
much is used in metabolism. Glucose is used in the process of respiration, to release energy for life
processes. Plants synthesize other carbohydrates, together with the lipids, proteins, growth factors and all
other metabolites they require. For this, they additionally need certain mineral ions, which they absorb from
the soil solution, for example nitrates which provides nitrogen and enable autotrophs to synthesize amino
acids. Synthesis of carbohydrates, amino acids and other carbon compounds uses the products of the Calvin
cycle and mineral nutrients. For example, triose phosphate can be further metabolized to produce
carbohydrates such as sugars, sugar phosphates and starch, and later lipids, amino acids such as alanine, and
organic acids such as malate.
A carbon sink is something that absorbs more carbon from the atmosphere than it releases, for example
plants, algae and the soil. Photosynthesis, which converts carbon dioxide and water into glucose and oxygen,
is the main process through which carbon dioxide is removed from the atmosphere and stored in plant (or
algal) biomass. In contrast, a carbon source is something that releases more carbon into the atmosphere than
it absorbs; for example, volcanic eruptions or the combustion of fossil fuels. Respiration of all organisms
releases carbon dioxide, as does combustion and decomposition. The difference between a carbon sink and a
carbon store is that a sink continues to accumulate carbon, whereas a carbon store maintains a constant
amount of carbon.
Carbon is in turn transformed from inorganic carbon dioxide to organic carbon-containing molecules, before
returning again to the atmosphere (the carbon cycle). Carbon is recycled in ecosystems by photosynthesis,
feeding and respiration.
Primary production is accumulation of carbon compounds in biomass by autotrophs. The world’s forests
store more carbon in plant biomass than any other biome. When forests are burnt or destroyed, the carbon is
released as carbon dioxide. When forests grow, either through expansion of forest area or because old forests
become denser and more carbon-rich, they convert carbon dioxide to carbon in the form of wood and other
biomass via the process of photosynthesis.
The process of afforestation involves planting trees in deforested areas or places that have never been
forested. New trees act as carbon sinks and can therefore help with climate change mitigation.
2 What are the roles of oxidation and reduction in biological systems?

Theme Chapter
B B4.2 Ecological niches
C1.3 Photosynthesis

Many chemical reactions involve reduction and oxidation. Reduction reactions involve the gain of electrons
in a chemical reaction: this can be by removing oxygen atoms or by adding hydrogen atoms. Oxidation
reactions involve the loss of electrons in a chemical reaction: this can be by adding oxygen atoms or by
removing hydrogen atoms. Redox reactions are linked reactions where one substance loses electrons while
the other gains electrons: the substance which gains the electron is said to be reduced while the one that lost
the electron is said to be oxidized. Redox reactions release energy, and so are useful in living organisms.
Both respiration and photosynthesis use redox reactions. Light is used as the external energy source in
photoautotrophs and oxidation reactions as the energy source in chemoautotrophs.
In biological oxidation, oxygen atoms may be added to a compound but, alternatively, hydrogen atoms may
be removed (dehydrogenation). In respiration, all the hydrogen atoms are gradually removed from glucose.
When hydrogen is removed from a substrate, the substrate has been oxidized. The hydrogen atoms are added
to hydrogen acceptors, which are themselves reduced. Since a hydrogen atom consists of an electron and a
proton, gaining hydrogen atom(s) (a case of reduction) involves gaining one or more electrons. Because
electrons are neither formed nor destroyed in a chemical reaction, if one atom or molecule is oxidized,
another must be reduced.
Iron-oxidizing bacteria are an example of a chemoautotroph. Common iron-oxidizing bacteria, including

Gallionella, Sphaerotilus, Crenothrix and Leptothrix species, oxidize iron(II) ions (Fe2+) to iron(III) ions
(Fe3+) to obtain energy for the synthesis of glucose. Iron-oxidizing bacteria take iron atoms out of the water
and remove electrons to release energy for metabolic processes: 4Fe2+ + O2→ 4Fe3+ + 2O2−
The iron(II) ions are oxidized to iron(III) ions and the oxygen molecules are reduced to oxide ions. This is a
redox (reduction–oxidation) reaction. Iron-oxidizing microbial communities can currently be found
associated with widespread hydrothermal vents at the ocean floor. While different to the metabolism
indicated for the Last Universal Common Ancestor (LUCA), the environment found at deep-sea
hydrothermal vents provides many opportunities for diverse forms of energy generation using
chemosynthetic pathways and suggests how early life may have released energy for metabolic activities.
Energy is released in both autotrophs and heterotrophs by the oxidation of carbon compounds in cell
respiration. The energy released maintains ecosystems and passes through food chains, ultimately being lost
as heat. Respiration takes place in every living cell and uses up nutrient molecules, making energy available
for metabolism, growth and reproduction. For respiration, many micro-organisms require oxygen; they can
only respire aerobically (obligate aerobes). An example of an obligate aerobe is Mycobacterium tuberculosis
(the bacteria that cause the disease TB). Other organisms only respire in the absence of oxygen (obligate
anaerobes): these microbes are poisoned by the presence of oxygen, because they lack defence mechanisms
to protect enzymes from oxidants. An example of obligate anaerobes are methane-producing archaea. A third
group of organisms normally respire aerobically but have the facility to switch to anaerobic respiration in the
absence of oxygen (facultative anaerobes), for example Escherichia coli (E. coli). This organism normally
lives in the intestines of animals but can also exist in water, food, soil or on surfaces that have been
contaminated with animal or human faeces.
Electron transfer reactions are central to many of the metabolic processes in living organisms. The flow of
electrons is responsible, directly or indirectly, for all work done by living organisms. These reactions depend
on the approach of an electron donor and an electron acceptor. In non-photosynthetic organisms, such as
animals, the sources of electrons are reduced compounds (food); in photosynthetic plants, the initial electron
donors are water molecules excited by the absorption of light.
Intermolecular electron transfer in biochemical reactions is common and occurs between sites on different
proteins. This leads to electron transport chains that function as a series of consecutive electron-transfer
reactions between metal sites within a protein or group of proteins. Electron transport chains are important in
photosynthesis (Figure B1.1.1) and respiration.
Figure B1.1.1 Electron transfer between photosystems I and II; chl-a refers to chlorophyll a
The citric acid or Krebs cycle (of aerobic respiration) includes a series of oxidation–reduction (redox)
reactions that result in the oxidation of an acetyl group to two molecules of carbon dioxide (Figure B1.1.2).
This oxidation generates high-energy electrons that will go on to be used to power the synthesis of ATP.
Figure B1.1.2 Citric acid cycle (Krebs cycle)
Photosynthesis is composed of the light-dependent reactions and the light-independent reactions. In the light-
dependent reactions, light energy is transformed into two forms of biochemical energy: reducing power (in
the form of carriers) and ATP. The products of the light-dependent reactions are then used in the light-
independent reactions (Calvin cycle) to drive the reduction of carbon dioxide and its conversion into glucose.
Many biochemical reactions are reduction–oxidation (redox) reactions that involve electron transfer, so the
reacting species in these reactions are electron carriers. Cells synthesize molecules that act as reducing
agents that transfer electrons.
Activated carriers are specialized to carry both high-energy electrons and hydrogen atoms. The most
important of these carriers are NADH (reduced nicotinamide adenine dinucleotide) and the closely related
molecule NADPH (reduced nicotinamide adenine dinucleotide phosphate).
Both NADH and NADPH carry energy in the form of two high-energy electrons plus a proton or hydrogen
ion (H+), which together form a hydride ion (H−). When these activated carriers pass their energy (in the
form of a hydride ion) to a donor molecule, they become oxidized to form NAD+ and NADP+, respectively.
Like ATP, NADPH is an activated carrier that participates in many important biosynthetic reactions that
would, unless it were involved, be energetically unfavourable.
A hydride ion is removed from the substrate molecule and added to the nicotinamide ring of NADP+ to form
NADPH. This is an oxidation–reduction reaction (redox reaction); the substrate is oxidized (loses hydrogen)
and NADP+ is reduced (gains hydrogen).
B1.2 Proteins
Page 222
1 How do abiotic factors influence the form of molecules?
Theme Chapter
A A1.1 Water
B B1.2 Proteins

An abiotic factor is a non-living, physical factor that can influence an organism or ecosystem – for example,
temperature, sunlight, pH, salinity or precipitation. These factors can also have an influence on the form of
molecules.
The complementary strands of the double helix of DNA can be made to come apart when a solution of DNA
is heated above physiological temperatures (to near 100 °C) or under conditions of high pH (alkaline), by a
process known as denaturation. However, this complete separation of DNA strands by denaturation is
reversible. When heated solutions of denatured DNA are slowly cooled, single strands often meet their
complementary strands and slowly reform double helices. The temperature at which DNA denatures is a
characteristic of each DNA that is largely determined by the G:C content of the DNA and the concentration
of ions in the solution.
Near the denaturation temperature, a small increase in temperature causes a rapid, near simultaneous loss of
the multiple weak interactions holding the strands together along the entire length of the DNA molecules,
leading to a sudden change in the absorption of ultraviolet radiation. This process is known as melting.
Mutations can lead to a change in protein structure. Gene mutation is the original source of all genetic
variation and causes structural changes to genes at the molecular level, which in turn lead to changes in the
proteins transcribed. Chemical mutagens and mutagenic forms of radiation, such as ultraviolet light, are
abiotic factors that influence the form of proteins. Mutation generates the variation on which natural
selection acts.
Thermal energy from heat, extremes of pH (acidity and alkalinity) that change the charges on amino acid
side chains, the presence of heavy metal ions (for example mercury) that interact with –S–S– links and high
concentrations of chemicals such as urea and ionic detergents, can all disrupt the weak non-covalent
interactions that stabilize the native conformation of a protein. The denaturation resulting from such
treatment causes a protein to lose both its native conformation (shape) and its biological activity.
2 What is the relationship between the genome and the proteome of an organism?
Theme Chapter
A2.2 Cell structure

The genome is the whole of the genetic information of an organism or cell. This includes DNA both in the
nucleus and in other organelles, such as the mitochondria. The genome includes all genes as well as non-
coding DNA sequences.
A proteome is the entire set of proteins produced by a cell, tissue, organ or organism at a specific time, under
defined conditions. The proteome is an expression of an organism’s genome.
Translation is the process by which genes are expressed as proteins, and so it is the protein-coding sections
of the genome (the genes) that are expressed as the proteome. Not all DNA is translated into proteins,
although some sections of DNA function to regulate gene expression.
The genome is relatively stable, but the proteome actively changes in response to various factors, such as the
developmental stage (of the cell, tissue, organism, and so on) and internal and external conditions. In
addition, proteins undergo modifications, which may occur after transcription (alternative splicing to produce
several proteins from one gene) or after translation (post-translational modification, for example covalent
attachment of carbohydrate (glycosylation) or phosphate (phosphorylation)). Because many coding genes are
transcribed into mRNA, which can be alternatively spliced, and those transcripts produce different proteins,
the proteome is larger than the genome.
The large-scale study of the proteome is called proteomics and it involves understanding the composition,
structure and function of proteins after they have been folded into their active conformations and how they
interact with one another in metabolic pathways.
The proteome can be studied using a variety of techniques. For example, two-dimensional gel
electrophoresis can be used to separate proteins by size and by their charges. The proteome can also be
studied using immunology and mass spectrometry, which identifies specific proteins within complex
samples.
Protein sequences and structures are assembled into databases. These are collections of thousands of
sequences that can then be compared and classified, for example into protein families. Proteins with similar
sequences belong to the same families and often have similar functions. Comparing protein sequences can
also yield information about how these proteins evolved.

Page 243
1 What processes depend on active transport in biological systems?
Theme Chapter
B3.2 Transport
B3.3 Muscle and motility (HL only)
D D3.3 Homeostasis
To move a dissolved solute (ions or molecules) against its concentration gradient, a membrane transport
protein must do work: it must drive the movement ‘uphill’ by coupling it to some other process that provides
an input of energy. The movement of a solute against its concentration gradient is therefore active transport.
It is carried out by special types of protein transporters called pumps (see Table B2.1.1 below), which link an
energy source to power the transport process. This energy can come from ATP hydrolysis, an ion gradient
across the membrane or sunlight (solar energy). Transporters transfer specific solutes across a membrane by
conformational changes (in shape) that expose the binding site first on one side of the membrane and then on
the other.
Table B2.1.1 outlines some of the processes dependent on active transport.
Table B2.1.1 Processes that depend on active transport in biological systems
Transporter Location Energy Function Why

source
Na+-driven membranes of Na+ active import of reabsorption of glucose in

glucose pump kidney and gradient glucose the kidney and absorption
intestinal cells of glucose in gut; glucose
is needed for respiration
Na+/H+ plasma membrane Na+ active export of H+ maintains homeostasis of

exchanger of animal cells gradient ions, pH regulation pH and sodium in, e.g., the
kidney
Na+/K+ pump plasma membrane ATP active export of maintains resting potential
(Na+/K+ ATPase) of neurons hydrolysis Na+ and import of
K+
Ca2+ pump plasma membrane ATP active export of reduces the amount of
(Ca2+ ATPase) of eukaryotic cells hydrolysis Ca2+ calcium to low levels,
preparing the cell for
signalling
Ca2+ pump sarcoplasmic ATP active export of pumps calcium ions back
(Ca2+ ATPase) reticulum hydrolysis Ca2+ into into muscle cells allowing
membrane of sarcoplasmic muscle to relax
muscle cells, ER of reticulum
most animal cells
H+ pump plasma membranes ATP active export of H+ creates a gradient of

(H+ ATPase) of plant cells, fungi hydrolysis hydrogen ions, allowing
and some bacteria H+ to pass through a
transporter, making
potential energy available
to make ATP
H+ pump membranes of ATP active export of H+ increases the acidity so

(H+ ATPase) lysosomes in hydrolysis into vacuole that specific enzymatic
animal cells and of reactions can occur
vacuoles in plant
and fungal cells
bacteriorhodopsin plasma membrane light active export of H+ allows light energy to be

(see Figure of some bacteria captured and used to move
B2.1.1 below) – a protons across the
protein used by membrane out of the cell;
archaea the resulting proton
gradient is subsequently
converted into chemical
energy
Figure B2.1.1 The molecular structure of bacteriorhodopsin
2 What are the roles of cell membranes in the interaction of a cell with its environment?
Theme Chapter
D2.2 Gene expression (HL only)

Cell membranes act as selective barriers. The plasma membrane separates a cell from its surroundings,
allowing the molecular composition of a cell to differ from that of its environment. If a cell is to survive,
grow and undergo cell division, nutrients must pass inward across the plasma membrane, and metabolic
waste products must pass out. To facilitate this exchange, the membrane is penetrated by highly selective
channels and transporters – proteins that allow specific, small molecules and ions to enter or leave the cell.
Other proteins in the membrane act as sensors, or receptors, that enable the cell to receive chemical signals
from the cell’s environment. Membrane proteins serve many functions, including anchoring the membrane to
macromolecules on either side of cells in a tissue or acting as enzymes. Some of the proteins in the plasma
membrane are glycoproteins and have covalently attached sugar chains, which form a carbohydrate layer that
helps protect and lubricate the cell surface, while also being involved in specific cell–cell recognition.
The cells in a multicellular organism must communicate with each other to coordinate their activities. This is
done by specific chemical signalling molecules, which include proteins, small peptides, amino acids,
nucleotides, steroids and amines. Receptors on the surface of membranes have binding sites for specific
signalling chemicals. In most cases, the signalling molecule cannot cross the cell membrane and must
therefore bind with a receptor on the outside of the plasma membrane. For example, hormones such as
insulin cause cells to respond to signals in specific ways. Insulin causes cells to store glucose as glycogen, or
to increase glucose metabolism. Hormones cause the expression of specific genes in cells. For example,
steroid hormones (such as oestradiol, progesterone and testosterone) bind to a site on a receptor, activating it.
The activated receptor binds to specific DNA sequences to promote gene transcription, which leads to the
production of specific proteins.
Neurotransmitters are chemical signals that cross the synapses of adjacent neurons. The neurotransmitter
binds to receptors in the postsynaptic membrane, causing sodium channels to open, depolarizing the
membrane and thereby initiating an action potential. In this way, changes in the environment (stimuli),
transduced into action potentials, can be passed and directed throughout the body to specific effectors, which
allow responses to the stimuli to occur.
Every organism has unique molecules on the surface of their cell membranes. These molecules include the
highly variable glycoproteins on the cell surface membrane. The glycoproteins that identify cells are the
major histocompatibility complex (MHC) antigens. The MHC antigens of individuals are genetically
determined. In inherited characteristics that are products of sexual reproduction, variations occur, so each of
us has distinctive MHC antigens present on our cell surface membranes. MHC antigens are unique (other
than in identical twins). Lymphocytes of the immune system have antigen receptors that recognize a person’s
own MHC antigens, and can tell them apart from any ‘foreign’ antigens detected in the body. It is critically
important that an individual’s cells are not attacked by their own immune system. This is the basis of the
‘self’ and ‘non-self’ recognition mechanism.
Antibodies initially occur attached to the cell surface membrane of B-cells, but later are mass produced and
secreted by cells derived from the B-cell. This occurs after the B-cell has undergone an activation step.
When a specific antigen enters the body, B-cells with surface receptors (antibodies) that recognize the
antigen bind to it. On binding to the B-cell, the antigen is taken into the cytoplasm by endocytosis. Then it is
expressed and displayed on the cell surface membrane of the B-cell (forming an antigen-specific B-cell).
Phagocytic cells, the macrophages, engulf any antigens they encounter. Once antigens have been taken up,
they are presented externally, attached to the MHC antigens, on the surface of the macrophages. T-cells
respond to antigens that are presented on the surface of other cells, as on the macrophages. As T-cells
encounter these macrophages and briefly bind to them, they are immediately activated, forming ‘armed’ or
activated helper T-cells. Activated helper T-cells bind to antigen-specific B-cells with the same antigen
expressed on their cell surface membrane. As a result, the B-cell is activated. It is now an ‘armed’ or
activated B-cell. After B-cells are activated, they divide rapidly by mitosis, forming a clone of plasma cells.
Clonal selection occurs, where a large number of plasma cells that produce one specific antibody type are
generated. A huge range of different antibody-secreting lymphocytes exists, each type recognizing one
specific antigen. The more antigens an individual encounters, the more antibodies they can form, should they
be required. In this way, the membranes of white blood cells play an essential role in defending the body
against infection.
B2.2 Organelles and compartmentalization

Page 255
1 What are examples of structure–function correlations at each level of biological organization?
This answer links material from all the themes.
As we have seen, structure and function are directly correlated. By understanding the structure of an object,
insight into its function can be gained. Similarly, if the function of a biological structure is known, it should
be possible to make predictions about its structure. There is always a relationship between the structure of a
biological object and its functions, and vice versa.
A thought exercise can be carried out when considering the correlation between structure and function of
biological structures:
1 What is the main function of the structure?

2 List all the parts of the structure (those that you can see and those you know about from your own
knowledge). Make a sketch to show the relationship of the parts.
3 What is the function of each part?
4 What would happen if the structure was different in some way (such as shape, size, composition or
other physical characteristics)? Why would it no longer perform its functions?
5 Finally, explain what is meant by the concept of structure–function correlation for the structure you
have explored.
Think now about examples of structure–function correlations at each level of biological organization:
molecules, cells, organisms and ecosystems. Think of an example from each level of organization and carry
out the thought exercise above for each. For example, how does the structure of a protein relate to its
function? What are the specific parts of the protein that relate to its function (such as the active site of an
enzyme)? What would happen if the structure of the protein was altered (you may want to consider what
happens when a protein denatures)? Structure–function relationships for molecules are explored in the first
part of each theme (A1, B1, C1 and D1); the second part of each theme looks at the cellular level (A2, B2,
C2 and D2); the third part (A3, B3, C3 and D3) covers the level of organisms; and the fourth and final part
(A4, B4, C4 and D4) discusses ecosystems.
2 What separation techniques are used by biologists?

Theme Chapter
B B2.2 Organelles and compartmentalization
C1.3 Photosynthesis

Any molecule, whether protein, carbohydrate or nucleic acid (DNA and RNA), can be separated, or resolved,
from other molecules based on their differences in one or more physical or chemical properties. For example,
the greater the number of differences between two biomolecules, the more easily and the more efficiently
they can be separated.
The two most widely used properties for separating proteins are size (defined as either length or molar mass)
and binding affinity for specific ligands, but these techniques are also useful for the separation of nucleic
acids and other biomolecules. Gel electrophoresis is a tool for separating fragments of DNA.
The most common initial step in protein purification is the separation of soluble proteins from insoluble
cellular material by differential ultracentrifugation (see Figure B2.2.1 in the Student’s book, page 245).
Centrifugation separates proteins based on their rates of sedimentation, which depend on their masses and
shapes.
Dialysis (see Figure B2.2.1 below) is a simple technique that separates large molecules from smaller ones.
Only small molecules can diffuse through the membrane (for example, Visking tubing) and large molecules
remain inside the membrane. At equilibrium, the concentration of small molecules is the same.
Figure B2.2.1 The principle of dialysis
Proteins and DNA can be separated by gel electrophoresis. When a mixture of proteins or DNA is placed in a
gel and an electric current is applied, smaller proteins or DNA migrate faster through the gel than larger
proteins do.
Another common technique for separating mixtures of proteins, as well as other molecules, is
chromatography. It is based on the principle that molecules dissolved in a solution will interact (bind and
leave) with a solid surface. If the solution is allowed to flow across the surface, then molecules that interact
often with the surface will spend more time bound to the surface and hence move more slowly than
molecules that interact less often with the surface.

