A Unity and Diversity

Monday, 15 January 2024

8:12 PM
Life Functions A2.2.7
 Metabolism
o Undertake essential chemical reactions
 Reproduction
o Produce offspring, either sexually or asexually
 Sensitivity
o Responsive to internal and external stimuli
 Homeostasis
o Maintain a stable internal environment
 Excretion
o Produce waste
 Nutrition
o Exchange materials and gases with the environment
 Growth/movement
o Move and change shape or size

MR SHEN

Cell theory A2.1

 The cell is the smallest unit of life
 Cells only arise from pre-existing cells
 All living things are made up of cells

Cell structure
Plasma membrane Have an outer border to maintain an internal chemistry to the
exterior (homeostasis)

Genetic material Must contain coded instructions (DNA) that function to

control internal activities within a cell

ribosomes Must contain ribosomes in order to translate the cell's coded

instructions into functional elements

cytosol Must contain an internal fluid that functions as a medium for

all necessary metabolic processes

Atypical cell structure in eukaryotes

 Sieve tube elements
o Sieve elements that line the phloem in plants are interconnected by
plasmodesmata into supracellular assemblies that transverse the length of a
plant
 o These sieve elements also lack nuclei and have few organelles, relying on local
companion cells for survival
o Phloem sieve tube elements challenge the idea that multicellular structures
are composed of anatomically independent cells
 Red blood cells
o Red blood cells have no nucleus or mitochondria when they are mature (the
organelles are ejected to allow more haemoglobin to be stored)
o Without any genetic material, red blood cells cannot independently replicate
and new cells must be continually produced within the bone marrow
o Red blood cells challenge the traditional definition of a eukaryotic cell as they
lack critical structures needed for autonomous survival
 Striated muscle fibres
o Individual muscle cells fuse together to form long striated muscle fibres
o These fibres are surrounded by a continuous plasma membrane and possess
multiple nuclei
o Striated muscle fibres challenge the idea that all living things are comprised of
discrete cell units
 Aseptate Fungal Hyphae
o Fungi may have filamentous structures called hyphae, which are used for
nutrient absorption and growth
o Hyphal cells are typically separated by internal walls (septa), but some hyphae
are not partitioned and have a continuous cytoplasm (with multiple nuclei)
o Aseptate fungal hyphae challenge the idea that living structures are
composed of autonomous cells

Microscopes - developments in microscopy A2.2.2/3

 Optical or Light microscopes
 Electron microscopes

Light microscopy
Light microscopes can be used to view living specimens in their natural colours
 These microscopes use glass lenses to bend light in order to magnify images (extent
of magnification is determined by the lenses used)
The clarity of cellular sub-structures can be improved via the use of fluorescent labelling
 Synthetic dyes can be used to bind particular cellular compounds in order to resolve
specific structures
o (e.g. DAPI is a fluorescent dye that stains DNA)
 Immunofluorescence staining uses antibodies that are conjugated to fluorescent
probes to specifically target a cellular component of choice
Electron microscopy
Electron microscopes can generate images at a much higher magnification and resolution,
however cannot view living specimens in natural colour
 These microscopes use electromagnets to focus electrons and produce
monochromatic images (to which false colour may be applied)
There are two main types of electron microscopes that allow for different visual
representations of a biological specimen
 Transmission electron microscopes (TEMs) pass electrons through a specimen to
generate a cross-section image
 Scanning electron microscopes (SEMs) scatter electrons over a surface to differentiate
depth and map in 3D
Cryogenic electron microscopy involves freezing samples prior to viewing in order to
generate images of a comparable standard to X-ray crystallography
 This allows for the determination of molecular structures at near atomic resolution
without requiring the crystallisation of the specimen
 If the frozen specimen is cracked along a plane via freeze fracturing, then internal
cellular structures can be studied
 Freeze fracturing was used to demonstrate the presence of integral membrane
proteins within the plasma membrane

