BABS1201 Course Notes

1: Life
LO1: List the major elements of life
CHONPS
1. Carbon
2. Hydrogen
3. Oxygen
4. Nitrogen
5. Phosphorus
6. Sulfur

All elements are quite homogenous in their relative amounts across organisms e.g., a worm and
human have the same amount of carbon relative to nitrogen

LO2: Describe some properties of water that make it essential for life
• Water  many biomolecules assume shape due to physical + chemical properties of water,
water is the medium for most biochemical reactions, water is generally associated with life
• H2O = 2 H atoms covalently bound to 1 O atom
- O is more electronegative than H = polar molecule
- Water molecules interact via strong hydrogen bonds
• Cohesion – water molecules attract each other
• Adhesion – water molecules attract other substances e.g., glass
• Water tension – water molecules on/near the surface interact with water molecules
adjacent to/below the surface  H2O surface molecules form more H-bonds with adjacent
molecules compared to H2O molecules in the bulk
- This gives rise to surface tension  water on the surface acts like a film, hence, it is
harder to penetrate the surface of water
e.g., human lungs are coated by water. The lungs produce a surfactant that reduces the
surface tension in the lung  premature babies who haven’t developed this surfactant
have difficulty breathing
• Water = universal solvent, as it dissolves more substances than any other liquid  dissolves
substances with polar regions
- Fats are hydrophobic as they are non-polar
- Soaps have a hydrophobic and hydrophilic end  breaks up fat and oil droplets which
can be washed away in water
• Density of ice (solid H2O) < density of water (liquid H2O)  water expands and floats when it
freezes
- In ice, 1 H2O molecule is H-bonded to 4 H2O neighbours in a 3D crystal  H-bonds are
stable and don’t move + crystal is spacious = fewer H2O molecules per unit of volume
- In liquid water, H-bonds continuously break and reform + molecules constantly move
about in close proximity = more H2O molecules per unit of volume
- Floating ice insulates liquid water from cold air – benefits marine organisms in cold
environments
LO3: Describe how changes in pH affect living organisms
• Water = amphoteric  behaves as an acid and base
H2O ⇌ H+ + OH-
• pH = -log10[H+]
- Neutral = pH 7  [H+]=[OH-]=10-7M
- Acidic = pH <7  [H+] > 10-7M  more protons, fewer hydroxides
- Basic = pH >7  [H+] < 10-7M  fewer protons, more hydroxides
• Buffer  substance that minimises the impact of adding an acid/base to a system  mall
changes in pH can disrupt cellular processes
- pH of blood = 7.4  the limits of blood pH are 7-7.8, anything above or below can be
lethal
Respiration  CO2+ H2O ⇌ H2CO3 ⇌ H+ + HCO3-  carbonic acid buffer maintains the pH
of blood and small intestine. For example, decreasing the [H+] leads to more H2CO3
dissociating to re-establish a normal pH
• The body is consistently maintaining a stable pH
- Skeletal muscles can stop functioning during strenuous exercise due to a build-up of
lactic acid decreasing muscle pH.
o The conversion of glycogen to lactate generates ATP  blood lactate rises from 1.6-
8.3mM  ↑[H+] = ↓pH of blood from 7.42-7.24  acidosis; hence, pace cannot be
sustained for long periods) athletes can train their body to process larger
amounts of exercise; lactic acid build-up = acidosis in muscles
- Untreated diabetes can lead to a coma  ketone bodies are released in the absence of
glucose; excess ketone bodies = ketoacidosis (i.e., acidification of blood)
• Water acidification

CO2 dissolves in water to form H2CO3

H2CO3 forms H+ and HCO3-

 H+ decreases pH

H+ combines with CO32- forming more

HCO3-

A lack of CO32- means calcification

cannot occur

 Calcification is necessary for

aquatic organisms to build shells etc
 Acidification may lead to a
significant loss in biodiversity
2: Cells
LO1 Explain how the diversity of life is classified
• Estimated 10-100 million species on earth; 1.8 million species identified
• Initially, species were classified according to similarities in structures, functions, and other
obvious features. Currently, species are classified according to similarities in their nucleic
acid composition – 16s rRNA codes for the 16s ribosome and is used to classify organisms
• Species have a two-part name  genus species e.g., Homo sapiens, Staphylococcus aureus