Page 272
1 What are the advantages of small size and large size in biological systems?
Theme Chapter
A A1.1 Water
B B2.3 Cell specialization
B3.1 Gas exchange
B3.2 Transport
‘For every type of animal there is a most convenient size, and a large change in size inevitably carries with it
a change of form.’
This quote is from the 1926 essay On Being the Right Size by biologist J.B.S. Haldane, where he discusses
how an organism’s structure is affected by a change in size (see the full paper here:
www.phys.ufl.edu/courses/phy3221/spring10/HaldaneRightSize.pdf).
Haldane’s essential point was that the size of an animal determines its structure. A proportional rise in an
object’s size causes its area to rise by the square, and its volume by the cube, of that increase. This is known
as the ‘square-cubed’ law. This means that as animals become larger, their body mass becomes more
significant compared to their surface area. As mass increases, structural adaptations (such as stronger, thicker
bones) are needed.
For animals, body size determines many aspects of an organism’s biology, such as anatomy, physiology,
reproductive success, life span and overall interactions with the physical and biological world.
Larger size results in a smaller surface area:volume ratio than smaller organisms, which means that
organisms cannot absorb materials across the surface of their body at a fast enough rate to support life
processes. Larger animals have adapted structures that increase surface area to increase diffusion. For
example, lungs contain alveoli which have a large surface area and are thin, increasing the rate of oxygen
diffusion into the blood and carbon dioxide into the alveolar air spaces. In addition, larger organisms need to
transport material over long distances and to every cell in the body: transport systems enable them to achieve
this. The circulatory system of larger animals, consisting of a heart, arteries, veins and capillaries, ensures
fast delivery of nutrients and oxygen, and a large surface area due to branching and narrow diameters, thin
walls and fenestrations (pores) in some capillaries where exchange needs to be particularly rapid. In plants,
xylem and phloem deliver water and organic compounds to areas where they are needed.
There are wide variations in size between closely related species, and even with the same species, and
between genders of the same species there can often be wide variation in size. Over the entire animal
kingdom there is a huge variation in mammal size, from very small bats and shrews to the blue whale.
Life on land imposes size limitations on animals because of gravity and the constraints of bone strength and
mass. However, the buoyancy of water lessens the effects of gravity to some extent. Therefore, marine
mammals can grow to very large sizes without the same muscle and skeletal structures that would be needed
by a similarly sized terrestrial animal.
Stabilizing natural selection should favour average individuals in a population to avoid selective pressures
against extreme phenotypes. The ones that survive and reproduce most effectively should not be too large or
too small but, to paraphrase Haldane, should be ‘just right’ in size.
However, there is a macroevolutionary tendency for species within a lineage to evolve towards an increase in
size. Evolutionary trends towards an increase in body size are common in the fossil record. For example, the
ancestors of modern horses were about the size of a dog, but horses have evolved to become as much as ten
times that mass.
Various explanations have been proposed for advantages of increased body size. Larger bodies are assumed
to contribute to a marked increase in survival and reproductive success. Large size may also provide
ecological advantages, such as the ability to kill and eat larger prey, and survive predator attacks or extreme
environmental conditions.
However, there are also several negative issues with larger body sizes. Although animal evolution often
favours large sizes, conversely, extinction favours small sizes. The occurrence of the mass extinction of
megafauna (large land animals), and the widespread extinction of giant animals during the ice age, shows
that large organisms are more susceptible to environmental crises, and the mass extinctions account for the
limit on body size increase.
In general, the gap of time from birth to reproductive age of a species is a function of scaling relationships,
so larger, slower-reproducing animal populations are generally unable to compensate for very strong natural
selection pressures.
Although large body size may provide a high ability to compete and occupy specialist niches in the short
term, small body sizes may have increased flexibility to survive and exploit an ecological niche, even under
increased selection pressures in the long term.
There will also be physically imposed limits to the size of some organisms as outlined by Haldane in his
essay; for example, insects must be small enough for oxygen to diffuse (via holes (spiracles) in their cuticle)
to all parts of their bodies, and flying birds must be light enough to fly.
2 How do cells become differentiated?

Theme Chapter
B B1.2 Proteins
D D2.1 Cell and nuclear division

The transformation from a zygote to a multicellular organism results from three interrelated processes:
mitosis, morphogenesis and cell differentiation. Once the animal is mature, differentiation occurs in only a
limited way – for the replacement of damaged or lost cells (from adult stem cells).
Many experiments, involving cloning, support the idea that nearly all the cells of an organism have genomic
equivalence: that is, they have the same genome. During the development of multicellular organisms,
differentiation processes form hundreds of cell types, each specialized for a particular function.
Many of the differences among differentiated cells are due to production of specific sets of proteins needed
to carry out the unique functions of each cell type. Only a subset of an organism’s genes from its genome is
transcribed at any specific time or in any specific cell.
Before differentiation is the process of cell determination, which involves the expression of genes for tissue-
specific proteins that allow differentiated cells to carry out their specific functions.
B3.1 Gas exchange

Page 294
1 How do multicellular organisms solve the problem of access to materials for all their cells?
Theme Chapter
B3.2 Transport

Small organisms, such as single-celled protists and bacteria, do not have any problem acquiring sufficient
quantities of oxygen and nutrients. Their very large surface area compared to their size, and the small
distances that molecules and ions need to travel, means that diffusion is rapid and highly effective.
Multicellular organisms have several issues to contend with, such as larger distances for respiratory gases
and nutrients to travel, higher energy and nutritional needs, and a smaller surface area:volume ratio.
Multicellular organisms solve the problem of size by having specialized structures to increase the surface
area for absorption. For the exchange of respiratory gases, mammals have lungs, fish have gills and insects
have a system of tubes called tracheoles; all of these increase the surface area available for gas exchange.
Amphibians can carry out gas exchange across their skin surface (if kept moist) due to a rich capillary
network, and they also have lungs which can be ventilated. Increased surface area, a small distance for
diffusion and the maintenance of concentration gradients are also achieved by digestive systems: mammals
have long intestines with folded walls containing finger-like villi and microvilli, with a rich blood supply to
quickly absorb nutrients and maintain a concentration difference of food molecules between the blood and
the lumen of the gut. A circulatory system delivers dissolved nutrients and oxygen to every cell – molecules
and ions diffuse from the blood capillaries into tissue fluid, and into the cells.
Plants increase the surface area available for gas exchange by having leaves, with stomata and a spongy
mesophyll layer. Root hair cells ensure a large surface area for the absorption of water and minerals. Xylem
vessels transport water around the plant, and phloem carry sugars, to ensure every cell is provided with
sufficient access to materials and removal of the products of cell metabolism.
Multicellular fungi have networks of hyphae that provide a large surface area for saprotrophic nutrition, and
the fused fungal cells allow for efficient transport of materials throughout the organism.
2 What is the relationship between gas exchange and metabolic processes in cells?
Theme Chapter
B B3.1 Gas exchange
C1.3 Photosynthesis
Respiration is one of the many metabolic processes that occur in cells. Aerobic respiration requires oxygen
and the removal of carbon dioxide. With increased levels of respiration, increased oxygen is required and
more carbon dioxide needs to be removed. Gas exchange provides the means of supplying the oxygen for
respiration and removing carbon dioxide. Respiratory gases, exchanged at the gas exchange surface (whether
this be the surface of a very small organism, or the adapted surface of an organ, such as lungs, in larger
organisms), travel to (oxygen) and from (carbon dioxide) cells allowing respiration to continue.
Gas exchange occurs in plants across the membranes of spongy mesophyll cells. Carbon dioxide diffuses
into cells and chloroplasts, and is used in the process of photosynthesis, where glucose and oxygen are
produced. Oxygen diffuses from cells in the leaf and into the air spaces of the spongy mesophyll, diffusing
from the leaf through stomata.
B3.2 Transport
Page 325
1 How do pressure differences contribute to the movement of materials in an organism?
Theme Chapter

Small organisms, such as bacteria and protists, do not need transport mechanisms because they have a very
large surface area compared to their size and can obtain nutrients and oxygen by diffusion direct into the cell
from their external environment. Large multicellular organisms have a relatively small surface area
compared to their size and so need specialized transport systems to move nutrients and oxygen to all cells,
and to remove waste products (such as carbon dioxide). Cells, tissues, organs and body systems are
organized as a hierarchy of subsystems that are integrated in a multicellular living organism – transport
systems form the link between individual cells and the tissues where material enters or leaves the body.
These transport systems either push material around the body (positive pressure) or pull under negative
pressure.
In plants, phloem transports sucrose and amino acids from sites of production (called a source) to a site of
need (called a sink). The typical direction of transport is downward from the primary source (leaves) to the
major sink (roots). Hydrostatic pressure ensures the movement of organic compounds, from an area of higher
pressure to an area of lower pressure. Higher pressure is generated by the movement of sucrose by active
transport at the source, and movement of water from the xylem into sieve tube elements by osmosis. Lower
pressure is created at the sink by the removal of sucrose for conversion into glucose for storage or use in
respiration, and by the movement of water into xylem by osmosis. The pressure gradient generated ensures
the mass flow of material around the plant. Studies on aphids feeding on phloem sap showed that sap was
‘pushed’ out of the plant showing the phloem is under pressure. More recent studies with sophisticated
pressure probes have shown a pressure gradient from source to sink.
In contrast, water and minerals are drawn up xylem vessels under tension (negative pressure). Loss of water
by transpiration from cell walls in leaf cells causes water to be drawn out of xylem vessels and through cell
walls by capillary action, generating tension (negative pressure potentials). It is this tension that draws water
up in the xylem. Cohesion ensures a continuous column of water. So, sucrose is ‘pushed’ and water ‘pulled’
through plant vascular tissue. Transpiration is powered by the Sun, which causes water to evaporate from
leaves. In contrast, sugars are moved into phloem by active transport.
Salts are actively transported into guard cells to draw water into them by osmosis. Increased volume in these
cells lead to an increase in pressure. Differential thickness of the cell wall of guard cells changes the shape of
the cells, opening stomata. The open stomata allow water to diffuse from the interior of the leaf to the
outside air, leading to the transportation pull which draws water up the plant.
In animals such as mammals, pressure differences are created by the heart. When the heart contracts,
pressure in the arteries leading from the heart increases, which moves blood throughout the body. Layers of
muscle and elastic tissue in the walls of arteries help them to withstand and maintain high blood pressures.
Tissue fluid is formed by pressure filtration of plasma in capillaries: this is promoted by the higher pressure
of blood from arterioles. Hydrostatic pressure in capillaries forces substances from the blood plasma into
tissue fluid. Substances can then move from tissue fluid into cells, and vice versa. Lower pressure in venules
allows tissue fluid to drain back into capillaries. Baroreceptors monitor blood pressure, and the medulla of
the brain coordinates responses and sends nerve impulses to the heart to change the heart’s stroke volume
and heart rate, which vary according to levels of activity or stress.
2 What processes happen in cycles at each level of biological organization?

Theme Chapter
C1.3 Photosynthesis
D3.1 Reproduction

Cycles occur at every level of biological organization. At the molecular level, metabolic cycles occur in the
cells of organisms. Oxidation and decarboxylation reactions in the Krebs cycle in the matrix of mitochondria
carry out processes in respiration. The Calvin cycle in the stroma of chloroplasts is a series of reduction
reactions in the light-independent reactions of photosynthesis.
At the cellular level, the cycle is the process by which a cell carries out its functions and then undergoes
division to form new cells. Mitosis is the production of genetically identical cells and meiosis is the
production of genetically different cells (or gametes).
Cycles occur at the level of organisms in both animals and plants. Angiosperms (flowering plants) that
complete their life cycles within one growing season (in the temperate zone) are known as annuals. A
number of angiosperms are biennial in the temperate zone: they grow vegetatively (asexually) for one
season. In the second growing season the plants flower and produce seeds, after which they die. Other
angiosperms are perennial and continue growing, flowering and producing seeds for a number of growing
seasons in a yearly cycle.
The duration and wavelength of light is critical in controlling the flowering of angiosperms. On the basis of
extensive experimental studies, flowering plants have been classified as ‘long-day’ or ‘short-day’ with
respect to their light requirements for flowering. A number of perennial and biennial plants require a prior
period of low temperature before they produce flowers.
The hormone abscisic acid (ABA) causes the abscission (dropping) of leaves. ABA accumulates as a
response to stressful environmental conditions, such as dehydration, low temperatures or short day lengths.
Its activity counteracts many of the growth-promoting effects of other plant hormones, such as auxin.
In humans, secretion of the hormone melatonin controls circadian rhythms (cycles of waking and sleeping).
The ovarian and uterine cycles together constitute the menstrual cycle. The ovarian cycle controls the release
of eggs (oocytes) and the release of oestradiol and progesterone. The uterine cycle controls the preparation
and maintenance of the lining of the uterus to receive a fertilized egg.
At the level of ecosystems, communities can cycle rather than reach a climax community, for example wood
pasture, which cycles from pasture to scrub to woodland and back to pasture.
The carbon cycle recycles carbon from living matter back to inorganic carbon in the atmosphere and non-
living parts of the biosphere. The water cycle is the movement of water between the biosphere (living part of
the Earth) and the atmosphere: water evaporates into water vapour, condenses to form clouds and
precipitates back to Earth in the form of rain and snow.

Page 340
1 What are the advantages and disadvantages of dispersal of offspring from their parents?
Theme Chapter
D D3.1 Reproduction
Dispersal is a type of movement. The dispersal of seeds ensures that they spread away from parent plants.
Modes of dispersal include water (for example coco-de-mer – the world’s biggest seed – also known as the
‘sea coconut’), animal (for example burdock), wind (for example dipterocarp seeds) and explosive
mechanisms (for example Japanese knotweed). Wind- and animal-dispersed species that produce seeds with
specialized features (such as wings and fleshy coats) tend to have smaller seeds than those dispersed through
explosive mechanisms with limited dispersal range.
The advantages dispersal provides include offspring avoiding competition with their parent and other
offspring from the same parent plant, for example for resources such as water and minerals, as well as
sunlight. In addition, dispersal means avoiding breeding with closely related individuals (i.e. reducing
chances of inbreeding).
There are evolutionary advantages of dispersal: if the habitat is fragmented, dispersal such as wind dispersal
means a plant can spread easily between patches of suitable habitat. In terms of populations, dispersal links
subpopulations, increasing connectivity and lowering the chance of local extinction.
Disadvantages of dispersal include the potential inability of offspring to find a suitable location to live within
the habitat of the species, and the need of parent plants to produce many offspring in the hope that enough
survive to maturity and reproduce. Specific adaptations for dispersal require energy to make, thus there are
fewer resources for the developing organism.
Animals also eventually need to move away from their parents, to avoid competition for food, water and
places to live within the habitat. Unlike plant dispersal, animal dispersal is linked to behaviour. Animals can
adjust their dispersal behaviour to changing conditions – something instrumental in overcoming challenges.
Reasons for dispersal may vary between male and female animals. For example, male dispersal results in
mating with unrelated females, whereas dispersal by female squirrels results in improved access to space in
which to establish maternal territories.
2 In what ways does locomotion contribute to evolution within living organisms?

Theme Chapter
D D1.3 Mutation and gene editing

Mutation is a change in the amount or the chemical structure (i.e. base sequence) of DNA of a chromosome.
Gene mutations are the original source of all genetic variation. In a species, mutations are essential for
evolution, with natural selection the mechanism driving evolutionary change. Alteration to the genome of a
species results in phenotypic changes, which can be behavioural, physiological or anatomical.
Change in locomotion can give individuals within a population a selective advantage. Examples of responses
to selective pressures can include migration, escaping from threats and looking for reproductive mates.
Sexual selection also plays a role in the evolution of species, with differences in physical and behavioural
traits being used as a sign of overall fitness, which affects success in attracting a mate. Males which have
means of locomotion, such as dancing displays, are more attractive to females and are more likely to
reproduce and pass on these adaptive alleles to the next generation.
Speciation is the splitting of one species into two or more species. Variation within a species, combined with
selection pressures, results in the conditions necessary for evolution to occur. Locomotion provides the
means for individuals within a species to move to new areas, such as finches migrating from mainland South
America to the Galápagos Islands. Environmental conditions on each island provided different selection
pressures, resulting in the evolution of new species. By changing location through locomotion, a species can
be subjected to new selection pressures or respond to changing niche requirements.
Speciation occurs through reproductive isolation. Geographical barriers can provide an isolating mechanism.
Individuals through locomotion may find themselves on opposite sides of a barrier and evolve into new
species if their selection pressures are different, such as evolution of bonobos and chimpanzees on opposite
sides of the Congo River. This is known as allopatric speciation. Sympatric speciation occurs when new
species evolve in the same locality. Again, changes in locomotion can result in sympatric speciation, where
individuals within a population can become spatially separate within the same ecosystem where
environmental conditions vary. For example, the tall trees within tropical rainforests provide opportunities
for alterations in niche requirements by giving a vertical dimension to the distribution of species – within a
population, some individuals may migrate vertically into the different conditions in the canopy which, over
time, can result in the evolution of new species, for example the flying lizards (Draco sp.) of South East
Asia.

Page 362
1 What are the properties of the components of biological systems?
Theme Chapter
A2.2 Cell structure
B3.1 Gas exchange
B3.2 Transport

A system can be defined as ‘an assemblage of parts and the relationships between them, which together
constitute an entity or whole’. A system can be divided into parts, or ‘components’, which can each be
studied separately: this is called a ‘reductionist’ approach. Alternatively, a system can also be studied as a
whole, and patterns and processes described for the whole system: this is called a ‘holistic’ approach. The
advantage of studying the whole system is that emergent properties appear that are not obvious if the
independent components are examined. For example:
• Consciousness is a property that emerges from the interaction of individual neurons in the brain;
emergent properties such as consciousness are an example of the consequences of interaction.
• Cells, tissues, organs and organ systems form a hierarchy of subsystems that are integrated in a
multicellular living organism: this integration is responsible for emergent properties; for example, a
cheetah becomes an effective predator by integration of its body systems.
• Polymerization of monomers results in emergent properties or polymers, such as proteins, lipids, starch
and nucleic acids (RNA and DNA).
For emergent properties, a hierarchical arrangement with reciprocal connections is needed. Emergence is
also a consequence of constraint.
Biological systems can be found at every level of organization, containing different structures (forms)
depending on the function of the system. At the smallest scale, systems include metabolic pathways
(connecting different molecules, for example enzymes and multi-enzyme complexes); at the cellular scale,
systems include cells and organelles; at the level of organisms, organ systems connect different organs which
serve a particular function, such as the circulatory system, respiratory system and nervous system; in plants,
vascular systems (xylem and phloem) connect different parts of the organism. Examples of biological
systems at the largest biological scale include communities and ecosystems. Biological systems therefore
exist as a hierarchy, from small to large scale. At each level, there is an exchange of energy and matter from
and within the components of the system. Interactions and feedback within each system maintain equilibrium
and ensure that the system is regulated.
Note: For extra reading, access this article, which looks at the history of ‘systems biology’:
www.ncbi.nlm.nih.gov/pmc/articles/PMC1626627
2 Is light essential for life?

Theme Chapter
C1.3 Photosynthesis
C2.1 Chemical signalling (HL only)

Life depends on photochemical processes – chemical and biochemical reactions driven by light (Figure
B4.1.1 below). The most important light-driven reaction is photosynthesis, since carbohydrates can be used
as energy sources by animals and oxygen can be used by organisms that carry out aerobic respiration. The
oxygen gas in the atmosphere is almost entirely the product of photosynthesis.
Figure B4.1.1 The visible spectrum
The oxygen released by photosynthesis (Figure B4.1.2) is derived from the photolysis of water molecules
into oxygen molecules, protons (used to reduce carbon dioxide) and electrons (to generate ATP).
The absorption and use of solar radiation depend on the presence of chlorophyll, which converts light energy
to chemical energy. The precise role of chlorophyll in the chloroplast under the influence of light is to cause
electron transfer (to the electron transport chain) and reduction–oxidation (redox) reactions.
Figure B4.1.2 Summary of photosynthesis
The solar energy of the Sun’s visible light and ultraviolet light promote processes that allow life to exist on
Earth and probably played an important role in the evolution of life from chemicals.
However, DNA and proteins are damaged by ultraviolet light with a wavelength shorter than about 290 nm.
The ozone layer absorbs the most harmful ultraviolet light before it reaches the Earth’s surface. Ozone, O3, is
formed photochemically from oxygen, O2, in the atmosphere and its levels in the stratosphere increased as
the oxygen levels increased following the evolution of the first cells that could photosynthesize.
Luciferase is an enzyme naturally found in fireflies (a type of beetle). When its substrate luciferin is present,
it catalyses a redox reaction which emits light, as shown by the equation below:
luciferin + ATP + oxygen → oxyluciferin + AMP + light
The bioluminescence is essential for a firefly to attract a mate. All fireflies have the same luciferin, but each
species produces a different colour of light. The colour was found to be determined by the luciferase that is
unique to each species of firefly. Bioluminescence is also seen in the marine bacterium Vibrio fischeri, which
produces the light-emitting enzyme luciferase when it reaches a critical cell population density in the light
organ of its host, the squid.
Ultimately, life is only possible on Earth due to the constant input of light energy. Photosynthetic organisms
create the oxygen needed for aerobic respiration. Radiation from the Sun also warms the planet, creating an
average temperature that is suitable for life to exist. Without sunlight, Earth’s temperature would be too low
to support life.