Calculating magnification
 Magnification = image size divided by actual size
In order to calculate magnification, both image size and actual size must be in the same units
 Metric conversions can be applied according to the following table:
Cell Types
Prokaryotic A2.2.5
 Single celled organisms with simple cell structure
o Do not posses any membrane-bound organelles
 Different shapes
o Rods (bacilli)
o Spheres (cocci)
o Spirals (spirilla)
o Commas (vibrio)
o Corkscrews (spirochetes)
 Two domains based on structure and genetics
o Bacteria
 Large and diverse range of organisms inc. pathogenic forms
o Archaea
Variety of extremophiles as well as those that exist in normal habitats
Structure
 Genetic material found in a region of the cytosol called the nucleoid (single DNA
strand called the genophore)
 May contain additional DNA molecules (plasmids) that can be exchanged via
bacterial conjugation (horizontal gene transfer)
 Ribosomes that are responsible for protein synthesis are characteristically small (70S)
 All possess a cell wall and may possess additional covering (slime capsule called
glycocalyx)
 May possess hair-like extensions called pili, that aid in adhesion (attachment pili) or
plasmid exchange (sex pili)
 Many possess several whip-like projections (flagella) that facilitate movement
Eukaryotic A2.2.6
 Organisms whose cells contain a nucleus and are compartmentalised by numerous
membrane-bound organelles
o Greater level of structural complexity
o Possibly evolved from prokaryotic via endosymbiosis
 Classified into kingdoms
o Animal
 No cell wall and undertake heterotrophic nutrition vie ingestion
o Plant
 Cell wall (made of cellulose) and undertake autotrophic nutrition via
photosynthesis
o Fungi
 Cell wall (made of chitin) and undertake heterotrophic nutrition via
absorption (saprotrophic)
o Protist
 Any eukaryotic organism that does not fit into the above criteria
Cell Structure
 Genetic material found in double-membraned nucleus
 Ribosomes within the cell that are responsible for protein synthesis comparatively
larger (80S)
 All share membrane bound organelles
o Mitochondria
o Endoplasmic reticulum
o Golgi apparatus
 o Vesicles
 Multicellular fungi form filamentous hyphae typically separated by internal walls
called septa

Exceptions A2.2.9
 Some cellular components not considered organelles
o Cells walls as they are extracellular
o Cytoskeletons and cytosol categorised as structural elements

Identifying Cells A2.2.8

 Different cell types categorised according to distinguished characteristics
o Prokaryotic vs eukaryotic
o Bacteria vs archaea
o Animal vs plant vs fungi

Prokaryotic vs Eukaryotic

Bacteria vs Archaea
Animal vs Plant vs Fungi

Viewing Cells A2.2.10

 Light microscopes possess low magnification and resolution, but view living
specimens in natural colours
o Eukaryotic cells larger than prokaryotic, however need staining to see more
than just nuclei and chloroplast

 Electron microscopes possess high magnification and resolution, but only view dead
specimens in monochrome (false colour often applied)
o Surfaces can be rendered via scanning electron microscopes
o Cross sections rendered via transmission electron microscopes
Drawing Cells A2.2.11
Prokaryotic
 Genophere (bacterial chromosome) drawn as a loop (prokaryotic DNA circular)
  Pili and flagella project from the cell wall (composed of peptidoglycan in bacteria)
 Ribosomes drawn as filled in dots (not empty) and labelled 70S for size
 Flagellum thicker and longer than pili
 Shape appropriate to the type of bacteria

Eukaryotic
Animals
 Nucleus is a double membraned structure with pores (any chromosomes are linear)
 ER network shown as connected membranes, golgi apparatus unconnected
 Ribosomes drawn as filled in dots and labelled 80S in size
 Mitochondria are sausage shaped and the inner membrane highly folded (into
cristae)
 Peroxisomes, lysosomes, and secretory vesicles should all look the same (except
labelling)
Plant
 Large central vacuole is included that occupies significant space
 Cell wall made of cellulose included as a thicker line external to the plasma
membrane
 Chloroplasts are double membraned structures with internal stacks of discs (grana)

