Introduction to Cells (1.

1):
 
The Cell Theory:
 Organs are made up from tissues, but cells are too small to be observed without a microscope.
 The cell theory was developed when similar features were noticed in the different cells of many
organisms.
 Unicellular organisms: organisms that consist of one cell.
 Multicellular organisms: organisms that are composed of many cells.
 Cells have several features in common, such as:
 Every cell is surrounded by a membrane, which separates the cell's contents from everything else
outside.
 Cells contain genetic material which stores all of the functions needed for cellular activity (DNA).
 Many of the cellular activities are chemical reactions, catalyzed by enzymes produced inside the cell.
 Cells have their own energy release system that powers all of its activities.
 There are some exceptions to the cell theory as some organisms' cells are not typical.
 
Using Light Microscopes
 
Drawing Cells:
 Use a sharp pencil with a hard lead to draw single sharp lines.
 Join up lines carefully to form continuous structures such as cells.
 Draw lines freehand, but use a ruler for labelling lines.
 
Calculation of Magnification and Actual Size:
 A typical school microscope has three levels of magnification:
 x40 (low power).
 x100 (medium power).
 x400 (high power).
 Magnification = size of image / actual size of specimen.
 
Testing the Cell Theory:
 There are several atypical examples that contradict the cell theory, including:
 Striated muscle fibers:
o They are extremely long in comparison to other cells (about 3cm long in humans).
o They have many nuclei, sometimes several hundreds.
 Hyphae:
o Hyphae make up fungi, and are sometimes divided into cell-like structures by walls called
septa.
o Some hyphae don’t have septa (e.g.: aseptate hyphae), making them seem as continuous
structures with multiple nuclei.
 Algae:
o Giant algae could reach up to 100mm in length with only one nucleus.
 
Unicellular Organisms:
 The one cell making up unicellular organisms must be able to carry out all the functions of life.
 Unicellular organisms are able to carry out at least 7 functions of life:
 Nutrition: obtaining food to provide the needed energy and materials for growth.
 Metabolism: chemical reactions inside the living cells such as respiration.
 Growth: an irreversible increase in size.
 Response: the ability to react to changes in the environment.
 Excretion: getting rid of the waste products of metabolism.
 Homeostasis: keeping conditions inside the organism within tolerable limits.
 Reproduction: producing an offspring, either sexually or asexually.
 Many unicellular organisms also have the ability to move.
 
Limitations on Cell Size:
 The metabolic rate of the cell is proportional to its volume.
 For metabolism to continue, the cell must absorb reactants and remove waste. The rate at which
substances move through the cell membrane depends on its surface area.
 A small volume-to-surface area ratio may prevent cells from efficiently letting substances in and out
of their membranes, and might cause them to overheat.
 As the cell grows, volume (cytoplasm) increases in ratio to the surface area (plasma membrane),
which causes:
 Many organelles forming that require more nutrients and produce more waste.
 Lack of energy as respiration does not occur fast enough.
 Excretion to be too slow.
 Diffusion to be too slow.
 Overheating.
 
Functions of Life in Unicellular Organisms:
 Paramecium is an organism that can be easily cultured in a laboratory.
 As a unicellular organism, the paramecium contains:
 A nucleus, which can divide for the often asexual reproduction in which one parent cell divides into
two daughter cells.
 Food vacuoles that contain organisms ingested by the paramecium.
 A cell membrane to control chemicals entering and leaving the cell.
 Contractile vacuoles that fill up with water and expel it through the cell plasma to keep the cell
within tolerable conditions (homeostasis and excretion).
 A cytoplasm in which chemical reactions take place.
 Cilia around the cell plasma to move the cell around (response).
o Learn to draw.
 Chlamydomonas is a unicellular organism that lives in soil and freshwater habitats. It carries out
photosynthesis but is not a plant, and its cell wall is not composed from cellulose.
 As a unicellular organism, the Chlamydomonas contains:
 A nucleus which can divide into another with identical genetic information as a form of asexual
reproduction or fuse and divide with another nucleus as a form of sexual reproduction.
 A cytoplasm in which chemical reactions take place.
 A freely permeable cell wall, not made of cellulose.
 A cell plasma to control what enters and leaves the cell.
 Contractile vacuoles at the base of the flagella to fill up with water and expel it through the cell
plasma to keep the cell within tolerable conditions (homeostasis and excretion).
 Chloroplasts used for photosynthesis (growth and nutrition).
 Two flagella that move the cell around, often to the areas with the most light according to the light-
sensitive "eyespot" (response).
o Learn to draw.
 
Multicellular Organisms:
 Multicellular organisms consist of a single mass of cells fused together.
 Undetailed.
 
Cell Differentiation in Multicellular Organisms:
 Differentiation: the development of cells in different ways to carry out specific functions.
 Cell differentiation can develop tissues in multicellular organisms.
 Through differentiation, cells become specialized and specific to a certain function.
 Specialized cells can develop ideal structures for their functions and make the necessary enzymes,
making them more efficient (e.g.: RBC's do not have a nucleus for more space).
 
Gene Expression and Cell Differentiation:
 Differentiation involves the expression of some genes and not others in a cell's genome.
 The human genome contains over 2,500 genes, but less than half of those are needed or used in a
single specialized cell.
  The genes used in a cell are said to be "expressed"
 The control of gene expression is the key to development.
 
Stem Cells:
 Early embryonic cells, also called stem cells, are capable of developing and differentiating into any
type of adult cells, granting stem cells therapeutic uses.
 Stem cells have two key properties:
 They can divide repeatedly to produce copious quantities of new cells. Therefore, they can be used
to replace or repair damaged organs.
 They are not fully differentiated, meaning that they can differentiate into different types of cells and
produce them.
 Stem cells can be used for therapeutic purposes and regenerate tissues such as those in the skin,
kidneys and hearts.
 Stem cells can be used for non-therapeutic purposes and divide into large quantities of striated
muscle fibers, or meat, consumable by humans (beef).
 At their early stages, stem cells are the most versatile as they are not differentiated and can
specialize into any type of cell. When committed, a cell can divide only into its type and is no longer a stem
cell.
 Stem cells are present in adult bodies, but in smaller quantities and more specific places such as the
bone marrow, skin and liver. They assist in reparations of various tissues.
 
Stargardt's Disease:
 The full name of the disease is Stargardt's macular dystrophy.
 It s a genetic disorder that develops for children between 6 and 12 years old.
 The disorder causes a membrane protein used for active transport in the retina cells to malfunction.
 The loss of vision can be so severe as to register a person as blind.
 Experimenting with mice stem cells showed that injecting them into eyes caused no rejection,
tumors or problems.
 The stem cells caused no side-effects and improved vision when tried on humans.
 
Heart Disease:
 
Ethics of Stem Cells:
 Stem cells can be obtained form a variety of sources:
 Deliberately fertilizing egg cells with sperm and allowing the zygote to develop into between 4 and
16 cells.
 Blood from the umbilical cord can be taken and the cells frozen for possible use later in the baby's
life.
 Some adult tissues such as bone marrow have stem cells.
 Stem cells are extremely helpful but have been regarded as unethical.
 Stem cells kill an embryo when taken from the embryonic cells. People argue that embryos only
become human when they develop more - after several weeks.
 In vitro fertilization (IVF) is creating humans for the sole purpose of taking stem cells, which is said to
be unethical.
 IVF involves hormone treatment for women as well surgical risks in extracting the stem cells. If
women are paid for this it could exploit vulnerable groups such as college girls.
 At the same time, they are very contributive to curing diseases.
 
 
Ultrastructure of Cells (1.2):
 
The Resolution of Electron Microscopes:
 Electron microscopes have much higher resolutions than light microscopes.
 The light microscope can have a maximum resolution of 0.2um (200nm), but not higher since It is
limited by the wavelength of light (400nm-700nm). This is why the maximum magnification of a light
microscope is often x400.
  Electron microscopes have a much higher resolution due to the shorter wavelength of an electron
beam. They have the resolution of 0.001um (1nm) which is 200 times higher than that of the light microscope,
allowing the to reveal the ultrastructure of cells.
  Resolution in Millimeters Resolution in Resolution in
(mm) Micrometers(um) Nanometers(nm)
Unaided Eyes 0.1 100 100,000
Light Microscope 0.0002 0.2 200
Electron 0.000001 0.001 1
Microscope
 
Prokaryotic Cell Structure:
 Prokaryotes have a simple cell structure without compartments.
 Prokaryotes do not have a nucleus, making them the first organisms to evolve on Earth and still the
simplest. They are everywhere.
 All cells have a cell membrane, but some, including prokaryotes, have a cell wall, which is much
stronger and gives the cell its structure and prevents it from bursting.
 The cell wall of prokaryotes contains peptidoglycan and is often said to be extracellular.
 Prokaryotes have an uninterrupted cytoplasm with no compartments or nucleus, but is still complex
with its enzymes and chemicals; less than eukaryotic cells, though.
 Prokaryotic cells only have ribosomes, smaller than those of eukaryotic cells, and a nucleoid in their
cytoplasm.
 The nucleoid (nucleus-like but not a true nucleus). appears lighter than other organelles in many
electron micrographs, and contains the naked DNA, which is not associated with proteins (that's why is
appears lighter in micrographs).
 
Cell Division In Prokaryotes:
 Prokaryotes divide by binary fission.
 Binary fission is used by prokaryotes as a form of asexual reproduction.
 In binary fission, prokaryotic cells' chromosomes are replicated, and the two copies move to
opposite ends of the cell, and the cytoplasm quickly divides afterwards, forming two genetically identical cells.
 Learn to draw.
 
Eukaryotic Cell Structure:
 Eukaryotes have a compartmentalized cell structure.
 Eukaryotic cells have structures inside them that are compartmentalized, and the partitions are
either single or double membranes.
 The internal structure of a eukaryotic cell is much more complex than that of a prokaryotic cell.
 The compartments in a eukaryotic cytoplasm are known as organelles.
 There are several advantages in being compartmentalized:
 Enzymes and substrates for a particular process can be much more concentrated than if they were
spread across the cytoplasm.
 Substances that can cause damage to the cell can be safely stored inside the membrane of an
organelle.
 Conditions such as PH can be maintained at an ideal level for a certain process.
 Organelles with their contents can be moved around within the cell.
 Learn to draw.
 The cell contains:
 Nucleus:
o The nuclear membrane is double and has pores through it. It contains chromosomes, which
contain DNA associated with histone proteins.
o Uncoiled proteins are spread through the nucleus and called chromatin. There are often
densely staining areas of chromatin around the edge of the nucleus.
o The nucleus is where DNA is replicated and transcribed to form mRNA, which is exported via
the nuclear pores to the cytoplasm.
  Rough Endoplasmic Reticulum (rER):
o The rER consists of flattened membrane sacs called cisternae which have ribosomes
attached to their outside.
o Ribosomes are larger than in prokaryotes and classified as 80S.
o The main function of the rER is to synthesize protein for secretion.
o Proteins synthesized by the rER are exported into the Golgi apparatus then outside the cell
by exocytosis.
 Golgi apparatus:
o The organelle consists of flattened membrane sacs called cisternae, like rER. However, these
are shorter, curved, do not have as many vesicles nearby and do not have ribosomes.
o The Golgi apparatus processes proteins brought in by the rER.
 Lysosome:
o These are approximately spherical with a single membrane. They are formed in Golgi
vesicles.
o They contain high concentrations of protein, which makes them dark in electron
micrographs.
o They contain digestive enzymes that break down ingested food, other organelles or even the
whole cell.
 Mitochondrion:
o A double membrane surrounds mitochondria, with the inner part invaginated to form
cristae.
o The fluid inside is called the matrix.
o The shape is variable, but usually spherical or ovoid.
o They produce ATP for the cell by aerobic cell respiration.
o Fat is digested here if it is used as an energy source.
 Free ribosomes:
o They appear as a dark granule in the cytoplasm and have no membrane.
o They, like rER ribosomes, are 80S.
o They synthesize proteins that work in the cytoplasm as enzymes, for example.
o They are constructed in a region of the nucleus called the nucleolus.
 Chloroplast:
o They have a double membrane.
o They contains stacks of thylakoids, which are flattened sacs of membrane.
o The shape is variable, but usually spherical or ovoid.
o They produce glucose and other organic compounds by photosynthesis.
o Starch grains may be present if rapid photosynthesis is taking place.
 Vacuoles and Vesicles:
o They consist of a single membrane with fluid inside.
o They are large in plant cells.
o Some animal cells digest food in them.
o Some unicellular organisms use them to expel excess water.
o Vesicles: very small vacuoles used to transport materials inside the cell.
 Microtubules and centrioles:
o Microtubules are small cylindrical fibers in the cytoplasm.
o They move chromosomes during cell division.
o Centrioles are in animal cells and contain two groups of nine triple microtubules.
o Centrioles form an anchor point for microtubules during cell division and for microtubules
inside cilia and flagella.
 Cilia and flagella:
o Cilia are whip-like structures projecting from the cell surface.
o Cilia contain a ring of nine double centrioles plus two central ones.
o Flagella are larger than cilia, and there is usually only one.
o They can be used for locomotion.
o Cilia can also be used to create a current in the fluid next to the cell.
 
Exocrine Gland Cells or the Pancreas:
 Gland cells secrete substances, releasing them through their plasma membrane.
 There are 2 types of glands cells in the pancreas:
 Endocrine cells secrete hormones into the bloodstream.
 Exocrine gland cells:
o They secrete digestive enzymes into a duct that carries them to the small intestine where
they digest foods.
o Since enzymes are proteins, they need to produce proteins in high amounts and process
them, so they have, as micrographs show:
o Plasma membrane.
o Golgi apparatus.
o Mitochondrion.
o Vesicles.
o Nucleus.
o Lysosomes.
o rER.
 
Palisade Mesophyll Cells:
 The function of the leaf is photosynthesis.
 The cell type that carries out the most photosynthesis in a leaf is palisade mesophyll.
 The shape of these cells is roughly cylindrical.
 They have:
 Cell wall.
 Plasma membrane.
 Chloroplasts.
 Mitochondrion.
 Vacuole.
 Nucleus.
 
 
Membrane Structure (1.3):
 
Phospholipid Bilayers:
 Phospholipids form bilayers in water due to the amphipathic properties of phospholipid molecules.
 Hydrophilic: a term used to describe substance which are chemically attracted to water. This
includes all substances that dissolve in water, as well as polar (e.g.: glucose), or charged (e.g.: sodium ions,
chloride ions) molecules, and substances that water adheres to (e.g.: cellulose).
 Hydrophobic: a term used to describe substances which do not dissolve in water. This also includes
nonpolar molecules and uncharged particles. The forces which cause two hydrophobic substances to join in
water are known are hydrophobic interactions.
 Amphipathic: a term used to describe substances that are partly hydrophilic and partly hydrophobic
 Phosphate heads in a phospholipid are hydrophilic.
 Hydrocarbon tails in a phospholipid are hydrophobic.
 When mixed in water, phosphate heads of a phospholipid are attracted to the water, while the
hydrocarbon tails are attracted to each other (hydrophobic interactions), which is why phospholipids form a
bilayer with the tails facing each other.
 
Davson-Danielli's Model of the Cell Membrane:
 In the 1930's, Davson and Danielli proposed a model demonstrating layers of protein adjacent to the
phospholipid bilayer of the cell membrane, on both of its sides.
 Davson and Danielli suggested that this model explains the effective blockage of membranes to the
movement of substances despite them being very thin.
 Davson and Danielli backed up their model since the electron micrographs made of the cell
membrane in the 1950's showed a railroad track appearance (two dark lines with a lighter band between,
noting that proteins appear dark in micrographs while phospholipids appear light).
  Problems with the Davson-Danielli model were:
 Freeze-etched electron micrographs: this caused fractures in weak parts of the cell, such as the
center of membranes. Globular proteins scattered through the center of the membrane in freeze-etched
images were interpreted as transmembrane proteins.
 Structure of membrane proteins: the proteins extracted from cell membranes were variable in size
and globular in shape, unlike those that would continuously cover the membrane. They were also at least
partly hydrophobic.
 Fluorescent antibody tagging: red and green-marked antibodies that bind into membrane proteins
tagged them as such. Within 40 minutes, the antibodies were mixed, meaning proteins are free to move
within the membrane, unlike what Davson and Danielli suggested.
 
Singer and Nelson's Model of the Cell Membrane:
 In 1966, Singer and Nelson proposed a cell membrane model which has proteins occupying different
parts of the membrane.
 Peripheral proteins were attached to the inner and outer surfaces, while integral proteins were
found within the phospholipid bilayer, protruding out of it in some cases from one or both sides.
 The model is also known as the fluid mosaic model since the proteins look like tiles in a mosaic, and
are free to move due to the same ability of phospholipids to do so.
 
Membrane Proteins:
 Membrane proteins are diverse in terms of structure, position in the membrane and function.
 Some functions of membrane proteins:
 They from binding sites for hormones, also known as hormone receptors. These include insulin.
 They can act as immobilized enzymes with their active site on the outside, such as in the small
intestines.
 Adhesion between them forms tight junctions between groups of cells in tissues and organs.
 They allow cell-to-cell communication, such as between receptors for neurotransmitters at synapses.
 They contain channels for passive transport to allow hydrophilic particles across by facilitated
diffusion.
 They contain pumps for active transport which use ATP to move particles across the membrane.
 They can act as electron carriers.
 The functions of membrane proteins allow them to be divided into 2 types:
 Integral proteins:
o Integral proteins are hydrophobic on at least part of their surface and therefore embedded
in the hydrocarbon chains inside the bilayer.
o Many integral proteins are transmembrane, meaning they extend across the membrane,
with hydrophilic parts projecting through the regions of phosphate heads on either side.
 Peripheral Proteins:
o Peripheral proteins are hydrophilic on their surface, so are not embedded in the membrane.
o Most peripheral proteins are attached to integral proteins and the attachment is often
reversible.
o Some peripheral proteins have a single hydrocarbon chain attached to them which anchors
them to the membrane.
 Membrane proteins are oriented correctly to function properly on either surface of the membrane
(inner or outer).
 The protein content of membranes is highly variable since membrane functions are different.
 The protein content on cells' plasma membranes is about 50%, while it reaches about 75% on
chloroplasts and mitochondria (the highest).
 
Drawing Membrane Structure:
 The following need to be shown in a membrane diagram:
 Phospholipids.
 Integral proteins.
 Peripheral proteins.
 Cholesterol.
 
Cholesterol In Membranes:
 Cholesterol is a component of animal cell membranes.
 Cholesterol is a lipid, but not a fat or an oil; it is a steroid.
 Most of the cholesterol molecule is hydrophobic, and hence attracted to the hydrocarbon tails, but
the -OH (hydroxyl) group on one of its ends is hydrophilic, and hence attracted to the phosphate heads.
 Cholesterol molecules are positioned between phospholipids in a membrane.
 The amount of cholesterol in animal cells varies.
 
The Role of Cholesterol in Membranes:
 Cholesterol in mammalian membranes reduces membrane fluidity and permeability to some solutes.
 The cell membrane is overall fluid since its components are free to move (hydrocarbon chains
behave as liquids while phosphate heads behave like solids).
 The fluidity of animal cells needs to be controlled; if they were too fluid, substance would easily pass
through, but if they were not fluid, transport would be restricted across them.
 Cholesterol:
 Disrupts the regular packing of hydrocarbon tails, preventing them from crystallizing and behaving
like solids.
 Restricts molecular motion and hence excess fluidity.
 Reduces the permeability of hydrophilic particles such as sodium and hydrogen ions.
 Can help cells curve into the concave shape which helps in the formation of vesicles through
endocytosis due to its shape.
 
 

Membrane Transport (1.4):

 
Endocytosis:
 The fluidity of membranes allow materials to be taken into cells by endocytosis or released by
exocytosis.
 Vesicle: a small sac of membrane with a droplet of fluid inside.
 Vesicles are spherical, often present in eukaryotic cells.
 Due to membrane fluidity and its ability to change shape, vesicles are constructed, move around,
then are deconstructed.
 To form a vesicle, a small region of the membrane is pulled of from the rest of it and pinches off.
Proteins in the membrane carry out this process, using energy from ATP.
 When vesicles form to take substances from outside into the cell itself, endocytosis occurs.
 Endocytosis vesicles could contain water and solutes, but also molecules too large to pass through
the plasma membrane that are needed by the cell (e.g.: white blood cells take in pathogens such as bacteria
and viruses by endocytosis then kill them).
 
Vesicle Movement In Cells:
 Vesicles move materials within cells.
 Sometimes, the content of the vesicle needs to be moved, while at other times it is the vesicle's
membrane.
 Protein is synthesized by the rough endoplasmic reticulum (rER) and then released through vesicles
in the Golgi apparatus. The Golgi apparatus processes the protein into its final form then releases it, once
again through vesicles, into the cell membrane to be secreted.
 In cell growth, phospholipids are produced next to the rER and inserted into it, where ribosomes add
proteins to the membrane and release it through vesicles into the membrane to increase its surface area by a
very small amount. This method can be used to increase the size of lysosomes and mitochondria.
 
Exocytosis:
  When vesicles form to transport substances through the cytoplasm and out of the cell (secretion),
exocytosis occurs.
 Digestive enzymes are released from gland cells by exocytosis, where the polypeptides are produced
in the rER, processed in the Golgi apparatus, and transported in vesicles in the plasma membrane, where the
vesicle fuses with the membrane while enzymes exit the cell (secretion).
 In paramecium, for example, waste can be expelled by transporting it in vesicles, sometimes called
contractile vacuoles, into the outside of the cell.
 
Simple Diffusion:
 Particles move across membranes by simple diffusion, facilitated diffusion, osmosis and active
transport.
 Diffusion: the spreading out of particles in liquids and gases that happens because the particles are
in continuous random motion.
 Particles diffuse from a higher concentration to a lower one (down the concentration gradient).
 Diffusion is a passive process since the cell does not require any energy to make it occur.
 Only particles that the phospholipid bilayer is permeable to can diffuse through he membrane (e.g.:
oxygen, a non-polar molecule, can easily pass through the membrane and diffuse in or out of the cell,
according to the concentration gradient).
 Since the center of the membrane is hydrophobic, polar particles cannot easily pass through, and are
only diffused at low rates (the smaller the particle, the easier the diffusion).
 
Facilitated Diffusion:
 Protein channels allow for polar substances to pass through them since they cannot perform simple
diffusion due to the membrane's hydrophobic interior.
 The chemical properties and diameter of the protein channels allow it to only pass one type of
material through it.
 The process is facilitated because channels are used to allow diffusion.
 Cells can control which channels are synthesized and placed in the membrane, and hence control
the types of particles diffusing in and out.
 