Page 379
1 What are the relative advantages of specificity and versatility?
Theme Chapter
B B1.2 Proteins
C1.3 Photosynthesis

Specificity within body mechanisms is found at every level of organization, helping to control and regulate
systems:
Molecules
• Regulation of transcription by proteins that bind to specific base sequences in DNA.

• Difference in shape between globular and fibrous proteins: their structures and therefore shapes make
them suitable for specific functions.
• Because of enzyme specificity, many different enzymes are required by living organisms, and control
over metabolism can be exerted through these enzymes. There are precise relationships between the
structure of the active site, enzyme–substrate specificity and denaturation.
• Absorption of specific wavelengths of light by photosynthetic pigments.
Cells
• Specific cyclins are required to pass each checkpoint in the cell cycle.
• The structure of channel proteins makes membranes selectively permeable by allowing specific ions to
diffuse through.
• Adaptive immune system responds in a specific way to pathogens. This enables a memory of the
pathogen to be stored so that if the same pathogen reinfects the body it can be dealt with quickly.
• Organelles as discrete subunits of cells that are adapted to perform specific functions.
Organisms
• Organisms play a specific role within the ecosystem (their niche).

• Each organism can be recognized by a specific name – this allows biodiversity to be classified.
• Organs within organisms play specific roles (for example the heart to pump blood, leaves to absorb
sunlight and carry out photosynthesis).
Ecosystems
• Ecosystem distribution is determined by specific abiotic factors (for example sunlight, precipitation and
temperature).
• Given any specific environmental conditions, ecological succession tends to lead to a particular type of
climax community.
There is the need for versatility in multicellular organisms in addition to specificity. Versatility and
specificity are linked. For example, the cell membrane has many specific proteins which play certain roles in
membrane function, such as facilitated diffusion, active transport and cell–cell recognition. By allowing
many different functions, the cells are versatile in their role within the body, for example some cells conduct
electrical impulses (neurons) and others insulate the body (adipose cells).
2 For each form of nutrition, what are the unique inputs, processes and outputs?
Theme Chapter
B1.2 Proteins
C1.3 Photosynthesis

Forms of nutrition can be divided into two groups: autotrophic and heterotrophic. The inputs of autotrophic
nutrition include inorganic carbon and either sunlight (photoautotrophic nutrition) or energy generated from
exothermic, oxidative chemical reactions (chemoautotrophic nutrition). The inputs of heterotrophic nutrition
are sources of organic carbon, including carbohydrates, lipids and proteins. Heterotrophs therefore use
carbon compounds obtained from other organisms to synthesize the carbon compounds that they require.
The processes of photoautotrophs include the light-dependent and light-independent reactions (Calvin cycle);
the processes of chemoautotrophs are oxidative reactions of inorganic substances resulting in the release of
energy that is then used to synthesize glucose. Outputs of autotrophs are glucose (stored chemical energy)
and, in the case of photoautotrophs, oxygen.
All heterotrophs are dependent, directly or indirectly, on organisms that manufacture their own food
(autotrophs). Inputs of heterotrophs therefore include food and, in many cases, oxygen (for aerobic
respiration). There are several types of heterotrophic nutrition, with different inputs. Herbivores feed on
producers, whereas carnivores feed on consumers. Omnivores feed on both producers and consumers.
Outputs of heterotrophs are undigested waste products such as fibre and small soluble molecules produced
from digestion such as glucose, amino acids, fatty acids and glycerol. Glucose and other organic molecules
are used in the process of respiration, to release energy and the outputs of water and carbon dioxide.
The processes of heterotrophs involve digestion of polymers into monomers, the absorption of digested
products and, finally, the assimilation of nutrients into cell structure and function. Some heterotrophs carry
out internal digestion and others external digestion. Internal digestion occurs when an animal takes in food
(complex organic matter) and digests it in the alimentary canal or gut, producing molecules that can be taken
up into the body’s cells via the blood circulation system. This is known as holozoic nutrition. Digestion
which occurs outside the organism is known as saprotrophic nutrition. Saprotrophs live on or in dead organic
matter, secreting digestive enzymes into it and absorbing the products of digestion. Feeding by saprotrophs
releases inorganic nutrients from the dead organic matter, including carbon dioxide, water, ammonia, amines
and ions such as nitrates and phosphates. These inorganic nutrients are then absorbed by green plants and
reused.
Some organisms can carry out both autotrophic and heterotrophic nutrition: these organisms are known as
mixotrophs, and their form of feeding mixotrophic nutrition. Pitcher plants are carnivorous, feeding on
captured insects, while also carrying out photosynthesis, for example. Some animals contain algae within
their tissues. Many marine flatworms have algae living symbiotically within their bodies, such as species of
Convoluta. Many species of coral can live in symbiosis with algae. Euglena is a well-known freshwater
example of a protist that is both autotrophic and heterotrophic. Some mixotrophs are obligate (meaning they
always carry out both forms of nutrition, such as Euglena) and others are facultative (sometimes carry out
both but can be either autotrophic or heterotrophic). Many phytoplankton (a type of alga), such as
Cryptomonas sp., are facultative mixotrophs because they take up dissolved organic carbon or, under
inorganic nutrient stress (when they lack access to key nutrients), use dissolved amino acids or other organic
sources of nitrogen.
Theme C Interaction and interdependence

C1.1 Enzymes and metabolism
Page 404
1 What are examples of structure–function relationships in biological macromolecules?
Theme Chapter
A2.2 Cell structure
B1.2 Proteins

Macromolecules are very large organic molecules (for example proteins, nucleic acids, lipids or
polysaccharides). There are many examples of structure–function relationships in biological
macromolecules, as discussed below.
The relationship between structure and function of proteins depends on the distinctive properties of the
amino acids, which are determined by their variable side chain group (R). The side chains of different amino
acids vary in size, shape, charge, hydrophobicity and reactivity. Amino acids with polar side chains are
hydrophilic and tend to be on the surfaces of proteins; by interacting with water, they make proteins soluble
(or partially soluble) in aqueous solutions and can form non-covalent interactions (such as hydrogen bonds)
with other water-soluble molecules. In contrast, amino acids with non-polar side chains are hydrophobic;
they avoid water molecules and often aggregate to form the water-insoluble cores of many proteins. The
polarity of amino acid side chains is responsible for shaping the final three-dimensional structure and hence
shape (conformation) of proteins.
Some proteins take up a tertiary structure that is a long, much-coiled chain; these are called fibrous proteins.
They have long, narrow shapes. Collagen is a fibrous, structural protein that occurs in skin, tendons,
cartilage, bone, teeth, the walls of blood vessels and the cornea of the eye. The collagen molecule consists of
three polypeptide chains, each in the shape of a helix. The chains are wound together as a triple helix
forming a stiff cable, strengthened by numerous hydrogen bonds. Many of these triple helixes lie side by
side, forming collagen fibres, held together by covalent cross-linkages. The ends of individual collagen
molecules are staggered so there are no weak points in collagen fibres, giving the whole structure high
tensile strength. This makes the protein well suited to provide structural support in skin, tendons and
cartilage.
Other proteins take up a more spherical shape and are known as globular proteins. They are mostly highly
soluble in water. Examples include enzymes, such as lysozyme and catalase, and hormones, such as insulin.
Insulin consists of two polypeptide chains linked by disulfide bridges. Insulin is a very small protein,
allowing it to move quickly through the blood. Its shape is recognized by specific receptors on its target cell
surfaces. It is difficult to make a small protein that will fold into a stable structure. This problem is solved by
synthesizing a longer protein chain, which folds into the proper structure. The extra pieces are removed,
leaving two small chains in the mature form. The structure is further stabilized by three disulfide bridges.
As we have seen above, variation in the form of monomers determines the structure and function of the
polymers formed by them. This is also the case in carbohydrates. Each polysaccharide contains only one type
of monomer, for example, starch is built from the monomer glucose. Alpha glucose forms polymers that
produce starch and glycogen, whereas beta glucose forms cellulose:
• Starch is a mixture of two polysaccharides: amylose is an unbranched chain of several thousand 1,4
linked α-glucose units, whereas amylopectin has shorter chains of 1,4 linked α-glucose units with, in
addition, branch points of α-1,6 glycosidic links along its chains. Starch is the major storage
carbohydrate of most plants. It is laid down as compact grains in plastids. Starch is an important energy
source in the diet of many animals, too. Its usefulness lies in the compactness and insolubility of its
molecule. It is readily hydrolysed to form sugar when required.
• Glycogen is a polymer of α-glucose, chemically very similar to amylopectin, although larger and more
highly branched. The function of glycogen is the same that of as starch – to store energy in a cell.
Glycogen is a useful store of energy in cells where there is a large amount of glucose because, as with
starch, the insoluble glycogen has no osmotic effects. The presence of extensive branching in glycogen
means it has a compact structure that allows for more glucose molecules to be stored within a small
volume. The presence of many non-reducing ends due to the branches allows for more rapid enzyme-
controlled hydrolysis of glycogen to release stored glucose when there is an increase in energy demand.
• Cellulose molecules are a polymer of β-glucose molecules. Cellulose molecules are straight and
uncoiled. Successive glucose units are linked at 180º to each other. A β-glucose molecule must be
rotated in orientation to the preceding molecules because a glycosidic bond is formed by removing
water from adjacent –OH groups: to ensure that the two –OH groups are pointing in the same direction
requires one of the two β-glucoses to rotate relative to the other. This structure is stabilized and
strengthened by hydrogen bonds between adjacent glucose units in the same strand and, in fibrils of
cellulose, by hydrogen bonds between parallel strands, too. In plant cell walls additional strength comes
from the cellulose fibres being laid down in layers that run in different directions. Many cellulose fibrils
form fibres. Due to cellulose’s form, it is an extremely strong material – insoluble, tough and durable,
and slightly elastic.
The long hydrocarbon tails present in fats and oils are typically of about 16–18 carbon atoms long, but may
be any even number between 14 and 22. The hydrophobic properties of triglycerides are due to these
hydrocarbon tails. A molecule of triglyceride is quite large, but relatively small when compared to polymers
such as starch and cellulose. It is only because of their hydrophobic properties that triglyceride molecules
clump together (aggregate) into huge globules in the presence of water, giving them the appearance of
polymers. Triglyceride structure allows for efficient energy storage. Mass for mass, fats and oils release
more than twice as much energy as carbohydrates do when they are respired. This is because fats are more
reduced (i.e. more hydrogen atoms relative to carbon and oxygen atoms compared to carbohydrates) than
carbohydrates. Fat therefore forms a concentrated, insoluble energy store.
Fatty acids can be saturated, monounsaturated or polyunsaturated, with the structure of each determining its
function. Fatty acids with one or more carbon–carbon double bond in their hydrocarbon tail are unsaturated.
Fatty acid molecules with no carbon–carbon double bonds are saturated. Differences between the melting
points of the fats is related to the number of C=C double bonds. Double bonds cause a bend in the carbon
chain, which prevents the chains from coming near each other and interacting strongly. In turn, the weak
bonds between the molecules make for a lower melting point.
Lipids built exclusively from saturated fatty acids are known as saturated fats. Saturated fatty acids are major
constituents of butter and cocoa butter. Lipids built from one or more unsaturated fatty acid are referred to as
unsaturated fats by dieticians. These occur in significant quantities in many common fats and oils – they
make up about 70% of the lipids present in olive oil. Where there is a single double bond in the carbon chain
of a fatty acid, the compound is referred to as a monounsaturated fatty acid. However, it is possible and
common for there to be two or more double bonds in the carbon chain. Lipids with two (and sometimes
three) double bonds occur in large amounts in vegetable seed oils, such as maize, soya and sunflower seed
oils. These are examples of polyunsaturated fatty acids. Fats with unsaturated fatty acids melt at a lower
temperature than those with saturated fatty acids, because their unsaturated hydrocarbon tails do not pack as
closely together as those of saturated fats. Polyunsaturated fats are important to the health of our arteries.
Plants use unsaturated fatty acids for energy storage, while endotherms (warm-blooded animals) use
saturated fatty acids. Plants and cold-blooded animals store unsaturated fatty acids in their cells because they
can utilize energy efficiently with less oxygen. Cold-blooded animals use a prevalence of unsaturated fatty
acids (including in the cell membrane) because they have lower melting points than saturated fats, and so
remain liquid at temperatures lower (usually 5 °C or lower) than those rich in saturated fatty acids. Warm-
blooded animals utilize saturated fatty acids because they become liquid at higher temperatures.
A plasma membrane is a structure common to all cells. The plasma membrane maintains the integrity of the
cell (it holds the cell’s contents together). It is also a barrier that all substances entering and leaving the cell
must cross. The lipid of membranes is predominantly phospholipid, together with other lipid types. The
phospholipid has a ‘head’ composed of a glycerol group, to which is attached one ionized phosphate group.
This latter part of the molecule has hydrophilic properties. Hydrogen bonds form readily between the
phosphate head and water molecules. The remainder of the phospholipid consists of two long fatty acid
residues consisting of hydrocarbon chains. These have hydrophobic properties and are repelled by water. So,
phospholipid is unusual in being partly hydrophilic and partly hydrophobic. This is referred to as
amphipathic. Phospholipid molecules arrange themselves as a bilayer, with the hydrocarbon tails facing
together. In the lipid bilayer, attractions between the hydrophobic hydrocarbon tails on the inside, and
between the hydrophilic glycerol/phosphate heads and the surrounding water on the outside, make a stable,
strong barrier.
The fourth group of biological molecules are the nucleic acids. Nucleic acids are very long, thread-like
(linear) macromolecules with alternating sugar and phosphate molecules forming the ‘backbone’. This part
of the nucleic acid molecule is uniform and unvarying. Sugar–phosphate bonding creates a continuous chain
of covalently bonded atoms in each strand of DNA (and also RNA) nucleotides, which forms a strong
backbone to the molecule. Along the strand, bases are attached to pentose sugar molecules. The bases project
sideways, forming the genetic code. Since the bases vary, they represent a unique sequence that carries the
coded information held by the nucleic acid. Hydrogen bonds between complementary bases, and the strong
backbone, provide great stability to DNA. The double strand of DNA can be split using enzymes and the
genetic code transcribed into mRNA. In this way, DNA’s structure makes it suitable for inheritance: it stores
the genetic code in a stable molecule that is replicated easily, which means that the genetic code is preserved
from one generation to the next.
2 What biological processes depend on differences or changes in concentration?

Theme Chapter
B3.1 Gas exchange
B3.2 Transport
C1.3 Photosynthesis
D D2.3 Water potential
D3.3 Homeostasis
Passive transport (simple diffusion, facilitated osmosis) and active transport are the two modes of transport
across the plasma membrane in living organisms. In passive transport, substances (for example carbon
dioxide and oxygen) move across the membrane by simple diffusion, without any use of energy as they are
moving down their concentration gradient. This diffusion of substances depends on their size, solubility in
water (a polar solvent) or organic solvents (non-polar solvents). Facilitated diffusion is a passive process that
involves specific proteins in the plasma membrane.
Gas exchange requires differences in concentration of oxygen and carbon dioxide. The concentration
gradient is maintained by movement of blood and ventilation.
Osmosis is a special type of diffusion of water across a selectively permeable membrane, which depends on
a concentration (and pressure) gradient. The net direction of flow of water by osmosis is determined by
solute potential and pressure potential. The osmotic behaviour of cells depends on the concentration of solute
in the surrounding solution.
Diffusion and osmosis are both passive transport processes that act to equalize the concentration of a solution
and are driven by changes in concentration of dissolved solute.
In active transport, energy in the form of ATP is utilized to move molecules or ions across membranes
against a concentration gradient. Pumps use energy from ATP to transfer specific particles across
membranes and can therefore move particles against a concentration gradient. In the kidney, active transport
of sodium ions takes place in the ascending limb to maintain high osmotic concentrations in the medulla,
facilitating water reabsorption in the collecting duct. Cotransporters are used in glucose absorption by cells
in the small intestine and in glucose reabsorption by cells in the nephron.
The rate of enzyme reactions depends on the concentrations of substrate and enzyme – an increase of either
leads to increased chance of collisions between enzyme and substrate, and increased enzyme–substrate
complexes.
End-product inhibition occurs when the product of the last reaction in a metabolic pathway inhibits the
enzyme that catalyses the first reaction of the pathway. In this type of inhibition, as the product molecules
accumulate, the steps in their production are switched off. However, these product molecules may now
become the substrates in subsequent metabolic reactions. If so, the accumulated product molecules will be
used up and production of new product molecules will recommence. An example of end-product inhibition is
a metabolic pathway that produces isoleucine. Bacteria can synthesize isoleucine from threonine. Isoleucine
acts as a non-competitive inhibitor by binding to the allosteric site of the enzyme threonine deaminase.
Threonine deaminase is an essential enzyme in the first stage of the metabolic pathway – its inhibition turns
off isoleucine production: this regulates the production of isoleucine. Initially, when isoleucine concentration
is still low, the metabolic pathway can proceed as there are low levels of non-competitive inhibition. As
isoleucine concentration increases, non-competitive inhibition takes place and the metabolic pathway is
regulated. As isoleucine is used in the cell for protein synthesis, its concentration falls and the allosteric sites
of threonine deaminase are no longer occupied, so the enzyme can once again act in the conversion of
threonine to isoleucine.
The resting potential is the potential difference across a nerve cell membrane when it is not being stimulated.
It is normally about −70 millivolts (mV). The resting potential difference is re-established across the neuron
membrane after a nerve impulse has been transmitted. The resting potential is the product of the active
transport of potassium ions (K+) inwards across the membrane and sodium ions (Na+) out across the
membrane. This takes place by means of a K+/Na+ pump, using energy from ATP. Three Na+ are pumped out
for every two K+ pumped in across the plasma membrane of the neuron. The tissue fluid outside the neuron
therefore contains many more positive ions than are present in the tiny amount of cytoplasm inside the
neuron. As a result, a negative charge is developed inside the cell compared to outside, and the resting
neuron is said to be polarized. The membrane potential is the difference in charge between the inside and
outside of a neuron, created due to the unequal distribution of ions on both sides of the cell.
Nerve impulses are action potentials that are propagated along nerve fibres. The action potential is the
potential difference produced across the plasma membrane of the nerve cell when stimulated, reversing the
resting potential from about −70 mV to about +40 mV. The nerve impulse is electrical because it involves
the movement of positively charged ions, leading to a potential difference (voltage) across the membrane.
The action potential is generated by sodium channels opening, allowing Na+ to flow down their
concentration gradient into the axon. When the sodium ions enter the neuron, their positive charges make the
membrane potential of that part of the membrane inside the cell more positive. The resting potential is
restored when potassium channels open, allowing K+ to flow down their concentration gradient to the outside
of the axon, thus making the inner side of the membrane more negatively charged again, with the sodium–
potassium pump completing the process.
Some homeostatic mechanisms depend on changes in concentration of substances in the body. For example,
the changes in blood sugar concentrations lead to the release of insulin (in the case of an increase in blood
sugar levels) or glucagon (if there is a decrease in sugar levels). The osmolarity (solute concentration) of the
blood is monitored by osmoreceptors in the hypothalamus, which cause the release of antidiuretic hormone if
blood becomes too concentrated.
In plants, substances need to be moved from where they are synthesized to other tissues or organs where they
are used by cells. Materials may need to be transported to storage sites and retrieved from storage sites.
Chemical signals, for example hormones, will also need to move. Translocation in plants relies on the active
loading of sucrose into sieve tube elements. Generation of root pressure in xylem vessels is also achieved by
active transport, where minerals are moved against their concentration gradient in order to lower water
potential in xylem vessels.
Both respiration and photosynthesis rely on the flow of protons down their electrochemical gradient to
synthesize ATP (a process known as chemiosmosis). A proton gradient is generated by the flow of electrons
along the electron transport chain.
In mitochondria, the electron-carrier proteins are arranged in the inner membrane in a highly ordered way.
These carrier proteins oxidize the reduced coenzymes and energy from the oxidation process. This process is
used to pump hydrogen ions (protons) from the matrix of the mitochondrion into the space between inner
and outer mitochondrial membranes. The hydrogen ions accumulate here. Because the inner membrane is
largely impermeable to ions, a significant gradient in hydrogen ion concentration builds up, generating a
potential difference across the membrane. This represents a store of potential energy. The protons
concentrated in the space between inner and outer mitochondrial membranes flow back into the matrix, via
the channels in the ATP synthase enzyme (ATPase), also found in the inner mitochondrial membrane. As the
protons flow down their concentration gradient, through the enzyme, the energy is transferred as ATP
synthesis occurs. ATP synthase therefore couples the release of energy from the proton gradient with
phosphorylation of ADP. ATPase has a rotational mechanism – energy generated by the rotation of the
enzyme leads to the production of ATP.
In the grana of chloroplasts, the synthesis of ATP is coupled to electron transport via the movement of
protons by chemiosmosis, as in mitochondria. Here, it is the hydrogen ions trapped within the thylakoid
space that activate the rotatory mechanism of ATP synthase enzymes, moving down their electrochemical
gradient. At the same time, ATP is synthesized from ADP and Pi. As excited electrons from photosystem II
pass along the electron transport chain or electron carriers, some of the energy causes the pumping of
hydrogen ions (protons) from the chloroplast’s matrix into the thylakoid spaces. Here, protons accumulate,
causing the pH to drop. The result is a proton gradient that is created across the thylakoid membrane, which
sustains the synthesis of ATP. Protons pass down their electrochemical gradient through ATPase, resulting in
the synthesis of ATP.