Domains of life  fully classified due to presence of rRNA in all living organisms
• Bacteria
- Have a range of morphologies (sizes and shapes)
- Most have a cell wall that can be classified as gram +ve or gram -ve
- Tend to have other features e.g., flagella for motility, or ability to produce endospores
(endospores are a dormant, non-reproductive structure produced by bacteria – allows
cell to remain dormant for extended period)
- Vary in their metabolism e.g., can be aerobic, anerobic, photosynthetic etc
• Archaea
- Similar size to bacteria (1μm-10 μm), but vary in shape
- Often associated with extreme environments e.g., methanogens, thermophiles,
haloarchaea
- Found in humans; non-pathogenic
- Share some traits with eukaryotes e.g., protein synthesis, processing of DNA
• Eukaryotes
- Kingdoms: animal, plants, fungi
- Protists
• Prokaryotes – informal term describing non-eukaryotes
- Initially was a domain that encompassed both archaea and bacteria
- Similarities between bacteria and archaea  size, cell membrane, lack membrane
bound organelles
- Differences between bacteria and archaea  cell membrane composition, process of
DNA replication
LO2 Define what a cell is
• Cell – smallest unit of organisation that can perform all activities essential for life. The
actions of organisms are based on the activities of cells
- Simplest collection of matter that can be considered a living entity
• Multicellular organisms – different cells with different roles e.g., muscle cells, nerve cells
LO3 List some characteristics of life
• Characteristics of life  reproduction, growth/development, response to environment (inc.
adaptation), metabolise to use and generate energy
• Viruses – nucleic acid, usually encased in a protein or lipid. Viruses infect a host by inserting
their genome into the host’s genome
- Can adapt to environment – characteristic of life …
- Simpler and smaller than cells, rely on a host to reproduce, cannot carry out metabolism
outside their host  they are not living
• Prion – misfolded version of a protein. The prion recognises similar proteins in their host,
and cause their proteins to misfold in a similar way  misfolded proteins = dysfunctional
- Prions cannot replicate themselves  they are not living
LO4 Explain the fundamental differences between prokaryotes and eukaryotes
• Eukaryotic cells
- Have membrane bound organelles, the largest of which is usually the nucleus
• Prokaryotic cells
- Mycoplasma is the smallest bacteria with a 0.1-1 μm diameter
- Contain at least one chromosome  may carry additional chromosomal DNA for
different features
• The factors that limit the minimum and maximum size of a cell
- Minimum – membrane needs to envelope DNA, and there needs to be sufficient
cytoplasmic space for metabolic activities
- Maximum – SA needs to be large enough to effectively take up nutrients

Eukaryotic Cells Prokaryotic Cells

Differences  Have membrane bound organelles  Lack membrane bound
 Chromosomal DNA contained in double organelles
membraned nucleus Contain a single chromosome
 Typically larger and more complex than concentrated in the nucleoid
prokaryotes region
 10-100 μm in diameter  Typically smaller and simpler
 Cytoplasm includes cytosol and organelles; than eukaryotes
doesn’t include nucleus 1-5 μm in diameter.
Similarities Plasma membrane – selective barrier that surrounds the cytosol
Genetic material – both cells have DNA/RNA
Ribosomes
 Organelles
Ribosomes (not technically an organelle) o Site of protein synthesis – mRNA is
e.g., the pancreas synthesises digestive translated into a polypeptide
enzymes, so it contains millions of ribosomes o Made up of ribosomal RNA (rRNA) and
protein
o Not surrounded by a membrane (not
considered an organelle)
o Can exist freely in the cytosol, or can be
bound to the rough endoplasmic reticulum
Plasma membrane o Structure separating intracellular space
from extracellular space
o Semi-permeable – controls movement of
substances into and out of the cell
o Comprised of a phospholipid bilayer
Mitochondria o Convert energy from one form to another
via respiration
Chloroplasts o Convert light energy to ATP via
photosynthesis