Osmosis:
 Osmosis: the net movement of water molecules entering and exiting cells.
 Sometimes the amount of water molecules moving in and out of the cell at the same rate, causing
no net movement.
 Osmosis occurs due to the difference in concentrations of the solutes in water.
 Substances dissolve in water by forming intermolecular bonds with its molecules, restricting its
movement. This causes a net movement from areas with low solute concentration to areas with high solute
concentration.
 Osmosis s a passive process since no direct energy is released to perform it.
 Osmosis can happen in all cells because water molecules, regardless of being hydrophilic, are small
enough to pass through the membrane.
 Some cells have aquaporins on their membranes, allowing a much higher permeability to water (e.g.:
kidney cells, root hair cells in soil).
 At their narrowest point, aquaporins are only slightly wider than water molecules, allowing them to
pass in a single file, and positive charges there prevent protons (H+) from passing through.
 
Active Transport:
 Cells sometimes take in substances even though their concentration is lower outside, going against
the concentration gradients.
 Most active transport uses ATP in order to occur, and each cell produces its own ATP through
respiration.
 Active transport is carried out by globular proteins in the membrane called pump proteins, and these
exist in many types to allow a cell to precisely control the content of its cytoplasm.
 
Active Transport of Sodium and Potassium in Axons:
 Axon: a narrow cell with cytoplasm inside which is part of neurons and the nerve system.
  Nerve impulses occur through rapid movement of sodium and potassium across the membrane of an
axon. This happens due to different gradients of them inside and outside the axon.
 Active transport in the Na-K pump uses 1 ATP in each cycle to perform the following steps:
 The axon contains a sodium-potassium pump protein which starts the process of facilitated diffusion
by opening up to the interior of the axon for three sodium ions to enter and attach to their binding sites.
 ATP is then used to transfer phosphate from itself to the pump, causing it to close.
 The interior of the pump opens for the three sodium ions to be released.
 Afterwards, two potassium ions can enter and attach to their binding sites.
 The potassium ions cause the phosphate group to be released, once again closing the protein pump.
 The interior of the pump opens again for the potassium ions to exit and sodium ions to enter once
again, repeating the same cycle.
 
Facilitated Diffusion of Potassium in Axons:
 Potassium channels consist of four protein subunits, and are 0.3nm wide at their narrowest point.
 Potassium is too large to pass through when associated with water as an ion, so the bonds are
broken and temporary bonds are formed between the ion and the pump.
 After the potassium passes through the narrowest part of the pore, it can once again be associated
with a shell of water molecules.
 The pump is specific to potassium since other positive ions are either too large to pass through or
too small to be separated from water molecules and attracted to the pump.
 Functioning of the potassium pump:
 Potassium pumps function through their voltage-based gate which opens according to the charge of
the membrane surrounding them.
 The ends of the gate are positively charged, while the inner membrane is negatively charged, causing
them to be attracted to each other so the gate is closed.
 At one point, though, the outer membrane becomes negative while the inner one becomes positive,
which attracts the gates to the outer membrane, making them open for potassium ions to enter.
 Within milliseconds of this, however, a small ball attached to the gates by a chain of flexible amino
acids fills the opening and keeps it closed until the gates close once again.
 
Preventing Osmosis In Excised Tissues and Organs:
 Animal cells can be damaged by osmosis.
 A solution with high osmolarity (hypertonic) has water leaving cells rapidly, causing the volume of
the cytoplasm to shrink while it maintains its plasma membrane's surface area, which develops indentation
(crenellations).
 A solution with low osmolarity (hypotonic) has water entering cells rapidly, causing them to swell up
and possibly eventually burst, leaving raptured plasma membranes called red cell ghosts.
 In isotonic solutions, water leaves and enters cells at the same rate, keeping them healthy.
 It is important to store human organs and tissues in isotonic solutions during medical procedures.
 Usually, an isotonic sodium chloride solution (normal saline) is used to store tissues, having an
osmolarity of about 300mOsm (milliOsmoles).
 Normal saline is used in many medical procedures; it can be:
 Safely introduced to a patients blood system via an intravenous drip.
 Used to rinse wounds and skin abrasions.
 Used to keep areas of damaged skin moistened prior to skin grafts.
 Frozen to the consistency of slush for the packing of donor organs until transplants.
 
 
The Origin of Cells (1.5):
 
Cell Division and the Origin of Cells:
 Cells can only be formed by division of pre-existing cells.
 Cells can only be created from previous cells, through DNA replication and division.
 
Spontaneous Generation and the Origin of Cells:
  Verifying the general principles that underlie the natural world: the principle that cells only come
from pre-existing cells needs to be verified.
 Spontaneous generation: the formation of living organisms from nonliving matter.
 After the 17th century, scientists proved in several ways that spontaneous generation is not possible
but some still believed it would be with the presence of air.
 Louis Pasteur used carefully designed apparatus and swan-necked flasks to falsify spontaneous
generation.
 Other reasons to suggest cells can only com from pre-existing cells include:
 Cells are very complex structures and no natural mechanism has been suggested to produce them
from simpler subunits.
 No example is known to increase the number of cells in an organism without cell division.
 Viruses are produced from simpler subunits but are not cells, and can only be produced in the host
cells they have infected.
 
Spontaneous Generation and Pasteur's Experiments:
 Evidence from Pasteur's experiments that spontaneous generation of cells and organisms does not
now occur on Earth.
 Pasteur proved that a nutrient broth of boiled water containing yeast and sugar was not
contaminated when kept in a sealed flask.
 The most famous of Pasteur's experiments involved the swan-necked flask, where he found that no
organisms would enter solutions if there is no path for them to do so, since the necks are bent.
 
Origin of the First Cells:
 The first cells must have arisen from nonliving material.
 Unless cells arrived to Earth from another part of the universe, they must have arisen from nonliving
material.
 The evolution of nonliving matter into living cells is thought to have taken hundreds of millions of
years.
 There are several ways through which nonliving matter could have evolved into living cells:
 Production of carbon compounds such as sugars and amino acids:
o When electrifying methane, hydrogen and ammonia (simulation of lightening effect),
common compounds of Earth's atmosphere, amino acids and other carbon compounds needed for life
were found to be produced.
 Assembly of carbon compounds into polymers:
o A first place for cells to evolve is likely to be deep-sea vents, which contain hot gushing
water carrying reduced inorganic chemicals such as iron sulphide.
o The chemicals in deep-sea vents represent readily accessible supplies of energy, perhaps the
source of energy for assembling carbon compounds.
 Formation of membranes:
o If phospholipids or other amphipathic compounds formed as the first carbon compounds,
they would automatically form bilayers and vesicles similar to plasma membranes, isolating their
internal chemistry than that of the surroundings, creating different conditions.
 Development of a mechanism for inheritance:
o DNA needs to replicate through the usage of enzymes for cell division, but genes are needed
to make enzymes.
o It is thought that RNA may have been instead of DNA earlier, as it can self-replicate while
still storing information.
 
Endosymbiosis and Eukaryotic Cells:
 The origin of eukaryotic cells can be explained by the endosymbiotic theory.
 The endosymbiotic theory states that mitochondria were once free-living prokaryotic cells that
developed aerobic respiration.
 Larger prokaryotes that could only respire anaerobically took mitochondria in by endocytosis, and
allowed them to stay in their cytoplasm.
 As long as mitochondria can divide fast enough, it can survive indefinitely in larger prokaryotic cells.
  According to the endosymbiotic theory, mitochondria have persisted for hundreds of millions of
years to become as they are today in eukaryotic cells.
 There formed a mutualistic relationship between the larger and smaller prokaryotes, where the
smaller ones would be supplied with food while the larger ones were efficiently supplied with energy through
the smaller cells' aerobic respiration. Natural selection therefore favored the cells with this endosymbiotic
relationship.
 The endosymbiotic theory also applied to plant cells and chloroplasts, where photosynthetic cells
were taken in by larger ones, supplied with food, and evolved into the current chloroplasts of eukaryotic cells.
 Although no longer capable of surviving alone, chloroplasts and mitochondria have features which
show they were once independent:
 They have their own genes, on a circular DNA molecule like that of prokaryotes.
 They have their own 70s ribosomes of a size and shape typical of some prokaryotes.
 They transcribe DNA and use the mRNA to synthesize some of their own proteins.
 They can only be produced by division of pre-existing mitochondria and chloroplasts.
 
 
Cell Division (1.6):
 
The Role of Mitosis:
 Mitosis: the division of a cell into two daughter cells, each with one of the nuclei and therefore
genetically identical to the other.
 Before mitosis occurs, all of the DNA in the nucleus must be replicated, which happens during the
interphase, before mitosis.
 During interphase, each chromosome is converted from a single DNA molecule into two identical
ones, called chromatids.
 During mitosis, one of the chromatids from every DNA passes to each daughter nucleus.
 Mitosis is involved whenever cells with genetically identical nuclei are needed in eukaryotes, such as
in growth, tissue repair and asexual reproduction.
 Mitosis, although a continuous process, has been divided into 4 phases:
 Prophase:
o The chromosomes becomes shorter and fatter by coiling (supercoiling).
o Microtubules grow from structures known as microtubule organizing centers (MTOC) to
form a spindle-shaped array that links the poles of the cell.
o At the end of the prophase the nuclear membrane breaks down.
 Metaphase:
o Microtubules continue to grow and attach to the centromeres on each chromosome.
o The two attachment points on opposite sides of each centromere allow the chromatids of a
chromosome to attach to microtubules from different sides.
o The microtubules are shortened at the centromeres to ensure correct attachment, and the
chromosomes are aligned at the equator (mitotic spindle).
 Anaphase:
o To start the anaphase, each centromere divides, allowing the pairs of sister chromatids to
separate.
o Spindle microtubules pull the sister chromatids to the two opposite poles, producing
genetically identical nuclei. This is ensured by the attachment of microtubules to centromeres in
metaphase.
 Telophase:
o The chromatids have now reached the poles and are called chromosomes.
o The chromosomes are pulled in a right group near the MTOC, and a nuclear membrane
reforms around them, creating a nucleolus after the chromosomes uncoil.
o By this stage the cell is already dividing and the two daughter cells enter interphase again.
 
Interphase:
 Interphase is a very active phase of the cell cycle with many processes occurring in the nucleus and
cytoplasm.
 Cell cycle: the sequence of events between one cell division and the next.
  The cell cycle has 2 main phases:
 Interphase.
 Cell division (discussed above).
 Interphase: a very active phase in the life of a cell when many metabolic reactions occur.
 DNA replication in the nucleus and protein synthesis in the cytoplasm only happen during
interphase.
 The number of mitochondria in the cell increases during metaphase due to growth and division.
 In plants, chloroplast increases like mitochondria, and cellulose is synthesized and vesicles are used
to add it to the cell wall.
 Interphase consists of 3 phases:
 G1: cellular contents, apart from the chromosomes are duplicated. Some cells do not need to
divide, and so enter a G0 phase instead, which may be temporary or permanent.
 S phase: the genetic material in the nucleus is replicated to have identical nuclei after mitosis.
 G2.
 
Supercoiling of Chromosomes:
 Chromosomes condense by supercoiling during mitosis.
 During the first stage of mitosis, condensation of chromosomes happens to fit them in the nuclei.
 Condensation happens by repeatedly coiling the DNA molecule to make the chromosome shorter
and wider (supercoiling).
 Proteins associated with chromosomes in eukaryotic DNA called histones help in supercoiling, and
enzymes are involved.
 
The Mitotic Index:
 Mitotic index: the ratio between the number of cells in mitosis in a tissue and the total number of
observed cells.
 Mitotic index = number of cells in mitosis/total number of cells.
 
Cytokinesis:
 Cytokinesis occurs after mitosis and is different in plant and animal cells.
 Cytokinesis: the process of cell division after mitosis.
 In animal cells:
o The plasma membrane is pulled inwards around the equator of the cell to form a cleavage
furrow. This is accomplished using a ring of contractile proteins immediately inside the plasma
membrane at the equator. The proteins are actin and myosin and are similar to proteins that cause
contractions in muscles.
o When the cleavage furrow reaches the center, the cell is pinched apart into two daughter
cells.
 In plant cells:
o Vesicles are moved to the equator where they fuse to form tubular structures across the
equator.
o With the fusion of more vesicles the tubular structures merge to form two layers of
membrane across the whole of the equator, which develop into the plasma membranes of the two
daughter cells and are connected to the existing plasma membrane at the sides of the cell, completing
the division of the cytoplasm.
o Pectins and other substances are brought in vesicles and deposited by exocytosis between
the two new membranes. This forms the middle lamella that will link the new cell walls.
o Both of the daughter cells bring cellulose to the equator and deposit it by exocytosis
adjacent to the middle lamella.
o Each cell builds its own cell wall adjacent to the equator.
 
Cyclins and the Control of the Cell Cycle:
 Cyclins: a group of proteins used to ensure the tasks of cell division are performed at the correct
time, and that the cell only moves on to the next stage of the cycle when appropriate.
 The cyclin cycle:
 Cyclins bind to enzymes called cyclin-dependent kinases.
  Kinases become active with cyclins bound to them and attach phosphate groups to other proteins in
the cell.
 The attachment of phosphate triggers other proteins to become active and start a stage of the cell
cycle.
 There are 4 main types of cyclin in human cells:
 Cyclin D triggers the cell to move from G0 to G1 and from G1 to the S phase.
 Cyclin E prepares the cell for DNA replication in the S phase.
 Cyclin A activates DNA replication inside the nucleus in the S phase.
 Cyclin B promotes the assembly of the mitotic spindle and other tasks in the cytoplasm to prepare
for mitosis.
 

Tumor Formation and Cancer:

 Mutagens, oncogenes and metastasis are involved in the development of primary and secondary
tumors.
 Tumors: abnormal groups of cells that develop at any stage of life in any part of the body.
 Malignant tumors, unlike benign tumors, can be life-threatening with development.
 Cancer: disease due to malignant tumors.
 Carcinogens: chemicals and agents that cause cancer.
 Mutagens: agents that cause gene mutation, which might lead to cancer.
 Mutations: random changes to the base sequences of genes.
 Oncogenes: the few genes that can cause cancer upon mutation.
 Oncogenes normally control cell division and the cell cycle, which is why a mutation in them may
cause abnormal division and therefore tumor formation.
 The chances of tumors forming are extremely small since multiple mutations are needed in a cell,
but the vast number of cells in human bodies make them significant.
 A tumor cell divides rapidly to multiply in number, forming a primary tumor.
 Metastasis: the movement of cells from a primary tumor to set up secondary tumors in other parts
of the body.
 
Smoking and Cancer:
 Correlation: a relationship between two variable factors.
 There are two types of correlation:
 Positive correlation: when both variable factors increase together.
 Negative correlation: when one variable increases while the other decreases.
 There is a positive correlation between cigarette smoking and the death rate due to cancer.
 Smoking leads to cancer mainly in organs where the smoke passes or makes contact with, but also in
other places.
 The correlation between smoking and cancer does not prove that smoking causes cancer, but the
links in this case are well-established.
 There are at least 40 carcinogens in cigarettes.
 

Molecules to Metabolism (2.1):

 
Molecules to Metabolism:
 Cells are made up of organelles (nucleus, mitochondria, endoplasmic reticulum, etc..)
 Organelles are made up of elements, compounds, and ions.
 Inside organelles, chemical reactions take place through the activation of enzymes.
 All enzyme-catalyzed chemical reactions inside biological cells are referred to as metabolisms.
 Anabolism: the synthesis of complex molecules from simpler molecules (e.g.:
a. Protein synthesis using ribosomes,
b. DNA synthesis during replication,
c. Photosynthesis, including production of glucose from carbon dioxide and water,
 d. Synthesis of complex carbohydrates including starch, cellulose and glycogen.
e. Condensation.
 Catabolism: the breakdown of complex molecules into simpler molecules (e.g.:
a. Digestion of food in the mouth,
b. Cell respiration in which glucose or lipids are oxidized to carbon dioxide and water.
c. Digestion of complex carbon compounds in dead organic matter by decomposers.
d. Hydrolysis.
 
Types of Bonding:
1. Intramolecular bonding: the bonding which occurs within the molecule.
Ionic bonds:
 Electrons are transferred from metal to nonmetal when undergoing an intramolecular bonding process (e.g.:
NaCl).
 An electrostatic attraction holds the compounds together.
 The reactants must be opposite in poles.
Covalent bonds:
 The reaction occurs between two nonmetals.
a. Nonpolar covalent bonds: covalent bonds where an equal sharing of electrons is present.
b. Polar covalent bonds: covalent bonds where an unequal sharing of electrons is present. One side of
such a compound would be slightly positive, while the other would be slightly negative. An important
polar covalent compound is H2O (water).
 
2. Intermolecular bonding: the bonding which occurs between molecules.
Hydrogen bonds:
 Hydrogen bonds connect molecules in order to hold them together.
 Hydrogen bonds are present between a slightly positive atom and a slightly negative atom.
 Hydrogen bonds are present between two polar molecules.
 
 
Water (2.2):
 
 Water is a polar molecule because when oxygen atom attracts the two hydrogen atoms towards itself, it
maintains a slightly negative charge, even though it shares it electrons with hydrogen, while the hydrogen
atoms are slightly more positive.
 
Properties of Water:
1. Cohesion: The ability of water molecules to stick to each other through hydrogen bonds.
 Cohesion allows water to be pulled inside the xylem along very long columns in trees (transport).
 Surface tension allows insects to walk on water (habitat).
 
1. Adhesion: The ability of water to stick to other surfaces through forming hydrogen bonds with other polar
molecules.
 Water adheres to cellulose molecules in leaf's cell walls, which keeps the walls moist.
 
1. Universal Solvent: Almost any substance can be dissolved in water due to polarity.
 Substances can be carried while dissolved in water (transport medium).
 Plants transport minerals in dissolved water.
 Metabolic reactions inside cells occur in aqueous solutions.
 
1. High Thermal Capacity: Water takes a long time to heat up, as well as to cool down, as a long time is needed
to break down the hydrogen bonds.
 Aquatic environments are thermally stable.
 Blood can carry water from warm to cooler parts (transport).
 
1. Cooling Effect From Evaporation: Water can evaporate before reaching its boiling point.
 Heat from the skin surface is used to evaporate water (sweat) which cools the body down.
 
1. High Boiling and Freezing Points: A lot of energy is required to break down water's hydrogen bonds, and
when it freezes is become less dense, as ice forms at the surface first.
 Water rarely boils in natural habitats (it is a thermally stable habitat).
 Ice on water surfaces insulates the water underneath, allowing organisms to survive.
 
Hydrophilic and Hydrophobic:
 Hydrophilic: a term used to describe substance which are chemically attracted to water. This includes all
substances that dissolve in water, as well as polar (e.g.: glucose), or charged (e.g.: sodium ions, chloride ions)
molecules, and substances that water adheres to (e.g.: cellulose).
 Hydrophobic: a term used to describe substances which do not dissolve in water. This also includes nonpolar
molecules and uncharged particles. The forces which cause two hydrophobic substances to join in water are
known are hydrophobic interactions.
 
 
Carbohydrates and Lipids (2.3):
 
Carbohydrates:
 Monosaccharides: single sugar molecules (e.g.: glucose, fructose, ribose).
 Disaccharides: consist of two monosaccharides linked together (e.g.: maltose -two glucose-, sucrose -glucose
and fructose-, lactose -galactose and glucose-).
 Polysaccharides: consists of many monosaccharides linked together (e.g.: starch, glycogen, cellulose -all of
them are made from linking glucose molecules together-).
 Starch consists of amylose and amylopectin.
 Condensation: a reaction in which two or more molecules combine to form a larger molecule, producing
H O as a byproduct.
 2

 Hydrolysis: the chemical breakdown of a large compound due to reaction with water.
 
Lipids:
 Lipids: a diverse group of carbon compounds that share the property of being insoluble in water.
 Triglyceride: a principle group of lipids made of three fatty acids which are combined to a single glycerol
molecule through condensation, producing three water molecules as a byproduct. they are used as a long-
term energy store (energy from them is released through aerobic respiration), as well as for insulation.
 Ester bond: the bond formed when an acid reacts with the -OH group in an alcohol (in the case of
triglyceride, it is between the -COOH (carboxyl) group on a fatty acid and an -OH on the glycerol).
 Lipids are a better long-term store of energy than carbohydrates because:
 
Fatty Acids:
 Most of the fatty acids used by living organisms have between 14 and 20 carbon atoms in them, which from
the hydrocarbon chains.
 In some fatty acids, all carbon atoms are linked together through single covalent bonds only, while in others
some of them are linked by double covalent bonds.
 Saturated fatty acid: fatty acids in which all carbon atoms are linked by single covalent bonds.
 Unsaturated fatty acids: fatty acids in which one or more carbon atoms are linked by double covalent bonds.
They can be:
1. Cis: the hydrogen atoms bonded to the carbon atoms which have a double covalent bond between them are
on the same side, which causes the molecule to be bent, and hence not stack easily, therefore having a lower
melting point.
2. Trans: the hydrogen atoms bonded to the carbon atoms which have a double covalent bond between them
are on opposite sides, which causes the molecule to be straight, and hence easily stack together, therefore
having a higher melting point.
 Unsaturated fatty acids are also divided as:
3. Monounsaturated fatty acids: fatty acids in which only one pair of carbon atoms is linked by a double
covalent bond.
4. Polyunsaturated fatty acids: fatty acids in which more than one pair of carbon atoms are linked by double
covalent bonds.
  Steroids include:
1. Testosterone.
2. Cortisone.
3. Vitamin D.
4. Cholesterol.
 
 
Proteins (2.4):
 
Amino Acids and Polypeptides:
 Polypeptides: chains of amino acids that are made by linking them together through peptide bonds in
condensation reactions. This happens in ribosomes through translation. They are the main, and often only,
component of proteins. Some proteins contain one polypeptide, while others contain more.
 The amino acid sequences of polypeptides are coded for by genes.
 The condensation reaction of amino acids involves the amine group (-NH2) of one amino acids the carboxyl
group (-COOH) of the other.
 Dipeptide: a molecule consisting of two amino acids linked together by a peptide bond.
 
The Diversity of Amino Acids:
 All amino acids have some identical structural features:
1. A carbon atom is at the center of the molecule.
2. The carbon atom is bonded to an amine group.
3. The carbon atom is bonded to a carboxyl group.
4. The carbon atom is bonded to a hydrogen atom.
5. The carbon atom is bonded to an R group, which is different in each amino acid.
 Since all 20 amino acids are very similar in structure, it is the R group which determines the chemical
property difference between them, creating such a vast diversity for each one's functions.
 Sometimes, amino acids are modified to differ than the 20 original ones, making different proteins. Collagen
polypeptides are an example, as they originally contains proline, but sometimes contains hydroxyproline
instead, which makes it more stable.
 