Abiogenesis A2
Living organisms are self-sustaining, meaning they are able to maintain the conditions
needed to continue their existence
 These conditions include: metabolism, reproduction, sensitivity (responsiveness),
homeostasis, excretion, nutrition and growth (movement)
 According to the cell theory, the cell is the smallest unit capable of self-sustaining life
(they can undertake all the functions of life)
 Smaller units, such as viruses, are not considered living because they cannot carry out
all life functions independently
 Viruses lack metabolism and must rely on metabolic events in a host cell to generate
its component parts
 A virus can therefore not reproduce autonomously and must infect a cell in order to
replicate
Cells are highly complex structures that can currently only be produced via the division of
pre-existing cells
 However the first cells must have spontaneously arisen from non-living material
(abiogenesis)
This process is theorised to have occurred over four key stages:
 Catalysis: Simple organic molecules were synthesised from primordial inorganic
molecules
 Self-Assembly: More complex polymers were constructed from these simple organic
molecules
 Self-Replication: Certain polymers formed the capacity to be duplicated (enabling
inheritance)
 Compartmentalisation: These molecules became packaged into membranes with
unique internal chemistry
The theory of abiogenesis has been difficult for scientists to test for a number of reasons:
 The exact conditions on pre-biotic Earth no longer exist and cannot be replicated
under controlled settings
 The first protocells did not form fossils and so there is limited evidence on which to
base hypotheses

Organic Material
All cells and organisms are constructed from complex carbon-based macromolecules
called organic compounds
 Organic compounds can vary greatly in structure and diversity due to the chemical
properties of carbon (can form four covalent bonds)
The generation of organic compounds from inorganic sources is considered to be a
fundamental requirement in the initial formation of cells
 The large variety of organic compounds allows cells to undertake a greater range of
chemical processes needed to sustain life
The spontaneous formation of simple organic compounds required specific pre-biotic
conditions:
 A lack of free oxygen in the atmosphere meant there was no ozone, which resulted in
higher levels of ultraviolet light penetration
 Higher atmospheric concentrations of carbon dioxide and methane resulted in
significantly higher temperatures
These conditions no longer exist on Earth and hence the chemical processes required for
carbon compounds to form spontaneously do not now occur

Self-Replication
The capacity for certain organic compounds to self-replicate is considered to be a
fundamental requirement in the initial formation of cells
 This allows for chemical processes to be reproduced in successive cells as the
necessary organic compounds are effectively inherited
RNA is presumed to have been the first genetic material due to two key qualities:
 Self-replicate: RNA can form a complementary template sequence that can be used
to produce new identical molecules
 Act as a catalyst: RNA catalysts (ribozymes) are involved in peptide bond formation
and intron splicing in modern cells
RNA is the only molecule that is capable of both self-replication and catalytic functioning,
but has since been superseded:
 DNA, through its superior chemical stability (double helical structure), has taken over
as the data storage form
 Protein, through its greater variability (20 amino acids as opposed to 4 bases), has
taken over as the catalytic form
RNA remains as a transitional form between DNA and protein in modern cells, suggestive of
its multi-faceted origins
Protocell Formation
The production of simple organic molecules facilitated the spontaneous formation of
membranes (and hence the organisation of protocells)
 In water, non-polar fatty acids will arrange to form micelles as the hydrophobic tails
coalesce to avoid contact with the polar solution
 When polar organic monomers are produced, they will attract the hydrophilic
glycerol heads of the fatty acids and a spherical bilayer will form
This formation of membrane-bound containers creates a hydrophobic barrier that allows the
internal chemistry of the vesicle to differ from the exterior
 This ordered aggregation of non-living components (protocell) would eventually lead
to the development of the first cells