LO5 Describe the concept of endosymbiosis

Chloroplasts
• Chloroplast – organelle found in plants and algae  site of photosynthesis
• Contains DNA and ribosomes unique to the organelle i.e., the chloroplast contains its own
genetic material
• Outer membrane – relatively permeable compared to inner membrane
• Inner membrane – selectively permeable
• Grana = stacked thylakoid membranes in the stroma
Mitochondria
• Present in almost all eukaryotic cells  site of respiration
• The number of mitochondria in a cell
depends on how aerobically
metabolically active the cell is
• Outer membrane – relatively
permeable compared to inner
membrane
• Inner membrane – selectively
permeable. Contains proteins that
assist with ATP synthesis
• Cristae – folded to increase its surface
area  contained within the inner
mitochondrial membrane
• Matrix includes mitochondrial DNA
and ribosomes
• Mitochondria contains its own genetic
material

Endosymbiosis

• Endosymbiotic theory –
ancestors of eukaryotes
took up oxygen using, non-
photosynthetic prokaryotic
cells  cells existed in
symbiosis and merged over
time to form a single
organism
• Evidence suggests that
chloroplasts developed from
endocytosis of
cyanobacteria
(photosynthetic bacteria)
• Evidence for theory:
mitochondria and
chloroplasts contain their
own DNA, mitochondria and
chloroplasts replicate in a
similar way to prokaryotes,
mitochondria and
chloroplasts contain an
inner and outer membrane
LO6 Identify characteristic structures of eukaryotic and bacterial cells, and describe their
basic functions
Prokaryotes – bacteria and archaea; lack membrane bound organelles

Eukaryotes- membrane bound organelles; compartmentalised = diverse environments within cell

Animal Cell
Plant cell

LO7 Describe the endomembrane system

• Endomembrane system – a group of membranes in eukaryotic cells that work to modify,
package, and transport and proteins  regulate protein traffic, perform metabolic functions
• Membranes in the endomembrane system interact by physical contact or vesicle
transformation
- Vesicle – parts of membrane bud off and form a circular membrane. Vesicles can
interact with other components of the cell by coming into contact with them and
engulfing them. Vesicles surround different substances in cells e.g., proteins
• Endoplasmic reticulum (ER)
- Smooth ER – outer surface that lacks ribosomes. Plays a diverse role in metabolic
processes e.g., drug detoxification, lipid synthesis, Ca2+ storage
- Rough ER – outer surface associated with ribosomes.
o As the polypeptide chain is extended from the ribosome, it is threaded into the ER
lumen through a pore  if a protein is unstable in the cytosol, it can pass through a
pore into a more suitable environment adjacent to the ER
o The finished protein is compartmentalised from the rest of the cell due to the ER
o The finished protein is transported via vesicles – membrane of ER buds off,
encapsulates protein and transports protein
o Rough ER can add membrane proteins to its membrane, and it can synthesise
phospholipids for the cell membrane
• Golgi apparatus – site where proteins are modified, stored, and transported onwards
- Golgi consists of cisternae – flattened membrane sacs with directionality  molecules
pass through the Golgi in a particular direction
- After leaving the ER, vesicles may travel to the Golgi apparatus for modification e.g.,
glycosylation (addition of a CHO) of protein to form a glycoprotein  modification may
occur in several stages
- After modification, new vesicles form and the protein travels to its target destination
• Lysosome – organelle that breaks down macromolecules into monomers that can be used by
the cell  removes ‘junk’ from the cell
- Membrane of lysosome segregates an acidic environment that contains enzymes which
hydrolyse macromolecules
- Phagocytosis – cell eating  lysosome engulfs and hydrolyses materials taken into the
cell e.g., macromolecules, bacteria, viral components