Denaturation of Proteins:
 A protein is denatured when the R bond between the amino acid and the radical is broken. The bond is
weak, and when it is broken, the protein is altered, or denatured.
 Denaturation is permanent, and soluble proteins often become insoluble after it due to the hydrophobic R
group being exposed to the water by change in conformation.
 Denaturation can either be caused by heat or PH.
 Egg white and albumin can be used in protein denaturation experiments.
 
Examples of Proteins:
1. Rubisco: originally recognized as ribolose biphosphate carboxylase, rubisco is arguably the most important
enzyme in the world. The active site and properties of rubisco allow it to catalyze the reactions involving
carbon dioxide in the atmosphere, making it a vital element in the production of carbon, which is a necessary
element in the composition of all organic matter, as well as all carbon compounds needed by living organisms.
Rubisco is present in high concentrations in plant leaves, making it the most abundant protein in the world.
2. Immunoglobulin: otherwise known as antibodies, this protein has sites on both its sides with attach to
bacteria and bind to their antigens. Its binding site is hyper-variable, and the immunoglobulin can act as a
marker for the pathogens to find phagocytes. The body can produce many different types of this protein with
different binding sites and in large amounts, making it the basis of specific immunity to diseases.
3. Collagen: the primary structure of collagen consists of rope-like proteins made of three polypeptides wound
together. Collagen, being the most abundant protein in the human body, forms almost a quarter of its
proteins. The function of this protein is to form a mesh of fibers circulating the walls of blood vessels and
ligaments, making them resist tearing and giving them immense strength. For protection from fractures,
collagen also forms part of the teeth and other bones.
4. Insulin: the insulin hormone functions by signaling variant cells in the body to absorb glucose, preventing it
from reaching high concentrations in the blood. Cells which respond to insulin have a special active site on
 their cell membrane to which only the insulin hormone with its unique structure can bind. This allows it to
signal them, but not other cells, to absorb glucose. Insulin is produced in the B cells of the pancreas and
transported by the blood.
5. Rhodopsin: this protein is present in the rod of the retina, located in the eyes, and is one of the pigments
which assists in absorbing light and allowing human vision. Rhodopsin consists of a light sensitive retinal
molecule, not amino acids, surrounded by opsin polypeptide. When the retinal molecule is exposed to light, it
alters shape, causing a change in the opsin, which is signaled to the brain, allowing it to recognize even low
intensities of light.
6. Spider Silk: dragline, a type of silk produced by spiders, is stronger than steel and tougher than Kevlar. It
makes the spokes of spider webs and the ropes on which spiders suspend themselves. Initially, dragline
consists of parallel polypeptide arrays. Gradually and with extension, though, the silk extends what primarily
seem to be disordered triangles in it along with the arrays, becoming very resistant to breaking.
 Proteome: the entire complement of proteins that is or can be expressed by a cell, tissue, or organism. Every
living organism can be recognized with a unique, distinct proteome. This partly occurs due to organismic
activity throughout the age of the organism, but also because of the slight difference in the arrangement and
sequence of amino acids, which form the organism's DNA, and hence determine its proteome.
 
 
Enzymes (2.5):
 
Active Sites and Enzymes:
 Enzymes: globular proteins that work as catalysts. Enzymes are often called biological catalysts because they
are made by living cells and speed up biochemical reactions.
 Substrates: the substances the enzymes convert into products through a biochemical reaction.
 Enzyme-substrate specificity: Each enzyme can one catalyze one type of substrate.
 Active site: a special region on the surface of an enzyme were substrates bind for synthesis or
decomposition. The active site of each enzyme has a specific shape which allows only one substrate to bind to
it.
 
Enzyme Activity:
 The catalysis of a reaction by an enzyme consists of three stages:
1. The substrate binds to the active site of the enzyme.
2. While the substrates are bound to the active site they change into different chemical substances, which are
the products of the reaction.
3. The products separate from the active site, leaving it vacant for substrates to bind again.
 Collision: the coming together of a substrate molecule and an active site.
 In most reactions the substrate is dissolved in water around the enzyme.
 Dissolved substances and enzymes move freely and randomly in water (diffusion), but most substrates are
lighter and so move faster than enzymes. Collision occurs due to the random movement, and a successful
collision is one in which the substrate is correctly aligned with the enzyme's active site.
 
Factors Affecting Enzyme Activity:
1. Heat: when liquids containing enzymes and substrates are heated, the particles gain more kinetic energy,
allowing both the enzymes and the substrates to move faster, hence colliding more. When enzymes are
heated, the bonds between them vibrate strongly, having a larger change of breaking. When the bonds break,
the enzyme's properties and active site are altered and it cannot function anymore. The enzyme is denatured.
Enzymes work best at their optimum temperature, often 37.
2. PH: enzymes work within a certain range of PH, and each one has an optimum PH. when the PH is altered
above or below the optimum PH, the enzyme is gradually denatured due to an alternation in structure.
3. Substrate concentration: As the concentration of a substrate increases in a solution, more frequent collisions
occur between it and the enzymes, allowing a higher rate of catalysis.
 Denaturation can occur to an enzymes due to unsuitable temperature or PH, and it often becomes insoluble
to form a precipitate in water.
 
Immobilized Enzymes:
 An extract of yeast containing no yeast cells would convert sucrose into alcohol.
  Enzyme immobilization: attaching enzymes to other materials in order to restrict their movement. This can
be done by attaching the enzyme to a glass surface, trapping them in an alginate gel, or bonding them
together to form enzyme aggregates of up to 0.1mm diameter.
 Enzymes immobilization has several advantages:
1. The enzyme can be easily separated from the products of the reaction, stopping the reaction at the ideal
time and preventing contamination of the products.
2. The enzyme can be recycled after retrieved from the reaction mixture. This saves money.
3. Immobilization decreases the effect of temperature and PH changes on enzymes, reducing their replacement
rate over time.
4. Substrates can be exposed to higher enzyme concentrations than with dissolved enzymes, speeding up
reaction rates.
 
Lactose-free Milk:
 Lactose intolerance occurs with the lack of lactase, which converts lactose into galactose and glucose. This
causes the conversion of lactose into different chemicals, such as carbon dioxide and methane. It leads to
cramps, distension, and acid diarrhea.
 Lactose-free milk is made when beads, containing immobilized lactase enzymes from yeast, are placed in a
column. Heat-treated skimmed milk is then passed through, and lactose-free milk is collected and recirculated
to ensure the full breakdown of lactose.
 Lactose-free milk is also used for:
1. Flavored milk products, as galactose and glucose are sweeter in taste than lactose, reducing the need for
additional sweeteners.
2. Galactose and glucose are more soluble than lactose, and produce a smooth texture when frozen, so they
are used to make ice-cream.
3. Bacteria ferment glucose and galactose more quickly than lactose, shortening the production time of
yoghurt.
 
 
Structure of DNA and RNA (2.6):
 
Nucleic Acids and Nucleotides:
 Nucleic acids: very large molecules that are constructed by linking together nucleotides to form a polymer.
 Nucleotides consists of three parts:
1. A sugar, which has five carbon atoms, hence a pentose.
2. A phosphate group, which is the acidic, negatively charged part of the nucleic acid.
3. A base that contains nitrogen, and has either one or two rings of atoms in its structure.
o The base and phosphate are linked to the pentose sugar by covalent bonds.
o Nucleotides are linked together by a covalent bond between the phosphate of one and the pentose
sugar of the other.
o The base of the nucleotide determines its type. There are 4 different bases, and they contain the
genetic information in pairs, protected by the phosphate and pentose sugar backbone.
 
Differences Between DNA and RNA:
Deoxyribonucleic Acid: Ribonucleic Acid:
The pentose sugar in DNA is deoxyribose. The sugar in RNA is ribose.
There are usually two polymers of nucleotides in There is only one polymer of nucleotides in
DNA. RNA.
The 4 nitrogenous bases of DNA are: Adenine, The 4 nitrogenous bases of RNA are: Adenine,
Cytosine, Guanine, and Thymine. Cytosine, Guanine, and Uracil
 
Structure of DNA:
 Each strand in a DNA consists of chains of nucleotides linked by covalent bonds.
 The strands are "antiparallel" since they are parallel but run in the opposite direction.
 The strands form a double helix when wound together.
  Complementary base pairing explains that Adenine (A) can only pair with Thymine (T), while Guanine (G) can
only pair with Cytosine (C ).
 
 
Respiration (2.8):
 
Release of Energy by Cell Energy:
 Cell respiration: the controlled release of energy from organic compounds to produce ATP.
 All living cells perform respiration.
 In respiration, organic compounds are broken down to release energy, like glucose broken down to carbon
dioxide and water.
 Human bodies use carbohydrates and lipids for respiration, but also protein if there is an excess.
 Plants use carbohydrates and lipids they make in photosynthesis for respiration.
 ATP is formed by adding a phosphate group to ADP, and it used for respiration. The energy to add a
phosphate group to ADP is obtained from organic compound breakdown.
 ATP is not transferred from cell to cell.
 
ATP is a Source of Energy:
 ATP from cell respiration is immediately available as a source of energy in the cell.
 Cells require energy for 3 main types of activity:
1. Synthesizing large molecules like DNA, RNA and proteins.
2. Pumping molecules or ions across membranes by active transport.
3. Moving things around the cell, such as vesicles, chromosomes, etc..
 ATP powers these processes and is readily available as ADP produces it with cell respiration, and it breaks
down back into ADP when it releases energy.
 Since ATP is converted to heat and that is lost to the environment, it has to be constantly synthesized.
 
Anaerobic Respiration:
 Anaerobic cell respiration gives a small yield of ATP from glucose.
 ATP is produced in small amounts but quickly in anaerobic respiration as glucose is broken down without
oxygen.
 Anaerobic respiration is used in 3 conditions:
1. When a short but rapid burst of ATP production is needed.
2. When oxygen supplies run out in respiring cells.
3. In environments that are deficient in oxygen, for example waterlogged soils.
 In humans, the product of anaerobic respiration is lactic acid, usually known as lactate in its dissolved form.
 In plants and yeast, glucose is converted to yeast and carbon dioxide.
 Both lactate and ethanol are toxic to cells in excess and so must be removed from cells that produce them or
be produced in very limited quantities.
 
Yeast and its Uses:
 Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking.
 Yeast: a unicellular fungus that naturally occurs in habitats where glucose or other sugars are available, such
as the surface of fruits.
 Yeast can respire aerobically or anaerobically.
 Anaerobic respiration in yeast is basis for the production of food, drinks and renewable energy.
 Yeast is often used to cause rising in bread as it is placed in dough, which is kept warm, and respires to
eventually consume oxygen and start carrying out anaerobic respiration. The carbon dioxide from anaerobic
respiration causes rising in the dough.
 Yeast also produces ethanol, but that is evaporated during baking.
 Yeast is also used to make bioethanol through its anaerobic respiration where it uses sugars from sugar
canes and corn, breaks them down and consumes them, to release ethanol which is processed and filtered to
improve its combustion.
 Bioethanol is often used to power vehicles.
 
Anaerobic Respiration in Humans:
  Lactate production in humans when anaerobic respiration is used to maximize the power of muscle
contractions.
 Sometimes anaerobic respiration must be used in the body.
 Examples where anaerobic respiration may be used include:
1. Weight lifters during the lift.
2. Short-distance runners in races up to 400 meters.
3. Long-distance runners, cyclists and rowers in their sprint finish.
 Anaerobic respiration cannot be used for long due to the accumulation of lactate in cells.
 Lactate removal requires oxygen.
 Oxygen debt: the demand for oxygen that builds up during a period of anaerobic respiration.
 
Aerobic Respiration:
 Aerobic respiration can produce over 30 ATP's per glucose molecules, while anaerobic respiration releases
only 2.
 Most of aerobic respiration occurs in the mitochondria.
 
Respirometers:
 Respirometer: any device that is used to measure respiration rate.
 Most respirometers involve the following parts:
1. A sealed glass or plastic container in which the organism or tissue is placed.
2. An alkali, such as potassium hydroxide, to absorb carbon dioxide.
3. A capillary tube containing fluid, connected to the container.
 Normally, the fluid in the capillary tube would move closer to the container as respiration takes places as
oxygen is being consumed and carbon dioxide absorbed.
 The temperature inside a respirometer should be controlled using a water bath to prevent volume
fluctuation of gases.
 Respirometers can be used in experiments such as:
1. The respiration rates of different organisms can be compared.
2. The effect of temperature on respiration rate could be investigated.
3. Respiration rates could be compared in active ad inactive organisms.
 
Ethics of Animal Use in Respirometers:
 Is it ethical to take animals from their natural habitat, experiment on them, and possibly not return them?
 Will the animals suffer any pain or harm from the experiment?
 Can harm effects on animals be minimized? Can contact with the alkali be prevented?
 Is the use of animals essential or are there alternatives?
 
 
Photosynthesis (2.9):
 
What is Photosynthesis?:
 Photosynthesis: the production of carbon compounds in cells using light energy.
 Photosynthesis is an example of energy conversion, as light energy is converted into chemical energy in
carbon compounds.
 
Wavelengths of Light:
 Visible light has a range of wavelengths with violet the shortest and red the longest.
 The wavelengths seen by humans are also the ones used in photosynthesis, as they penetrate the
atmosphere in larger quantities than other wavelengths.
 
Light Absorption by Chlorophyll:
 Chlorophyll absorbs red and blue light most effectively and reflects green light more than other colors.
 Pigments make leaves appear green because they reflect green light.
 Chlorophyll is the main light-absorbing pigment in plants, and always appears green because I absorbs red
and blue light most effectively.
 
Oxygen Production in Photosynthesis:
 Oxygen is produced in photosynthesis from photolysis of water.
 Photolysis breaks down water to take in the hydrogen atoms as electrons into the electron carrier
plastoquinone, and releases oxygen as a waste product.
 
Effect of Photosynthesis on the Earth:
 Changes to the Earth's atmosphere, oceans and rock deposition due to photosynthesis.
 Prokaryotes performed photosynthesis first, and were then joined by plants.
 Great oxidation effect: the rising of oxygen rates in the atmosphere due to photosynthesis.
 Oxygenation may have weakened the greenhouse effect and hence caused glaciation.
 Oxygen caused the oxidation of iron dissolves in seawater, which caused precipitates of iron (banded iron
formations) at the seabed.
 Banded iron formations are most important iron ores, providing supplied of steel and iron.
 
Production of Carbohydrates:
 Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide.
 Plants use photosynthesis to make carbohydrates.
 Reaction involving the making of oxygen are often endothermic.
 Synthesis and condensation reactions are often endothermic.
 The energy obtained for photosynthesis is from light, which is why photosynthesis can only happen with
light in presence.
 Light energy does not disappear but is converted to chemical energy.
 
Limiting Factors:
 The rate of photosynthesis in plants can be affected by:
1. Temperature.
2. Light intensity.
3. Carbon dioxide concentration.
 Only the most unavailable of these factors is considered the limiting factor, as improving it would cause an
increase in the rate of photosynthesis while manipulating other factors would cause no change as long as it is
the limiting factor.
 
Controlled Variables in Limiting Factor Experiments:
 Which limiting factor will you investigate? (independent variable).
 How will you measure the rate of photosynthesis? (dependent variable).
 How will you keep the other limiting factors at a constant and optimal level? (controlled variable).
 
 

Genes (3.1):
 
What is a Gene?:
 Gene: an inheritable factor that consists of a length of DNA and influences a specific characteristic.
 Genetics comes from the word genesis, meaning origin.
  It was confirmed in the 19th century that heritable factors that influenced the characteristics of a living
organisms existed.
 Research into genetics was intense in the early 20th century, and by its middle it was found that genes are
found in DNA.
 There are 46 DNA molecules in a human cell, but thousands of genes.
 
Where are Genes Located?
 A gene occupies a specific position on one type of chromosome.
 Locus: the position of a gene in its type of chromosome.
 
What are Alleles:
 The various specific forms of a gene are alleles.
 Gregor Mendel concluded that there can be various types of a certain genes, and those determine inherited
factors of the offspring of breeding organisms.
 There are three alleles to the color coating of mice, and a large number of alleles for fruit fly eye color.
 There are 3 alleles that determine humans' ABO blood groups.
 As alleles are different forms of the same gene, they occupy the same locus on a chromosome.
 Only one allele can occupy the locus of a gene on a chromosome.
 Most animals have two copies of every chromosomes, which means possibly two different alleles of a gene
in each cell.
 
Differences Between Alleles:
 Alleles differ from each other by one or a few bases only.
 A gene consists of a length of DNA, with a base sequence that can be hundreds or thousand of genes long.
 Alleles often forms due to only slight differences in base sequences of a gene.
 Single nucleotide polymorphisms (SNPs - pronounced snips): positions in a gene where more than one base
sequence can be present.
 Several snips can be present in a gene, but even then the alleles of the gene differ by only a few bases.
 
Mutation:
 New alleles are formed by mutation.
 Mutations are random changes with no particular mechanism for them to be carried out.
 The most significant type of mutation is base substitution, where one base in a gene is replaced by another
(e.g.: adenine is replaced by cytosine, guanine or thymine).
 Mutations are mostly neutral of harmful, and can be lethal.
 Mutations are eliminated when a mutated cell dies (in frame mutation), but if the mutated cells develop into
gametes, the mutations can be passed down to an offspring, possibly causing genetic disease.
 
Sickle Cell Anemia:
 Sickle-cell anemia is the commonest genetic disease in the world.
 Sickle-cell anemia is due to a mutation in the gene that codes for the alpha-globin polypeptide hemoglobin,
which has the symbol Hb.
 Most humans have the allele HbA.
 HbS is a mutated gene that formed when the sixth codon of HbA is converted from GAG to GTG.
 The mutation is only passed down to an offspring if it forms in the ovary or testis that develops into an egg or
sperm.
 When the HbS is transcribed, the mRNA produced has GUG as its sixth codon instead of GAG. When this
mRNA is transcribed, the sixth amino acid in the polypeptide is valine instead of glutamic acid.
 Valine causes hemoglobin molecules to stick in tissues with low concentrations of oxygen.
 The bundles of hemoglobin molecules formed are rigid enough to distort red blood cells into a sickle shape.
 Sickle cells damage cells by blocking blood capillaries to disrupt blood flow.
 Red blood cells are restored to there normal condition once they reach the lungs with high oxygen
concentrations.
 The lifespan of sickle-cell red blood cells can be shortened to as little as 4 days, and the inability of the body
to replace all these cells at a fast enough rate causes anemia.
 It is not known how often this mutation occurs but it can be very common.
  In parts of East Africa, up to 5% of newborn babies have two copies of the HbS allele and so develop severe
anemia, while 35% have one copy and so develop mild anemia.
 
What is a Genome?:
 Genome: the whole of the genetic information of an organism.
 Genetic information is contained in DNA, so the genome is the entire base sequence of each DNA molecule
in an organism.
 Genomes vary in different species:
1. In humans the genome consists of 46 DNA molecules from which the chromosomes in the nucleus are
formed, plus the DNA molecule in the mitochondrion. The same pattern applies for other animals but usually
with different chromosome numbers.
2. In plant species the genome is the DNA molecules in the nucleus and those in the mitochondrion and
chloroplast.
3. The genome of prokaryotes includes the circular chromosome plus any plasmids.
 
The Human Genome Project:
 The entire base sequence of human genes was sequenced in the Human Genome Project.
 The Human Genome Project started in 1990, but rapid improvements in sequencing techniques allowed it to
be completed by 2003.
 The knowledge of the entire base sequence did not give an immediate and total understanding of genetics,
but can be used for example to find the number of base sequences responsible for protein coding, which is
approximately 23000 in humans.
 Most of the human genome is not transcribed. The "junk" regions (junk DNA) contain elements that affect
gene expression and highly repetitive sequences. These are called satellite DNA.
 The genome sequenced is only one amongst many. There are many variations in snips that cause human
diversity, but the genome is mostly the same.
 Comparing the base sequences of humans and other species reveals information about evolution and
previously unknown species.
 
 
Chromosomes (3.2):
 
Bacterial Chromosomes:
 Prokaryotes have one chromosome consisting of a circular DNA molecule.
 The DNA in prokaryotes is called "naked DNA" because it is not associated with proteins.
 Due to one chromosome being present in them, prokaryotes often have only one copy of every gene. At a
certain stage, the chromosome replicates, but the cell is split shortly after.
 
Plasmids:
 Some prokaryotes also have plasmids but eukaryotes do not.
 Plasmids: naked circular structures that contain genes useful for the cell but not responsible for the basic
functions of life.
 Plasmids do not replicate at the same time or rate as chromosomes, which may prevent them from being
passed into the two daughter cells of a divided cell. There may also be multiple copies of plasmids in a single
cell.
 Copies of plasmids can be transferred from a cell to another or even cross the species barrier if the
prokaryotic cell releasing it dies and it is absorbed by another cell or species.
 Plasmids are used by biologist to artificially transfer genes between species.
 
Using Autoradiography to Measure DNA Molecules:
 Developments in scientific research follow improvements in techniques: autoradiography was used to
establish the length of DNA molecules in chromosomes.
 In biology, images can sometimes be stronger evidences than quantitative data for or against a hypothesis.
 Autoradiography was used by biologists from the 1940's onwards to discover where specific substances were
located in cells or tissues.
  John Cairns use autoradiography I the 1960's to investigate whole DNA molecules from E.coli cells and found
that there was more than one DNA molecule in a chromosome, and revealed for the first time DNAs'
replication forks.
 
Measuring the Length of DNA Molecules:
 John Cairns produced images of DNA molecules from E.coli using this technique:
1. Cells were grown for two generations in a culture medium containing titrated thymidine. Thymidine consists
of the base thymine and deoxyribose, used by E.coli to make DNA nucleotides for replication. Tritium, a
radioactive isotope of hydrogen, was placed in titrated thymidine to make the DNA molecules produced by
E.coli cells radioactively labelled.
2. The cells were placed onto a dialysis membrane and there cell walls digested using the enzyme lysozyme.
The cells were gently burst the release their DNA onto the surface of the dialysis membrane.
3. A thin film of photographic emulsion was applied to the surface of the membrane and left in darkness for 2
months. During that time some tritium molecules within the DNA decayed an emitted high-energy electrons
that react with the film.
4. At the end of the 2 months the film was examined with a microscope. At each point where a tritium atom
decayed a dark grain would be present, which showed the positions of DNA.
 Cairns' research showed that the single DNA molecule in E.coli cells is 1,100µm long, noting that the cell
itself is 2µm long.
 Eukaryotes contain linear chromosomes instead of circular ones.
 Cairn's method was used afterwards on plants and other organisms.
 