Page 424
1 In what forms is energy stored in living organisms?
Theme Chapter
C1.3 Photosynthesis

The proton gradients generated by proton pumping during the electron transport chain are a stored form of
energy. When protons move down their electrochemical gradient (from the intermembrane space to the
matrix in mitochondria), they cause a rotatory mechanism in ATP synthase, an enzyme embedded in the
inner mitochondrial membrane, to generate ATP.
Polysaccharides are used as energy storage compounds in animals and plants because of their coiling and
branching during polymerization and their relative insolubility (due to their large molecular size) and the
relative ease of adding or removing alpha-glucose monomers by condensation and hydrolysis to build or
mobilize energy stores. Starch is the storage polysaccharide used in plants and glycogen is the storage
polysaccharide used in animals.
Triglycerides are also used to store energy in organisms. Triglycerides store more energy per unit mass than
polysaccharides, and they are suited to long-term energy storage functions.
Energy stored as biological matter is known as biomass. New biomass is produced by producers through the
process of photosynthesis and is known as primary production. Due to loss of biomass when carbon
compounds are converted to carbon dioxide and water in cell respiration, secondary production is lower than
primary production in an ecosystem. As energy is transferred along food chains, the amount of energy
becomes less, which ultimately limits the length of food chains.
2 What are the consequences of respiration for ecosystems?

Theme Chapter
C C1.3 Photosynthesis

Energy is transferred from one organism to another in a food chain, but only some of the energy transferred
becomes available to the next organism in the food chain. Energy is therefore lost between trophic levels in a
food chain.
Reasons for energy loss:
• Much of the energy is used for cell respiration to provide energy for growth, movement, feeding and all
other essential life processes. Energy from respiration is ultimately lost as heat.
• Not all food eaten can be digested. Some passes out with the faeces. Indigestible matter includes bones,
hair and feathers in animals, and lignified fibres in plants.
• Not all organisms at each trophic level are eaten. Some escape predation.
Only about 10% of what is eaten by a consumer is converted into new biomass and can therefore then be
transferred on through the food chain. There are two consequences of this:
• Food chains in ecosystems are short. Little of what is eaten by one consumer is potentially available to
those in the next trophic level, and so only a few transfers can be sustained. It is uncommon for food
chains to have more than four or five links between a producer (green plant) and a top carnivore.
• Feeding relationships in a food chain may be structured like a pyramid. At the start of the chain is a very
large amount of living matter (biomass) of green plants, and therefore more energy. This supports a
smaller biomass of primary consumers that, in turn, supports an even smaller biomass of secondary
consumers, and so on.
Ecosystems are open systems in which both energy and matter can enter and exit. Sunlight energy ensures
that energy lost in the form of heat energy, as a result of respiration, is replaced through the process of
photosynthesis, maintaining the stability of ecosystems. Ecosystem respiration is the combination of

autotrophic and heterotrophic respiration, resulting in the loss of carbon from the ecosystem to the
atmosphere.
C1.3 Photosynthesis
Page 449
1 What are the consequences of photosynthesis for ecosystems?
Theme Chapter
B B3.1 Gas exchange
C1.3 Photosynthesis

Ecosystems are open systems in which both energy and matter can enter and exit. Sunlight energy ensures
that energy, lost as heat energy because of respiration, is replaced through the process of photosynthesis,
maintaining the stability of ecosystems.
Photosynthesis provides the oxygen required by organisms for aerobic respiration. The increase in free
oxygen in the atmosphere early on in the Earth’s history has enabled sufficient levels of aerobic respiration
in organisms, leading to the evolution of multicellular organisms. The creation of ozone in the atmosphere
protected the surface of Earth from harmful ultraviolet radiation, enabling animals to move from water onto
land.
The advent of photosynthesis led to a reduction in carbon dioxide in the atmosphere. Changes in levels of
photosynthesis have been linked to changes in carbon dioxide levels over geological history, which have
resulted in global warming and global cooling events, and to the mass extinction of organisms.
The evolution of plants led to the development of leaves, which lose water in the process of transpiration.
Transpiration forms part of the water cycle, which impacts on ecosystems in several ways: rainfall leads to
rock and soil erosion, which shapes ecosystems, and the water is needed by all organisms to support life and
is one of the key molecules needed for photosynthesis.
The feeding relationships between organisms are represented in food chains. Most food chains begin with
photosynthetic organisms. Plants are the primary producers in the food chain; other organisms feed on them.
Some do so directly (the herbivores); others do so indirectly, by feeding on the herbivores or on organisms
that do. So, virtually all life (including human life) is dependent on green plant nutrition, that is, on
photosynthesis.
2 What are the functions of pigments in living organisms?

Theme Chapter
B B3.2 Transport
C1.3 Photosynthesis
D D3.1 Reproduction
D3.2 Inheritance

Biological pigments are coloured compounds that are produced by metabolism (enzyme-controlled reactions
inside cells). For example, melanin is a biological pigment responsible for the colour of skin, hair and eyes.
There are many different pigments and accessory pigments in photosynthetic organisms:
• Anthocyanins are aromatic, water-soluble polyphenol pigments found in fruit, vegetables and flowers.
The colour of anthocyanin molecules is affected by the presence of cations, pH and temperature. They
can act as acid–base indicators.
• Carotenoids are lipid-soluble plant pigments involved in the absorption of blue light during
photosynthesis. Carotenoids are found in yellow and orange vegetables and fruits, and in many dark
green vegetables. β-carotene (a precursor to vitamin A) is found in carrots and has a characteristic
orange colour. It appears orange when viewed in white light since its molecules absorb strongly in the
violet–blue (400–510 nm) region of the electromagnetic spectrum.
• Chlorophylls are the main photosynthetic pigments in leaves and are involved in absorbing the light
needed in the process of photosynthesis. Chlorophyll molecules ionize and donate an electron to the
electron transport chain. Chlorophyll occurs in plants in two closely related forms: chlorophyll a (blue–
green) and chlorophyll b (yellow–green).
The porphyrins are a series of related nitrogen-containing macrocyclic (large single ring with multiple donor
sites) conjugated ligands that are able to coordinate strongly with a specific metal cation. Examples of
porphyrins and their cations are chlorophyll (Mg2+); haemoglobin (Fe2+), which is used to transport oxygen
in the blood; myoglobin (Fe2+), a protein found in striated muscles that is used to supply oxygen to muscle
cells; and the cytochromes (Fe2+ and Fe3+, depending on their oxidation state), which are involved in the
electron transport chain in mitochondria and chloroplasts.
In plants, pigments act as visible signals to attract insects, birds and other animals for pollination and seed
dispersal. Pigments also protect plants from damage caused by UV and visible light, such as the purple
pigment betalain (see page 233 of the Student’s book). Many pigment-rich fruits are consumed in the human
diet. The pigment content of fruits is due to the wide variety of compounds that are present and is responsible
for the characteristic green, yellow, orange, red, blue and purple colours. Fruits change colour as they ripen.
The evolution of colour vision in primates is thought to be linked to the colour of ripe fruit – by being able to
see red, primates were able to select ripe fruit, rather than fruit that was green and underdeveloped.
Although animals cannot synthesize carotenoids, some animal foods contain them because animals absorb,
modify and deposit dietary carotenoids in tissues. The yellow in egg yolk, for example, is due to carotenoids.

Page 466
1 What patterns exist in communication in biological systems?
Theme Chapter

Cells respond to changes in their environment by receiving and integrating signals from other cells. In this
way, communication takes place between different biological systems in an organism. Most cell signals are
coordinated by chemical signal molecules called ligands. For example, motile single-celled organisms detect
nutrients in their environment and move towards the source. Bacteria also use chemical signalling.
In multicellular organisms, chemical signals include growth factors, morphogens, cytokines and hormones
that may have come from neighbouring cells or from more distant sources. Neurotransmitters are chemical
signals that cross the synapses of adjacent neurons.
In cell differentiation, morphogens occur across a gradient of concentrations: these gradients drive the
process of differentiation of unspecialized stem cells into different cell types. Different concentrations of the
morphogen result in the initiation or inhibition of gene expression, which in turn determines the way in
which cells differentiate and develop into specific tissues. The concentration of the morphogen in each
particular cell then determines a series of subsequent signals (cascades). Responses to these signals
determine the direction and extent of cell growth and development, ultimately forming all the tissues and
organs of the body. The expression of such gradients also controls the length of body structures such as toes
and fingers, the location of the nose and other body patterns. The pattern of morphogen distribution therefore
communicates to cells the timing and degree of specialization.
Cells can detect these signals because of receptors in their plasma membrane to which the ligand binds. This
then triggers an internal response. This transference of signal is known as signal transduction and the cell’s
response to a chemical signal (ligand) may be fast or slow.
Receptors are typically transmembrane proteins, which, when the ligand binds to them, activate internal
signalling pathways. However, some receptors occur within the cell nucleus. These particular receptors are
stimulated by ligands (non-polar molecules) that pass through the plasma membrane. The activation of a
receptor (internal or external) initiates a chain of responses (often amplified) and often involves a second
messenger.
2 In what ways is negative feedback evident at all levels of organization?

Theme Chapter
B B3.2 Transport
D3.1 Reproduction
D3.3 Homeostasis
Negative feedback occurs at all levels of biological organization, from the biochemical level to the
ecosystem level.
An example of negative feedback at the biochemical level is when an enzyme acting early in a reaction
pathway is inhibited by a later product of that pathway, known as end-product inhibition. When large
amounts of the final product begin to accumulate, the product binds to an earlier enzyme and slows down its
catalytic action, limiting further entry of substrates into that reaction pathway.
At the tissue level, negative feedback occurs in the menstrual cycle. The developing follicle secretes
oestradiol, which stimulates the building up of the endometrium (the lining of the uterus). This prepares the
uterus for possible implantation of an embryo, if fertilization takes place. The concentration of oestradiol
continues to increase to a peak value just before the midpoint of the cycle. When oestradiol reaches its
highest level, it inhibits further secretion of FSH from the pituitary gland. This prevents the possibility of
further follicles being stimulated to develop (an example of negative feedback).
At the organism level, in mammals, regulation of body temperature, blood glucose level and the
concentration of water and ions (osmolarity) in blood and tissue fluid (osmoregulation) are all regulated by
negative feedback involving various hormones, for example, ADH, insulin and glucagon (Figure C2.1.1).
Figure C2.1.1 Negative feedback
At the ecosystem level, population interactions can lead to negative feedback loops. For example, in
predator–prey interactions, as the prey increases in population density, the predator population also
increases. The increase in the predator numbers eventually leads to a reduction in prey numbers, which in
turn leads to a reduction in the predator. The cycle then continues to repeat.

Page 489
1 In what ways are biological systems regulated?
Theme Chapter
C1.3 Photosynthesis
D D2.2 Gene expression (HL only)
D2.3 Water potential
D3.1 Reproduction
D3.3 Homeostasis
Homeostasis is the life process that maintains internal conditions in the body within narrow limits.
Homeostatic mechanisms include:
• Thermoregulation
o Birds and mammals regulate their body temperature by physiological and behavioural means.
o Thermoregulation in humans involves vasodilation, vasoconstriction, shivering, sweating, uncoupled
respiration in brown adipose tissue and hair erection.
• Regulation of blood glucose
o This involves the control of secretion of insulin and glucagon by pancreatic endocrine cells, transport
of the hormones in the blood, and the effects on target cells (muscles and the liver).
• The kidney’s role in osmoregulation and excretion.
Homeostasis involves negative feedback, where homeostatic variables are returned to the set point from
values above and below the set point.
Changes during the ovarian and uterine cycles involve hormonal regulation. Oestradiol, progesterone,
luteinizing hormone (LH) and follicle-stimulating hormone (FSH) interact to regulate the menstrual cycle,
which involves both positive and negative feedback mechanisms.
Ventilation and heart rate are controlled by feedback mechanisms. Feedback control of heart rate follows
sensory input from baroreceptors and chemoreceptors: baroreceptors monitor blood pressure and
chemoreceptors monitor blood pH and concentrations of oxygen and carbon dioxide. The medulla
coordinates responses by sending nerve impulses to the heart to change the heart’s stroke volume and heart
rate. Feedback control of ventilation rate follows sensory input from chemoreceptors. Changes in pH, as the
result of increased or decreased carbon dioxide dissolved in the blood plasma, are monitored by
chemoreceptors in the brainstem and lead to the control of ventilation rate using electrical impulses to the
diaphragm and intercostal muscles.
Metabolic pathways have a variety of processes that regulate them. Feedback inhibition uses products to
inhibit enzyme reactions. In respiration and photosynthesis, coenzymes (NAD, FAD and NADPH) transfer
hydrogen (and therefore electrons), which regulates these processes.
Transcription and translation are regulated to ensure control of protein synthesis. Regulation of transcription
involves proteins (promoters, enhancers and transcription factors) that bind to specific base sequences in
DNA. Control of the degradation of mRNA is a means of regulating translation. In human cells, mRNA may
persist for time periods from minutes up to days, before being broken down by nucleases.
Although water moves freely into and out of cells, its movement can be controlled by pumping ions against
their concentration gradient, altering the solute potential of the cell. Active transport regulates the movement
of nutrients and ions across the cell membrane: for example in the kidney, sodium ions in the ascending limb
of the loop of Henle help to maintain high osmotic concentrations in the medulla, facilitating water
reabsorption in the collecting ducts.
Synapses regulate the transfer of electrical signals around the body. Regulation of cell signalling pathways
involves positive and negative feedback.
In plants, interactions between auxin and cytokinin regulate root and shoot growth. Root tips produce
cytokinin, which is transported to shoots, and shoot tips produce auxin, which is transported to roots.
Interactions between these phytohormones help to ensure that root and shoot growth are integrated.
2 How is the structure of specialized cells related to function?

Theme Chapter
B3.1 Gas exchange
B3.2 Transport

Unspecialized cells are formed following fertilization, and subsequently develop into specialized cells by
differentiation, involving different patterns of gene expression within an early-stage embryo. Cell
differentiation is the process for developing specialized tissues in multicellular organisms. The basis for
differentiation is often triggered by changes in the environment. Cell size is an aspect of specialization.
Examples in humans include male and female gametes, red and white blood cells, neurons and striated
muscle fibres.
The human egg cell (ovum) is around 110 µm in diameter, whereas the main body of the sperm is 5 µm wide
with a mid-piece (containing mitochondria) and flagellum of 50 µm. The larger cell body of the egg allows it
to store nutrients for the early development of the fertilized egg, whereas the cell body of the sperm only
needs to hold the nucleus, for delivery to the egg, and so can be much smaller. The long flagellum of the
sperm provides propulsion.
Red blood cells (erythrocytes) are around 8 µm in diameter, much smaller than white blood cells (around
12–17 µm). Red blood cells need to be small so that they can fit through the small lumen of capillaries. In
addition, their small size and shape mean that red blood cells have a larger surface area compared to their
cell size, allowing oxygen to diffuse in and out from the cell at a faster rate.
Neurons (nerve cells) transmit electrochemical impulses through the body, allowing coordination and
response to stimuli to occur. Their length enables the electrical impulse to be sent without interruption over a
long distance. Responses to stimuli, especially those concerned with pain, need to be dealt with quickly, so
fast transmission of the impulse is needed – something achieved by the long length of the myelinated neuron.
Striated muscle fibres are multinucleated cells that attach to muscles to allow movement. Instead of being
made from many individual cells, muscle fibres are extended cellular structures that can be several
centimetres long. This extended length allows them to coordinate contraction and has a significant effect on
muscle force generation.
Ciliated cells are specialized cells that are used in animals to move substances within the body. Cilia occur in
large numbers on certain cells, such as the ciliated lining (epithelium) of the air tubes serving the lungs
(bronchi), where they cause the movement of mucus across the cell surface. It is the cilia of this ‘bronchial
tree’ that cigarette smoke destroys over time. They are also found inside the oviduct where they help move
the egg (ovum) from the ovary to the uterus.
Goblet cells are cells that secrete mucus. They are found in the breathing system in the trachea and bronchi,
and in the digestive system in the small and large intestines. In the breathing system, mucus traps micro-
organisms and particles in the air, and is moved to the mouth using cilia. In the digestive system, mucus
protects the lining of the alimentary canal, such as in the stomach where acid conditions and digestive
enzymes would otherwise damage the stomach wall. The mucus also lubricates food to ensure smooth
passage through the gut.
Phloem tissue transports sugars in plants. Phloem cells are composed of two different types of cell: sieve
tubes and companion cells. Sieve tubes are narrow, elongated elements, connected end to end to form tubes.
The end walls, known as sieve plates, are perforated by pores. The cytoplasm of a mature sieve tube has no
nucleus, nor many of the other organelles of a cell. Each sieve tube is connected to a companion cell by
strands of cytoplasm, called plasmodesmata, which pass through narrow gaps in the cell walls. The
companion cells service and maintain the cytoplasm of the sieve tube, which has lost its nucleus. The sieve
tube elements are an example of an atypical cell structure in eukaryotes, as they do not contain a nucleus.
Other specialized plant cells include guard cells, palisade cells, spongy mesophyll and root hairs.
• Stomata open and close due to the change in turgor pressure of the guard cells. They open when water is
absorbed by the guard cells from the surrounding epidermal cells. When the guard cells become fully
turgid, they each push into the epidermal cell beside them (because of the way cellulose is laid down in
the cell walls). A pore develops between the guard cells. When water is lost and the guard cells become
flaccid, the pore closes again.
• Palisade mesophyll forms a single layer of cells towards the top of the leaf; they are full of chloroplasts
to maximize photosynthesis.
• Spongy mesophyll contains air spaces where gas exchange occurs.
• Root hair cells ensure a large surface area for the absorption of water and minerals into plants.

Page 516
1 What are examples of branching (dendritic) and net-like (reticulate) patterns of organization?
Theme Chapter
B3.1 Gas exchange
B3.2 Transport
D D3.1 Reproduction

Branching patterns are seen at different levels of organization. At the molecular level, the branching pattern
of polymers such as starch and glycogen, which occurs during polymerization, leads to their relative
insolubility (due to their large molecular size) and the relative ease of adding or removing alpha-glucose
monomers by condensation and hydrolysis to build or mobilize energy stores. At the cellular level, in the
nervous system, neurons have dendrites that link to many other neurons via synapses. This type of branching
is known as ‘dendritic’ organization. The amount of branching is correlated to the function of the neuron.
Some tissues have a branching pattern. Cardiac muscle tissue has a branching structure, which helps the
heart muscle to contract in three dimensions. Organs themselves can have a branching structure. For
example, the mammalian lung is composed of a tree of branching tubes (trachea branch into bronchi, which
in turn divide into many bronchioles, at the end of which are the alveoli). The branching structure ensures
that the alveoli are filled with air approximately uniformly. The branching structure of capillaries in animals
ensures that every cell in the body of a multicellular animal receives sufficient quantities of nutrients and
oxygen. In plants, branching structures include the roots and branches of trees, ensuring that a large surface
area is covered for maximum absorption of light (leaves on branches), water and minerals (roots).
Evolution can follow a branching pattern, with ancestral species leading to many new species through
processes such as adaptive radiation. The relationship between all species is known as the ‘tree of life’,
where all species are ultimately related, and are descended from a universal common ancestor.
‘Reticulate’ comes from the Latin reticulum, which means ‘net’. Reticulation, and the exchange of genetic
information this leads to, can occur at many different biological levels: chromosomal level (meiotic
recombination, which causes the shuffling of genes at the chromosomal level), population level (through
sexual reproduction between individuals – sexual recombination) and species level.
Evolution at the species level is normally seen as the accumulation of mutational changes within
evolutionary lineages that are passed on to the new generation leading to a bifurcating evolutionary pattern.
However, reticulate evolution suggests that genetic changes may also arise from gene transfer between
different lineages.
The most obvious reticulate processes that may occur at the species level are related to hybridization (such as
hybrid speciation) and horizontal gene transfer (the exchange of genetic material between bacteria – or via an
external vector such as a virus).
At the ecosystem level, food webs form a net-like structure, with many interconnections between different
food chains. This is because most prey species have to escape the attentions of more than one predator.
Predators, as well as having preferences, need to exploit alternative food sources when one source becomes
limited. They also take full advantage of gluts of food as particular prey populations become temporarily
abundant. Food webs represent the flow of matter and energy through communities, and can be used to
predict the effect of perturbation on ecosystems (for example, if a top predator is removed). Reduction in the
top predator can lead to an increase in the number of prey that it feeds on, which in turn leads to a reduction
in subsequent species in the food chain. Reduction of lower trophic levels can have a knock-on effect on
producers, leading to population growth due to decreased predation. This interdependence means that if one
essential organism is removed from the chain, for example due to human impacts such as habitat loss, then
the food web could collapse. This may endanger the entire ecosystem, especially when keystone species are
affected.
2 What are the consequences of positive feedback in biological systems?