- Autophagy – cell cleaning  lysosome breaks down damaged intracellular materials

e.g., damaged organelles

• Vacuoles – type of vesicle derived from the ER and Golgi apparatus. The environment of a
vacuole depends on its function and is different to the cytosol
- Unicellular eukaryotes in freshwater may have contractile vacuoles that remove water
to maintain ion concentrations
- The central vacuole of plant cells acts as an inorganic ion repository
- Vacuoles take up a large volume of plant cells
- Some vacuoles take up gases  allows cell to float in water
LO8 List the main components of the cytoskeleton and briefly describe their roles in the cell
• Cytoskeleton – network of dynamic fibres that extend throughout the cytoplasm of
eukaryotic cells  cytoskeleton provides support and motility for the cell
• Bacteria have a similar network, but the components differ
• The 3 fibres of the cytoskeleton are: microtubules, microfilaments, and intermediate
filaments
• Microtubules – hollow tubes comprised of two types
of globular proteins
- Give the cell its shape
- Provide tracks for organelles to move along
- Specialised microtubules allow cilia (hair-like
structures for movement) and flagella (tail of a
cell) to function in cell motion e.g., sperm
• Microfilaments (a.k.a. actin filaments) – twisted double chains of globular actin proteins
- Provide the cell with shape
- Provide a pulling force in the cell  actin filaments can be
polymerised (added to) or depolymerised (taken away) 
allows filaments to extend or pull back within a cell i.e.,
expand/contract in a cell
- Microfilaments make up the core of microvilli, play a role in
muscle contraction, are involved in cytoplasmic streaming in
plants (movement of the cytoplasm), and allow amoeba and
some white blood cells to move via contractions
• Intermediate filaments – diverse group of filaments made up of various fibrous proteins that
are coiled into cables  present in only some animals including vertebrates
- Example: keratin (structural protein) filaments are present in dead cells on the outer
layer of skin. Defective keratin in the skin tissue is associated with disorders where the
skin cannot withstand force i.e., the skin breaks when force is applied due to weak
structural components
3: Macromolecules
LO1 Provide a broad definition of the term “macromolecule”.
• Macromolecule – large polymer that is comprised of monomers held together by covalent
bonds
• Polymer – long, chain-like structure comprised of similar/identical smaller molecules held
together by covalent bonds
• Monomer – small molecules that make up a polymer

LO2 Explain the way in which macromolecules are generally synthesised and broken down by
organisms.
Synthesis  dehydration (loss of H2O molecule) to form a new covalent bond

Breakdown (hydrolysis)  addition of water across a covalent bond to split the bond