Eukaryote Chromosomes:
 Eukaryote chromosomes are linear DNA molecules associated with histone proteins.
 Chromosomes in eukaryotes are composed of DNA and protein.
 Histones are globular in shape and wider than DNA molecules.
 DNA molecules are wrapped in strands around histone proteins, separated by small distances with DNA
without histones. This gives a eukaryotic chromosome the appearance of a string of beads during interphase.
 
Differences Between Chromosomes:
 In a eukaryote species there are different chromosomes that carry different genes.
 Eukaryote chromosomes are too narrow to be visible with a light microscope during interphase.
 During mitosis or meiosis, chromosomes become visible under light microscopes due to supercoiling, and
can be seen to be double as each one is replicated.
 Chromosomes differ in length and the position of their centromeres, ranging from near the end of a
chromatid to its center. The minimum number of different chromosomes in eukaryotes is 2.
 Many chromosomes contain over 1000 genes, each with its own locus.
 The arrangement of genes allows for correct crossing over in meiosis.
 
Homologous Chromosomes:
 Homologous chromosomes carry the same sequence of genes but not necessarily the same alleles of those
genes.
 Homologous chromosomes are usually not identical because at least a few alleles are different in them.
 In identical species, at least every chromosome in one organism is homologous to the other, allowing for
interbreeding.
 
Comparing the Genome Sizes:
 The smallest genome of living organisms is that of viruses, although they are in many cases not regarded as
living organisms.
 Prokaryotes often have smaller genomes than eukaryotes.
 The size of a eukaryote's genome depends on the size and number of its chromosomes.
 The genome size of an organism is correlated to its complexity, but not directly proportional since the
proportion of DNA that is functional varies, as well as the amount of gene duplication.
 
Haploid Nuclei:
 Haploid nuclei have one chromosome of each pair.
  Haploid nuclei in humans contain 23 chromosomes, 1 of each type.
 Gametes: cells that fuse together during sexual reproduction.
 Gametes have haploid nuclei, each containing 23 chromosomes in humans.
 
Diploid Nuclei:
 Diploid nuclei have pairs of homologous chromosomes.
 Diploid nuclei in humans contain 46 chromosomes, 2 of each type.
 The fusion of haploid gametes forms a diploid zygote, and these divide by mitosis to forms more diploid
cells.
 Many organisms consist entirely of diploid cells, except for the cells they use to produce gametes for sexual
reproduction.
 Diploid nuclei have two copies of every gene, except those on sex chromosomes.
 An advantage of diploid nuclei is that a harmful recessive mutation can be avoided if the dominant gene is
present.
 Organisms are more vigorous if they have 2 copies of each gene instead of 1 (hybrid vigor).
 
Chromosome Numbers:
 The number of chromosomes is a characteristic feature of members of a species.
 One of the most fundamental characteristics of a species is the number of chromosomes.
 Organisms with different numbers of chromosomes are unlikely to be able to interbreed so all the
interbreeding members of a species need to have the same number of chromosomes.
 Evolution can cause changes in the number of chromosomes, an increase with splits or a decrease with
fusion, but the number is likely to stay the same.
 
Sex Determination:
 Sex is determined by sex chromosomes and autosomes are chromosomes that do not determine sex.
 There are 2 chromosomes in humans that determine sex:
1. The X chromosome: relatively large and has its centromere near the middle.
2. The Y chromosome: much smaller and has its centromere near the end.
 The X chromosome has essential genes for both males and females, and so must be present in all humans.
 The Y chromosome has a small number of genes, some of which are the same as the ones in the X
chromosome, but it only needs to be present in males.
 A gene in the Y chromosome called either SRY or TDF develops the fetus into a male, causing the formation
of testes and production of testosterone, for example.
 If the Y chromosome is not found in the fetus, it develops an ovary instead of testes and female hormones
instead of testosterone.
 Females have 2 X chromosomes, and so can only pass on the X chromosome.
 Males determine the sex of a fetus, as they can either pass the X or Y chromosome.
 
Karyograms:
 A karyogram shows the chromosomes of an organism in homologous pairs of decreasing length.
 Chromosomes are most visible in the metaphase stage of mitosis.
 Stains are used to make chromosomes visible under microscopes, and some give each chromosome a
distinctive branding pattern.
 Chromosomes can now digitally be arranged by type, according to the position of their centromeres if their
sizes are similar.
 
Karyotypes and Down Syndrome:
 Karyogram: an image of the chromosomes of an organism.
 Karyotype: the number and type of chromosomes that the organism has in its nuclei.
 Karyotypes can be used in 2 ways:
1. To deduce whether the individual is a male or a female.
2. To diagnose down syndrome and other genetic conditions. This is usually done using fetal cells taken from
the uterus.
 If three copies of chromosome 21 are present, Down syndrome/trisomy 21 is caused.
 
 
Meiosis (3.3):
 
The Discovery of Meiosis:
 Meiosis was discovered by microscope examination of dividing germ-line cells.
 When chromosomes were observed through advanced microscopes, German scientists began studying them
and the process of cell division until mitosis and meiosis were revealed.
 Meiosis was very hard to study due to cells having to be treated very carefully, and often no cells being
studied were going through meiosis, or images were not clear enough for observation. Tissue cells were
obtained form the anthers of lily buds or testis from dissected locust.
 In the horse threadworm it was found that there are 2 chromosomes in the nuclei of egg and sperm cells but
4 in a fertilized egg.
 The number of chromosomes is doubled by fertilization. Hence it was concluded that there must be a
special nuclear division that halves the number of chromosomes.
 Meiosis: a process of nuclear division unlike mitosis that halves the number of chromosomes in a fertilized
egg.
 
Meiosis in Outline:
 One diploid nucleus divides by meiosis to produce four haploid nuclei.
 Meiosis is one of two ways by which a eukaryotic cell's nucleus can divide.
 Meiosis include 2 nucleus divisions, producing 4 nuclei in the end. The 2 divisions are known as meiosis I and
meiosis II.
 The nucleus that undergoes the first division is diploid, having 2 of each chromosome.
 Homologous chromosomes: chromosomes of the same type but different alleles.
 The chromosomes produced by meiosis are haploid, having 1 of each chromosome.
 Meiosis I is called reduction division since it involves halving the number of chromosomes.
 The 2 nuclei produced by meiosis I are haploid, but each chromosome has its 2 sister chromatids.
 In meiosis II, the sister chromatids separate to produce 4 haploid nuclei with each chromosome having only
1 chromatid.
 
Meiosis and Sexual Life Cycles:
 The halving of the chromosome number allows a sexual life cycle with fusion of gametes.
 The life cycles of living organisms can be sexual or asexual. In asexual life cycle the offspring have the same
chromosomes as the parent and so are genetically identical.
 In eukaryotic organisms, sexual reproduction involves the process of fertilization.
 Fertilization: the union of sex cells, or gametes, usually from two different parents.
 Fertilization doubles the number of chromosomes each time it occurs, so they must be halved through
meiosis.
 Meiosis can occur at any stage during a sexual life cycle, but in animals it happens during the process of
creating gametes, so body cells are diploid and have 2 copies of most genes.
 Without meiosis there cannot be gamete fusion, and hence the life cycle of eukaryotes could not occur.
 
Replication of DNA Before Meiosis:
 DNA is replicated before meiosis so that all chromosomes consist of two sister chromatids.
 During the early stages of meiosis chromosomes gradually shorten by supercoiling.
 Chromosomes consist of two sister chromatids at the beginning of meiosis due to their replication in the
interphase. The two sister chromatids of each chromosomes are genetically identical due to the accuracy of
replication.
 DNA does not replicate after meiosis I, which explains the end-product of meiosis II being 4 haploid nuclei
that contain only 1 chromatid of each chromosome.
 
Bivalents Formation and Crossing Over:
 The early stages of meiosis involve pairing of homologous chromosomes and crossing over followed by
condensation.
 Before supercoiling and division, homologous chromosomes pair up with each other, forming bivalents, each
associated with 4 DNA molecules (chromatids).
  The process of forming bivalents is sometimes called synapsis.
 Crossing over happens soon after synapsis, where a part of a chromatid in one chromosome of a bivalent
breaks and joins the other chromosome, at precisely the same location of the other chromatid, and vice versa.
 Every bivalent has at least one cross over, and there may be several.
 Because bivalents contain homologous but not identical chromosomes, allele exchange allows for the
production of chromatids with new allele combinations.
 
Random Orientation of Bivalents:
 Orientation of pairs of homologous chromosomes prior to separation is random.
 During the supercoiling of homologous chromosomes, spindle microtubules grow on opposite poles of the
cell. After the breakdown of the nuclear membrane, spindle microtubules attach to the centromeres of
chromosomes, but each chromosome from a bivalent attached only to one pole/spindle microtubule.
 The attachment of spindle microtubules to centromeres in meiosis is different from that in mitosis in that:
1. Each chromosome is attached to 1 pole only, not to both.
2. The 2 homologous chromosomes in a bivalent are attached to different poles.
3. The pole to which a homologous chromosome is attached depends on the way a homologous pair is facing.
This is called orientation.
4. The orientation of bivalents is random, so each chromosome has an equal chance to be drawn into either
pole.
5. The orientation of one bivalent does not affect other bivalents.
 
Halving the Chromosome Number:
 Separation of pairs of homologous chromosomes in the first division of meiosis halves the chromosome
number.
 Initially the chromosomes of a bivalent are held together by chiasmata, but this slides to their ends as the
spindle microtubules pull them apart, until they separate.
 Disjunction: the separation of homologous chromosomes.
 The separation of homologous chromosomes to opposite pairs halves their number. Therefore, meiosis I is
the reduction division. The two cells resultant from meiosis I are haploid.
 
Obtaining Cells From a Fetus
 
Diagrams of the Stages of Meiosis:
 In meiosis, unlike in mitosis, the 4 stages occur twice, in meiosis I and again in meiosis II:
1. Meiosis I:
a. Prophase I:
o Cell has diploid (2n) chromosomes.
o Synapsis occurs.
o Crossing over occur.
b. Metaphase I:
o Spindle microtubules move bivalents to the cell's equator.
o Orientation of paternal and maternal chromosomes on either side of the equator is random and
independent of other homologous pairs.
o Anaphase I:
o Homologous pairs are separated. One chromosome of each pair moves to each pole.
o Telophase I:
o Chromosomes uncoil. During interphase that follows, no replication occurs.
o Reduction of chromosome number from diploid to haploid occurs.
o Cytokinesis occurs.
o Meiosis II:
o Prophase II:
o Chromosomes, which still consist of 2 chromatids, condense and become visible (supercoiling).
o Metaphase II:
o Spindle microtubules attach to the centromere of each chromosome.
o Anaphase II:
o Centromeres separate and chromatids are moved to opposite poles.
 o Telophase II:
o Chromatids reach opposite poles.
o Nuclear envelope forms.
o Cytokinesis occurs.
 
Meiosis and Genetic Division:
 Crossing over and random orientation promotes genetic variation.
 Apart from the genes on the X and Y chromosomes, humans have 2 copies of each gene. In some cases 2
copies are the same allele and there will be one copy in every gamete produced.
 There are likely to be thousands of genes in a parent's genome where the 2 alleles are different, and each of
the alleles has an equal chance of being passed on to the gamete. Hence, a fertilized egg may inherit any
combination of the alleles passed on by the parents.
 There are 2 processes in meiosis that generate the diversity of genes:
1. Random orientation of bivalents:
o For every bivalent present in a nucleus, the number of combinations of genes possible double,
meaning for a haploid (n) nucleus, the number of possible gene combination equals 2^n.
2. Crossing over:
o Crossing over is the key to mixing up gene combinations and creating the possibility for different
ones instead of only the paternal and maternal ones being available.
 
Fertilization and Genetic Variation:
 The fusion of 2 gametes to form a zygote is very important as:
1. It is the start of a new life.
2. It allows alleles from different individuals to be combined in one new individual.
3. The combination of alleles is likely to never have existed before.
4. Fusion of gametes therefore promotes genetic variation in a species.
5. Genetic variation is essential for evolution.
 
Non-disjunction and Down Syndrome:
 Non-disjunction can cause Down syndrome and other chromosome abnormalities.
 Disjunction: an error in meiosis where homologous chromosomes are unable to separate at anaphase.
 In non-disjunction, the homologous pair moves to one size as a whole, causing one gamete to have an extra
chromosome while the other would be deficient by a chromosome.
 If a gamete resulting from non-disjunction is involved in human fertilization, it would have either 45 or 47
chromosomes.
 An abnormal number of chromosomes often leads to syndromes (collections of physical signs or symptoms).
 Down syndrome (trisomy 21) results from an extra chromosome 21.
 Most trisomies are so fatal they prevent the offspring from surviving. Babies are sometimes born with
trisomy 13 or 18.
 Non-disjunction can lead to the birth of babies with abnormal sex chromosome numbers (Klinefelter's
syndrome - XXX, Turner's syndrome - X).
 
Parental Age and Non-disjunction:
 Studies show a positive correlation between the age of the parent and the chances of non-disjunction
occurring.
 
 
Inheritance (3.4):
 
Mendel and the Principles of Inheritance:
 Mendel discovered the principles of inheritance with experiments in which large numbers of pea plants were
crossed.
 Organisms have characteristics that they pass on to an offspring for inheritance, and others that cannot be
inherited.
 Similarities were noticed sometimes between children and their grandparents more than their parents in the
19th century, which introduced "blending inheritance".
  Mendel chose a variety of pea plants with different characteristics that would have grown alike on their own.
He crossed those varieties together by pollinating female parts of each pea plant with the pollen of another
plant. He noticed that the offspring had combined characteristics of the male and female plants producing it.
 Mendel's research was ignored for over 30 years, until biologists attempted and confirmed his research after
rediscovering it in 1900.
 Mendel's theory explained the basis of inheritance in all plants and animals.
 
Replicates and Reliability in Mendel's Experiments:
 Different pea plants have distinctive properties such as flower color that can be easily followed from one
generation to the other. They can also be crossed to produce hybrids of allowed to self-pollinate.
 Before Mendel, Thomas Andrew Knight made several important discoveries experimenting with pea plants:
1. Male and female parents contribute equally to the offspring.
2. Characters can be not found in the organism but passed on to its offspring, being discrete rather than
blending.
3. One character may show a "stronger tendency" than another.
 Mendel used the principle of repetition to increase accuracy and exclude irrelevant data, and this was later
followed by all scientists.
 
Gametes:
 Gametes are haploid so contain one allele of each gene.
 Gametes: cells that fuse together to produce the single cell that is the start of a new life.
 Zygote: the single cell produced when a male and female gamete fuse.
 The male gamete is generally smaller than the female one and has the ability to move.
 Parents pass genes on to their offspring in gametes.
 Gametes are haploid, containing only 1 allele of each gene.
 Male and female gametes make an equal genetic contribution to their offspring, despite the size difference
of their gametes.
 
Zygotes:
 Fusion of gametes results in diploid zygotes with two alleles of each gene that may be the same allele or
different alleles.
 The nucleus of a zygote is diploid, containing those of both male and female gametes. It hence contains 2
alleles of each gene.
 If alleles A and a existed for a gene, 3 combinations are possible:
1. AA.
2. Aa.
3. aa.
 Some genes contain more than 2 alleles.
 The gene for ABO blood groups contains 3 alleles: IA, IB and i. Hence, 6 combinations are possible:
1. I AI A.
2. IBIB.
3. ii.
4. I AI B .
5. IAi.
6. IBi.
 
Segregation of Alleles:
 The two alleles of each gene separate into different haploid daughter nuclei during meiosis.
 The diploid nucleus of meiosis contains 2 copies of each gene, while the haploid nuclei contain 1.
 If the 2 genes of the diploid nucleus in meiosis contain the same allele, then each haploid daughter cell will
receive a copy of that cell (e.g.: if the diploid cell contains the alleles PP, each daughter cell will receive a P).
 If the 2 genes of the diploid nucleus in meiosis contain different alleles, then each haploid 50% of the
daughter nuclei receive one allele, while the other 50% receive the other allele (e.g.: if the diploid cell contains
the alleles Pp, 50% of daughter nuclei will receive P, while the other 50% will receive p).
 Segregation: the separation of alleles into different nuclei.
 Segregation breaks up existing allele combinations and allows for the formation of new ones in the offspring.
 
Dominant, Recessive and Co-dominant Alleles:
 Dominant alleles mask the effects of recessive alleles but co-dominant alleles have joint effects.
 In Mendel's experiments examining pea plant length, plants with a tall and a dwarf parent were tall since tall
are dominant to dwarf alleles (one parent had the gene TT (tall), while the other had tt (dwarf), and the
offspring ended up with Tt, being tall but a carrier of the dwarf gene).
 Alleles can be co-dominant, where the effects of both alleles show on an offspring that has them both (e.g.:
CR is the allele for red flowers, while CW is for white flowers. CRCW produce pink flowers due to co-dominance).
 An allele is usually dominant because it codes for a protein that is active and carries out a function, while the
recessive allele codes for a non-functional protein.
 
Punnett Grids:
 Monohybrid crosses involve only one gene between the parents, meaning that parents have the same allele.
 Most crosses start with pure-breeding parents, each one having only one allele per gene, and hence only
being able to donate it to the offspring.
 The first offspring, known as the F1 generation, would have two different alleles, one from each parent, and
hence be able to form 4 different zygotes with another F1 generation member.
 Punnett grids show the possible genes to be formed from the crossing of one generation.
 The offspring of a cross between two F1 organisms is called the F2 generation.
 
ABO Blood Groups:
 ABO blood groups in humans are an important example of co-dominance; before performing transfusions,
compatibility of blood types needs to be checked.
1. IAIA gives the genotype of blood group A.
2. IBIB gives the genotype of blood group A.
3. ii give the genotype of blood group O.
4. IAIB gives the genotype of blood group AB due to co-dominance.
5. IAi gives the genotype of blood group A since i is recessive.
6. IBi gives the genotype of blood group B since i is recessive.
 The reasons behind the co-dominance of IA and IB and the recession of i are as follows:
1. All three alleles cause the production of a glycoprotein in the membrane of red blood cells.
2. IA alters the production of the glycoprotein by addition of acytel-galactosamine. This altered glycoprotein is
absent from people who do not have the allele IA, so if exposed to it the make anti-A antibodies.
3. IB alters the production of the glycoprotein by addition of galactose. This altered glycoprotein is not present
in people who do not have the allele IB, so if exposed to it the make anti-A antibodies.
4. IAIB alters the production of the glycoprotein by addition of acytel-galactosamine and galactose. As a
consequence neither anti-A nor anti-B antibodies are produced, and a different phenotype is given due to co-
dominance.
5. i can only produce the basic glycoprotein, making it recessive. The presence of IA or IB with i makes it
recessive since the glycoprotein is altered with the addition of acytel-galactosamine or galactose.
 
Testing Predictions in Cross-breeding Experiments:
 The actual outcomes of genetic crosses do not usually match the predicted ones.
 Chance plays a role in the inheritance of genes.
 The greater the difference between observed and expected results, the less likely that prediction errors are
due to chance, and the more likely they're due to irrelevance.
 Chi-square tests can be used to assess the relevance of genetic crossing predictions to actual outcomes.
Cross Predicted Outcomes Example
Pure-breeding parents, All the offspring will have the All offspring of a cross
one with dominant alleles same character as the parent with between pure-breeding tall
and one with recessive the dominant alleles. and dwarf pea plants will be
alleles, are crossed. tall.
Pure-breeding parents All the offspring will have the All the offspring of a cross
that have different co- same character, different from between red and white-
dominant alleles are either parent. flowered Mirabilis jalapa plant
 crossed. will have pink flowers.
Two parents each with Three times as many offspring will 3:1 ratio of tall to dwarf pea
one dominant and one have the character of the parent plants from a cross of parents
recessive allele are with the dominant alleles as have each with a tall and dwarf
crossed. the character of the parent with allele.
the recessive alleles.
A parent with one Equal chance of the offspring 1:1 ratio of tall to dwarf pea
dominant and one having the dominant character or plants from a cross of parents,
recessive allele is crossed the recessive one from the alleles. one dwarf and the other tall
with a parent with two with one tall allele and one
recessive alleles. dwarf allele.
 
Genetic Diseases Due to Recessive Alleles:
 Many genetic diseases in humans are due to recessive alleles of autosomal genes.
 Genetic disease: an illness caused by a gene.
 Most genetic diseases are caused by recessive alleles.
 If an individual has the recessive allele of a genetic disease and another dominant one, he wouldn't have the
disease but is a carrier and may pass it on to offspring.
 An offspring being born with a recessive genetic disease is often unpredicted as both parents would be
carriers not suffering the symptoms themselves.
 There is a 25% chance of an offspring being born with a recessive genetic disease if both his parents are
carriers.
 
Other Causes of Genetic Diseases:
 Some genetic diseases are sex-linked and some are due to dominant or co-dominant alleles.
 A few genetic diseases can be caused by a dominant allele. The person cannot be a carrier of the disease in
this case; only a victim since it’s a dominant allele.
 If a parent has the allele for a dominant genetic disease, there is a 50% chance of the offspring inheriting it.
 Huntington's disease is caused by a dominant allele.
 Sickle-cell anemia is caused by co-dominant alleles, which is rare.
 Most genetic diseases affect males and females the same way, but some show different patterns of
inheritance in them.
 Sex-linkage: a difference in the patterns of inheritance of a genetic disease due to gender (male or female).
 Red-green color-blindness and hemophilia are sex-linked genetic diseases.
 
Cystic Fibrosis and Huntington's Disease:
 Cystic fibrosis is the commonest genetic disease in parts of Europe.
 Cystic fibrosis is due to a recessive allele in the CFTR gene.
 The CFTR gene is found in chromosome 7 and produces a chloride ion channel that is involved in the
secretion of sweat, mucus and digestive juices.
 The recessive alleles of the CFTR genes cause the production of chloride ion channels that do not function
properly. Sweat would contain excess sodium chloride amounts while digestive juices and mucus are secreted
with insufficient amounts, making them very viscous.
 Cystic fibrosis causes sticky mucus to build up in the lungs causing infections and the pancreatic duct is
usually blocked so digestive enzyme secreted by the pancreas do not reach the small intestine.
 In some parts of Europe 1 in 20 people have cystic fibrosis. The chance of an offspring being born with the
disease from 2 carrier parents is 1/20 * 1/20 = 1/400.
 Huntington's disease is due to a dominant allele in the HTT gene.
 The HTT gene is found on chromosome 4 and produces the protein Huntingtin, function still being
researched.
 The dominant allele of the HTT gene causes degenerative changes in the brain, usually starting at between
30 and 50 years of age. Changes in behavior, thinking and emotions become increasingly severe.
 Life expectancy after Huntington's is diagnosed is about 20 years, and the patient usually eventually needs
full nursing care, succumbing to heart failure, pneumonia or another infectious disease.
  Because Huntington's is diagnosed at a late stage, most people with the dominant allele already have
children by the time they are diagnosed.
 A genetic test can show whether the Huntington's dominant allele is present, but most people at risk choose
not to have the test.
 About 1 in 10,000 people have the dominant allele, but only one parent with it is needed since it is
dominant.
 