Theme Chapter
D D3.1 Reproduction
D3.3 Homeostasis
D4.3 Climate change

Positive feedback is a process that increases change, promoting deviation away from an equilibrium.
In plants, positive feedback is used in fruit ripening. Ethylene, a phytohormone, is produced by a fruit which
then causes neighbouring fruit to ripen. These fruits, in turn, produce ethylene, which causes increased fruit
ripening. This system ensures the rapid and synchronized production of ripe fruit.
Generally, animals are looking to maintain equilibrium within narrow limits, via homeostatic mechanisms.
Negative rather than positive feedback is used in homeostatic control, where negative feedback returns
homeostatic variables to the set point from values above and below the equilibrium.
However, there are some examples of positive feedback loops that exist in animal bodies. One is found in the
cascade of chemical reactions that result in blood clotting, or coagulation. As one clotting factor is activated,
it activates the next factor in sequence until a fibrin clot is achieved.
Ovulation (the release of a mature egg cell from the ovarian follicle and its release from the ovary) also
involves a positive feedback loop. FSH, secreted by the pituitary gland, stimulates the development of
several immature egg cells (in primary follicles) in the ovary. The developing follicle then secretes
oestradiol, which leads to an increase in FSH receptors in the follicles, increasing oestradiol production
further. The high level of oestradiol stimulates the secretion of LH by the pituitary gland. LH stimulates
ovulation on day 14 of the cycle.
Another example of positive feedback in humans occurs in the hormonal control of childbirth, where
changes during childbirth are triggered by a decrease in progesterone levels, allowing increases in oxytocin
secretion due to positive feedback. Contractions of the uterine wall stimulate stretch receptors, which signal
the brain to release the hormone oxytocin from the posterior pituitary. Oxytocin levels increase and stimulate
the wall of the uterus and the contractions become stronger. This stimulates the stretch receptors, causing
more oxytocin release (positive feedback). Oxytocin also relaxes the elastic fibres that join the bones of the
pelvic girdle, especially at the front, helping the dilation of the cervix so that the head of the baby (the widest
part of the offspring) can pass through. Control of contractions during birth occurs via a positive feedback
loop. The resulting powerful, intermittent waves of contraction of the muscles of the uterus wall start at the
top of the uterus and move towards the cervix. The rate and strength of the contractions increase, until they
expel the offspring. Finally, less powerful uterine contractions separate the placenta from the endometrium,
and cause the discharge of the placenta and remains of the umbilical cord as the afterbirth.
In ecology, destabilizing positive feedback mechanisms will drive systems towards tipping points, where a
new equilibrium is reached. There are examples of positive feedback in the process of global warming.
Positive feedback mechanisms involve increasing temperatures, melting permafrost and the release of
methane. As methane is a greenhouse gas, it has the potential to increase temperatures, thereby reinforcing
the rise in temperature. Other positive feedback mechanisms causing the enhanced greenhouse effect involve
the release of carbon dioxide from the deep ocean; increases in absorption of solar radiation due to loss of
reflective snow and ice; accelerating rates of decomposition of peat and previously undecomposed organic
matter in permafrost; and increases in droughts and forest fires.

Page 547
1 How do animals protect themselves from threats?
Theme Chapter
B B3.3 Muscle and motility (HL only)
D3.1 Reproduction

Different forms of locomotion allow animals to escape danger and avoid predation. Adaptations in marine
mammals, such as limbs that form flippers and a tail that forms a fluke with up-and-down movement, allow
fast movement through the water to escape predators, for example seals and sea lions avoiding predation by
killer whales.
Adaptations of prey include defences and warning signals, such as bright coloration. Physical defences, such
as the hard shell on tortoises and turtles, or the spines of a hedgehog (a small mammal found throughout
parts of Europe, Asia and Africa), prevent the predator from being able to eat the prey or cause pain to the
predator, thereby discouraging animal predation. Animals such as woodlice and millipedes roll into a ball
when threatened by a predator – a physical and behavioural adaptation.
Some species have evolved camouflage as an adaptation where the organisms resemble their background.
This means that they are less visible to predators. Chameleons have some of the best-known camouflage of
any animal. They are lizards in the family Chamaeleonidae and are found in Africa, Madagascar, southern
Europe and southern Asia. Fischer’s chameleon, for example, is found in Tanzania.
Warning colouration is used by some species to warn predators that the prey species may be toxic and not
good to eat. For example, the caterpillars of the cinnabar moth have distinctive black and yellow stripes –
this combination of colours is often used in the animal kingdom to indicate that an animal is poisonous. The
caterpillar absorbs toxins from the ragwort on which it feeds. Predators that eat the caterpillar will
experience an unpleasant taste and the presence of toxic chemicals, and so learn not to eat those caterpillars
in future. This type of defensive mechanism is called aposematic or warning colouration, and is a type of
chemical adaptation to avoid predation.
Some species mimic the colour, size and shape of venomous species, for example non-venomous king
snakes mimic coral snakes, one of the most poisonous snakes on Earth. Predators are tricked into thinking
that king snakes are poisonous and so avoid them. King snakes do not have to invest in making poison but
have all the advantages of coral snakes in avoiding predation.
Animal adaptations that protect against threats are the result of evolution by natural selection. Mutation and
sexual reproduction generates the variation on which natural selection acts. Intraspecific competition within
a species leads to differential survival value and reproductive potential of specific genotypes, which in turn
result in adaptations, such as physical, physiological or behavioural changes, that protect against threat.
2 How can false-positive and false-negative results be avoided in diagnostic tests?

Theme Chapter
A2.2 Cell structure
D3.1 Reproduction
Diagnostic tests are used in detecting disease and for monitoring its progression. Diagnostic tools and
equipment are also used in guiding treatment and evaluating its effectiveness.
A false-positive test is a test result that indicates that a person has a specific disease or condition when the
person does not have the disease or condition. A false-negative test is one that indicates that a person does
not have a specific disease or condition when the person does actually have the disease or condition (Table
C3.2.1).
Table C3.2.1 The range of outcomes from the diagnostic tests for a disease
Without disease With disease
Positive test false-positive true positive
Negative test true negative false-negative

Diagnostic tests can be invasive and non-invasive, and include biopsy (a sample of tissue taken for
examination), colonoscopy (a thin tube with a camera inserted into the anus to view inside the bowel), CT
scan (X-rays used to create detailed pictures inside the body), hearing tests (wearing headphones and
responding when sounds are heard at different volumes), ultrasound (real-time images inside your body
using sound waves produced by a transducer pressed against your body) and blood tests.
Various tests are available to assess the presence of bacteria and viruses as the cause of infection. These
include staining and examination under a microscope, culturing (placed in conditions that encourage the
growth of micro-organisms), testing for antibodies, testing for antigens (for example lateral flow tests) and
testing for genetic material (such as DNA or RNA) from the pathogen. Pregnancy testing uses detection of
human chorionic gonadotropin secretion. PCR (polymerase chain reaction) tests are a fast, highly accurate
way to diagnose certain infectious diseases and genetic changes. The tests work by finding the DNA or RNA
of a pathogen or abnormal cells in a sample.
Commercial genetic tests can yield information about potential future health and disease risk. One possible
impact is that, without expert interpretation, this information could be difficult to understand.
Some non-invasive diagnostic tests use imaging (image-guided diagnostic testing) as a diagnostic tool, for
example X-rays, MRI and fMRI. Although not using the same techniques as, for example, lateral flow tests,
they are still capable of generating false-positive and false-negative diagnoses.
The likelihood of false results (both false-positive and false-negative) is an important issue for diagnostic
tests and has to be determined at the time of establishing the test.
All tests will have a threshold level for detection and, if the signal is below that, the test will appear negative.
This is a universal feature of tests, and unavoidable, so it is important to know what the limit of detection is.
If the threshold level is too high, the proportion of false-negative results is likely to also be unacceptably
high.
False-positives are more difficult to avoid, because they arise when the test responds to something other than
the target. The probability of false-positive results should be established during test development, but it is not
easy to test every possible contaminant that might be present.
The usual approach to try to reduce the risk of false results is to include a positive control, i.e. a sample that
contains a known amount of the target. A number of samples, each with different amounts of the target to
take account of the threshold, are an even better option. Negative samples should be included as controls as
well. By including these controls the possibility of being fooled by a false result is reduced and there is
increased confidence that the results obtained are reliable.
Ideally all diagnostic tests should be carried out with multiple samples: measurements are repeated to
strengthen the reliability of data. Two or three replicates, at least, of each test sample would be necessary to
give greater reliability in the results; however, that is not always possible or practical, for example as with
the COVID-19 lateral flow tests that have been in common use (and which are often only 80% reliable).
Testing replicates is always best practice.

Page 577
1 What are the benefits of models in studying biology?
Theme Chapter
B1.2 Proteins
C C4.1 Populations and communities

Models in biology are artificial representations of natural phenomena and are used to understand biological
processes or structures. There are many benefits to using models in biology, such as:
• to increase knowledge about biological systems

• to estimate or predict variables of interest
• to help explain how something works or to describe how something is structured
• to make predictions or to explain observations
• to simplify complex or abstract systems.
In 1953, James Watson and Francis Crick developed the first model of DNA, revealing for the first time that
it is a double helix made of two antiparallel strands of nucleotides. Biochemical reactions can also be
demonstrated using either physical or digital molecular models, for example condensation reactions forming
dipeptides and longer chains of amino acids, or polysaccharides forming from sugar monomers.
In 1935, chemical analysis of cell membranes indicated the presence of large amounts of protein, along with
phospholipid molecules. Scientists Hugh Davson and James Danielli suggested that the phospholipid bilayer
was located between two layers of proteins (i.e. sandwiched between them). Pores were thought to be present
in places in the membrane. The Davson–Danielli model was accepted for many years. The model was
ultimately proved to be incorrect (i.e. it was falsified). Analysis of the falsification of the Davson–Danielli
model led to the Singer–Nicolson model. This fluid mosaic model, proposed by Jonathan Singer and Garth
Nicolson in 1972, is the model accepted today. The model integrates peripheral and integral proteins,
glycoproteins, phospholipids and cholesterol.
When skeletal muscle contracts, the actin and myosin filaments slide past each other in response to nervous
stimulation, causing shortening of the sarcomeres. This occurs in a series of steps, sometimes described as a
ratchet mechanism. A great deal of ATP is used in the contraction process. The cyclic interactions in muscle
contraction and their dependence on ATP was demonstrated by attaching fluorescent dye to the myosin
molecules, prior to causing them to ‘row’ along the actin filament. When electromagnetic radiation of a
particular wavelength illuminated this contracting tissue, the cyclic movement of the myosin heads was
detectable. The velocity of movement observed could be correlated with changing ATP concentrations. This
so-called ‘sliding filament’ model helps to explain the contraction of all muscles, including cardiac and
skeletal muscle.
Population growth is modelled using S-shaped (sigmoid) population growth curves. Population growth slows
as a population reaches the carrying capacity of the environment. The curve represents an idealized graphical
model – in reality, population growth may show variation or fluctuations from the model.
Studying natural ecosystems can be difficult because there are many variables that cannot be controlled, such
as temperature, wind and rainfall. Mesocosms overcome such difficulties and provide a way of studying the
effects of independent variables on the structure and functioning of an ecosystem. Mesocosms are a model
used to investigate the effect of variables on ecosystem sustainability. They can be set up in open tanks, but
sealed glass vessels are preferable because entry and exit of matter can be prevented but energy transfer is
still possible. Mesocosms enable all variables other than the independent and dependent variable to be kept
constant. Precise manipulation of the independent variable can be made, along with accurate measurement of
the dependent variable. The sustainability of an ecosystem may change when an external factor disrupts the
natural balance. Mesocosms can investigate the effect of altering one variable on the stability of an
ecosystem and establish whether the changes are sustainable.
2 What factors can limit capacity in biological systems?

Theme Chapter

At the cellular level, there is a limit to the capacity of cells to divide endlessly and differentiate along
different pathways. Early embryonic stem cells have the capacity to become any cell type in the body,
including the placenta, but later stem cells can only become specific tissues.
Species have a range of tolerance for limiting factors, such as temperature, salinity, pH and availability of
water. The law of tolerance states that an organism or population has certain minimum, maximum and
optimum environmental factors that determine success. These critical minimal and critical maximum limits
are a species’ limits of tolerance.
Biomes are groups of ecosystems with similar communities due to similar abiotic conditions and convergent
evolution. Abiotic factors determine terrestrial biome distribution. For any given temperature and rainfall
pattern, one natural ecosystem type is likely to develop. Graphs can be used to show the distribution of
biomes with these two climatic variables on the horizontal and vertical axes. Specific climate conditions
characterize the tropical forest, temperate forest, taiga, grassland, tundra and hot desert biomes.
Concentrations of carbon dioxide, light intensity or temperature are limiting factors on the rate of
photosynthesis and, therefore, productivity. Primary production is the accumulation of carbon compounds in
biomass by autotrophs. Biomes vary in their capacity to accumulate biomass, depending on the climatic
conditions where they are found.
Factors that limit capacity have been a driving force in evolution by natural selection. Overproduction of
offspring and competition for resources are factors that promote natural selection. Factors that may limit
carrying capacity include food and other resources.

Page 601
1 What are the direct and indirect consequences of rising carbon dioxide levels in the atmosphere?
Theme Chapter
A A1.1 Water
B1.2 Proteins
B3.1 Gas exchange
B3.2 Transport
D4.3 Climate change

The direct effects of rising carbon dioxide in the atmosphere include ocean acidification and global warming.
Ocean acidification leads to collapse of coral ecosystems. Global warming has many direct effects:
Polar ice melt
At the North Pole, Arctic sea ice is being lost at a rate of almost 13% per decade, meaning that there may be
no ice by the summer of 2060. The associated Greenland ice is similarly in decline. At the South Pole,
Antarctica has lost approximately three trillion tons of ice since the early 1990s. Research has shown that
Greenland and Antarctic ice sheets are losing ice six times faster than they were in the 1990s.
Glacier retreats
Since 1980, glaciers worldwide have been in rapid retreat. Mid-latitude mountain ranges such as the
Himalayas, the Tibetan plateau, Alps, Rockies and the southern Andes, plus the tropical summit of
Kilimanjaro, show the greatest losses of glacier ice. Rivers below these mountain ranges are glacier-fed, so
the melting of glaciers will have an increasing impact on the water supplies for millions of people.
Rising sea levels
The impact of global warming on sea levels is due to the thermal expansion of sea water and the widespread
melting of polar ice. The global sea level rose at an average rate of 1.8 mm per year in the period 1960–2003
but, during the latter part of that period, the rate was far higher than at the beginning. If this acceleration
continues at the current rate, sea levels could rise by at least 30 cm in this century. This phenomenon will
threaten low-lying islands and countries, such as Bangladesh, and major city communities such as London,
Shanghai, New York and Tokyo.
Changing weather and ocean current patterns
At the poles cold, salty water sinks and is replaced by surface water that is warmed in the tropics. Melting ice
decreases ocean salinity, which then slows the great ocean currents. Ocean currents convey heat energy from
warmer to colder regions through their pattern of convection. So, for example, as the Gulf Stream (which, to
date, has kept temperatures in Europe relatively warmer than those in Canada) slows down, more heat is
retained in the Gulf of Mexico. Here, hurricanes get their energy from hot water and are becoming more
frequent and more severe.
Alterations in the patterns of heat and rainfall distribution over continental land masses are predicted to cause
Russia and Canada to experience the largest mean temperature rises, followed by several Asian countries and
already drought-ridden countries in West Africa.
Coral bleaching
Corals are colonies of small animals embedded in a calcium carbonate shell that they secrete, with a
mutualistic relationship with algae (see page 353 of the Student’s book). When under environmental stress
(such as high water temperatures), the algae are expelled (causing loss of colour) and the coral starts to die.
Mass bleaching events occurred in the Great Barrier Reef in 1998, 2002, 2016, 2017 and 2020. Today, coral
reefs are dying all around the world. The effects of thermal stress are likely to be exacerbated under future
climate scenarios.
There are also indirect consequences of rising carbon dioxide levels in the atmosphere. Rising carbon
dioxide levels affect plants directly by increasing rates of photosynthesis and reducing the loss of water
(plant transpiration) by reducing the opening of stomata. This leads to several indirect effects. For example,
when plants reduce the aperture of their stomata, they use less soil water. Research has shown that elevated
carbon dioxide leads to a decrease in whole plant water use of 5–20%. This leads to a change in the amount
of soil water available to other plants. At the same time, altered water availability and enhanced
photosynthesis can change the amount of leaf, root and soil biomass, resulting in changes to ecosystem
functioning. The indirect effects of elevated carbon dioxide explain, on average, 28% of the total plant
productivity response, and are almost equal to the size of direct effects on evapotranspiration.
Elevated carbon dioxide also leads to changes in the chemical composition of plant tissues. Due to increased
photosynthetic activity, non-structural carbohydrates (sugars and starches) per unit leaf area increase on
average by 30–40% under elevated carbon dioxide. Nitrogen concentrations in plant tissues typically
decrease, with nitrogen per unit leaf mass decreasing on average by 13%. These changes would have
repercussions for human nutrition. Protein concentrations in grains of wheat, rice and barley, and in potatoes,
decrease by 5–14% under elevated carbon dioxide.
Under elevated carbon dioxide most plant species therefore show higher rates of photosynthesis, increased
growth, decreased water use and lowered tissue concentrations of nitrogen and protein. Rising carbon
dioxide over the next century is likely to affect both agricultural production and food quality.
2 How does the transformation of energy from one form to another make biological processes possible?
Theme Chapter
A A1.1 Water
B B3.3 Muscle and motility (HL only)
C1.3 Photosynthesis
D D4.3 Climate change

Transformations are processes within systems that involve the formation of a new end product, or a change
of state (for example liquid to gas). Some examples of transformations include:
• energy transformation: visible light (short-wave radiation) absorbed by Earth’s surface and emitted as
long-wave radiation (heat)
• energy-to-matter transformation: photosynthesis converting sunlight energy with carbon dioxide and
water into glucose
• matter-to-energy transformation: respiration breaking down glucose into water, carbon dioxide and
energy.
The transformation of light energy to chemical energy, when carbon compounds are produced in
photosynthesis, ensures an ongoing input of energy into food chains. This energy transformation supplies
most of the chemical energy needed for life processes in ecosystems. As energy is transferred along a food
chain, it is ultimately lost as heat by respiration. Reductions in energy availability at each successive stage in
food chains are due to large energy losses between trophic levels. Decomposers, feeding on waste and dead
organisms, ensure that the energy in detritus is returned to the environment as heat when they use absorbed
material for respiration.
Energy transformations occur in anabolic and catabolic reactions. Anabolism includes the formation of
macromolecules from monomers by condensation reactions, including protein synthesis, glycogen formation
and photosynthesis. Catabolism includes the hydrolysis of macromolecules into monomers in digestion and
oxidation of substrates in respiration. Cell respiration is a catabolic system for producing ATP within the cell
using energy released from carbon compounds, while photosynthesis is an anabolic system for trapping
sunlight energy in glucose.
When skeletal muscle contracts, actin and myosin filaments slide past each other in response to nervous
stimulation, causing shortening of the sarcomeres. This occurs in a series of steps, described as a ratchet
mechanism. ATP and the transformation of energy is necessary for the contraction process. The myofibril is
stimulated to contract by the arrival of an action potential, which triggers the release of calcium ions from
the sarcoplasmic reticulum to surround the actin molecules. Calcium ions now react with the protein troponin
which, when activated in this way, triggers the removal of the blocking molecule, tropomyosin. The binding
sites are now exposed. Each bulbous head of myosin, to which ADP and Pi are attached (called a charged
bulbous head), reacts with a binding site on the actin molecule beside it. The phosphate group (Pi) is
dislodged (removed) from the head at this moment. The ADP molecule is then released from the bulbous
head and this is the trigger for the rowing movement of the head, which tilts by an angle of about 45º,
pushing the actin filament along. At this step, the power stroke, the myofibril has been shortened
(contraction). Finally, a new molecule of ATP binds to the bulbous head. The protein of the bulbous head
includes the enzyme ATPase, which catalyses the hydrolysis of ATP. When this reaction occurs, the ADP
and inorganic phosphate (Pi) formed remain attached, and the bulbous head is now ‘charged’ again. The
charged head detaches from the binding site and straightens. Repeated contractions result in movement.
In food chains, the release of energy occurs in both autotrophs and heterotrophs by oxidation of carbon
compounds in cell respiration. Energy is ultimately returned to the environment through heat loss: this occurs
in both autotrophs and heterotrophs due to conversion of chemical energy to heat in cell respiration. Energy
transfers are not 100% efficient, so heat is produced both when ATP is produced in cell respiration and when
it is used in cells.
Life on land on the early Earth was not possible due to high levels of ultraviolet radiation. The subsequent
evolution of photosynthetic bacteria, and an increase in oxygen levels in the atmosphere, led to the creation
of ozone, which blocked UV light and made life on land possible. Ozone is a greenhouse gas, along with
carbon dioxide, nitrous oxide (N2O), methane, water vapour and CFCs. Greenhouse gases in the atmosphere
trap infrared light and heat the atmosphere, making life on Earth possible. Without the greenhouse effect, the
average temperature on Earth would be 33 °C cooler (i.e. −18 °C).
Theme D Continuity and change

D1.1 DNA replication
Page 614
1 How is genetic continuity ensured between generations?
Theme Chapter
B B1.2 Proteins
D3.1 Reproduction
D3.2 Inheritance
DNA replication allows the genetic code to be copied from one cell to two daughter cells. Reproduction is
the means by which the code contained within the genome is passed on to new generations. In asexual
reproduction, mitosis ensures that genetically identical offspring are produced, that are adapted to an existing
environment. Sexual reproduction, where gametes are produced by the process of meiosis, produces
offspring with new gene combinations, and therefore variation. This variation is needed for adaptation to a
possibly changing environment.
Meiosis ensures that the number of chromosomes is maintained from one generation to the next. It does this
by halving the number of chromosomes in gametes (so that they have one set of chromosomes rather than
two), so that at fertilization the diploid number of chromosomes is restored.
The genome codes for the proteome of an organism – continuity between generations ensures that the same
genome is passed on, with DNA translation and transcription ensuring that proteins are synthesized in a
predictable and consistent way. Mutations lead to changes in the genetic code: evolution and natural
selection select against unwanted mutations, which helps ensure genetic continuity of useful traits that help a
species survive.
2 What biological mechanisms rely on directionality?