Role of Water
The presence of water is an essential requirement for the formation of life
 The polarity of water will cause non-polar lipids to spontaneously form lipid bilayers
when in solution
 The thermal properties of water will help to maintain a stable internal environment
needed for homeostasis
 Water will dissolve any polar or charged substance, making it an excellent medium
for metabolic reactions
 The assembly of complex organic molecules requires water as a reagent
(condensation polymerisation)
Water on Earth
When the Earth was forming, the materials involved in its accretion would have contained a
sizeable quantity of water vapour
 However, high temperatures would have prevented this water from condensing and
low gravity would have resulted in most of the vapour being lost to space
Consequently, the large bodies of water on Earth are hypothesised to have instead
originated from asteroids formed further from the Sun
 These asteroids formed at a distance from the Sun where the cooler temperatures
would have allowed the water to be frozen as ice
 When the asteroids collided with Earth, the planet had achieved sufficient mass (and
gravity) to retain the water and had cooled enough for it to condense
The presence of liquid water is an essential condition when searching for other habitable
planets with extraterrestrial lifeforms
 The Goldilocks zone is the range of distance from a star where the right temperatures
would exist for liquid water to exist on a planet
 The relevant distances will depend on the size and temperature of the star – the
habitable zone will be further away from hotter stars
 Very few planets discovered within a Goldilocks zone also possess a suitable mass or
atmosphere for liquid water to exist on the planetary surface
LUCA Evidence
All lifeforms on Earth share certain characteristics, suggesting that all extant organisms are
derived from a common source
 The last universal common ancestor (LUCA) is the most recent population from which
all organisms on Earth share a common descent
 The LUCA would represent the immediate antecessor of the three current domains of
life (bacteria, archaea and eukaryotes)
Evidence for the existence of a last universal common ancestor include the fact that:
 The genetic code is universal and all life shares a common mechanism of
transcription and translation
 Certain genes are broadly distributed across all cellular organisms (e.g. instructions
for DNA replication)
The LUCA does not represent the first cellular organism and it is probable that other
lifeforms coexisted at the time of the LUCA
 Due to horizontal gene transfer (e.g. viral integration), the genome of the LUCA is
likely representative an ancient community of organisms that evolved independently
but became extinct due to competition from the LUCA and its descendants
Because microbes do not typically leave discernable fossils, major uncertainties exist
regarding the dates of key events that led to the evolution of life on Earth
Scientists can use biochemical evidence or phylogenetic comparisons to estimate dates of
the first living cells and the LUCA
Biochemical Evidence
Biosignatures are the chemicals produced by cellular processes that provide evidence of past
or present life
 The earliest evidence of life dates to 3.7 billion years ago in the form of stromatolites
– a layer of sediment laid down by microbes

Phylogenetic Comparisons
Scientists can also compare the genome of different species in order to develop a timeline
for evolutionary divergence
 The more differences between the genomic sequences of two species, the longer the
time period since the two species shared a common ancestor

To establish the original genome of the LUCA, scientists searched for genes present in both
prokaryotic domains (bacteria and archaea)
 Genes that were not highly conserved within a domain were disregarded (these could
have been shared by horizontal gene transfer and not been present in the LUCA)
  This led to the identification of 355 genes that are proposed to have originated
directly from the LUCA

Molecular Clock
The specific timing of evolutionary divergence can be estimated from genomic comparisons
by using the molecular clock technique
 This technique uses the mutation rate of biomolecules (DNA, RNA or proteins) to
deduce the time since two or more life forms diverges
The molecular clock technique is predicated on the assumption that there is a direct
correlation between number of sequence differences and the time since two species
diverged
 Example: If a gene mutates at a rate of 1 bp per 100,000 years and two species have 6
differences in their gene sequences, then divergence occurred 600,000 years ago
There are a number of limitations with using the molecular clock technique to estimate dates
of evolutionary events:
 The mutation rate is not constant across all genes and all species
 Future mutations may reverse earlier mutations, obscuring the specific number of
mutations that have occurred
Based on phylogenetic comparisons and the molecular clock technique, the LUCA’s evolution
into archaea and bacteria could have occurred at any point between 2 to 4 billion years ago