Sex-linked Genes:
 The pattern of inheritance is different with sex-linked genes due to their location on sex chromosomes.
 Hermaphrodite: able to produce both male and female gametes.
 Plants such as peas are hermaphrodite.
 Thomas Andrew Knight discovered that the results of crossing experiments were the same whichever
character was in the male gamete and which in the female gamete.
 The following crosses gave the same results:
1. Pollen from a plant with green stems placed onto on the stigma of a plant with purple stems.
2. Pollen from a plant with purple stems placed onto on the stigma of a plant with green stems.
 Sex linkage: an inheritance pattern where the ratios are different in males and females.
 Sex linkage in animals is dependent on the genes in the X and Y chromosomes.
 
Red-green Color-blindness and Hemophilia:
 Almost all sex linkages are due to genes on the X chromosome since the Y chromosome is very small and
contains few genes.
 Red-green color-blindness is caused by a recessive allele of a gene for one of the photoreceptor proteins.
 Males, since they only have an X chromosome from their mother, are red-green color-blind if they receive
the recessive allele from their mother. The percentage is about 8%.
 Females must receive the recessive allele from both the mother and the father in order to have red-green
color-blindness. The percentage is about 0.5% since there is a lower chance for both genes to be recessive.
 Hemophilia is a life-threatening genetic disease, mostly caused by the inability to make Factor VIII, one of the
proteins involved in the clotting of blood.
 Hemophilia is treated by infusing Factor VIII, purified from the blood of donors. The life expectancy of
untreated patients is 10 years.
 The gene for Factor VIII is located on the X chromosome, and is recessive.
 The frequency of the hemophilia allele is about 1 in 10,000, hence the frequency in boys. Females can be
carriers, but only develop the disease if they receive the recessive allele from both parents (chances are
theoretically 1 in 100,000,000).
 The father would have to be a hemophiliac and take the risk of reproducing for a chance to be there to pass
it on to his daughter.
 
Pedigree Charts:
 Pedigree charts are used to deduce a pattern of inheritance, which Punnett grids cannot do.
 The usual conventions for constructing pedigree charts are:
1. Males are shown as squares.
2. Females are shown as circles.
3. Squares are circles are shaded or cross-hatched to indicate whether an individual is affected by the disease.
4. Parents and children are linked using a T, with the top bar of the T between the parents.
5. Roman numerals indicate generations.
6. Arabic numbers are used for individuals in each generation.
 
Genetic Disease in Humans:
 Many genetic diseases have been identified in humans but are very rare.
 Most humans don't suffer genetic diseases because they are caused by very rare recessive alleles which
follow Mendelian patterns of inheritance.
 The human genome for an individual can now be sequenced relatively cheaply and quickly.
 Genomes of different people are being sequenced to compare the number of recessive disease alleles being
carried, and it is about 75-200 amongst the 2500 or so genes in the genome.
  An offspring can only have the genetic disease of a recessive allele if he receives that allele from both
parents.
 
Causes of Mutation:
 Radiation and mutagenic chemicals increase the mutation rate and can cause genetic disease and cancer.
 A gene consists of a length of DNA, with a base sequence that can be hundreds or thousands of bases long.
 New alleles are formed from other alleles by gene mutation.
 Mutation: a random change to the base sequence of a gene.
 2 types of factor can increase the mutation rate:
1. Radiation increases the mutation rate if it has enough energy to cause chemical changes in DNA. Gamma
rays and alpha particles from radioactive isotopes, short-wave ultraviolet radiation and X-rays are all
mutagenic.
2. Some chemical substances cause chemical changes in DNA and so are mutagenic. Examples are
benzo[a]pyrene. And nitrosamines found in tobacco smoke and mustard gas used as a chemical weapon in the
First World War.
 Mutations can be a cause of cancer when cells divide endlessly to develop into a tumor.
 Mutation numbers in ovaries and testes must be minimized to reduce genetic diseases.
 
Consequences of Nuclear Bombing and Accidents at Nuclear Power Stations:
 The release of radioactive isotopes exposes people to dangerous levels of radiation.
 The Hiroshima and Nagasaki bombings killed 15,000-250,000 people either directly or within a few months.
 Nearly 100,000 survivors were experimented on, 26,000 being a controlled sample. By 2011 the survivors
had developed 17,448 tumors, but only 853 could be attributed to the effects of radiation from the atomic
bombs. 10,000 children that were fetuses at the time of the detonations and 77,000 children born later were
observed, but not was associated with mutations, probably because they were too few to be recognized.
There was reluctance towards marriage due to fear of the offspring having genetic diseases.
 The effects of Chernobyl, Ukraine, in 1986 involved explosions and fire at the core of a nuclear reactor. The
effects were widespread and severe:
1. 4km2 of pine forest downwind of the reactor turned ginger brown and died.
2. Horses and cattle near the plant died from damage to their thyroid glands.
3. Lynx, eagle owl, wild boar and other wildlife subsequently started to thrive in a zone around Chernobyl from
which humans were excluded.
4. Bioaccumulation cause high levels of radioactive caesium in fish as fay away as Scandinavia and Germany
and consumption of lamb contaminated with radioactive caesium was banned for some time as far away as
Wales.
5. Concentrations of radioactive iodine in the environment rose and resulted in drinking water and milk with
unacceptably high levels.
6. More than 6,000 cases of thyroid cancer have been reported that can be attributed to radioactive iodine
released during the accident.
7. There hasn't been official reports of increases in solid cancers or leukemia due to radiation in the most
affected populations.
 
 
Genetic Modification and Biotechnology (3.5):
 
Gel Electrophoresis:
 Gel electrophoresis is used to separate proteins or fragments of DNA according to size.
 Gel electrophoresis involves the placement of molecules in gel, emersed in conducting fluid. An electric
current is then applied, and positively charged and negatively charged particles move in opposite directions.
Proteins can be positively or negatively charged, and hence separated by this method.
 The gel used in gel electrophoresis resists movement of molecules in it. The DNA of eukaryotes, for example,
is too long to move in it. DNA hence breaks down into smaller fragments, all negatively charged, that move
toward the positive electric field, not at the same rate (smaller fragments ove faster).
 
DNA amplification by PCR:
 PCR can be used to amplify small amounts of DNA.
  The polymerase chain reaction is used to make large numbers of copies of DNA. Within an hour or two,
millions of copies can be made, which makes it easier to study DNA without worrying about limited samples.
 Very small amounts of DNA from blood, hair or semen can be amplified by PCR for forensic investigation
uses.
 PCR is used to copy parts of a human's genome or DNA, obtained from chromosomes in white blood cells or
semen.
 A sequence for PCR amplification is selected using a primer that binds to the starting point of the desired
sequence by complementary base pairing.
 
DNA Profiling:
 DNA profiling involves comparison of DNA.
 DNA profiling involves 6 stages:
1. A sample of DNA is obtained.
2. Sequences in the DNA that vary considerably between individuals are selected and copied by PCR.
3. The copied DA is split into fragments using restriction endonucleases.
4. The fragments ae separated using gel electrophoresis.
5. A pattern of bands that is always the same with the DNA of a single individual is produced.
6. Profiles of different individuals are compared to see which bands are the same and which are different.
 
Paternity and Forensic Investigations:
 DNA profiling is used in forensic investigations:
1. Blood stains on a suspect's clothing could be shown to come from the victim.
2. Blood stains at the crime scene, not for the victim, could be from a suspect.
3. A single hair at the crime scene could be from a suspect.
4. Semen from a sexual crime scene could be from a suspect.
 Comparing DNA bands in crime scenes to those of suspects reveals criminals in many cases.
 DNA profiling is also used in paternity investigations, required for reasons such as:
1. The man claiming he isn’t the father to avoid paying the mother for child care.
2. Women who've had multiple partners may wish to identify the biological father.
3. A child may wish to prove a deceased man is their father to show that they are their heir.
 For paternity investigations, DNA of the father, mother and child are needed. Profiles are prepared and
bands are compared. If any bands in the child's profile do not occur in the profile of the mother or man, the
man isn’t the father.
 
Analysis of DNA Profiles:
 The bands of DNA profiles from a crime scene are compared to those of a suspect and victim to find out the
criminal.
 In paternity tests, the bands of a child's DNA profile are compared to those of both the mother and man, and
each band has to be found in one of them or the man isn't the father.
 
Genetic Modification:
 Genetic modification is carried out by gene transfer between species.
 Genetic modification (GM): the transfer of genes from one species to another.
 GM is possible because the genetic code is universal, allowing same polypeptides to be produced.
 The gene for making human insulin was transferred to a bacterium for large quantities of the hormone to be
produced to treat diabetics.
 Goats have been produced that secrete milk containing spider silk for commercial use.
 Genetic modifications are significant in the farming industry.
 
Techniques for Gene Transfer to Bacteria:
 Genetic engineering: the techniques of transferring genes to bacteria.
 Gene transfer to bacteria often involves plasmids, restrictions enzymes and DNA ligase:
1. With plasmids:
o Plasmid: a small extra circle of DNA.
o The smallest plasmids have about 1,000 base pairs (1kbp), but they can have over 1,000 kbp.
o Plasmids are very common in bacteria.
 o The most abundant plasmids are those that encourage their replication in the cytoplasm and their
transfer from one bacterium to another.
o Natural selection favors plasmids that benefit a bacterium over disadvantageous ones.
o Bacteria use plasmids to exchange genes, so naturally absorb them and incorporate them into their
main circular DNA molecule.
o Plasmids are very useful in genetic engineering.
2. Restriction enzymes:
o Restriction enzymes/endonucleases: enzymes that cut DNA molecules at specific base sequences.
o Endonucleases can be used to cut plasmids open or cut desired genes from larger DNA molecules.
o Some endonucleases have the useful property of cutting the two strands of a DNA molecule at
different points, leaving single-stranded sections called sticky ends.
o Sticky ends cut by an endonuclease have complementary base sequences and so can be used to link
together pieces of DNA, by hydrogen bonding between the bases.
3. DNA ligase:
o DNA ligase: an enzyme that joins DNA molecules together firmly by making sugar-phosphate bonds
between nucleotides.
o When sticky ends link a desired gene to a plasmid, there as still nicks in the sugar-phosphate
backbone, but these can be sealed with DNA ligase.
o It is easier to obtain messenger RNA transcripts of a gene than the gene itself.
o Reverse transcriptase: an enzyme that makes DNA copies out of RNA molecules called cDNA.
o Revere transcriptase can be used to make the DNA needed for gene transfer from messenger RNA.
 
Assessing the Risks of Genetic Modification:
 Fears from genetic engineering started in the 1970's when Paul Berg planned to transfer SV40 (a monkey
virus that caused cancer in mice), to E.coli, which naturally lived in human intestines. There was fear of causing
cancer in humans.
 The risk of such processes as genetic engineering can be assessed using 2 questions:
1. What is the chance of an accident or other harmful consequence happening?
2. How harmful would the consequence be?
 If there is a high chance of consequences or they are very harmful then research should not be done.
 
Risks and Benefits of GM Crops:
 Potential benefits of GM crops can be grouped into environmental, health and agricultural benefits.
 Financial benefits of GM crops are not assessed because they can’t be on a scientific basis using
experimental evidence.
 Claims about environmental benefits of GM crops:
1. Plants can be made resistant to pests by transferring a gene that makes them toxic to pests, reducing the
need for insecticides that harm bees and other beneficial insects.
2. Use of GM crop varieties reduces the need for plowing and spraying crops, so less fuel is needed for farm
machinery.
3. The shelf-life of fruit and vegetables can be improved, reducing wastage and reducing the area of crops hat
have to be grown.
 Claims about the health benefits of GM crops:
1. The nutritional value of crops can be increased, for example the vitamin content.
2. Varieties of crops can be produced lacking allergens or toxins that are naturally present in them.
3. GM crops could be engineered that produce edible vaccines so by eating the crop person would be
vaccinated against a disease.
 Claims about agricultural benefits of GM crops:
1. Varieties resistant to drought, cold and salinity can be produced by gene transfer, expending the range over
which crops can be produced and increasing total yields.
2. A gene for herbicide resistance can be transferred to prevent other plants from growing nearby, such as
weed, which increases the yield of crop plants.
3. Crop varieties can be produced that are resistant to diseases caused by viruses.
 The risks concerning GM crops, excluding financial ones, are grouped into health, environmental and
agricultural risks.
 Claims made about health risks of GM crops:
 1. Proteins produced by transcription and translation of transferred genes could be toxic or cause allergic
reactions in humans or livestock that eat GM crops.
2. Antibiotic resistance genes used as markers during gene transfer could spread to pathogenic bacteria.
3. Transferred genes could cause problems through unexpected mutations.
 Claims made about environmental risks of GM crops:
1. Non-target organisms could be affected by toxins released by GM crops.
2. Genes transferred to crops to make them herbicide resistant could be transferred to wild plants, turning
them into uncontrollable super-weeds.
3. Biodiversity could be reduced with the dominance of crops resistant to insects and wild plants increasing.
 Claims made about agricultural risks of GM crops:
1. Seeds from crops randomly germinate sometimes to grow into unwanted plants that need to be controlled,
but this is very difficult with herbicide resistance genes.
2. Widespread use of GM plants with pest-killing toxins will allow pests to develop immunity against the toxin.
3. Strains adapted to local conditions cannot be developed since farmers are not allowed to re-grow GM crops
from their seeds.
 
Analyzing Risks to Monarch Butterflies of Bt Corn:
 Bt toxin is a gene derived from a bacterium -Bactillus thuringiensis- and codes for Bt toxin, a protein that kills
members of insect orders that contain butterflies, moths, flies, beetles, bees and ants.
 Genetically modified corn varieties produce Bt toxin in all parts of them, including pollen.
 Concerns have been expressed about the effect of Bt corn on non-target species such as the monarch
butterfly.
 Monarch butterfly larvae feed on milkweed leaves, a plant sometimes grown close enough to corn crops to
be dusted with pollen of GM corn. The larvae may hence be poisoned by Bt toxin.
 The risk of GM corn on monarch butterflies has been experimentally tested, and data is available for
analysis.
 
Clones:
 Clones: groups of genetically identical organisms, derived from a single original parent cell.
 All zygotes are different since they are produced by sexual reproduction, and they develop into an adult
organism.
 With sexual reproduction, an offspring is genetically different from parents.
 With asexual reproduction, an identical offspring to the parent is produced.
 Cloning: the production of genetically identical organisms.
 The smallest clone that can exist is a pair of identical twins.
 Identical twins are formed when the zygote splits into two cells, each of which develop into an embryo, or
when an embryo splits into two parts that develop into separate individuals.
 Identical twins have different fingerprints, and a better term for them is monozygotic.
 Triplets, quadruplets and quintuplets have been more rarely produced.
 Clones can sometimes consists of very large numbers of organisms (e.g.: commercially grown potato
varieties).
 Large clones are formed by cloning happening again and again, but all clones may be traced back to one
original parent cell.
 
Natural Methods of Cloning:
 Many plant species and some animal species have natural methods of cloning.
 A single garlic bulb, when planted, uses it food stores to grow leaves. These leaves produce enough food by
photosynthesis to grow a group of bulbs. The bulbs are genetically identical, making them a clone.
 A strawberry plant grows long horizontal stems with plantlets at the end. These plantlets grow roots into the
soil and photosynthesize using their leaves, so can become independent of the parent plant. A healthy
strawberry plant can produce 10 or more genetically identical new plants in this way during a growing season.
 Natural methods of cloning are less common in animals, but some, like Hydra, can do it.
 Female aphids can give birth to offspring entirely produced from diploid egg cells that were produced by
mitosis rather than meiosis. The offspring are therefore clones of their mother.
 
Cloning Animal Embryos:
  Animals can be cloned at the embryo stage by breaking up the embryo into more than one group of cells.
 Cells are pluripotent at their early stages of development in an animal embryo.
 Splitting/fragmentation: the process of an embryo splitting into 2 or more parts, each developing into a
functioning organism.
 Coral embryos are known to clone themselves repeatedly, sometimes reaching one cell per clone, to
increase the chance of offspring survival.
 The formation of identical twins can be regarded as splitting, but most animal species do not appear to do
this naturally.
 Animal embryos can be split artificially, and in some cases the separated parts may develop into multiple
embryos.
 The splitting of embryos is often most successful at the 8-cell stage.
 In livestock, an egg can be fertilized in vitro and allowed to develop into a multicellular embryo. Cells are
then taken from the embryo while still pluripotent and transplanted into surrogate mothers.
 Cells can only be taken from embryos for cloning in limited numbers since after several divisions the embryo
cells stop being pluripotent.
 There is very little interest in artificial cloning because it is not possible to assess at the embryo level whether
an offspring or its clones will have desirable characteristics.
 
Cloning Adult Animals Using Differentiated Cells:
 Methods have been developed for cloning adult animals using differentiated cells.
 It is relatively easy to clone animal embryos, but impossible to know whether the product will have desirable
characteristics.
 Clones made form adult animals have predictable characteristics, but are very hard to make since most cells
in adults are specialized, when pluripotent cells are needed for cloning.
 John Gurdon cloned a frog species by extracting nuclei from its cells and placing them in egg cells from which
nuclei have been removed. He was awarded a Noble Prize for his pioneering research.
 The first mammal to be cloned was Dolly the Sheep in 1996.
 Aside from reproductive purposes, cloning can be used for therapeutic reasons, where the cone of a person
would have identical tissues that can be used to regenerate adult tissues after the cloned embryo have
developed.
 
Methods Used to Produce Dolly:
 The method of cloning used to make Dolly the sheep is called somatic-cell nuclear transfer.
 Somatic cell: a normal body cell with diploid nucleus.
 Somatic-cell nuclear transfer is done through 3 steps:
1. Adult cells of a sheep were taken and grown in a laboratory, using a medium containing low concentrations
of nutrients. This made genes in the cell inactive so that the pattern of differentiation was lost.
2. Unfertilized eggs were taken from sheep ovaries, and the nuclei removed from them.one of the cultures cells
was placed next to each egg cell inside the zona pellucida around the egg, a protective coating of gel.
3. A small electric pulse was used to fuse the two cells together, and about 10% of fused cells developed like a
zygote into an embryo.
4. The embryos, when 7 days old, were injected into other female sheep as surrogate mothers (as in IVF). Only
1 out of 29 implanted embryos developed successfully, Dolly.
Species, Communities and Ecosystems (4.1):
 
Ecology: the study of relationships between living organisms and their environments.
 
Species:
 Species: groups of organisms that can potentially interbreed to produce fertile offspring.
 Interbreeding: the process of producing an offspring through the mating of two identical species.
 Cross-breeding: the process of producing an offspring through the mating of two different species. The
offspring of cross-breeding is almost always infertile to prevent the mix-up of two species' genes.
 
Populations:
 Population: a group of organisms of the same species who live in the same area at the same time.
 Populations in different areas, if they do not interbreed, develop differences in their characters. They are still
of the same species until they cannot interbreed and produce an offspring.
 
Autotrophic and Heterotrophic Nutrition:
 Autotrophic organisms: organism which make their own carbon compounds from carbon dioxide and other
simple substances.
 Heterotrophic organisms: organisms which obtain their carbon compounds from other organisms.
 Some unicellular organisms use both methods of nutrition.
 Plants and algae carry out photosynthesis in chloroplasts, using light, carbon dioxide and other simple
compounds to make their own complex organic compounds.
 Parasitic plants are not autotrophic, and obtain carbon compounds from other plants, harming them.
 Plants and algae are considered autotroph since only 1% are parasitic.
 
Consumers:
 Consumers: heterotrophs that feed on living organisms by ingestion.
 Consumers feed on other organisms through ingestion, eating them, digesting them, and absorbing the
needed carbon compounds. They feed on organism either alive or shortly dead. Unicellular consumers feed on
organisms through endocytosis an digest it inside vacuoles.
 Consumers are divided to trophic groups (primary consumer eats autotroph, secondary consumer eats
primary consumer, etc..)
Detritivores:
 Detritivores: heterotrophs which obtain organic nutrients from ditritus by internal digestion.
 Detritivores feed on dead organic matter such as dead leaves, feathers, and feces.
 Large ditritivores digest food into gut (earthworms) while unicellular ones ingest it into food vacuoles.
 
Communities:
  Community: populations of different species living together and interacting with each other.
 All species are dependent on others for long-term survival.
 Typical communities consists of hundreds or even thousand of species living together in an area.
 
Ecosystems:
 Ecosystem: a community and its interactions with the abiotic environment.
 Biotic organisms: living components of an environment.
 Abiotic components: non-living components of an environment.
 Biotic organisms depend on abiotic environments for survival.
 Abiotic environments can have a powerful influence on biotic organisms, such as forming habitat.
 Biome: a collection of ecosystems that are similar to each other.
 Biosphere: all biomes (living components) that cover Earth.
 
 
Inorganic Nutrients:
 Inorganic nutrients are gained by autotrophs and heterotrophs through abiotic environments.
 Living organisms need a supply of chemical elements:
1. Carbon, hydrogen and oxygen to make carbohydrates, and carbon compounds.
2. Nitrogen and phosphorus.
3. Approximately 15 other elements, which are minute but essential.
 Autotrophs need those inorganic compounds.
 Heterotrophs obtain those from food, but still need sodium, calcium and potassium.
 
Nutrient Cycles:
 Nutrients are usually passed between biotic organisms before returning to the abiotic environment to be
recycled.
 Inorganic nutrients are maintained by nutrient cycling.
 
Sustainability of Ecosystems:
 Ecosystems have the ability to be sustainable over long periods of time.
 Something is sustainable if can continue indefinitely.
 There are 3 requirements for sustainability in ecosystems:
1. Nutrient availability.
2. Detoxification of waste products.
3. Energy availability.
 Sustainability depends on continued energy supplies to ecosystems, mostly the sun.
 
Mesocosms:
 Mesocosm: a small experimental area se up as an ecological experiment.
 Mesocosms can be used to test what types of ecosystems are sustainable.
 
Energy Flow (4.2):
 
Sunlight and Ecosystems:
 Most ecosystems rely on the initial supply of energy from sunlight.
 Living organisms can harvest sunlight energy through photosynthesis.
 Three autotrophs can carry out photosynthesis (producers):
1. Plants.
2. Eukaryotic algae.
3. Cyanobacteria.
 Heterotrophs are also divided into:
4. Saprotrophs.
5. Detritivores.
6. Consumers.
 Saprotrophs indirectly rely on energy from the sun as they feed on carbon compounds.
 Sunlight availability varies in different regions around the world, and hence to different organisms.
  