Theme Chapter
B B1.2 Proteins
B3.2 Transport
D3.1 Reproduction

Directionality can be seen at every level of biological organization, from the micro to the macro scale.
At the molecular level, DNA, RNA and proteins are all sequences – if you read them in the opposite
direction they do not work. This is obviously true for DNA, with its codon triplets, but equally the case for
proteins, where inverted sequences do not fold and have no function. The form of beta-sheets and alpha-
helices depends on the bonds that form between amino acid residues and, therefore, on the directionality of
the amino acid sequence.
At the cellular level, the mechanisms of movement across membranes can also be seen as directional –
letting molecules and ions enter or leave the cell cytoplasm in one direction. A large part of membrane
function is to maintain different pH, voltage and ion concentrations on each side of the membrane.
Membranes also help to generate energy, by allowing protons through the membrane to drive the rotary
ATPase protein complex.
Tissues, organs and organ systems show directionality at the organism level. In eukaryotes there are three
main systems that produce movement. One system is actin fibres and myosin, the motor that moves along
actin in muscles. In mammals, the heart is adapted for delivering pressurized, oxygenated blood to the
arteries. This one-directional flow ensures that oxygen is absorbed into the blood in the lungs and then
delivered rapidly to respiring tissue. Valves in veins ensure that blood flows back to the heart in one
direction through the body.
In the nervous system, neurotransmitters are produced in vesicles in the presynaptic knob, and then diffuse
across the synapse to receptors on the postsynaptic membrane. This ensures that signals travel in one
direction through the nervous system, from receptors to effectors.
In plants, xylem vessels provide hollow tubes in which water moves up the plant through the process of
transpiration. Evaporation from the leaves, powered by the Sun, generates the transpiration pull and so water
movement through plants is unidirectional. Pollen tube growth is also in one direction – from the pollen on
the stigma down to the ovum within the ovule and ovary. Tropisms in plants are also directional processes,
as a response to stimuli such as light and gravity.
At the ecosystem level, energy flow through food chains is from producers to consumers. The directionality
of energy flow supports ecosystems, but ultimately means that all energy is lost as heat due to inefficient
energy transformations. This means that food chains tend to be short, with insufficient energy remaining to
support higher consumers.

Page 636
1 How does the diversity of proteins produced contribute to the functioning of a cell?
Theme Chapter
A2.2 Cell structure
B B1.2 Proteins
B2.2 Organelles and compartmentalization
C1.3 Photosynthesis
D3.1 Reproduction
Proteins play a variety of roles in the functioning of a cell. They are responsible for nearly every aspect of
cell structure and function, including cell shape and inner organization, product manufacture and removal of
waste products. Proteins also receive signals from outside the cell and activate intracellular responses, in a
process known as cell signalling.
The amino acid sequence of proteins determines the way they fold and their ultimate shape. Fully folded
proteins have distinct characteristics that determine how they interact with other molecules. Structural
proteins maintain cell shape and compose structural elements in connective tissues such as cartilage and
bone in vertebrates. Enzymes are proteins that catalyse biochemical reactions that occur in cells, and control
metabolic pathways such as respiration and photosynthesis. They form the electron transport chain, which
generates a proton gradient within mitochondria and chloroplasts, which leads to the generation of ATP.
DNA replication, transcription, translation and recombination are regulated by proteins. Enzymes, such as
helicase and DNA polymerase, control DNA replication; RNA polymerase is one of several enzymes that are
involved in transcription. Transcription is also regulated by proteins that bind to specific base sequences in
DNA.
Cyclins are a family of proteins that control the cell cycle by activating cyclin-dependent kinase (CDK)
enzymes. Proteins are also involved in cell division. Microtubules play a major role in organizing the
cytoplasm and in the distribution of organelles. They also form the mitotic spindle during cell division.
Proteins of the cytoskeleton pinch the cell membrane in cytokinesis and separate the cytoplasm between two
cells. Histone proteins in eukaryotes help condense the DNA so that it can be supercoiled and moved around
the cell during cell division.
Proteins in the plasma membrane have several different roles, each of which contributes to the functioning of
the cell. Proteins receive chemical signals from outside the cell, translating chemical signals into intracellular
action. Other proteins anchor the cell in a particular location. Glycoproteins (a carbohydrate chain attached
to a protein) are involved in cell–cell recognition. Most antigens are glycoproteins or other proteins. Integral
transmembrane proteins transfer ions and molecules from one side of the membrane to the other. Active
transport moves specific molecules such as glucose from a lower concentration outside the cell to a higher
concentration within the cell, using energy from respiration; facilitated diffusion transports ions and
molecules down their concentration gradient. Aquaporins are small channels in the cell membrane that are
involved in the movement of water.
Actin filaments are involved in various forms of cell movement, including cell locomotion. Actin in the tail
of sperm is involved in the regulation of sperm motility, and its presence in the head helps in the acrosome
reaction.
2 What biological processes depend on hydrogen bonding?

Theme Chapter
A A1.1 Water
A1.2 Nucleic acids
B1.2 Proteins
B3.2 Transport

A hydrogen bond is a weak bond caused by electrostatic attraction between a positively charged part of one
molecule and a negatively charged part of another. Many biological processes depend on hydrogen bonding.
The structure of proteins relates to their function, which in turn controls many biological processes, such as
muscle contraction and enzyme activity. The secondary structure of proteins is maintained by hydrogen
bonds (–NH⋯O=) between C=O and –NH groups of the peptide backbone. The tertiary structure is
maintained by hydrogen bonds between R-groups of the same polypeptide to allow the protein to fold into a
functional conformation. Quaternary structure is maintained by a number of interactions including hydrogen
bonds between R-groups of different polypeptides, allowing for interaction between different subunits of the
same protein. For example, in collagen molecules, hydrogen bonds between R-groups of adjacent
polypeptides in a collagen molecule give the structure high tensile strength.
Hydrogen bonding in enzyme molecules confers the three-dimensional conformation of their active site,
which is crucial to their function, for example the binding of a specific substrate. Interactions involving the
enzyme active site and substrate may also involve hydrogen bonds, which help to bind the active site to the
substrate and hold them in the correct orientation for the reaction to occur.
Hydrogen bonding also plays a role in the structure and function of carbohydrates. Cellulose fibres have
hydrogen bonds between cellulose chains, which confer high tensile strength. The cell walls of plants depend
on this strength to withstand hydrostatic pressure that builds up in the cell following movement of water
from a lower solute concentration to a higher solute concentration. Turgor pressure in plant cells supports the
plant tissue and enables processes such as photosynthesis and phototropism. In plant transpiration, hydrogen
bonds form between water molecules, allowing water uptake via transpiration and capillary action.
In a largely aqueous environment, the ability of molecules to form hydrogen bonds with water means that
they are soluble, so that molecules can diffuse, be transported or be metabolized.
Hydrogen bonds between complementary bases cause DNA to be a stable, double-stranded molecule. This
stability gives the DNA molecule durability and allows replication and transcription to be carried out reliably
and repeatedly. Hydrogen bonds between complementary bases are weak intermolecular forces that can
break easily so that the DNA can separate into two strands to allow for DNA replication and transcription.
DNA replication uses one strand as a template to synthesize a new strand: free nucleotides form hydrogen
bonds with bases on the DNA strand. Transcription, in contrast, uses free ribonucleotides to form hydrogen
bonds with the DNA strand.
During translation, tRNA transfers amino acids to the mRNA at the ribosome. tRNA has intramolecular
hydrogen bonds which maintain its three-dimensional conformation in order that tRNA can fit into the active
site of aminoacyl-tRNA synthetase, so that it can be joined to its corresponding amino acid. During
translation, the anticodon on tRNA forms hydrogen bonds with the complementary codon on mRNA, which
allows the polypeptide synthesized to have an amino acid sequence corresponding to the codon sequence on
mRNA.
Ligand–receptor interactions may also involve hydrogen bonds, allowing a ligand to bind, causing
conformational changes and triggering cell signalling. As hydrogen bonds are weak interactions, this allows
for the ligand to bind and dissociate (i.e. binding is temporary) from the receptor.

Page 647
1 How can natural selection lead to both a reduction in variation and an increase in biological diversity?
Theme Chapter
B B1.2 Proteins
C C4.2 Transfers of energy and matter
D3.1 Reproduction

Natural selection is the mechanism through which evolution takes place. Mutation and sexual reproduction
(through the process of meiosis) generate the variation on which natural selection acts. Random mutation
causes variation, from which those best adapted to the environment survive and pass on their ‘successful’
alleles to the next generation. Variation in a characteristic is associated with variation in fitness (the average
overall reproduction of individuals with a given genotype relative to that of individuals with other
genotypes). Natural selection operates continuously and over billions of years, resulting in the biodiversity of
life on Earth.
Natural selection leads to both a reduction in variation and an increase in biological diversity. Natural
selection can lead to reduction of alleles in a gene pool by selecting for or against a specific gene or gene
combination (leading to directional selection). Fewer alleles are present in the gene pool, which leads to a
reduction in variation. On the other hand, natural selection can lead to adaptive radiation where populations
of a species are exposed to new environmental selection pressures, resulting in niche diversification and, if
reproductive isolation takes place, to speciation.
Biodiversity is the variety of life in all its forms, levels and combinations, including ecosystem diversity,
species diversity and genetic diversity. Increasing species diversity through speciation leads to increased
genetic diversity. Increased diversity of producers leads to increased complexity of food webs and ultimately
to increased ecosystem diversity. With varied adaptations of producers to trap sunlight, the flow of energy
through ecosystems can be maximized, which increases the complexity of food webs and the stability of the
ecosystem. All these factors lead to an increase in biological diversity, generated through the process of
natural selection.
2 How does variation in subunit composition of polymers contribute to function?

Theme Chapter
A2.2 Cell structure
B1.2 Proteins

Polymers are large organic molecules made up of repeating subunits called monomers, for example
polypeptides are made from many amino acids. Variation in monomers determines the structure and function
of the polymers formed by them. For example, alpha glucose forms polymers that produce starch and
glycogen, whereas beta glucose forms cellulose. The orientation of beta glucose allows hydrogen bonds to
form between adjacent molecules in cellulose, which strengthens the structure. The consequences of these
differences are that cellulose is insoluble in water and so has a structural function, whereas starch and
glycogen are used for storage. The structure of cellulose makes it an extremely strong material: insoluble,
tough and durable, and slightly elastic. The presence of extensive branching in glycogen and starch means
that these molecules have a compact structure that allows for more glucose molecules to be stored within a
small volume. Both starch and glycogen can be readily hydrolysed to form glucose when required to provide
energy for the body.
Nucleotides form the monomers of nucleic acids. DNA nucleotides contain deoxyribose and the bases
adenine (A), cytosine (C), thymine (T) and guanine (G). RNA contains ribose and the bases A, C, U (uracil)
and G. DNA forms the nucleic acid that stores genetic information, while RNA is synthesized as an essential
intermediate molecule formed by transcription of the DNA template. RNA allows the genetic code to be
translated to form proteins. The structural difference between the sugars deoxyribose and ribose gives DNA
added stability, making DNA more suitable for the storage of genetic information, whereas the relative
instability of RNA makes it more suitable for its shorter-term functions. Most types of RNA molecules show
extensive intramolecular base pairing between complementary sequences within the RNA strand, causing
folding of the molecule and creating predictable three-dimensional structures that are essential for their
function. tRNA, for example, has short (70–90 nucleotides) stable lengths of RNA with extensive
intramolecular base pairing, which contains an amino acid binding site and an mRNA binding site. The
earliest life is believed to have had RNA as its form of nucleic acid because of the catalytic properties the
molecules have, as well as the role of RNA in passing the genetic code from one generation to the next.
A protein’s primary structure is determined by the order of amino acids, which is in turn determined by the
sequence of codons in mRNA, itself determined by the series of codons in DNA. The order of amino acid
residues determines the structure and ultimate function of the protein. Single amino acid changes, caused by
mutations, can lead to an alteration in protein structure and can result in diseases such as sickle cell anaemia,
caused by a change to haemoglobin. A single amino acid change to Ras proteins (proteins involved with
growth, proliferation and migration of cells) makes cancers about four times more likely.
At a larger scale, replacing one protein subunit with another can result in different functions. Lactate
dehydrogenase (LDH), also known as lactic acid dehydrogenase, is an enzyme involved in cellular
respiration. It exists in five different forms. LDH enzymes are found in many tissues in the body, including
red blood cells, the heart, liver, kidneys, brain, lungs and skeletal muscles. Each LDH enzyme has a slightly
different structure, with different concentrations in different tissues. For example, LDH-1 is found mostly in
red blood cells and heart muscle; LDH-3 is concentrated in the lungs.

Page 669
1 What processes support the growth of organisms?
Theme Chapter
A2.2 Cell structure
B B1.2 Proteins
C1.3 Photosynthesis
D3.1 Reproduction
Growth is one of the life processes, which means an increase in size either through an increase in the number
of cells or through an increase in the size of each individual cell.
At a molecular level, the synthesis of polymers, such as polypeptides, from monomers (amino acids, in the
case of proteins) provides the structural biomolecules for growing cells and organisms. DNA replication is
required for reproduction, and for growth and tissue replacement in multicellular organisms. New cells
require new DNA, which is synthesized in parent cells prior to cell division. Mitosis forms two daughter
cells from one parent cell, allowing cells to proliferate and new tissues to form. In plants, growth occurs in
the embryo with the support of nutrient reserves in the seed during germination. In animals, growth of the
embryo is initially supported by nutrient reserves in the zygote, and then (in placental animals) by food and
oxygen from the mother via the placenta.
In plants, the zygote grows by repeated mitotic division to produce cells that form an embryonic plant,
consisting of an embryo root, an embryo stem and either a single cotyledon (seed leaf) or two cotyledons.
Once the seed is in favourable conditions, germination allows the plant to grow: the plant produces a shoot,
leaves and roots. For germination to take place, food reserves are mobilized (i.e. stored food such as starch is
made available to the growing embryo). A particular plant growth substance (known as gibberellic acid, GA)
is produced by the cells of the embryo. This growth-promoting substance passes to the food stored in the
cotyledons. Here, protein reserves are converted to hydrolytic enzymes that mobilize the stored food
reserves. The main event is the production of the enzyme amylase, which hydrolyses starch to maltose. This
disaccharide is then hydrolysed to glucose. The resulting soluble sugar (and other compounds) sustain
respiration and also provide the building blocks for synthesis of the intermediates essential for new cells.
Once a plant has grown past the early embryo stage, all later growth of the plant occurs by proliferation at
restricted points in the plant, called meristems. A meristem is a group of cells that retains the ability to divide
by mitosis. These cells are small, with thin cellulose walls and dense cytoplasmic contents. Vacuoles in the
cytoplasm are mostly absent, marking them apart from typical mature plant cells (which have large fluid-
filled vacuoles). Meristems occur either at terminal growing points of stems and roots, or they are found
laterally.
Directional growth in plants is achieved through the hormone auxin. The positively phototropic response of
plants occurs when a light stimulus causes auxin to be released from the growing tip of the coleoptile. Light
from the illuminated side of the plant causes auxin to accumulate on the darkened side of the stem,
increasing its concentration. Auxin on the darkened side causes cells to elongate there, bending the stem
towards the light. This directs leaves towards a source of light, enabling photosynthesis to be maximized.
Anabolic processes, such as photosynthesis, lead to the growth of producers. Limiting factors, such as carbon
dioxide concentration, temperature and levels of sunlight, determine the rate of photosynthesis, which
supports growth in plants. Ecosystems that exist in climates that maximize rainfall, temperature and
insolation have greater rates of primary production and storage of energy in biomass than ecosystems in less
optimal environments.
The oxidation of organic substrates in respiration, a catabolic process, releases energy to support life
processes, including growth. Consumption of organisms by consumers in food chains maintains the growth
of individuals and populations, through the transfer of energy and biomass.
2 How does the variation produced by sexual reproduction contribute to evolution?

Theme Chapter
B B1.2 Proteins
D D3.1 Reproduction

The individuals in a species are not all identical, but show variations in their characteristics. Variation arises
in meiosis in gamete formation, and in sexual reproduction at fertilization. Genetic variations in meiosis arise
via random assortment of paternal and maternal chromosomes in the process of gamete formation. The
crossing over of segments of individual maternal and paternal homologous chromosomes results in new
combinations of genes on the chromosomes of the haploid gametes. These processes operate each time
meiosis occurs and is followed by fertilization. Fusion of male and female gametes in sexual reproduction is
random, meaning that any sperm can fertilize any egg. The results are new combinations of existing
characteristics that may favour individuals in their lifetime – they may affect survival and opportunities to
reproduce. If so, a particular individual’s success in reproduction will result in certain alleles being passed on
to the next generation in greater proportions than other alleles.
As a result of all these factors, the individual offspring of parents are not identical. Rather, they show
variations in their characteristics. Each offspring has a genome different to that of their parents; if sufficient
changes to the gene pool take place, alterations to the proteome of a species can lead to increased
reproductive success (fitness). Through time, changes to the gene pool, combined with reproductive
isolation, can lead to speciation.
Natural selection results in offspring with favourable characteristics. Genetic variation has arisen in
organisms when:
• the favourable characteristics are expressed in the phenotypes of some of the offspring
• these offspring may be better able to survive and reproduce in a particular environment; others will be
less able to compete successfully to survive and reproduce.
Thus, natural selection operates to determine the survivors and the genes that are perpetuated in future
progeny. In time, this selection process may lead to new varieties and new species. For example, the fittest of
the wildebeest (herbivores) of the African savannah may be those with the most acute senses, fastest reflexes
and strongest leg muscles for efficient escape from predators. By natural selection for these characteristics,
the health and survival of wildebeest is maintained.

Page 680
1 What mechanisms are there for inhibition in biological systems?
Theme Chapter

Inhibition affects all levels of biological systems, from the molecular level with enzymes to the population
level with species population growth.
Inhibition in enzymes can be non-competitive or competitive. In non-competitive inhibition, specific

substances can bind to an allosteric site in the enzyme. This causes interactions within an enzyme that lead to
changes in the enzyme shape, altering the active site enough to prevent catalysis. In these interactions,
binding is reversible. Competitive inhibition occurs when an inhibitor binds reversibly to an active site; it is
in competition with the enzyme’s substrate.
Some metabolic pathways are regulated by feedback inhibition. In end-product inhibition, as the product
molecules accumulate, the steps in their production are switched off. But these product molecules may now
become the substrates in subsequent metabolic reactions. If so, the accumulated product molecules will be
removed and production of new product molecules will recommence. For example, isoleucine is an end
product that acts as an inhibitor of an enzyme used in the initial stage of the pathway.
In other metabolic pathways, mechanism-based inhibition is the result of chemical changes to the active site
caused by the irreversible binding of an inhibitor, for example the effect of penicillin on bacterial cell walls.
Penicillin inhibits DD-transpeptidase, a bacterial enzyme that forms cross-links between murein strands in
the cell wall, strengthening the structure. By inhibiting transpeptidase, the cell walls are not cross-linked so
are weak. Without a strong cell wall, a bacterial cell is vulnerable to the movement of water into the cell by
osmosis, which kills the bacteria by lysis (the increased pressure of water inside the cell causes the
membrane to burst).
In populations, numbers of individuals increase until the carrying capacity is reached, i.e. the maximum
number of a species that can be supported by a given environment. Numbers of individuals in a population
may fluctuate due to density-independent factors, but density-dependent factors tend to push the population
back towards the carrying capacity. Intraspecific competition affects the carrying capacity of a population.
Populations with high numbers per area (i.e. higher density) will experience more intraspecific competition
and therefore have a lower carrying capacity due to the lower amount of food available. In interspecific
competition, species with similar niches will compete for similar resources, lowering the carrying capacity of
one or both of the species. In this way, further population growth is inhibited and the population size kept to
sustainable limits. Overproduction of offspring and competition for resources, such as food and other factors
that may limit carrying capacity, promote natural selection.
2 In what ways does the environment stimulate diversification?