Hydrothermal Vents
Current evidence suggests that the last universal common ancestor likely
existed in the vicinity of hydrothermal vents
 Hydrothermal vents can develop wherever a heat source comes into
close contact with fluid system from within the Earth’s crust, resulting
in the convective flow of fluid to the seafloor
 This fluid is rich in minerals that precipitate upon reaching the seafloor,
creating chimney-like structures or vents
Fossil Evidence
The precipitation of minerals from vent fluids also occurs on biological structures, resulting in
their subsequent mineralisation and preservation
 Fossilized evidence of bacteria have been discovered in ancient seafloor
hydrothermal vent precipitates that are dated as being ~3.7 billion years old
Genomic Evidence
Genomic analysis also supports the idea the last universal common ancestor developed in
close proximity to hydrothermal vents
 Genes proposed to belong to LUCA are involved in the use of molecular hydrogen as
an energy source (hydrothermal vents are rich in hydrogen)
 LUCA is also thought to have possessed a gene that is currently found in
extremophiles existing in high temperature environments (like hydrothermal vents)

Endosymbiosis
Eukaryotic cells are believed to have evolved via endosymbiosis – whereby one cell was
engulfed by another and became assimilated into its cellular structure
  Current evidence suggests that all eukaryotes evolved from a common unicellular
prokaryote that had a nucleus and reproduced sexually
 This prokaryotic ancestor engulfed another aerobic bacterium, which over time lost
its independent utility and developed into the mitochondria
 A subsequent internalisation of a photosynthetic cyanobacterium likely contributed
to the development of the chloroplast in plant cells
Evidence for Endosymbiosis
Mitochondria and chloroplasts are both organelles suggested to have arisen via
endosymbiosis
 These organelles are therefore expected to share characteristics with bacteria as a
consequence of their prokaryotic origins
Evidence that supports the extracellular origins of these organelles include:
 Membrane: They both have a double membrane (the outer membrane may have
been vesicular in origin
 Antibiotics: Both organelles display susceptibility to certain antibiotics (antibiotics
target prokaryotic features
 DNA: Mitochondria and chloroplast possess their own DNA, which is naked and
circular (like in prokaryotes
 Division: Both organelles divide by a process similar to binary fission (the bacterial
reproduction method
 Ribosomes: They both have 70S ribosomes, which are also found in prokaryotic cells

Multicellularity
Multicellular organisms are composed of multiple cells operating in unison to support the
total lifeforms
 All plant and animal species are multicellular, along with most fungi and several
species of eukaryotic algae
Multicellularity has evolved repeatedly and offers several distinct survival advantages
 Being multicellular allows an organism to exceed size limits normally imposed by
SA:Vol ratio limitations
 Multicellular organisms can have longer lifespans as the organism can survive the
death of an individual cell
 Multicellularity fosters complexity by allowing the differentiation of cell types within a
single organism
One challenge faced by multicellular organisms is the occurrence of cancer – whereby cells
fail to regulate their normal pattern of growth within the organism

Multicellullar organisms are capable of completing functions that unicellular organisms could
not undertake – this is due to the collective actions of individual cells combining to create
new synergistic effects
 These new functions are called emergent properties and arise as a consequence of
cell specialisation
In a multicellular organism, the differential expression of genes causes cells to become
specialised and develop unique functions
 The differing patterns of gene expression may be coordinated by extracellular signals
or triggered by changes in the environment
In multicellular organisms:
 Cells of the same type may be grouped together to form tissues
 The functional grouping of multiple tissues results in the formation of organs
 Organs may interact to form organ systems capable of carrying out specific body
functions
 Organ systems collectively carry out the life functions of the complete organism