Energy Conversion:
 Light energy is converted to chemical energy in carbon compounds by photosynthesis.
 Plants absorb sunlight using chlorophyll and other photosynthetic pigments.
 Plants use the conversion of light energy to chemical energy to produce carbohydrates, lipids and other
carbon compounds.
 Plants use part of their energy for cell respiration to achieve cellular activities, but the majority remains in its
cells and tissues, available for saprotrophs.
 
Energy in Food Chains:
 Chemical energy in carbon compounds flows through food chains by means of feeding.
 Food chain: a sequence of organisms, each of which feeds on the previous one.
 There is usually between two and five organisms in a food chain.
 The food chain always starts with a producer, followed by consumers (primary consumers feeds on
producer, secondary consumer feeds on primary consumer, etc..).
 Consumers obtain energy from the carbon compounds of the organism they feed on.
 The arrows in a food chain indicate the flow of energy from one organism to another.
 Food web: a diagram that shows how food chains are linked together into more complex feeding
relationships.
 Food webs are hard to construct because:
1. Organisms often occupy two trophic levels.
2. Not all feeding habits or organisms are known.
3. Feeding habits of organisms may vary seasonally.
4. Less energy is available as the food web progresses.
 
Respiration and Energy Release:
 Energy released by respiration is used in living organisms and converted to heat.
 The laws of thermodynamics are:
1. Energy is neither created not destroyed, but changed from one form to another:
o Living organisms need energy for cellular activities such as:
o Synthesizing large molecules like DNA, RNA and proteins.
o Pumping molecules or ions across membranes by active transport.
o Moving things around inside the cell, such as chromosomes or vesicles, or in muscle cells the protein
fibers that cause muscle contraction.
o ATP: adenosine triphosphate.
o ADP: adenosine diphosphate.
o ATP supplies energy for such activities, and each cell produces its own ATP supply.
o In ATP conversion to ADP, carbon compounds such as carbohydrates and lipids are oxidized.
o Oxidation reactions are exothermic, so the energy released is used in endothermic reactions to
produce ATP.
o Cell respiration transfers chemical energy from glucose and other carbon compounds into ATP to be
directly used by cells, as other carbon compounds can't.
2. Whenever energy is transformed, there is a loss of it through the release of heat:
o Energy transfers are never 100% efficient.
o In metabolic processes, a high amount of energy is transformed into and lost as heat.
o Heat is a disordered form of energy and mostly cannot be used.
o Heat is eventually lost from the ecosystem.
 
Heat Energy in Ecosystems:
 Living organisms cannot convert heat to other forms of energy.
 Living organisms can, however, perform various energy conversions:
1. Light energy to chemical energy (photosynthesis).
2. Chemical energy to kinetic energy (muscle contraction).
3. Chemical energy to electrical energy (nerve cells).
4. Chemical energy to heat energy (heat-generating adipose tissue).
 
Heat Losses from Ecosystems:
 Heat resulting from cell respiration makes organisms warmer.
 According to physics' laws of thermodynamics, heat is passed from hotter to colder bodies. This means that
the heat produced by living organisms is ultimately lost to the abiotic environment.
 
Energy Losses and Ecosystems:
 Energy losses between trophic levels restrict the length of food chains and the biomass of higher trophic
levels.
 Biomass: the dry mass of an organism, which consists of tissues and organic compounds.
 Since organic compounds have energy, biomass has energy.
 Ecologists can measure the amount of energy is added per year by groups of organisms to their biomass.
 As trophic levels increase, biomass decreases because:
1. Energy is released in cellular respiration (loss of CO2).
2. Not all of the organism is consumed by the consumers (inedible parts/uneaten material).
3. Not all of the ingested food is digested and absorbed (indigestible material is excreted as feces).
 The number of trophic levels in a food chain is restricted because as they progress, energy is constantly lost,
until the remaining energy is not sufficient for consumers.
 Pyramids of energy: quantitative representations of energy flow using pyramids of energy. These often use
the unit of kilojoules per meter squared per year (kj/m^2/yr).
 
 

Carbon Cycling (4.3):

 
Carbon Fixation:
 Autotrophs convert carbon dioxide into carbohydrates and other carbon compounds.
 Autotrophs' usage of carbon dioxide reduces its concentration in the atmosphere, as it is lower in locations
where photosynthesis rates are higher.
 
Carbon Dioxide in Solution:
 In aquatic habitats carbon dioxide is present as a dissolved gas and hydrogen carbonate ions.
 CO2 in water can either remain a dissolved gas or react with H2O to form H2CO3 (carbonic acid). H2CO3 is
dissociated to form H+ and HCO3- (hydrogen and hydrogen carbonate ions), which explains why CO2 reduces the
PH of water.
 Dissolved CO2 and HCO3 ions are both used by aquatic autotrophs to make carbon compounds.
 
Absorption of Carbon Dioxide:
 Carbon dioxide diffuses from the atmosphere or water into autotrophs.
 The usage of autotrophs for CO2 decreases its concentration inside their cells, so CO2 in their environment
diffuses into their cells.
 In land plants, diffusion of CO2 often occurs in the stomata of leaves (underside), while aquatic plants are
wholly permeable to CO2, allowing it to diffuse from any part of them.
 
Release of Carbon Dioxide from Cell Respiration:
 Carbon dioxide is produced by respiration and diffuses out of organisms into water or the atmosphere.
 CO2 is a waste product of aerobic cell respiration.
 CO2 is produced by:
1. Non-photosynthetic cells in producers.
2. Animal cells.
3. Saprotrophs.
 CO2 diffuses into the atmosphere once produced by living organisms.
 
Methanogenisis:
 Methanogenisis: the production of methane from organic matter in aerobic conditions by methanogenic
archaeans, and some diffuses into the atmosphere.
 Three different groups of anaerobic prokaryotes are involved in methanogenisis:
 1. Bacteria that convert organic matter into a mixture of organic acids, alcohol, hydrogen and carbon dioxide.
2. Bacteria that use the organic acids and alcohol to produce acetate, carbon dioxide and hydrogen.
3. Archaeans that produce methane from carbon dioxide, hydrogen and acetate through two chemical
reactions:
a. CO2 + 4H2 ---> CH4 + 2H2O.
b. CH3COOH ---> CH4 + CO2.
o Archaeans carry out methanogenisis in anaerobic environments such as:
c. Mud along shores and in the beds of lakes.
d. Swamps, mires, mangrove forests and other wetlands where the soil or peat deposits are
waterlogged.
e. Guts of termites and of ruminant mammals such as cattle and sheep.
f. Landfill sites where organic matter is in wastes that have been buried.
o Some of the carbon dioxide produced by archaeans diffuses into the atmosphere while the other is
trapped and burned as fuel.
 
Oxidation of Methane:
 Methane is oxidized to carbon dioxide and water in the atmosphere.
 Methane remains in the stratosphere for an average of only 12 years since is reacts with monoatomic
oxygen (O) and hydroxyl radicals (OH), which explains why its concentrations are not so high in the
atmosphere even though is it produced in large amounts.
 
Peat Formation:
 Peat forms when organic matter is not fully decomposed because of anaerobic conditions in waterlogged
soils.
 Saprotrophs cannot thrive in anaerobic conditions (waterlogged soils), so organic matter is not fully
decomposed there, creating acidic conditions which further inhibit saprotrophs and methanogens as they
develop -the acidic conditions-.
 About 3% of Earth's surface consists of peat (dark brown acidic material), which stretches in some areas to a
depth of 10 meters, showing its immense amounts.
 
Fossilized Organic Matter:
 Fossilized organic matter: partially decomposed organic matter from past geological eras was converted into
oil and gas in porous rocks or into coal.
 Carbon can remain unchanged in rocks for millions of years due to its stability.
 Coal is formed when deposits of peat are buried under other sediments. The peat is heated and compressed
until coal is formed.
 Oil and natural gas are formed in the mud at the bottom of seas and lakes. Organic matter is often not
completely decomposed due to anaerobic conditions, so it is fossilized under heat and pressure to form
complex liquid or gaseous carbon mixtures known as crude oil and natural gas.
 Natural gas mainly consists of methane.
 

 Carbon dioxide is produced by the combustion of biomass and fossilized organic matter.
 The products of complete combustion are carbon dioxide and water.
 It is natural in some places for fires so periodically occur in forests and green lands, so the community is
often adaptive and regenerates quickly. Such fires release carbon dioxide.
 Carbon atoms in carbon dioxide may have been removed by photosynthesizing plants hundreds of millions
of years ago.
 
Limestone:
 Animals such as reef-building corals and mollusks have hard parts that are composed of calcium carbonate
and can become fossilized in limestone.
 When animals with hard body parts composed of calcium carbonate die, the calcium carbonate dissolves in
water under acidic conditions, but would be deposited at the bottom under alkaline conditions, forming
limestone. In shallow tropical seas calcium carbonate can also be deposited by precipitation in the water.
  10% of sedimentary rocks on Earth are limestone, and 12% of calcium carbonate's mass is carbon, so huge
amounts of the element are trapped in limestone.
 Animals with hard body parts consisting of calcium carbonate include:
1. Mollusk shells.
2. Hard corals that build reefs, which produce their exoskeletons by secreting calcium carbonate.
 
 
Climate Change (4.4):
 
Greenhouse Gases:
 Carbon dioxide (CO2) and water vapor (H2O) are the most significant greenhouse gases.
 Greenhouse gases: gases in the atmosphere which retain heat within the atmosphere. They simulate the
effect of glass in greenhouses, which traps heat, hence the name.
 Carbon dioxide is released into the atmosphere through cell respiration by living organisms, as well as the
combustion of biomass and fossil fuels. It is removed by the photosynthesis of plants and by dissolving in the
ocean.
 Water vapor is formed through water evaporation from the oceans and transpiration in plants. It is removed
from the atmosphere by rainfall and snow.
 Water droplets continue to retain heat while vaporized as it condenses back into liquid water in clouds. This
causes temperatures to change at quicker rates during the night, as skies are clearer from clouds as water
reflects and traps heat energy.
 
Other Greenhouse Gases:
 Greenhouse gases such as methane and nitrogen oxides have a lesser impact than that of carbon dioxide
and water vapor.
 Methane is the third most significant greenhouse gas. It is emitted from marshes and other waterlogged
habitats, as well as from landfill sites where organic wastes have been dumped. It is also released during the
extraction of fossil fuels and from melting ice in polar regions.
 Nitrous oxide is also a significant greenhouse gas released naturally by bacteria in some habitats, and by
agriculture and vehicle exhausts.
 Oxygen and nitrogen, the most abundant gases on Earth, are both not greenhouse gases as they do not
absorb longer-wave radiation. Hence, all greenhouse gases make up less than 1% of the atmosphere.
 
Assessing the Impact of Greenhouse Gases:
 The impact of gas depends on its ability to absorb longer-wave radiation as well as on its concentration in
the atmosphere.
 Methane causes much more warming per molecule than carbon dioxide, but is existent in much lower
concentrations and so has a lesser effect on the greenhouse effect and global warming.
 The concentration of a gas depends on the rate at which it is released into the atmosphere and for how long
it remains there on average.
 Water vapor is emitted into the atmosphere at immense rates, but remains there for only 9 days, while
methane remains for an average of 12 years, and carbon dioxide even more.
 
Long-wavelength emissions from Earth:
 The warmed Earth emits longer-wave radiation.
 The warm surface of Earth absorbs short-length waves, but emits them at much longer ones, often as
infrared rays.
 The peak wavelength of solar radiation is 400nm, while the warm surface of Earth emits these waves after
absorbing them at a peak wavelength of 10,000nm.
 
Greenhouse Gases:
 Longer-wavelength radiation is reabsorbed by greenhouse gases, which retains the heat in the atmosphere.
 25-30% of the heat in the short-wavelength radiations emitted by the sun is absorbed before reaching the
Earth's surface. Most of it is UV light, absorbed by ozone.
 70-75% of solar radiation therefore enters the Earth, much of which is converted to heat.
  About 70-85% of the loner-wavelength radiations re-emitted by Earth's surface are captured by greenhouse
gases before they reach outer space. This energy is re-emitted, some back to Earth, as heat, which causes
global warming.
 Without the greenhouse effect, the mean temperature of Earth would be about -18ºC.
 Greenhouse gases in Earth's atmosphere absorb heat within specific wavebands. The re-emitted
wavelengths vary between 5-70nm.
 
Global Temperatures and Carbon Dioxide Concentrations:
 With the change of concentration of a greenhouse gas in the atmosphere, a change in the climate should be
expected.
 To study the difference in carbon dioxide concentrations along time, ice from the Antarctic would be drilled
as it contains bubbles of gas, and the ratio of carbon dioxide would be studied.
 There is a very striking correlation between carbon dioxide concentrations and climate change (as carbon
dioxide rises in concentration, so do global temperatures).
 
Greenhouse Gases and Climate Patterns:
 Global temperatures and climate patterns are influenced by concentrations of greenhouse gases.
 Mean temperatures are expected to be 32ºC higher with greenhouse gases than without on Earth's surface.
 It is expected that global temperatures will increase with the rise of greenhouse gas concentrations as more
heat is retained.
 The relationship between greenhouse gas concentrations and global temperatures is not necessarily
proportional, as other factors contribute into their change such as:
1. The Milankovitch cycles in the Earth's orbit.
2. The variation in sunspot activity.
 Higher temperatures would cause other changes in global climates, such as:
1. Increased evaporation of water, and therefore more frequent rains.
2. Increased amounts of rain delivered throughout thunderstorms and other intense bursts.
3. Increased number of hurricanes and tropical storms due to higher ocean temperatures (faster wind speeds
and more powerful disasters).
 Not all areas would become warmer with climate change, and not all would have rain increase in them
(some face the opposite conditions).
 Weather patterns are unpredictable, but a few degrees increased may cause dramatic effects on the planet.
 
Industrialization and Climate Change:
 There is a correlation between rising atmospheric concentrations of carbon dioxide since the starts of the
industrial revolution two hundred years ago and average global temperatures.
 There have been large fluctuations in carbon dioxide concentrations over the last 800,000 years.
 Carbon dioxide concentrations have risen to reach nearly 400ppm recently.
 Unnatural carbon dioxide concentration increases are expected to have started in the 18th century when
some countries began industrializing, but it is impossible to predict the exact date as other factors contribute.
 temperature rises due to carbon dioxide concentration remarkably began to rise during and after the
1950's.
 
Burning Fossil Fuels:
 Recent increases in atmospheric carbon dioxide are largely due to increases in the combustion of fossilized
organic matter.
 The burning and usage of oil, natural gas and coal became increasingly widespread in the 19th century,
increasing carbon dioxide emissions.
 The popularity of fossil fuels started peaking since the 1950's and onwards, matching the period of the
steepest increases in carbon dioxide rates. This furthermore elaborates on the contribution of fossil fuels in
the emission of carbon dioxide, and hence global warming.
 
Opposition to the Climate Change Science:
 Many argue that climate change is not directly related to carbon dioxide emissions and human actions, as
there were several random fluctuations in temperature as well.
 The claim is not supported by evidence, which makes it scientifically weak and unproven.
 
Coral Reefs and Carbon Dioxide:
 Over 500 billion tons of carbon dioxide have dissolved in ocean water since the industrial revolution.
 The PH of ocean water dropped from 8.179 to 8.104 between the late 18th century and mid-1990's. It is
currently 8.069, and this means 30% acidification. The acidification would continue to increase with the rise of
carbon dioxide rates.
 After carbon dioxide is turned into hydrogen carbonate ions and hydrogen ions in the ocean, the hydrogen
reacts with carbonates to reduce their concentration, although it is already low.
 Marine animals such as reef-building corals that deposit calcium carbonate in their skeletons need to absorb
carbonate ions from seawater, and its lack makes it harder for them to do so.
 If hydrogen carbonate levels continue to increase, hence reducing calcium carbonates, even existing corals
and coral reefs are threatened as the calcium carbonate in their skeletons tends to dissolve.
 In the area of acidified waters corals, coral reefs, sea urchins and other animals which use calcium carbonate
in making their skeletons are not usually found. Instead, there are invasive algae and sea grasses flourishing in
such areas.
 
The Precautionary Principle:
 The precautionary principle explains that a change suggested by humans, if large, should be firstly proven to
have no negative implications on the environment.
 Since science doesn’t always have the answer, caution should be exercised first, then science, in the case of
uncertainty.
 Precautionary measures should be taken to reduce the harm of a change on the environment.
 The precautionary principle allows for protection from the possibility of late reactions toward change (e.g.: it
is predicted that a reaction to the greenhouse effect after it has proven effectivity would have been too late).
 The precautionary principle:
1. Limits innovation.
2. Could prevent new ideas.
3. Prevents environmental damage, which is easier than repairing it on the long term.
4. Shifts the burden of proof from the protectors to the proposers of an action.
Levels of Protein Structure (7.3):
 
 The shape of a protein determines its function. It consists of one or more polypeptides, and the sequence of
amino acids determine its shape.
 There are four levels in a protein structure:
1. Primary structure: the sequence of amino acids in a polypeptide.
o It is determined by inherited genetic information.
o It is linked together by peptide bonds.
o There is a very high number of combinations, since 20 different amino acids exist.
o It determines the higher levels of protein structure and its biological function.
2. Secondary structure: the coils and folds of proteins resultant from hydrogen bonds between CO and NH
groups.
o Typical secondary structures:
o Beta pleated sheet: hydrogen bonds between chains.
o Alpha helix (coil): hydrogen bonds between the hydrogen of an amino acid and the oxygen of a
carboxyl.
2. Tertiary structure: further folding because various parts on the ….
o It is determined by interactions between R groups (e.g.: hydrogen bonds, ionic bonds, hydrophobic
interactions, and Van Der Waal's interactions.
o Strong covalent bonds called disulfide bridges may form between neighboring cysteine amino acids.
3. Quaternary structure: this is not present in all proteins.
o It results when two or more polypeptides aggregate together (e.g.: collagen - three polypeptides
coiled, hemoglobin - four polypeptides.
 Hemoglobin consists 4 polypeptide units joined together. Each subunit has a heme (containing Fe) group at
the chain's center, which binds to oxygen molecules.
  Fibrous proteins are insoluble in water, physically tough, and long and narrow. They consists of parallel
polypeptide chains in long fibers or sheets (repetitive amino acid sequences) (e.g.: collagen, contractile -
myosin component of muscles).
 Globular proteins are soluble in water, and the tertiary structure is critical for their functions. It consists of
irregular amino acid sequences, and polupetide chains folded into a spherical shape (e.g.: hemoglobin and
myogoblin - transport, insulin and growth hormone - hormones, enzymes - catalysts, immunoglobulin -
antibodies.

Metabolism (8.1):
 
Metabolic Pathways:
 Metabolic Pathway: the sequence of small steps in which a chemical reaction takes place.
 Most metabolic pathways involve a chain of reactions.
 Some metabolic pathways form a cycle instead of a chain, forming a product which is the reactant for the
rest of the pathway.
 
Enzymes and Activation Energy:
 The binding between an enzyme and a substrate lowers the overall energy level of the transition state.
 The activation energy is used to weaken or break the bonds in a substrate. As the activation energy is
reduced, the rate of reaction is greatly increased.
 
Types of Enzyme Inhibitors:
 Enzyme inhibitors: chemical substances which bind to enzymes and reduce the activity of the enzyme.
 Competitive inhibitors: enzyme inhibitors which interfere with the active site so that the substrate cannot
bind (e.g.: para-aminobenzoate is a substrate for the enzyme dihydropetroate synthetase, which is inhibited
by sulfadiazine).
 Non-competitive inhibitors: enzyme inhibitors which bind at a location other than the active site, changing
the shape of the enzyme so that it cannot bind to a substrate (e.g.: fructose-6-phosphate is a substrate for the
enzyme phosphofructokinase, which is inhibited by xylitol-5-phosphate).
  When inhibited by competitive inhibitors, enzymes do not bind to substrates, but if a much higher
concentration of substrates is present than that of the inhibitors, the uninhibited enzyme will reach its
maximum rate.
 Non-competitive inhibitors change the structure of the enzyme, preventing substrates from binding to it.
Uninhibited enzymes function normally, but the overall rate would be lower with inhibitors.
 
End-product Inhibition:
 Many enzymes are regulated by chemical substances to special sites, called the allosteric sites, away from
the active site. These are called allosteric interactions.
 In many cases, the substances binding to the allosteric sites are end-products of a pathway, while the
enzyme they bind to catalyzes the first reactions in a metabolic pathway. Hence, the enzyme can work rapidly
in a pathway where end-products are with a shortage, but completely stops with an excess of them.
 As the concentration of end products increases, the rate of reaction decreases, and eventually stops when
the concentration of the products is very high.
 An example of end-product inhibition is the inhibition of threonine deaminase, which catalyzes threonine (an
amino acid), by isoleucine.
 
 
Cell Respiration (8.2):
 
Oxidation and Reduction:
 Cell respiration involves the oxidation and reduction of compounds.
 Oxidation: the loss of electrons from a substance.
 Reduction: the gain of electrons by a substance.
 Electron carriers: substances that can accept and give up electrons as required.
 Electron carriers often link oxidations and reductions in cells.
 In respiration, the main electron carrier used is NAD, while in photosynthesis it is a phosphorylated version
of NAD, which is NADP.
 NAD + 2 electrons ---> reduced NAD.
 NAD originally exists as a positively charged NAD+, and accepts electrons by receiving 2 H molecules from the
compound being reduced.
 One H molecule from the reduced compound splits into a proton and electron, and NAD+ takes in only the
electron to become NAD while the proton is released. The other H is accepted as a whole to from NADH.
 NAD+ + 2H+ + 2 electrons ---> NADH + H+.
 Reduction can be achieved by accepting hydrogen atoms, because they have an electron. Oxidation can
therefore be achieved by losing hydrogen atoms.
 Accepting oxygen atoms causes oxidation due to its high electron affinity that draws electrons from other
parts of the molecule or ion, while losing them causes reduction.
 
Phosphorylation:
 Phosphorylation of molecules makes them less stable.
 Phosphorylation: the addition of a phosphate molecule (PO43-) to an organic molecule.
 Biochemists indicate that some amino acid combinations on proteins act as binding sites for phosphate
molecules.
 Phosphorylation can be said to activate the molecule since it increases its reactivity by making it more
unstable.
 The hydrolysis of ATP releases energy and hence is exergonic.
 Many metabolisms are endergonic, and hence need an exergonic reaction to give them energy for activation.
 The conversion of glucose to glucose-6-phosphate is endergonic and proceeds with the hydrolysis of ATP
(exergonic), as do many other metabolisms.
 