Theme Chapter
B B1.2 Proteins
D D2.2 Gene expression (HL only)
D3.1 Reproduction
D3.2 Inheritance

During early-stage embryo development, complex mechanisms of gene expression determine the ways in
which cells differentiate and take up specific roles. This leads to diversification of cell and tissue type, and
ultimately to the development of organs and organ systems. The basis for differentiation is different patterns
of gene expression often triggered by changes in the environment. A small number of genes are involved in
determining body patterns during development. The specific signalling molecules that are involved in gene
expression are called morphogens. These molecules are extracellular (i.e. exist outside the cells of a tissue)
and occur across a gradient of concentrations: these gradients drive the process of differentiation of
unspecialized stem cells into different cell types. Different concentrations of the morphogen result in the
initiation or inhibition of gene expression, which in turn determines the way in which cells differentiate and
develop into specific tissues. The concentration of the morphogen in each particular cell then determines a
series of subsequent signals (cascades): responses to these signals determine the direction and extent of cell
growth and development, ultimately forming all the tissues and organs of the body. The expression of such
gradients also controls the length of body structures such as toes and fingers, the location of the nose and
other body patterns.
Methylation of DNA and histones affects gene expression in cells. These affect which proteins are produced
and the diversity present within the proteome. The environment of cells also affects proteins in a different
way. In most proteins within the cell environment, folding is a rapid process in which some accessory
proteins, including enzymes, are normally involved. These may determine the shape as much or more than
the amino acid sequence does.
Asexual reproduction is suited to populations that are adapted to an existing environment and so
diversification does not take place. In sexual reproduction, however, offspring are produced with new gene
combinations and thus variation needed for adaptation to a changing environment is generated.
Phenotype refers to the observable traits of an organism resulting from genotype and environmental factors.
Some traits are due to genotype only, for example blood type, and so the environment plays no role. Some
traits are due to environment only and others are due to interaction between genotype and environment. If a
trait is affected by the environment, variation in the phenotype of a population is apparent. Phenotypic
plasticity is the capacity to develop traits suited to the environment experienced by an organism, by varying
patterns of gene expression. Phenotypic plasticity is not due to changes in genotype, and the changes in traits
may be reversible during the lifetime of an individual.
Ecological succession is the change in a community through time. Change in the community is brought
about by the interaction between a community of organisms and the physical environment in which they live.
Succession can be triggered by changes in both the abiotic environment and in biotic factors. Over time,
changes to the environment, such as increase in soil and corresponding retention of water, lead to a
succession ultimately resulting in a climax community. Different species are found at each stage of the
succession, with each seral stage having distinctive abiotic conditions that attract species with niches that
correspond to the specific conditions. As the abiotic and biotic conditions change, so too do the species
within a community. Diversification therefore occurs throughout the succession, with the climax community
usually providing conditions that offer the greatest habitat complexity and therefore containing the greatest
diversity.
Variation within a population combined with selection pressure can lead to speciation and diversification. If
environmental conditions change, organisms within a population can be better adapted, survive and
reproduce, and pass on alleles that confer an advantage. If reproductive isolation occurs, due to geographical,
behavioural or ecological barriers, the separated populations can evolve into separate species, resulting in
increased biodiversity.

Page 692
1 What variables influence the direction of movement of materials in tissues?
Theme Chapter
A A1.1 Water
B3.2 Transport
C1.3 Photosynthesis

In tissues, water moves from a higher osmotic concentration to a lower osmotic concentration. The solute
concentration in cells determines osmotic concentration, which in turn determines direction of movement of
water through a tissue. When glucose is used in respiration, the solute concentration of a cell is reduced.
Similarly, when glucose as stored as glycogen (in animal cells) or starch (in plant cells), the solute
concentration is reduced, which affects the osmotic concentration and the movement of water into or out
from the cell.
Xylem tissue transports water and minerals in plants from the roots to the leaves. The osmotic concentration
in the xylem tissue of the root determines the speed and direction of water movement. Endodermal cells of
the root contain a Casparian strip made of a waterproof substance (suberin) which blocks the apoplast
pathway, directing water through the symplast pathway. This ensures water flows into the xylem and not out,
enabling the plant to control water movement. In addition to the Casparian strip, endodermal cells pump salts
into the xylem. This lowers the water potential of the xylem (i.e. increases solute concentration) enabling
water to move down a water potential gradient. This creates a positive pressure potential, moving water and
dissolved minerals a short distance up the xylem. Root pressure is generated to cause water movement in
roots and stems when transport in the xylem due to transpiration is insufficient, for example when high
humidity prevents transpiration or in spring, before leaves on deciduous plants have opened.
Abiotic factors determine the rate of transpiration from leaves. Decreased humidity and increased sunlight,
wind and temperature all increase transpiration. The transpiration pull is generated by energy from the Sun
causing water to evaporate from leaves. The movement of water in xylem tissue is therefore in one direction.
As water molecules leave the leaf by evaporation, cohesive forces between water molecules, due to hydrogen
bonding, ensure that a column of water is pulled up the plant in xylem tissue.
In the phloem, sucrose is loaded into the phloem sieve tubes in the leaf by active transport. The accumulation
of sugar in the phloem tissue raises the solute potential and water follows the sucrose by osmosis. This
creates a high hydrostatic pressure in the sieve tubes of the source area. Meanwhile, in living cells elsewhere
in the plant – often, but not necessarily, in the roots – sucrose may be converted into insoluble starch
deposits. This is a sink area. As sucrose flows out of the sieve tubes here, the solute potential is lowered.
Water then diffuses out and the hydrostatic pressure is lowered. These processes create the difference in
hydrostatic pressures in source and sink areas that drive mass flow in the phloem. The direction of movement
of sucrose is determined by the rate of glucose metabolism, which in turn is determined by variables such as
demand for glucose for respiration or storage as starch. Increased temperature can increase the rate of
sucrose movement in plants due to increased rates of respiration and, therefore, active transport.
2 What are the implications of solubility differences between chemical substances for living organisms?
Theme Chapter
B1.2 Proteins
B3.2 Transport
Blood is the transport medium of the body in animals: many metabolites are carried around the body in the
blood plasma. However, not all metabolites are soluble in water. The following table shows how a selection
of essential metabolites are carried compared with their solubility in water.
Table D2.3.1 Transport of metabolites in the blood
Metabolite Solubility in water Mechanism of transport in the blood
glucose highly soluble dissolved in the blood plasma
amino acids soluble dissolved in the blood plasma
cholesterol insoluble in particles called low-density lipoproteins (LDLs, or

‘bad cholesterol’), complexes of thousands of
cholesterol molecules bound to proteins, and in high-
density lipoprotein particles (HDLs, or ‘good
cholesterol’) (page 402 of the Student’s book)
fats (lipids) insoluble absorbed in the gut as droplets; transported about the
body (from fat store sites to respiring cells) as water-
soluble lipoproteins
oxygen low solubility in the plasma combined with haemoglobin in the red blood cells (page
292 of the Student’s book) – about 200 cm3 per litre of
blood can be transported
sodium chloride highly soluble as Na+ and Cl– ions, dissolved in the plasma
Glucose is a polar molecule and so dissolves in water due to the formation of hydrogen bonds with their
slightly charged hydroxyl groups (–OH). The negatively charged oxygen ions in water attract and surround
the positively charged hydroxyl groups in glucose. Its solubility in water makes it possible to be transported
in blood plasma.
Carbohydrates that dissolve in water have an osmotic effect on cells. If they are in a higher concentration
within a cell than the surrounding tissue fluid, water will move into the cell by osmosis. If the solute
concentration is lower inside a cell than the surrounding solution, water will leave the cell by osmosis.
Lipids, starch and glycogen are insoluble and so have no osmotic effects on the cells where they are stored.
Glycogen molecules, for example, have a large molar mass, which gives them a very low solubility.
Therefore, they have a negligible contribution to the osmotic pressure of the cell. In contrast, each molecule
of an equivalent number of glucose molecules contributes to osmotic pressure. If the glucose molecules were
not covalently bonded to form glycogen, the cell’s plasma membrane would burst (a process known as lysis).
D3.1 Reproduction
Page 724
1 How can interspecific relationships assist in the reproductive strategies of living organisms?
Theme Chapter
A A4.2 Conservation of biodiversity
D D3.1 Reproduction
Interspecific relationships are those between two different species. Symbiotic relationships are one example
of an interspecific relationship. Symbiotic relationships occur when two organisms live together closely.
Mutualism is a specific type of symbiotic relationship in which both species derive benefit. Mutualism can
increase the carrying capacity of both species in the relationship. Root nodules in Fabaceae (the legume
family), mycorrhizae in Orchidaceae (the orchid family) and zooxanthellae in hard corals are all examples of
mutualistic relationships.
Pollination is the transfer of pollen from a mature anther to a receptive stigma, often brought about by
animals. Pollinators include insects, such as butterflies or bees. In other flowers, it may be bird or bat visitors
that unwittingly carry out pollination. The pollinator is typically attracted by colour or scent (or both), and is
rewarded by a sugar solution called nectar and pollen, which usually form a key part of the diet. In return,
they accidentally transfer pollen between flowers and between plants. Thus, there is a mutualistic
relationship between pollinator and plant in plant sexual reproduction.
An example of this interdependence between pollinator and plant comes from the tropical rainforests of
Brazil. The Brazil nut tree (Bertholletia excelsa) occurs in the countries of the Amazon region, widely
dispersed in the rainforests there. Key features of the Brazil nut life cycle are as follows:
• The trees flower during the dry season, between October and December – a relatively short period in
which pollination must occur.
• The large flowers can only be pollinated by orchid bees – it is the female orchid bee that is the
pollinator. Only a powerful, large-bodied bee can prise open the protective ‘flower hood’ to access the
nectar, incidentally bringing about cross-pollination.
• The chief habitat of the orchid bee is undisturbed forest. Attempts to manage and maintain colonies of
orchid bees on plantations have been unsuccessful.
• The male orchid bees cannot mate successfully with the females without first visiting the flowers of
small orchids that grow high on the branches of the canopy of the Brazil nut tree.
• These orchid flowers are pollinated by the male orchid bee, which visits them for exposure to a perfume
present in the waxy secretion that these flowers exclusively produce.
• With this perfume, the male bees can compete for a mate, successfully breed, and so maintain orchid
bee populations. Without the orchid bees and the epiphytic orchids, Brazil nut trees would not be able to
reproduce and produce seeds.
• After pollination, a further year elapses before the fruits develop. These contain 10–25 Brazil nuts
(seeds) within an extremely hard shell.
In the past, conservation has focused on individual species with seriously dwindling numbers. Now it is clear
that exclusive attention to the survival of an individual endangered species is mistaken – we need to protect
entire ecosystems, because of the interspecific relationships that exist between species.
Both organisms in a mutualistic relationship ensure that both species live well within their range of
tolerance, and optimize their mode of nutrition, with the environment providing ideal conditions for growth
and reproduction.
Other interspecific relationships involve competition between species – these will reproductively benefit a
predator at the expense of prey populations.
2 What are the roles of barriers in living systems?

Theme Chapter
D D3.1 Reproduction
D3.3 Homeostasis

Barriers in biological systems can be both biochemical and physical. The plasma membrane is the barrier
controlling entry to and exit from the cell. Hydrophobic hydrocarbon chains that form the core of a
membrane have low permeability to large molecules and hydrophilic particles, including ions and polar
molecules, so membranes function as effective barriers between aqueous solutions. The cell membrane
allows non-polar molecules such as steroid hormones to cross into intracellular space, but large polar
molecules such as peptide hormones cannot pass the barrier as they are repelled by the hydrophobic interior
of the membrane.
The skin acts as both a physical and chemical barrier to pathogens. The skin forms a physical barrier to
pathogens by blocking their entry into the body. If the skin is wounded, the clotting reaction seals the
damaged area and ensures that the barrier is maintained. Clotting factors from platelets, and the subsequent
cascade pathway, result in rapid conversion of fibrinogen to fibrin by thrombin, which traps erythrocytes to
form a clot. Mucous membranes produce mucus that traps pathogens and, in the case of the trachea, is
transported away from the interior of the body by cilia action. In terms of chemical defences, the surface of
the skin has hydrolytic enzymes that destroy bacteria, and the interior of the stomach produces hydrochloric
acid which acts as a barrier to pathogens.
In the kidney, the Bowman’s capsule forms a barrier between the blood and the filtrate. In the glomerulus,
much of the water and many relatively small molecules present in the blood plasma, including useful ions,
glucose and amino acids, are forced out of the capillaries, along with urea, into the lumen of the capsule.
This fluid is called the glomerular filtrate and the process is described as ultrafiltration, because it is powered
by the pressure of the blood (hydrostatic pressure). The blood pressure here is high enough for ultrafiltration
because the input capillary (afferent arteriole) is significantly wider than the output capillary (efferent
arteriole). The barrier between the blood plasma and the lumen of the Bowman’s capsule functions as a filter
or ‘sieve’ through which ultrafiltration occurs. This sieve is made of two layers of cells (the endothelium of
the capillaries of the glomerulus and the epithelium of the capsule wall), between which is a basement
membrane. The cells of the inner wall of the capsule are podocytes, which wrap around the capillaries of the
glomerulus, leaving a network of slits between the extensions. Similarly, the endothelium of the capillaries
has pores. These are large enough for fluid to pass through, but not large enough for the passage of blood
cells. This detail has only become known because of studies using electron microscopes; these filtration gaps
are very small indeed. Finally, there is the basement membrane, a layer that surrounds and supports the
capillary walls. This structure consists of a meshwork of glycoproteins that allows the filtrate to pass, but
that retains almost all of the plasma proteins. The fluid that has filtered through into the renal capsule is very
similar to blood plasma, but it has a significant difference. Not only are blood cells retained in plasma, but
the majority of blood proteins and polypeptides also remain there.
From early in their development, embryos are contained, supported and protected by a membranous, fluid-
filled sac, called the amniotic sac. This forms a barrier between the embryo and the uterus, and serves as a
physical barrier to infection. It is the outer layers of the tissues of the embryo that grow and give rise to the
membranes and that also form the placenta. The placenta is a disc-shaped structure composed of maternal
(endometrial) and foetal membrane tissues. Here the maternal and foetal blood circulations are brought very
close together over a huge surface area, but they do not mix, and the placenta acts as a barrier between
maternal and foetal blood systems. The placenta and foetus are connected by arteries and a vein in the
umbilical cord. Exchange in the placenta is by diffusion and active transport, where materials needed by the
foetus move into the foetal blood (such as glucose and oxygen) and waste products are moved out (such as
carbon dioxide and urea).
Barriers have resulted in natural selection and speciation. Natural selection is the mechanism driving
evolutionary change and has led to the diversity of life seen on Earth. Speciation is the process through
which new species are formed. Barriers such as geographical, behavioural or temporal isolation can lead to
reproductive isolation of populations of a species. Geographical isolation can arise from the formation of
rivers or mountain ranges, which divide populations. Behavioural differences include different mating
rituals. Temporal differences include individuals being fertile at different times or seasons. Populations are
interacting groups of organisms of the same species living in an area. When they become isolated in different
areas, with different environmental selection pressures, this leads to a divergence in the gene pool of both
species (from mutations, meiosis and sexual reproduction). Over time, the isolated populations may become
so genetically different that they become different species. Alternatively, a new population may form from a
tiny sample that became separated from a much larger population. While the number of individuals in the
new population may rapidly increase, the gene pool from which they formed may have been totally
unrepresentative of the original, with many alleles lost altogether. In this way, populations of the same
species can change, through accumulation of gradual changes in the genotype over time, to eventually form
new, genetically distinct species.
The biological species concept states that a species is a group of organisms that can breed and produce fertile
offspring. There are barriers to prevent interbreeding between closely related species, which prevents the
mixing of alleles between species. The barriers that prevent interbreeding between closely related species
occur either before fertilization can be attempted (pre-zygotic isolation) or after fertilization has occurred
(post-zygotic isolation). Hybrids formed are not viable and die prematurely, or are formed and are infertile
because the chromosomes cannot pair up in meiosis to produce haploid gametes. Where hybrids are fertile,
with each succeeding generation, fewer survive, leading to them eventually all dying out.
D3.2 Inheritance
Page 759
1 What are the principles of effective sampling in biological research?
Theme Chapter

In many investigations, such as ecological studies, it is not possible to study every organism or cover the full
extent of the ecosystem. Limitations are put on how many organisms and parts of the ecosystem are studied.
Therefore, samples are taken. In ecology, the sampling system used depends on the areas being sampled.
Random sampling ensures that every individual in the community has an equal chance of being selected and
so a representative sample is assured, to avoid bias. Quadrats are used to sample ecological populations and
to estimate the abundance of plants and non-mobile organisms. Random sampling is appropriate if the study
area is homogeneous (the same throughout), but not appropriate if sampling along a line transect, where
there is an environmental gradient and a change in species composition. For example, if an area of woodland
is being studied, there are likely to be different types of habitat within it: random sampling may miss one or
more of these and so stratified sampling is used. This technique considers the proportional area of each
habitat type within the woodland and samples each one accordingly. The technique can also be used to
compare undisturbed and disturbed areas. Random sampling inevitably results in sampling error. The
difference between the estimate of population size and the true size of the whole population is the sampling
error.
Systematic sampling is used along a transect where there is an environmental gradient, such as the change
from the edge of a woodland adjoining open land into interior forest where, for example, warmer and lighter
conditions predominate at the edge of the forest and cooler, darker ones in the interior.
Succession is an example where there are changes in a community through time, although this is usually
expressed as change along an environmental gradient. Succession can be triggered by changes in an abiotic
factor, and also in biotic factors. Systematic sampling along the environmental gradient ensures that abiotic
factors can be measured at regular intervals, and all communities sampled.
2 What biological processes involve doubling and halving?

Theme Chapter
B1.2 Proteins
D3.1 Reproduction
D3.2 Inheritance
Examples of doubling occur at every level of biological organization.
At the molecular level, DNA replication means one strand of DNA becomes two. DNA replication is the
production of exact copies of DNA with identical base sequences, which is required for reproduction, growth
and tissue replacement in multicellular organisms. DNA replication is a prerequisite for both mitosis and
meiosis. Replication is semiconservative, which means that one strand of the original DNA is used as a
template for the new strand, thereby doubling the amount of DNA. Complementary base pairing and the
processes involved in replication ensure a high degree of accuracy in copying base sequences. Replication
allows DNA to be passed on to new cells.
In addition, when two carbohydrate or amino acid monomers join through condensation reactions, single
molecules join to form either disaccharides or dipeptides.
At the cellular level, mitosis results in the doubling of cells at each division. Cell proliferation is needed for
growth, cell replacement and tissue repair. Cell proliferation occurs during routine cell replacement and
during wound healing. Stem cell niches in adult humans maintain cells or promote their proliferation.
Proliferation for growth occurs within plant meristems and early-stage animal embryos. In meiosis, each
division generates two new cells, although at the end of meiotic division, four cells are produced rather than
the two in mitosis. Two divisions of meiosis produce four haploid nuclei from one diploid nucleus. Meiotic
division allows female and male gametes to fuse at fertilization, restoring the diploid number of
chromosomes. In this way, the genetic code from two individuals can be mixed and combined to form
offspring that are genetically unique, in the process of inheritance.
At the ecosystem level, populations colonizing new areas, where limiting factors do not limit population
growth, show exponential growth, with populations doubling in each generation. This occurs until the
population reaches the carrying capacity of the environment, and density-dependent factors limit further
population growth.
There are also examples of halving in biological systems. An example of halving in meiosis is known as a
reduction division, where diploid cells produce haploid gametes containing half the number of chromosomes
compared to the parent cell. A diploid cell has two copies of each autosomal gene whereas a haploid gamete
has one copy. Production of haploid gametes in parents enables the diploid number to be restored after the
fusion of male and female gametes in fertilization. This pattern of inheritance is common to all eukaryotes
with a sexual life cycle. Halving occurs during the hydrolysis of biological molecules. Digestion of
disaccharide sugars, such as maltose, results in subunits that are half the size of the original molecule.
Halving of dipeptides, into amino acids, occurs by digestive enzymes for absorption.
Some biological processes involve both doubling and halving. For example, DNA replication involves both
halving (two separate DNA strands) and doubling to form two new molecules. Doubling of each DNA
molecule occurs in interphase and halving at anaphase of mitosis.
D3.3 Homeostasis
Page 778
1 For what reasons do organisms need to distribute materials and energy?
Theme Chapter
B3.1 Gas exchange
B3.2 Transport
C1.3 Photosynthesis
There are a variety of ways that organisms distribute materials and energy. In each case, materials and
energy need to be moved from one location to another, to redistribute resources to areas that need them.
Carbohydrates, such as glucose, can be stored in cells by converting monosaccharides to polysaccharides via
condensation reactions. The compact nature of starch in plants and glycogen in animals is due to coiling and
branching of the molecules during polymerization. The relative insolubility of these compounds is due to
large molecular size. It is relatively easy to add or remove alpha-glucose monomers by condensation and
hydrolysis to build or mobilize energy stores. This redistribution of biomolecules ensures that the osmotic
concentration of the cell, and more widely the blood plasma and tissue fluid, is maintained within safe limits.
This enables the cell to remain isotonic to the surrounding area.
Triglycerides can be distributed to the subcutaneous layer of the skin. Triglycerides in adipose tissues are
used as energy storage and thermal insulation. The properties of triglycerides make them suited to long-term
energy storage functions. The use of triglycerides as thermal insulators can be related to body temperature
and habitat.
In DNA replication, one strand of DNA becomes two. DNA replication is the production of exact copies of
DNA with identical base sequences, which is required for reproduction, growth and tissue replacement in
multicellular organisms. DNA replication is a prerequisite for both mitosis and meiosis. These processes
distribute the components of DNA (deoxyribose, phosphate and base) into new DNA molecules, so that the
genetic code can be passed on to new cells.
ATP (adenosine triphosphate) is the molecule that distributes energy within cells. Energy transfers occur
during interconversions between ATP and ADP (adenosine diphosphate). Energy is released by hydrolysis of
ATP to ADP and phosphate, whereas energy is required to synthesize ATP from ADP and phosphate. Like
many organic molecules of its size, ATP contains a good deal of chemical energy locked in its structure.
What makes ATP special as a reservoir of chemical energy is its role as a common intermediate between
energy-yielding reactions and energy-requiring reactions and processes. Energy-yielding reactions include
many of the individual steps in respiration. Energy-requiring reactions include the synthesis of cellulose
from glucose, the synthesis of proteins from amino acids, and the contraction of muscle fibres. ATP
therefore distributes energy through cells to support many life processes, such as the active transport of
molecules and ions across membranes by membrane pumps, synthesis of macromolecules (anabolism), the
movement of the whole cell, and movement of cell components such as chromosomes.
Proteins in the plasma membrane are used to distribute ions and molecules. Substances required by cells,
such as glucose, can be actively moved into cells using protein pumps. The pumps use energy from ATP to
transfer specific ions or molecules across membranes, against a concentration gradient. Protein pumps are
also used to generate the resting potential in neurons. Sodium and potassium ions are pumped in opposite
directions across the plasma membrane of neurons.
In photosynthesis, light energy is transformed into chemical energy when carbon compounds are produced.
Specific wavelengths of light are absorbed by photosynthetic pigments; the light excites electrons within a
pigment molecule. This energy transformation supplies most of the chemical energy needed for life
processes in ecosystems. Matter and energy are passed through food chains, where matter is recycled and
energy released as heat. The constant input of energy and matter maintains ecosystems. In both respiration
and photosynthesis, electron carriers transfer energy to the electron transport chain, which results in the
generation of ATP through movement of protons down their electrochemical gradient via ATPase.
Cell division redistributes matter and energy into new cells. Organelles and energy are needed in the new
cells in order to carry out life functions. In meiosis, redistribution of matter and energy is needed to form
gametes, which are required for sexual reproduction.
In the digestive system, food is moved through the gut by peristalsis, under the control of the central nervous
system (CNS) and enteric nervous system (ENS). Swallowing of food and egestion of faeces is under
voluntary control by the CNS. Peristalsis is under involuntary control by the ENS. The action of the ENS
ensures passage of material through the gut is coordinated, and nutrients contained in the food are distributed
through the body via the blood systems and into cells, where the biomolecules are used to synthesize new
molecules or used in metabolic processes such as respiration.
The transport systems of animals and plants distribute water, minerals and organic molecules, as well as
hormones and other substances needed throughout the organisms. These substances are required to support
life processes and for metabolic reactions such as respiration in cells.
2 What biological systems are sensitive to temperature changes?