Glycolysis and ATP:
 Glycolysis gives a small net gain of ATP without the use of oxygen.
 Glycolysis happens in a cell's cytoplasm.
 By converting glucose (6-carbon molecule) to pyruvate (3-carbon molecule), glycolysis can release small
ratios of ATP without using oxygen.
  Glycolysis occurs through a pathway of reactions.
1. Firstly, ATP is used to phosphorylate the sugars:
Glucose --ATP-> Glucose-6-phosphate --> Fructose-6-phosphate --ATP-> Fructose-1,6-biphosphate.
2. Fructose-1,6-biphosphate is split to form 2 molecules of triose phosphate.
3. Triose phosphate molecules are oxidized as hydrogen atoms are removed from them -not H+ ions but whole
atoms- and become glycerate-3-phosphate, releasing enough energy to make ATP.
4. The hydrogen atoms released from triose phosphate bind to NAD+ to form NADH + H+.
5. In the final stages of glycolysis, the phosphate group is transferred to ADP to produce ATP and pyruvate.
 These steps occur twice per glucose molecule.
 The net products of glycolysis are:
1. 2 ATP.
2. 1 NADH ---> 2FADH2.
3. 2 pyruvates.
 
The Fate of Pyruvate, The Link Reaction:
 In aerobic cell respiration pyruvate is decarboxylated and oxidized.
 In the link reaction pyruvate is converted into acetyl coenzyme A.
 If oxygen is available, pyruvates are taken into the mitochondria's matrix for full oxidation in the link
reaction, but this isn't a single-step process.
 The link reaction:
1. Pyruvates are decarboxylated, releasing oxygen and carbon in the form of carbon dioxide to form an acetyl
group.
2. Pyruvates are oxidized by releasing hydrogen atoms.
3. Hydrogen atoms are accepted by NAD+ and a related carrier called FAD, which pass them on to the electron
transport chain where oxidative phosphorylation will later occur.
 The link reaction has its name because it links glycolysis with the cycle of reactions that follows.
 The link reaction involves one decarboxylation and one oxidation.
 The acetyl formed in the link cycle is attached to coenzyme A to from acetyl coenzyme A.
 Two link reactions occur for every cycle since 2 pyruvates are produced in glycolysis.
 The net products of the link reaction are:
1. 2 NADH.
2. 2 carbon dioxide.
3. 2 acetyl coenzyme A (CoA).
 Carbohydrates, proteins and lipids are all converted into CoA at on point in their metabolism.
 
The Krebs Cycle:
 In the Krebs cycle, the oxidation of acetyl groups is coupled to the reduction of hydrogen carriers.
 If the body's ATP is low, it goes through Krebs cycle. If the body's ATP is high, CoA is stored as fat.
 Krebs cycle involves 2 decarboxylations and 4 oxidations.
 Most of the energy released during Krebs cycle is used to reduce hydrogen carriers (NAD+ and FAD).
 The reduction of NAD+ and FAD allows for storage of chemical energy to be later used in oxidative
phosphorylation.
 For every Krebs cycle, the production of reduced NAD occurs 3 times, 1 time for reduced FAD, and
decarboxylation occurs twice. 1 molecule of ATP is also generated.
 Krebs cycle:
1. Acetyl CoA (2-carbon molecule) ---> Citrate (6-carbon molecule).
2. Citrate (6-carbon molecule) ---> 6-carbon molecule.
3. 6-carbon molecule --NAD+-> 5-carbon molecule (CO2 + NADH + H+).
4. 5-carbon molecule --NAD+-> 4-carbon molecule (CO2 + NADH + H+).
5. 4-carbon molecule --ADP-> 4-carbon molecule (ATP).
6. 4-carbon molecule ---> 4-carbon molecule (FADH2).
7. 4-carbon molecule ---> 4-carbon molecule.
8. 4-carbon molecule --NAD+-> oxaloacetate (4-carbon molecule) (NADH + H+).
  The net products of Krebs cycle are:
1. 6 NADH.
2. 2 FADH2.
3. 4 CO2.
4. 2 ATP.
5. All 6 glucose carbons are oxidized to CO2.
 Krebs cycle occurs twice for every glucose molecule, which explains the net products.
 
Oxidative Phosphorylation, The Electron Transport Chain:
 Energy released by oxidation reactions is carried to the cristae of the mitochondria by reduced NAD and FAD.
 Oxidative phosphorylation is the final part of aerobic respiration, where ADP is phosphorylated to produce
ATP, using energy released by oxidation.
 The main oxidized substance in oxidative phosphorylation is reduced NAD.
 As reduced NAD and FAD donate their electrons to electron carriers in the inner mitochondrial membrane,
passing them from carrier to carrier, the energy is utilized to push hydrogen protons from the matrix, through
the inner membrane and into the intermembrane space. Hydrogen protons then have to pass through a
channel protein known as ATP synthase in order to reenter the matrix, and hence produce ATP.
 
Chemiosmosis:
 In chemiosmosis protons diffuse through ATP synthase to generate ATP.
 Chemiosmosis: the mechanism used to couple the release of energy by oxidation to ATP production.
 Chemiosmosis has its name because the hydrogen protons (chemical substance) move across a membrane
down the concentration gradient.
 Electrons release energy every time they pass from carrier to carrier.
 Chemiosmosis:
1. NADH + H+ supplies pairs of hydrogen atoms to the first carrier in the chain, with the NAD+ returning to the
matrix.
2. The hydrogen atoms are split to release two electrons, which pass from carrier to carrier in the chain.
3. Energy is released as electrons pass from carrier to carrier, and 3 carriers use this energy to transfer
hydrogen protons from the matrix, across the inner membrane, and into the intermembrane space.
 4. As electrons move across carriers, a proton gradient is built which acts as a store of potential energy.
5. At the end of the carriers, oxygen acts as a receptor and takes in both positively and negatively charged
hydrogen ions to form water.
6. Protons pass back into the matrix through ATP synthase, producing ATP in the process.
 
The Chemiosmotic Theory:
 Peter Mitchell proposed the chemiosmotic theory in 1961 in order to explain the coupling of electron
transport in the inner mitochondrial membrane to ATP synthesis.
 
Structure and Function in the Mitochondrion:
 The structure of the mitochondrion is adapted to the function it performs.
 Adaptation: a change in structure so that something caries out its function more efficiently.
 The mitochondrion is a semi-autonomous organelle, meaning it can grow and reproduce alone but still
depends on the cell for resources. 70S ribosomes and naked DNA are found in the mitochondrion within the
matrix.
 Adaptations of the mitochondria include:
1. Mitochondria are responsible for aerobic respiration, and their outer membrane separates them from the
rest of the cell, creating a compartment specialized for aerobic respiration.
2. The inner mitochondrial membrane is the site for oxidative phosphorylation, containing transport chains and
ATP synthase.
3. Cristae are tubular extensions of the inner membrane that increase the surface area for oxidative
phosphorylation.
4. The intermembrane space has little space for storage of hydrogen protons, and so the concentration
gradient can build up rapidly.
5. The matrix contains the enzymes necessary to carry out the link reaction and Krebs cycle.
 
Mitochondrial Membranes are Dynamic:
 The technique of electron tomography has allowed 3D images of the mitochondrial structure to be
developed.
 "Cristae are not simple infoldings but are invaginations."
 Cristae originate at narrow openings and restrict the diffusion of proteins between compartments.
 Membranes are not only very flexible but also dynamic, undergoing fusion and fission in response to
metabolisms.
 
 
Photosynthesis (8.3):
 
Location of Light-dependent Reactions:
 Light-dependent reactions take place in the intermembrane space of thylakoids.
 Photosynthesis is divided into two different processes; light-dependent and light-independent.
 Light-dependent reactions rely on light directly, while light-independent reactions do not directly rely on
light, but can only carry on without it for a few seconds since they use the products of light-dependent-
photosynthesis, which run out very rapidly.
 Chloroplasts have an outer and inner membrane.
 A chloroplast's inner membrane encloses another set of interconnected membranes called thylakoid
membranes.
 Light-dependent reactions take place in the thylakoid space and across the thylakoid membranes.
 
The Products of the Light-dependent Reactions:
 Reduced NADP and ATP are produced in the light-dependent reactions.
 Light energy is converted into ATP and reduced NADP in light-dependent reactions, which serve as energy
sources in light-independent reactions.
 
The Location of the Light-independent Reactions:
 Light-independent reactions take place in the stroma.
 The inner membrane encloses a compartment called the stroma.
  Stroma: a thick protein-rich medium containing enzymes for use in the light-independent reactions, also
known as the Calvin cycle.
 Calvin cycle: an anabolic pathway that requires endergonic reactions to be coupled to the hydrolysis of ATP
and the oxidation of reduced NADP.
Light-dependent Reactions Light-independent Reactions
Photolysis. Carbon fixation.
Photoactivation. Carboxylation of RuBP.
Electron transport. Production of triose phosphate.
Chemiosmosis. ATP and NADPH as energy sources.
ATP synthesis. ATP used to regenerate RuBP.
Reduction of NADP. ATP used to produce carbohydrates.
 
Photoactivation:
 Absorption of light by photosystems generates exited electrons.
 Photosystems: light-harvesting arrays that group together the chlorophyll and accessory pigments.
 Photosystems I and II light-harvest arrays and have reaction centers.
 Photosystems absorb light energy using chlorophylls and pass it on to 2 special chlorophyll molecules in the
reaction center that also have their electrons excited when they receive light.
 The special chlorophylls are said to be photoactivated, and they have the ability to donate their excited
electron to electron acceptors.
 Light-dependent reactions occur in photosystem II.
 Plastoquinone: the electron acceptor in photosystem II.
 Plastoquinone is reduced by accepting 2 light photons/electrons from a special chloroplast.
 Plastoquinone is hydrophobic and so cannot exit the membrane even though it does not have a fixed
position.
 
Photolysis:
 Once the plastoquinone is reduced, the chlorophyll in the reaction center then becomes a strong oxidizing
agent to split water molecules nearest to it and take their electrons to replace the ones it has lost.
 2H2O ---> O2 + H+ + 4 electrons.
 Photolysis: the splitting of water.
 Photolysis explains the release of oxygen in photosynthesis.
 Photolysis happens in the membrane of thylakoids.
 The waste product of photosystem II is oxygen and so it is diffused away.
 The useful product of photosystem II is the reduced plastoquinone, carrying not only 2 electrons, but much
of the energy absorbed by light as well. This energy drives all the subsequent reactions of photosynthesis.
 
The Electron Transport Chain:
 Transfer of excited electrons occurs between carriers in thylakoid membranes.
 Photophosphorylation: the production of ATP using energy derived from light.
 Photophosphorylation is carried out by thylakoids.
 Thylakoid membranes include:
1. Photosystem II.
2. ATP synthase.
3. A chain of electron carriers.
4. Photosystem I.
 Plastoquinone is needed to carry the electron pairs form the reaction center of photosystem II to the start of
the chain of electron carriers.
 
The Proton Gradient:
 Excited electrons from photosystem II are used to generate a proton gradient.
 When plastoquinone drops the electron pairs into the electron carriers, energy is used to pump hydrogen
protons across the membrane to the inner space of the thylakoid.
  Hydrogen protons in the thylakoid's inner space are stored as a source of potential energy.
 Photolysis also contributes to the proton gradient in thylakoids since it takes place in the thylakoid
membrane.
 
Chemiosmosis:
 ATP synthase in thylakoids generates ATP using the proton gradient.
 Hydrogen protons can travel back across the membrane, against the concentration gradient, through ATP
synthase.
 This process is very similar between the mitochondrion and chloroplast
 When electrons pass through all electro carriers in a pathway, they are passed to plastocyanin, a water-
soluble electron acceptor in the fluid inside of thylakoids. Reduced plastocyanin is needed in the next stage of
photosynthesis.
 
Reduction of NADP (Photosystem I):
 Excited electrons from photosystem I are used to reduced NADP.
 The remaining parts of light-dependent reactions involve photosystem I.
 NADP is needed for light-independent reactions and as a similar role to NAD in respiration, which is carrying
electrons for reduction.
 Photosystem I, just like photosystem II, goes through photoactivation and the electron pair plus a hydrogen
proton from the stroma are used to reduce NADP into NADPH + H+ with an enzyme called NADP+ reductase.
 Missing electrons in photosystem I are replaced by electrons from plastocyanin from photosystem II.
 Noncyclic photophosphorylation: producing ATP using energy from excited electrons in photosystem II.
 
Carbon Fixation:
 In the light-independent reactions a carboxylase catalyzes the carboxylation of ribulose biphosphate.
 The reaction that converts carbon dioxide in plants to other carbon compound is arguably the most
important in all living organisms.
 In plants and algae, the reaction above occurs in the stroma, the fluid that surrounds thylakoids in the
chloroplast.
 The product of the carbon fixation reaction is a 3-carbon molecule: glycerate-3-phosphate.
 Carbon dioxide reacts with a 5-carbon molecule, ribulose biphosphate (RuBP), in order to produce 2
glycerate-3-phosphate molecules at a time. The reaction is catalyzed by ribulose biphosphate carboxylase, or
rubisco.
 2CO2 + 3RuBP (5C) ---> 3unstable (6C) ---> 6 glycerate-3-phosphate (3C).
 Rubisco is present in high concentrations in the stroma in order to maximize carbon fixation.
 
The Role of Reduced NADP and ATP in the Calvin Cycle:
 Glycerate-3-phosphate is reduced to triose phosphate using reduced NADP and ATP.
 The ratio of hydrogen to oxygen must be increased when RuBP is converted to glycerate-3-phosphate, and
reduced NADP and ATP are used to do so.
 ATP provides energy, while reduced NADP provides the hydrogen atoms to reduce glycerate-3-phosphate
into triose phosphate.
 
The Fate of Triose Phosphate:
 Triose phosphate is used to regenerate RuBP and produce carbohydrates.
 The first carbohydrate produced by light-independent reactions in photosynthesis is triose phosphate.
 Triose phosphate can form hexose phosphate using 2 of its molecules, and that can pile up through
condensation to form starch, but if all triose phosphate was used up like that RuBP would run out.
 The production of triose phosphate from RuBP and its reversal into RuBP are all part of the Calvin Cycle.
 Since 6 triose phosphates are produced in a Calvin cycle, 5 are used, along with 3 ATP, to be converted back
into 3 RuBP molecules, while one is stored as starch. Hence 2 Calvin cycle are needed to produce one glucose
molecule, since each triose phosphate contains 3 carbons.
 
RuBP Regeneration:
 Ribulose biphosphate is reformed using ATP.
  In the last phase of the Calvin cycle, triose phosphate is reconverted back to RuBP, which helps allows for the
fixation of carbon dioxide, repeating the Calvin cycle.

 
Chloroplast Structure and Function:
 The structure of the chloroplast is adapted to its function in photosynthesis.
 Chloroplasts are quite variable in shape but share certain features:
1. A double membrane forming the outer chloroplast envelope.
2. An extensive system of internal membranes called thylakoids, which are an intense green color.
3. Small fluid-filled spaces inside the thylakoid.
4. A colorless fluid around the thylakoids, called the stroma, which contains many different enzymes.
5. Grana, which are stacks of thylakoids.
6. Starch grains or lipid droplets, if the chloroplast has been photosynthesizing rapidly.
 
Chloroplast Structure-function Relationship:
 There is a clear relationship between the structure of the chloroplast and its function:
1. Chloroplasts absorb light. Grana, consisting of thylakoids, have pigments and can maximize light absorption
through the large area of their membranes.
2. Chloroplasts produce ATP through photophosphorylation. A proton gradient is needed. The area of the fluid
in the thylakoids is very small, allowing a gradient to from very quickly and hence allowing ATP synthesis to
begin.
3. Chloroplasts carry out the many chemical reactions of the Calvin cycle. The stroma contains high
concentrations of all enzymes involved in the Calvin cycle, and ATP and reduced NADP are easily available
since thylakoids, where they are made, are distributed within the stroma.
Transport in the Xylem of Plants (9.1):
 
Transpiration:
 Transpiration is the inevitable consequence of gas exchange in the leaf.
 Plant leaves are the primary organ of photosynthesis, which involves the synthesis of carbohydrates using
light energy. Carbon dioxide is used in this process, while oxygen is released as a waste product; the exchange
of these two gases is necessary for photosynthesis.
 Since cuticles (waxy layers on the top of leaves) have low permeability, pores on the epidermis are needed
to absorb carbon dioxide (stomata). Stomata usually allow water vapor to escape.
  Transpiration: the loss of water vapor from the leaves and stems of plants.
 Guard cells are used by plants to minimize water loss through stomata. They are found on either side of a
stoma, and control its aperture, being able to open wide or fully close. They are found in all land plants, except
liverworts.
 Guard cells close the stoma when they are flaccid. They open up when they are turgid, having potassium ions
accumulated in them, and water filling their vacuoles.
 
Using a Potometer:
 Potometer: a device used to measure water uptake in plants.
 A potometer consists of a leafy shoot in a tube, a reservoir, and a graduated capillary tube.
 A bubble in the capillary tube marks the zero point, and moves along it as the plant takes up water through
its roots.
 A tap below the reservoir allows it to be reset for new trials.
 Factors that affect transpiration:
1. Light intensity (positive correlation): light stimulates the opening of stomata, as guard cells open during the
day.
2. Temperature (positive correlation): higher temperatures evaporate water more rapidly, increase diffusion
rate, reduce relative air humidity, and sometimes cause stomata to close. Some plants open their stomata
under high temperatures to cool down by transpiration.
3. Humidity (negative correlation): water diffuses out of the leaf when there is a concentration gradient
between air spaces inside the leaf and the air outside.
4. Wind (positive correlation): wind blows air saturated with water vapor away.
 
Xylem Structure Helps Withstand Low Pressure:
 The cohesive property of water and the structure of the xylem vessels allow transport under tension.
 Xylem vessels are long continuous tubes, with thickened walls impregnated with a polymer called lignin,
which strengthens the walls to make them withstand low pressures without collapsing.
 Xylem vessels are formed from files of cells, arranged end-to-end.
 Cell walls between adjacent xylem cells are largely removed and plasma membranes, as well as cell contents,
break down in flowering plants.
 In mature plants, xylem vessels are nonliving, so water transport must be a passive process.
 Pressure in xylem vessels is much lower than atmospheric pressure, but their rigidity prevents them from
collapsing.
 Cohesion between water molecules in the xylem, and their adhesion to its hydrophilic walls, allow water to
be transported in a stream along xylem vessels.
 
Tension in Leaf Cell Walls Maintains the Transpiration Stream:
 The adhesive property of water and evaporation generate tension forces in leaf cell walls.
 The adhesion of water molecules to xylem walls allows it to be sucked out, furthermore reducing the already
low pressure.
 Transpiration pull: the pulling force generated by low pressure that is transmitted through the water in the
xylem vessels down the stem and to the ends of the xylem in roots.
 Transpiration pull is strong enough to pull water upwards, against gravity, to the top of the tallest tree.
 Transpiration pull is a passive process energized by the thermal energy that causes transpiration.
 Cavitation: the breaking down of liquid columns due to their inability to consistently move up the xylem for
the lack of strong cohesion between their molecules and their incapability to resist the very low pressures in
xylem vessels.
 Cavitation can even happen with water, but is unusual.
 Xylem cells with a narrower diameter (tracheids) better resist cavitation than wider diameter ones (vessels),
since water is more unlikely to break up due to bubble formation with a narrower diameter.
 
Active Transport of Minerals in the Roots:
 Active uptake of mineral ions in the roots causes absorption of water by osmosis.
 Roots use protein pumps and active transport to absorb minerals from the soil ,which act as a solute of
water.
  Since solute concentrations in roots would be about 100 times higher than the ones in soil, water would
diffuse into the roots due to gradient difference, through osmosis. Ions can make contact with protein pumps
through diffusion or mass flow, when water carrying the ions moves drains through the soil.
 Some ions move very slowly within soil due to bonds they establish with the surface of soil particles. To
overcome this problem, plants have formed a relationship with fungus where the long, thread-like structure of
hyphae absorbs mineral phosphates in the soil and supplies it to roots, allowing plants to efficiently grow in
mineral-deficient soils.
 This mutualistic relationship is found between fungus and members of the heather family orchids and many
trees, as plants provide the fungus with sugars and nutrients for the minerals they obtain.
 Root hair cells have many mitochondria to produce ATP for active transport, as well as a large surface area.
 
Replacing Losses from Transpiration:
 Plants transport water from roots to leaves to replace losses from transpiration.
 The movement of water:
1. Water evaporated from plants through the stomata by transpiration is replaced from the xylem.
2. Transpiration-pull, cohesion and adhesion allows water to climb up the xylem.
3. Water moves from the soil into the roots by osmosis due to the active transport of minerals into roots.
4. Water travels from roots to the xylem through cell walls (apoplast pathway), and from the xylem to leaves
through the cytoplasm (symplast pathway).
 
Adaptations for Water Conservation:
 Adaptation of plants in deserts and in saline soils for water conservation.
 Xerophytes: plants adapted to growing in deserts and other dry habitats.
 Some xerophytes are ephemeral, having a very short life-cycle which is completed just after rainfall in
deserts when water is available. They then remain dormant as embryos in seeds until the following rainfall,
sometimes years after.
 Xerophytes can also be perennial, relying on a storage of water in specialized leaves, stems or roots.
 Most cacti are xerophytes that have:
1. Leaves reduced in size to the degree where they appear as spines.
2. Pleats in their stems that allow them to expand and contract in volume rapidly, as the stem stores water.
3. A very waxy and thick cuticle to prevent water evaporation.
4. Stomata that are more widely spaced than in normal plants.
5. Stomata often open at night in cacti as temperature is lower, reducing transpiration.
6. Crassulacean acid metabolism (C4 metabolism).
 Crassulacean acid metabolism (CAM): In the night, cacti absorb carbon and store it in the form of a four-
carbon compound, malic acid. In the morning, cacti release carbon dioxide from the malic acid they store at
night, performing photosynthesis even with their stomata closed.
 Cacti are classified as CAM plants.
 Many xerophytes have similar adaptations to cactus.
 Marram grass is a xerophyte that has:
1. Rolled leaves in order to create a closed environment that reduces water loss through evaporation.
2. Stomata within the rolled leaves that sit within the curls, making them less likely to open up and lose water.
3. Hairs within the rolled leaves to reduce air movement, once again cutting down water loss.
 Saline soils: soils with high concentrations of salts.
 Halophytes: plants that live in saline soils.
 Halophytes have several adaptations:
1. Leaves are reduced to small scaly structures or spines.
2. Leaves are shed when the water is scarce, while the stem becomes green and adopts heir function of
photosynthesis.
3. Water storage structures develop in the leaves.
4. Thick cuticles and a multiple-layered epidermis.
5. Sunken stomata.
6. Long roots which go in search of water.
7. Structures for removing salt build-up.
 
Drawing Xylem Vessels:
  Primary xylem vessels are visible in cross sections of young stems such as in young Helianthus.
 The primary wall of the xylem is permeable and thin, being unlignified.
 Secondary thickening of the wall is lignified and either annular or helical, allowing growth.
 When the plant is fully grown, a secondary, extensively lignified xylem is produced which is strong but
doesn't grow.
 Learn to draw.
 
 
Transport in the Phloem of Plants (9.2):
 
Translocation Occurs from Source to Sink:
 Phloem tissues are found throughout the plants in stems, roots and leaves.
 Phloem tissue is made of sieve tubes, made from specialized, column-arranged sieve tube cells, separated by
perforated walls called sieve plates.
 Sieve tube cells are closely associated with companion cells.
 Translocation: the transport of organic solutes in plants. The phloem is responsible for translocation.
 Phloem links parts of the plants that need certain nutrients to parts that have a surplus of it.
 Sources: locations where the phloem obtains the organic solutes to transport.
 Sinks: locations where the phloem drops organic solutes.
 Sources and sinks switch sometimes, so the phloem needs to be able to transport solutes in both directions,
and unlike blood vessels, it has no valves.
 Like blood vessels, the phloem uses pressure gradients for transport, and uses energy, making transport an
active process in it.
Sources Sinks
Mature green leaves (photosynthetic tissue) Roots that use cell respiration for growth or
absorption.
Green stems (photosynthetic tissue) Developing fruits (parts growing or developing
food stores).
Storage tissues in germinating seeds (storage Developing seeds (parts growing or developing
tissue) food stores).
Tap roots or tubers at the start of the growth Growing leaves (parts growing or developing food
season (storage tissue) stores).
  Developing tap roots or tubers (parts growing or
developing food stores).
 
Phloem Loading:
 Active transport is used to load organic compounds into phloem sieve tubes at the source.
 Sucrose is not directly metabolized by plants, and so is a good carbohydrate for transport as it wouldn't be
metabolized during the transport.
 Phloem loading: the mechanism by which plants bring sugars into the phloem.
 Apoplast route: the method of sugar transport where sugar enters the cell walls of companion and
sometimes sieve tube cells from mesophyll cells in significant amounts, after which a sugar transport protein
transports the sugar into the phloem.
 In the apoplast route:
1. The concentration gradient of sucrose is established by active transport. 
2. H+ ions are actively transported out of the companion cell from surrounding tissues using ATP as an energy
source. 
3. The build up of H+ flows down its concentration gradient through a co-transport protein with the energy
released is used to carry sucrose into the companion cell-sieve tube complex.
 Symplast route: the method of sugar transport where sugar travels between cells through connections called
plasmodesmata.
 Once it reaches the companion cell, sucrose is converted to an oligosaccharide to maintain its concentration
gradient.
 
Pressure and Water Potential Differences Play a Role in Translocation:
 Incompressibility of water allows transport by hydrostatic pressure gradients.
 The build up of sucrose and other carbohydrates draws water into the companion cell through osmosis.  
 Pressure builds up due to the combination of rigid cell walls and incompressibility of water, leading to water
flowing from the area of high pressure to an area of low pressure. 
 Sucrose is withdrawn from the phloem at the sink end, and is either: 
1. Utilized as an energy source for such processes as growth. 
2. Converted to starch. 
 In both cases, the loss of solute causes a reduction in osmotic pressure and the water that carried the solute
so the sink is then drawn back in to the transpiration stream in the xylem.
 
Phloem Sieve Tubes:
 The functions of the phloem include loading carbohydrates from sources, transporting them through long
distances, and unloading them at sinks.
 Unlike the vascular elements of the xylem, the elements of sieve tubes are living, but have reduced
cytoplasm quantities and no nucleus.
 One reason why sieve tube elements need to be living is to maintain the concentration gradient of sucrose
and organic molecules that they achieve through active transport.
 Sieve tube cells and companion cells share the same parent cell.
 Companion cells perform many of the genetic and metabolic functions of the sieve tube cells:
1. Increased number of mitochondria in companion cells allow it to support active transport.
2. The in-folding of companion cells' plasma membrane allows an increased phloem loading capacity in the
apoplastic route.
 Plasmodesmata connect companion and sieve tube cells and are larger between them than in other parts of
the plant in order to allow the transport of oligosaccharides and genetic elements.
 The accumulation of sucrose in companion-sieve tube cells requires the presence of active transport
proteins or enzymes to produce oligosaccharides.
 The rigid cell wall of sieve tube cells allows the establishment of the necessary pressure to achieve the flow
of phloem in the cell.
 Sieve plates are the remnants of cell walls that separate sieve tube cells.
 Sieve plates and the reduced cytoplasm of sieve tube cells means less resistance to the flow of phloem sap.
 
Experiments Using Aphid Stylets:
 Phloem sap is relatively nutrient-rich, and contains dissolved nutrients that do not need to be digested.
 The only animals to feed on phloem sap as the main part of their diet are aphids.
 Aphids penetrate the plant tissues to reach the phloem using mouth parts called stylets. The phloem sap
continues to flow into the stylet once it enters, into the aphid. The closer the stylet is to the sink, the slower
the flow of phloem sap out into the aphid.
 
Radioisotopes as Important Tools in Studying Translocation:
 Developments in scientific research follow improvements in apparatus: experimental methods for measuring
phloem transport rates using aphid stylets and radioactively-labelled carbon dioxide were only possible when
radioisotopes became available.
 Carbon-14 is an isotope of carbon that is radioactive.
 Radioactively-labelled carbon within carbon dioxide can be fixed by plants during photosynthesis, releasing
radiation that can be detected using film or radiation detectors.
 As the carbon is metabolized in the plant, it will be found in different molecules within it, meaning both its
formation and movement can be traced.
 The Geiger counter is a device that can be used to measure radiation levels in a plant.
 
Identifying Xylem and Phloem in Light Micrographs:
 Xylem cells are generally larger than phloem cells.
 Within one vascular bundle, phloem cells tend to be closer to the outside of the plant in stems and roots.
 
 
Growth in Plants (9.3):
 
Growth in Plants:
 Undifferentiated cells in the meristems of plants allow indeterminate growth.
 Determinate growth: growth where there is a defined juvenile or embryonic period, or growth stops when a
certain size is reached or a structure is fully formed.
 Indeterminate growth: growth where cells continue to divide indefinitely.
 Many plant cells, even fully specialized ones, have the capacity to generate full plants, being totipotent.
 Growth in plants is confined to regions known as meristems.
 Meristems are composed of undifferentiated cells undergoing active division.
 Apical meristems: primary meristems found at the tips of stems and roots.
 Many dicotyledonous plants develop lateral meristems.
 
Role of Mitosis in Stem Extension and Leaf Development:
 Mitosis and cell division in the shoot apex provide cells needed for extension of the stem and development
of leaves.
 Cells in meristems divide repeatedly through a short cycle of mitosis and cytokinesis.
 New cells absorb nutrients and water to grow in mass and volume.
 The root apical meristem is responsible for root growth.
 The shoot apical meristem provides needed cells for stem growth as well as the production of leaves and
flowers.
 In cell division in the shoot apical meristem, one cell remains there while the other becomes differentiated
as it is pushes away from the meristem.
 Meristems can give rise to other meristems, such as the protoderm, procambium, and ground meristem.
 Protoderm: a meristem responsible for epidermis growth.
 Procambium: a meristem responsible for vascular tissue growth.
 Ground meristem: a meristem responsible for pith growth.
 Chemical influences play a large role in determining the type of specialized cell and unspecialized cells give
rise to.
 Leaf primordia: young leaves produced at the sides of the shoot apical meristem, appearing as small bump.
 
Plant Hormones Affect Shoot Growth:
 Plant hormones control growth in the shoot apex.
 Hormone: a chemical message produced and released in one part of an organism to have an effect in
another part of the organism.
 Auxins: hormones that have a broad range of functions including initiating the growth of roots, influencing
the development of fruits and regulating leaf development.
 IAA: indole-3-acetic acid (IAA), the most abundant auxin in plants.
 IAA controls growth in the shoot apex, and promotes the elongation of cells in stems.
 IAA is synthesized in the apical meristem of the shoot and transported down the stem to stimulate growth.
 At high concentrations, IAA can inhibit growth.
 Axillary buds: shoots that form at the junction, or node, of the stem and the base of a leaf.
 Apical dominance: the limitation of axillary bud growth by auxin produced in the shoot apical meristem.
 The further an axillary bud is from the shoot apical meristem, the less likely its growth is to be inhibited by
auxin.
 Cytokinins: hormones produced in the roots which promote axillary bud growth.
 The relative ratio of cytokinins to auxins determines the growth and development of axillary buds.
 Gibberellins: a category of hormones that contributes to stem elongation.
 
Plant Tropisms:
 Plants respond to the environment by tropisms.
 The direction in which stems grow can be affected by 2 stimuli:
1. Light.
2. Gravity.
 Tropisms: directional growth responses to directional external stimuli.
 Phototropism: growth towards light.
 Gravitropism: growth in response to gravitational force.
  Stems grow with phototropism and anti-gravitropism.
 
Auxin Influences Gene Expression:
 Auxin influences cell growth rates by changing the pattern of gene expression.
 The first step in phototropism is the absorption of light by photoreceptors called phototropins, which are
proteins.
 When absorbing light in the right wavelength, the conformation of phototropins changes and they bind to
receptors within a cell which control the transcription of specific genes.
 PIN3 proteins: glycoproteins found in the plasma membrane of cells in the stem that transport auxin from
cell to cell.
 The genes involved in phototropism are thought to be ones coding for PIN3 proteins.
 
Intracellular Pumps:
 Auxin efflux pumps can set up concentration gradients of auxin in plant tissue.
 Phototropism is dependent on auxin.
 If phototropins in the tip detect a greater intensity of light on one side of the stem than the other, auxin is
transported laterally form the side with brighter light to the more shaded side.
 High concentration of auxin on the shadier side of the stem cause greater growth on the side, so the stem
grows in a curve towards the source of brighter light.
 More light will be received by the leaf with phototropism and it will be able to photosynthesize at a greater
rate.
 Gravitropism is dependent on auxin.
 The upward growth of shoots and the downward growth of roots occur in response to gravity.
 If a root is placed on its side, statoliths (cellular organelles) accumulate on the lower side of cells due to
gravity.
 The distribution of PIN3 transporter proteins that direct auxin transport to the bottom of the cells occurs.
 High concentrations of the auxin inhibit root cell elongations so the top of cells elongate at a higher rate than
the bottom cells causing the root to bend downward.
 Opposite pattern - In the shoot, auxin promotes elongation. In the root, auxin inhibits shoot elongation.
 
Micropropagation of Plants:
 Micropropagation is an in vitro procedure that produces large numbers of identical plants.
 Micropropagation depends on the totipotency of plant tissues, and a stock plant with a desirable feature is
often chosen.
 Explants: tissues from the stock plant that are sterilized and cut.
 For most applications, the least differentiated tissue of the explant, mostly meristems, is used for
micropropagation.
 The explant is placed in a sterilized growth media that includes plant hormones such as auxin and cytokinin.
 Callus: a mass of undifferentiated cells created by placing the explant tissue in the growth media.
 If the ratio of auxin to cytokinin in the growth media is more than 10:1, then it is called a rooting media and
the explant grows roots.
 If the ratio of auxin to cytokinin in the growth media is less than 1:10, then it is called a shoot media and
shoots develop.
 Once roots and shoots are developed, the cloned plant can be transferred to soil.
 
Micropropagation is Used for Rapid Bulking Up:
 Micropropagation techniques can be used to produce virus-free strains of plants.
 Viruses are transported in plants through vascular tissues and plasmodesmata.
 The apical meristem is often free of viruses.
 Micropropagation is faster and needs less area than other, traditional methods of production.
 The micropropagation of orchids allows for sustaining their population and using them commercially to
remove their threat of extinction.
 Orchid seeds are hard to germinate, and asexual reproduction is often more successful.
 Cryopreservation: the storing of micropropagated plantlets in liquid nitrogen, creating a seed bank.
 Ophrys lutea is a threatened orchid in Malta, and was collected form the wild, micropropagated, and
redistributed and kept as stock.
 
 
Reproduction in Plants (9.4):
 
Flowering and Gene Expression:
 Flowering involves a change in gene expression in the shoot apex.
 When a seed germinates, a young plant is formed that grows roots, stems and leaves (vegetative phase).
 Vegetative structure: roots, stems and leaves.
 The vegetative phase can last for weeks, months and years before the plant enters its reproductive phase to
produce flowers.
 The change from vegetative phase to reproductive phase occurs with the growth of meristems in the shoot
into flowers instead of leaves.
 Flowers: structures produced by the shoot apical meristem that allow for sexual reproduction, thereby
increasing variety.
 Flowers can be classified as short-day or long-day, the period of darkness playing a key role in their
formation. Temperature can also play a role.
 Light plays a role in the production of inhibitors or promoters of genes that control flowering.
 
Photoperiods and Flowering:
 The switch to flowering is a response to the length of light and dark periods in many plants.
 Long-day plants flower in the summer, when there are short nights.
 Short-day plants flower in the autumn, when there are long nights.
 Plants use a pigment in their leaves to measure night length, which is the phytochrome.
 Phytochromes exist in two forms:
1. Pr (phytochrome red): turns into Pfr when absorbing red light.
2. Pfr (phytochrome far red): turns into Pr when absorbing far red light.
 In normal sunlight, Pr is rapidly converted to Pfr, causing a lot of it to be available in the night.
 During the night, Pfr is gradually converted back to Pr.
 Pfr is the active phytochrome form.
 In long-day plants, enough Pfr remains at the end of the night to bind to the receptors that promote the
transcription of genes needed for flowering.
 In short-day plants, Pfr inhibits the receptors which promote the transcription of genes needed for
flowering. At the end of long nights, Pfr is very little in amount and fails to inhibit flowering.
 
Inducing Plants to Flower Out of Season:
 Flower forcing: a procedure designed to get flowers to bloom out of season or at specific times such as
holidays.
 Growers can manipulate the length of the days and nights to force flowering, by providing lighting, humidity
and nutrition.
 
Draw an Animal Pollinated Flower:
 Stamen: male reproductive system in flowers.
 Carpel/pistil: female reproductive system in flowers.
 The flower contains:
1. Filament (stamen).
2. Anther (stamen).
3. Stigma (carpel).
4. Style (carpel).
5. Ovary (carpel).
6. Petal.
7. Sepal.
8. Stem.
 
Mutualism Between Flowers and Pollinators:
 Most flowering plants use mutualistic relationships with pollinators in sexual reproduction.
 Sexual reproduction in flowers depends on the transfer of pollen from the stamen to the stigma.
  Pollen can be transported by wind, sometimes water, but mostly pollinators.
 Mutualism: a close association between organisms where they both benefit from the relationship.
 Pollinators get food from the nectar, while the plant gets its pollen transferred.
 
Pollination, Fertilization and Seed Dispersal:
 Success in plant reproduction depends on pollination, fertilization and seed dispersal.
 After pollination comes fertilization, where each pollen on the stigma extends a tube containing a male
gamete which goes through the style to reach the ovules inside the ovary.
 The fertilized ovule develops into a seed while the ovary develops into a fruit.
 Seed dispersal: the process by which seeds are transferred from the plant for reproduction.
 Seed dispersal reduces competition between the parent and offspring plants, as well as spreading the
species.
 The type of seed dispersal depends on the type of fruit (animals can eat it, it can attach to them through
hooks, or it can be winged to glide through).
 
Preserving Habitats as a Conservation Measure:
 Paradigm shifts: more than 85% of the world's 250,000 species of flowering plants depend on pollinators for
reproduction. This knowledge has led to protecting entire ecosystems rather than individual species.
 Traditionally, conservation methods took into regards only certain species or populations.
 The relation between pollinators and flowers shows the importance of protecting the ecosystem and
biological processes.
 Saguaro cacti act as perching and nesting sites for many animals.
 Once the saguaro fruit ripens, bats and other birds consume the fruits, dispersing the seeds by ingesting
then excreting them, noting that they are not digested.
 Cacti flowers bloom for only one evening per year, attracting bats and birds to their nectar, which enables
pollination for them.
 
The Structure of Seeds:
 Seed: a package containing an embryo plant and food reserves, all inside a protective seed coat.
 The seed contains:
1. Seed coat (testa).
2. Scar, where the seed was once attached to the ovary.
3. Micropyle, next to the scar.
4. Embryo root (radicle).
5. Embryo shoot (plumule).
6. One or two cotyledons, depending on whether the plant is monocotyledonous or dicotyledonous.
 
Germination Experiment Design:
 Germination: the early growth of a seed which involves the growth of the embryo shoot and root.
 Dormancy: the property of seeds where they do not directly germinate, which allows seed dispersal.
 In order to germinate, seeds need:
1. Water; Some seeds are dry and need hydration, while other contain a hormone which inhibits germination
and needs water to wash it away.
2. Oxygen, for aerobic respiration to grow and perform metabolic processes.
3. Warmth, in order to perform metabolic reactions.
 During germination, the plant hormone gibberellin is produced.
 Gibberellin stimulates mitosis and cell division in the embryo, as well as amylase production and breaking
down starch in food reserves into maltose. Other enzymes break down maltose into glucose or sucrose.
 Starch is immobile, while glucose and sucrose can move around in the seed, and are needed for cellular
growth.
 Most vegetable seeds germinate quickly, with only a short dormancy period.
 Some problems that prevent seeds to germinate:
1. The seed is too old.
2. The soil is not hydrated enough.
3. The temperature is too high or low.
4. The soil is waterlogged, preventing aerobic respiration.
Meiosis (10.1):
 
Chromosome Replication:
 Chromosomes replicate in interphase before meiosis.
 Meiosis follows a period of interphase with the cell cycle phases of G1, S and G2, like mitosis.
 During the S phase, DNA is replicated so that each chromosome consists of 2 sister chromatids.
 At the start of meiosis, the chromosomes supercoil to become more visible.
 Unlike in mitosis, synapsis occurs with the alignment of homologous chromosomes together.
 Tetrad: the combination of 2 homologous chromosomes, consisting of 4 chromatids.
 Synaptonemal complex: a protein-based structure formed between homologous chromosomes.
 
Exchange of Genetic Material:
 Crossing over: the exchange of DNA material between non-sister homologous chromatids.
 Chiasma (plural: chiasmata): the connection points at which non-sister homologous chromatids exchange
genetic information.
 Research suggests that chiasmata are essential for meiosis to occur successfully.
 
Explaining Discrepancies in Mendelian Ratios:
 Mendel's paper was published in 1866.
 Discrepancies appeared in Mendel's principle of independent assortment:
1. William Bateson and Punnett conducted crosses with sweet peas.
2. One of the parent plants had long pollen (LL) and purple flowers (PP), while the other had short pollen (ll)
and red flowers (pp).
3. As expected, the F1 had long pollen and purple flowers (LlPp).
4. The F2 generation of dihybrid cross had surprising results; instead of the 9:3:3:1 ratio, there were far more
offspring with the parental phenotypes seen in the P generation and much smaller numbers of the non-
parental phenotypes, known as recombinants.
 
New Combinations of Alleles:
 Crossing over produces new combinations of alleles on the chromosomes of haploid cells.
 New combinations of alleles can be produced due to different loci at crossing over.
 
Meiosis I:
 Homologous chromosomes separate in meiosis.
 There are a number of ways in which meiosis I is different from meiosis II:
1. Sister chromatids remain associated with each other.
2. The homologous chromosomes behave in a coordinated fashion in prophase.
3. Homologous chromosomes exchange DNA leading to genetic recombination.
4. Meiosis I is a reduction division in that it reduced the chromosome number by half.
 
Independent Assortment:
 Independent assortment of genes is due to the random orientation of pairs of homologous chromosomes in
meiosis I.
 Independent orientation explains that the orientation of one homologous pair of chromosomes is unrelated
to the others. Also, it is random to which pole every chromosome of a homologous pair moves.
 A heterozygote passes on one allele into each new cell produced in meiosis I. Each allele has a 50% chance to
move into each pole due to random orientation.
 The genotype AaBb has 4 possible products with an equal chance of being formed, each 25%:
1. AB.
2. Ab.
3. aB.
4. Ab.
 
Meiosis II;
 Sister chromatids separate in meiosis II.
  After meiosis I, the daughter cells enter meiosis II without going though interphase.
 Meiosis II is similar to mitosis in that the chromatids are separated into different poles.
 The sister chromatids separated in meiosis properties are unlikely to be identical due to crossing over.
 
 
Inheritance (10.2):
 
Segregation and Independent Assortment:
 Unlinked genes segregate independently as a result of meiosis.
 Segregation: the separation of the two alleles of every gene that occurs during meiosis.
 Independent assortment: the theory that the alleles of two genes pass into gametes without influencing
each other.
 The genes on a single chromosome are linked and so do not segregate independently, except for those far
apart on it.
 Crossing over occurs the most in genes separated the furthest, and can make it appear that the genes are
unlinked.
 
Punnett Squares for Dihybrid Traits:
 In dihybrid crosses, the inheritance of 2 genes is investigated together.
 Mendel crossed pure-breeding peas that had round yellow seeds with pure-breeding peas that had wrinkled
green seeds:
o When Mendel allowed the F1 plants to self-pollinate, they all had round yellow seeds, those alleles
being dominant.
o 4 different phenotypes appeared in the F2 generation:
o Round yellow: one of the original parental phenotypes.
o Round green: a new phenotype.
o Wrinkled yellow: another new phenotype.
o Wrinkled green: the other original parental phenotype.
o The phenotype ratio for such breeding is 9 yellow round: 3 green round: 3 yellow wrinkled: 1 green
wrinkled.
o The four possible genotypes of F1 hybrids with SsYy each have a 1/4 of occurring, since each allele
has a 1/2 chance of passing to a gamete (independent assortment):
o SY.
o Sy.
o sY.
o sy.
 Punnett square: a table that is used to systematically combine every possible combination of maternal allele
and paternal allele.
 Punnett squares directly show all possible genotypes, but phenotypes can also be concluded from them.
 To create a Punnett square:
1. Determine the genotypes of the parents.
2. Identify the different varieties of gametes the parents can produce. One copy of each gene must be present
in the gamete according to Mendel's principle of segregation.
3. Setup a Punnett grid, with as many rows as there are male gametes (sperms), and as many gamete as there
are female gametes (eggs).
4. Fill in the offspring genotypes.
5. Determine the genotype ratio for the predicted offspring.
6. Determine the phenotype ratio for the predicted offspring.
 

Pcr machine is used to diagnose malaria