Theme Chapter
B1.2 Proteins
C1.3 Photosynthesis
D4.3 Climate change

Biological systems at every level of organization are sensitive to temperature changes.
DNA is a double helix made of two antiparallel strands of nucleotides with two strands linked by hydrogen
bonding between complementary base pairs. In response to high temperatures, the hydrogen bonds break and
the strands separate. This is used in the process of the polymerase chain reaction, where DNA molecules are
amplified.
Metabolic reactions in cells are sensitive to temperature. The rates of both respiration and photosynthesis
increase at higher temperatures, up to optimal temperatures. The kinetic energy of molecules increases,
increasing the reaction rate.
Enzymes are proteins that have a specific conformation, enabling catalytic conversions to occur in cells and
within an organism. Enzymes work best at an optimal temperature: if this temperature is exceeded, the
enzyme denatures (i.e. there is a change to the shape of the active site so that the substrate can no longer bind
to it). If the enzymes involved in respiration or photosynthesis exceed their optimal temperature level, the
rate of these reactions will reduce and, at excessive temperature, will cease.
Cell membranes are sensitive to changes in temperature. Cholesterol acts as a modulator (adjustor) of
membrane fluidity, stabilizing membranes at higher temperatures and preventing stiffening at lower
temperatures. Also in the membrane, the fatty acid chains of the phospholipids can be modified to adapt to
changes in temperature. The composition of fatty acids in lipid bilayers affects the fluidity of the membrane.
Unsaturated fatty acids in lipid bilayers have lower melting points, so membranes are fluid and therefore
flexible at temperatures experienced by a cell. Saturated fatty acids have higher melting points and make
membranes stronger at higher temperatures.
Receptors in the skin and brain are sensitive to temperature changes. Free nerve endings detect increases and
decreases in temperature, which lead to negative feedback loops that restore equilibrium and return the
internal body temperature to a set point.
Species show a range of tolerance to limiting factors, including temperature. The range of tolerance is
determined by the niche of a species. A temperature change within the range of tolerance will not affect the
niche of a species, whereas fluctuations beyond the range may lead to species extinction or the need to
migrate to a new area.
At the ecosystem level, abiotic factors such as temperature can act as selection pressures. High or low
temperatures may affect survival of individuals in a population. Temperature patterns can also influence the
timing of biological events such as flowering, budburst and bud set in deciduous trees, bird migration and
nesting. With increased global temperatures, through global warming, the synchrony of phenological events
may be disrupted.
Abiotic factors, including temperature, determine the distribution of terrestrial biomes. Changes in
temperature can lead to the biome shifting so that its optimal conditions can be met. Increases in temperature
can have a severe effect on some ecosystems. Increases in water temperature are a cause of coral bleaching,
and the loss of corals causes the collapse of reef ecosystems. Warmer temperatures and decreased winter
snowfall lead to increased incidence of drought and reductions in primary production in the taiga biome,
with forest browning, and increases in the frequency and intensity of forest fires, which results in legacy
carbon combustion. In this way, ecosystems can change from net carbon accumulation to net loss, which can
result in a tipping point and lead to ecosystem collapse.

Page 797
1 How do intraspecific interactions differ from interspecific interactions?
Theme Chapter

Intraspecific interactions are interactions between individuals of the same species, whereas interspecific
interactions are between different species. When resources are limited, populations will compete to survive.
Competition can be either intraspecific or interspecific. Interspecific competition exists when the niches of
different species overlap. No two species can occupy the same niche, so the degree to which niches overlap
determines the degree of interspecific competition. Interspecific interactions can also include mutualism,
predation, parasitism and pathogenicity.
If two species share the same resource at the same place and the same time, then the dominant species will
outcompete the other species. The inferior competitor will either die out or move away to avoid the
competition. This is competitive exclusion.
Natural selection is the result of intraspecific competition, i.e. competition between individuals of the same
species. Individuals will usually interact with more members of their own species than of other species.
Individuals of the same species share the same niche and so intraspecific competition plays a stronger role in
evolution than interspecific competition (competition between individuals of different species), because in
intraspecific competition individuals compete for the same resources and have the same biotic and abiotic
interactions that influence the growth, survival and reproduction of the species. Any mutation that gives
individuals in a population a selective advantage improves their chance of surviving intraspecific
competition.
2 What mechanisms minimize competition?

Theme Chapter

Populations do not show rapidly increasing numbers in most habitats or, at least, not for long. Population
size is naturally limited by environmental factors. These include space, light and the availability of food.
These factors limit carrying capacity. The never-ending competition for resources means that the majority of
organisms fail to survive and reproduce. In effect, the environment can only support a certain number of
organisms, and the number of individuals in a species remains more or less constant over a period of time.
Overproduction of offspring and competition for resources are therefore factors that promote natural
selection.
In his book On the Origin of Species (1859), Darwin proposed his ‘principle of divergence of character’ to
explain the origin and diversity of species. He hypothesized that competition is a key driving force of
divergent selection: when organisms compete for scarce resources, natural selection favours those
individuals that are least like their competitors. This divergent selection thereby causes competing groups of
organisms (that is, populations and species) to evolve to become more different from each other in resource
use and associated traits.
Competition is strongest within a species. Each individual will usually interact with more members of its
own species than of other species. The members of its own species are more similar to it, exploiting the same
resources. One way to avoid competition is to become different, and for new niches to evolve: hence there
will be a selective evolutionary force pushing similar competing types to become different. Competition
between similar individuals will lead to the evolution of new adaptations in each that reduce the intensity of
competition; divergence will therefore occur. The division of a species into spatially or temporarily separate
populations leads to reproductive isolation and, ultimately, to new species.

Page 819
1 What is the distinction between artificial and natural processes?
Theme Chapter
D3.1 Reproduction

Natural processes are ones that have evolved and are naturally occurring. Artificial processes are ones that
have been devised by humans. Artificial selection, for example, is a human-made process, whereas natural
selection takes place in natural populations under natural conditions. Artificial selection is carried out in crop
plants and domesticated animals by choosing individuals for breeding that have desirable traits. Artificial
selection takes place in domesticated populations and produces new varieties desired by human societies and
has no adaptive advantage. Under natural selection, fitness determines the chances of survival and can lead
to the evolution of new species.
The stability of ecosystems is a natural process but can be affected by artificial processes of humans, such as
agriculture, deforestation and pollution. Rewilding an ecosystem is an artificial process that is trying to
reflect a natural process.
Succession is the orderly process of change over time in a community. It is a natural process leading to a
climax community that is more or less stable and in equilibrium with the natural environmental conditions.
Interrupting succession can be an artificial process, if humans are involved, such as farming and the draining
of wetlands. Succession can also happen after an artificial process of interruption.
In IVF treatment, female hormones are controlled, with artificial doses of hormones used to induce
superovulation. Some techniques, such as gene editing, use natural processes that are manipulated by
humans to bring about desired consequences.
2 Over what timescales do things change in different biological systems?

Theme Chapter
C1.3 Photosynthesis
D4.3 Climate change

Some ecosystems, such as tropical rainforests, have been around for millions of years. All ecosystems are
established through the process of succession, where one community replaces another due to changes in
abiotic and biotic conditions.
The carbon cycle provides a good example of the range of timescales in which biological processes operate.
Biological and geological processes move carbon between stores, and these vary both temporally and
quantitatively. Physical processes control the movement of carbon between stores on land, the oceans and
the atmosphere. Processes are the physical mechanisms that drive the inputs, outputs and flows of the cycle.
Carbon cycle processes include: photosynthesis, respiration, decomposition, fossilization and combustion
(including natural and fossil fuel use), which operate over a large range of different timescales (see Table
D4.2.1).
Table D4.2.1 How carbon is circulated between stores, and the timescale on which processes operate
Processes by which carbon is circulated Operational

timescales
Diffusion carbon dioxide diffuses from the atmosphere or water into seconds
autotrophs (plants and other photosynthetic organisms)
Photosynthesis autotrophs convert CO2 from the atmosphere into carbohydrates seconds
and other organic compounds
aquatic plants use dissolved CO2 and hydrogencarbonate ions
(HCO3−) from the water in the same way
Respiration CO2 is produced as a waste product and diffuses out into the seconds
atmosphere or water
Feeding/ animals feed on plants to obtain glucose and other nutrients minutes/hours
consumption biomass passed from one animal to the next in a food chain
Decay/ dead organic matter is decomposed to CO2, water, ammonia and hours/days
decomposition mineral ions by micro-organisms
CO2 produced diffuses out into the atmosphere or dissolves in
water (as HCO3− ions)
Peat formation in acidic and anaerobic conditions, dead organic matter is not fully centuries
decomposed but accumulates as peat
peat decays slowly when exposed to oxygen, releasing CO2 into
the atmosphere
Methane organic matter held under anaerobic conditions (such as in minutes

formation waterlogged soil or in the mud of deep ponds) is decayed by
methane-producing bacteria (methanogenic archaeans)
methane accumulates in the ground in porous rocks or under
water, but may diffuse into the atmosphere
in air and light, methane (CH4) is oxidized to CO2 and water
Fossilization partially decomposed organic matter from past geological eras millennia
was converted either into coal or into oil and gas that accumulate
in porous rocks
peat in past geological eras was converted to coal
Combustion releases CO2 into the atmosphere seconds

since the start of the Industrial Revolution in Europe, CO2 has
been released at an increasing rate by the combustion of biomass
and fossilized organic matter
Shell and coral many organisms combine HCO3− with calcium ions to form millennia
formation calcium carbonate shells and coral skeletons (animals such as
reef-building corals and molluscs such as shellfish)
shells and reef-building coral can become fossilized and form
sedimentary rocks (chalk and limestone) over long periods of
geological time
Evolution is the development of life, from its earliest beginnings to the diversity of organisms we know
about today, living and extinct. Evolution has occurred over geological time, but modern evidence shows
that evolution can happen over much more rapid timescales (such as the evolution of bacteria and viruses).
D4.3 Climate change

Page 837
1 What are the impacts of climate change at each level of biological organization?
Theme Chapter
C1.3 Photosynthesis
D3.3 Homeostasis
D4.3 Climate change

Climate change is the long-term change in global or regional climate patterns caused by natural or human
factors. Climate change since the mid- to late-twentieth century onwards is attributed primarily to the
increased levels of atmospheric greenhouse gases produced by the use of fossil fuels and land-use change
(such as deforestation and cattle farming). Climate change impacts every level of biological organization.
At a cellular level, temperature affects enzyme activity. Increased temperature increases the kinetic energy of
enzymes and substrates, leading to increased successful collision and, therefore, rate of reaction. Both
respiration and photosynthesis are controlled by enzymic reactions, so increased temperature, up to optimum
conditions, will increase the rate of these processes.
Increased extreme weather events, resulting from climate change, can result in increased rainfall and
flooding. Flooded soils contain less oxygen than well-aerated soils, and saturated soils can lead to the death
of aerobic bacteria, some of which are decomposers. Reduced rates of decomposition can affect nutrient
uptake in plants and, therefore, primary productivity.
At the level of organisms, dry weather caused by climate change will lead to increased dehydration in both
animals and plants. Dehydration in animals is countered by the hormone ADH, which causes the kidney to
reabsorb more water. The physiology of mammals is adjusted as temperatures increase. Evaporative cooling
enables mammals to lose heat when exposed to extreme temperature. Homeostatic mechanisms enable
animals to survive in a range of different environments, but increased average temperatures may put these
systems under stress, especially that of increased sweating if water sources become less abundant.
Increased temperature and dehydration in plants can result in cells losing water, causing plasmolysis in cells:
the cytoplasm pulls away from parts of the cell wall and the cell becomes flaccid, resulting in wilting.
Changes to phenological seasonal events occur with climate change, such as the timing of budburst, nesting
and migration. The timing of some life cycles is changed, such as the increased incidence of reproductive
cycles in bark beetles. In the UK, where average spring temperatures have increased by 0.5 °C, butterflies
have been seen earlier, by between three days and a week on average. Evolution resulting from climate
change has been observed in the tawny owl: the owl is found in two different feather colours, grey and
brown. Grey-coloured owls usually dominate in Finland, but research has found that the number of brown
tawny owls has been increasing because of the decrease in snow and rise in temperatures.
Temperature has also been shown to affect the fatty acid composition of adipose tissue. Some phospholipids
have saturated fatty acid tails (no double bonds between a pair of carbon atoms) and some have unsaturated
fatty acid tails (double bonds between carbon atoms). Organisms have been found to vary the balance
between saturated and unsaturated fatty acids (and the amount of cholesterol in their membranes) as ambient
temperatures change. In this way, organisms maintain a properly functioning membrane, even at very low
temperatures. For example, investigations into the Lake sturgeon (Acipenser fulvescens), a North American
temperate freshwater fish, has shown that when the temperature decreases, both mono- and polyunsaturated
fatty acids of phospholipids significantly increase, and saturated fatty acids decrease. With global warming
there may be a selection for fatty acid compositions that favour the increased average global temperatures.
At the population level, food webs can be disrupted if species are lost from a food chain or new competitive
species enter. Interspecific relationships can disturb community structure because of the introduction of
exotic, alien species. Major losses of biodiversity are predicted because of global climate change and higher
rates of species extinction (above the current rates and the rates from fossil records).
All types of natural selection reduce variation within a population, although climate change can further lower
a population’s genetic diversity through directional selection. Changes in the environment will favour some
within a population and these will be selected for, altering the allele frequency and narrowing the gene pool.
Species sensitive to the increased temperatures will need to adapt or risk extinction if environmental
conditions are no longer suitable for them. The niche of a species determines its distribution: if conditions
vary to the extent that a species’ niche can no longer be expressed, the species will become extinct. For
example, on mountain ranges, high-altitude species will have nowhere else to go as upslope shifts occur due
to climate change. Species may shift, adapt to the environment or become extinct depending on their
exposure, sensitivity and resilience to the new environment. When a species adapts, it may remain in a new
environment but change genetic composition or use phenotypic plasticity. Change in distribution, genetic
composition and phenotypes may cause disruption in species interactions, ecosystem function and structure.
The distribution of ecosystems, such as tundra, taigas, grasslands, tropical rainforests, temperate deciduous
forests and deserts, depend on insolation, precipitation and temperature. Primary productivity increases with
increased rainfall and ideal temperatures, due to the requirements of photosynthesis. Primary productivity
will also increase due to increased rates of photosynthesis. Changes in climate (for example increased
average temperature, decreased rainfall and changes in seasonality) and extreme events (such as increased
hot days, fire, increased frequency and intensity of heatwaves and intensified wet seasons) can bring changes
to biomes and the biodiversity they contain. Ecosystems are at high risk of changes in composition and
structure due to climate change. For example, tropical coral reefs require very specific abiotic factors to
grow, including the ideal temperature. Increased temperatures lead to coral bleaching, which can bring about
the collapse of coral ecosystems.
2 What processes determine the distribution of organisms on Earth?

Theme Chapter

Abiotic and biotic variables affect species distribution. Limiting factors are the components of an ecosystem,
either biotic or abiotic, which limit the distribution or numbers of a population. Limiting biotic factors
include interactions between organisms, such as competition or predation, and limiting abiotic factors
include physical components of the environment, such as temperature, salinity, pH, oxygen, carbon dioxide,
light, hydrostatic pressure, water current, wind velocity, substratum type (layer of rock or soil beneath the
surface of the ground), rainfall amount and humidity. Species operate within limits of tolerance, which
determine the niche and, ultimately, the distribution of a species.
Insolation (amount of sunlight), temperature and precipitation affect the type of ecosystem that develops in
any given area. Each element of the climate plays a role in structuring communities within the abiotic
environment they inhabit. Temperature affects the rate of enzyme reactions in the cells of all organisms,
affecting the rate of primary productivity through photosynthesis and decomposition. Temperature also
affects the rate of transpiration. Precipitation affects the rate of photosynthesis and primary productivity.
Insolation also affects the rate of photosynthesis and primary productivity. Information about the relative
contributions of two climatic factors, precipitation and temperature, can be used to predict the type of stable
ecosystem that can be expected in an area. Biomes are groups of ecosystems that share similar abiotic
conditions, and so develop similar communities through convergent evolution.
Climate change affects the distribution of species as the niche requirements of a species shift geographically.
For example, as warmer temperatures are found at higher altitudes, montane species move upwards as the
conditions change. If the environmental conditions required by a species are no longer found due to these
vertical shifts, then the species will become extinct if only found in montane ecosystems. Biomes, which
require specific abiotic conditions, are affected by climate change. Changes in patterns of rainfall associated
with climate change, and alterations in land and sea surface temperature, will lead to shifts in the distribution
of biomes. As biomes shift, so will the species that live in them.
Natural selection is the process where organisms better adapted to their environment survive and produce
more offspring than competitors and is the mechanism through which evolution occurs. Variation within a
species, combined with selection pressures, confers fitness on some members of a population. If reproductive
isolation occurs, new species can evolve that are better adapted to their environment. Through evolutionary
history, the biodiversity of life on Earth has emerged as part of a continuous process caused by changes to
the abiotic and biotic environment of species, reproductive isolation and natural selection. The distribution of
individual species has ultimately depended on biogeographical processes. Biogeography is the study of the
processes that determine the spatial and temporal distributions of organisms and their attributes, such as
genetics and traits, across the Earth.

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Biology for the IB Diploma – Answers

Theme A Unity and diversity

A1.2 Nucleic acids

B4.1 Adaptation to environment

C C1.1 Enzymes and metabolism

C1.2 Cell respiration

C3.1 Integration of body systems

D D1.1 DNA replication

D1.2 Protein synthesis

2 Which biological processes only happen at or near surfaces?

A2.3 Viruses (HL only)

B B2.1 Membranes and membrane transport

B2.3 Cell specialization

B3.1 Gas exchange

C C2.2 Neural signalling

C3.2 Defence against disease

D D1.1 DNA replication

D4.2 Stability and change

A1.2 Nucleic acids

2 How can polymerization result in emergent properties?

A2.1 Origins of cells (HL only)

B B1.1 Carbohydrates and lipids

C C2.1 Chemical signalling (HL only)

D D1.2 Protein synthesis

A2.1 Origins of cells (HL only)

A A1.2 Nucleic acids

A2.1 Origins of cells (HL only)

A4.1 Evolution and speciation

D D1.1 DNA replication

D2.1 Cell and nuclear division

D4.1 Natural selection

2 What is needed for structures to be able to evolve by natural selection?

A A4.1 Evolution and speciation

C C3.2 Defence against disease

D D1.2 Protein synthesis

D1.3 Mutation and gene editing

D2.1 Cell and nuclear division

D4.1 Natural selection

D4.3 Climate change

A2.2 Cell structure

A1.2 Nucleic acids

A2.2 Cell structure

B B1.1 Carbohydrates and lipids

B2.1 Membranes and membrane transport

C C1.1 Enzymes and metabolism

C2.2 Neural signalling

D D4.1 Natural selection

Figure A2.2.1 The synthesis of biological macromolecules from monomers

2 What are the features of a compelling theory?

A A2.2 Cell structure

A4.1 Evolution and speciation

D D4.1 Natural selection

Some examples of compelling theories:

A2.3 Viruses (HL only)

A A4.1 Evolution and speciation

B B4.1 Adaptation to environment

B4.2 Ecological niches

D D1.2 Protein synthesis

D4.1 Natural selection

2 To what extent is the history of life characterized by increasing complexity or simplicity?

A A4.1 Evolution and speciation

B4.2 Ecological niches

D4.1 Natural selection

A3.1 Diversity of organisms