Synthesis and hydrolysis are catalysed by enzymes

LO3 Briefly describe the general structural features of each of the four major classes of
macromolecules.
Carbohydrates
• Monomer = monosaccharide  comprised of C, H, and O (CH2O)
• Bonds between monosaccharides = glycosidic bonds
• Monosaccharides can either be an aldose or ketose depending on the location of the
carbonyl group
- Stereoisomers of monosaccharides exist e.g., glucose and galactose enantiomers
• Carbohydrates include:
- Monosaccharides – 1 molecule e.g., glucose (C6H12O6)
- Disaccharides – 2 monosaccharides bound by a glycosidic bond e.g., maltose is
comprised of two glucose molecules, sucrose is comprised of one glucose and one
fructose molecule, lactose is comprised of one glucose and one galactose molecule
- Polysaccharides – polymer comprised of several (up to thousands) of monosaccharides
joined by glycosidic bonds e.g., starch
Lipids
• Lipids are macromolecules
but are not polymers
• Triacylglycerol (TAG) – 3
fatty acid molecules + 1
glycerol molecule joined by
an ester bond (dehydration
between each molecule to form new bond)
- Fatty acids vary in length and saturation (no. of double bonds)
o Saturated – fatty acids (and fats) have no double bonds in HC chain – C bound to
max. no. of H atoms
o Unsaturated – fatty acids (and fats) have 1 or more double bonds in HC chain –
double bonds can cause kinks in molecule
Proteins
• Monomer = amino acid
• Bonds between amino acids = peptide bond
• Polypeptide = several amino acids joined together by peptide bonds
• Protein = 1+ polypeptides folded into a specific 3D structure  proteins are biologically
active polypeptides
• Amino acids have a
common structure:
- α-carbon (central
carbon)
- Amino group (NH3+)
- Carboxyl group (COO-)
- Hydrogen atom
- Variable side chain (R) –
differentiates amino
acids
- There are 20 amino acids that make up 1000s of proteins
o Side chains can be polar, non-polar, or ionic
Non-polar
o Valine, leucine, and isoleucine – broken down in muscles during intense exercise
o Methionine – first amino acid in a polypeptide – encoded for by start codon
o Proline – helix breaker – prevents proteins from forming certain structures
Polar
o Cysteine – 2x cysteine molecules can form strong disulphide bonds
Ionic
o Aspartic acid & glutamic acid – proton donors
o Lysine, arginine & histidine – proton acceptors
 • Proteins are synthesised via enzyme catalysed dehydration
- Amino acids are linked together by peptide bonds  polypeptide chain
- Direction of synthesis is from the amino end (N-terminus, start of chain) to the carboxyl
end (C-terminus, end of chain)
- Bonds are formed by a dehydration reaction between the carboxyl group of one amino
acid and the amino group of the next  amide linkage (peptide bond)
- Proteins – backbone of peptide bonds; side chains project from backbone
- Protein adopts its shape from the folding of a polypeptide chain  specific 3D structure
determines the function of the protein
• Proteins can adopt 4 different structures
1. Primary structure – sequence of amino acids  just a polypeptide chain
2. Secondary structure – conformation adopted by local regions of polypeptide chains. The
structure is stabilised by H-bonding between C=O and N-H groups of backbone
- α-helix – coiled polypeptide chain
- β-strand/sheets – parallel or
antiparallel polypeptide sheets
o Parallel sheets – connected by
loops and angled H-bonds. Each
sheet runs in the same direction
CN or NC
o Anti-parallel sheets – connected by
turns and perpendicular H-bonds.
Each sheet runs in the opposite
direction i.e., CN and NC
3. Tertiary structure – 3D shape of a single polypeptide chain, stabilised by interactions
between the side chains of amino acids
- Stabilised by weak interactions including hydrophobic interactions, H-bonds, and
ionic/electrostatic bonds  individual interactions are weak, cumulative effect is strong
- Disulphide bridges (covalent bond) can form between 2x cysteine side chains
- Fibrous tertiary structure – mostly comprised of α-helices, elongated/rod-like structure,
often insoluble in water
- Globular tertiary structure – compact, complex structures, can contain α-helices and β-
sheets, have a hydrophobic core and hydrophilic surface
4. Quaternary structure – protein consisting of >1 polypeptide chain, each chain in the
structure is called a sub-unit
- Sub-units stabilised by non-covalent interactions e.g., H-bonds

Denaturation occurs when conditions e.g., heat. pH, disrupt a protein’s structure = loss of function
Nucleic Acids
• Monomer = nucleotides
• Bonds between nucleotides = phosphodiester
• Nucleic acids initially discovered in 1868 by Friedrich Miescher – termed nuclein
• Early research sought to differentiate whether proteins or DNA were genetic material
- Proteins = highly complex, and only 20 monomers, DNA = regular structure, only 4
monomers
- Hershey and Chase in 1953 used bacteriophage T2 (bacterial virus) to demonstrate DNA
is genetic material  when virus infects E.coli, something heredity is passed on
o Phages contain protein (high sulfur content) and nucleic acids (high phosphorus
content)
o Phage was tagged with radioactive sulfur and radioactive phosphorus and
infected cell  infected cell was centrifuged; no sulfur was present in cell after
centrifugation, phosphorus was present in cell after centrifugation
o Demonstrated DNA = component transferred to cell  DNA = genetic material
• DNA and RNA are both nucleic acids
- DNA contains Thymine, RNA contains Uracil
- DNA contains deoxyribose (H on C2), RNA contains ribose (OH on C2)
- DNA is usually double stranded, RNA is usually single stranded
• Sugar in nucleic acids
- DNA = deoxyribose
- RNA = ribose
• Nucleotides
- Nucleotide = phosphate bound to 5’ C of
sugar, nitrogenous base bound to 1’ C
- Adenine and guanine are purines (double ring), thymine and cytosine are pyrimidines
(single ring)
DNA structure:
• Watson and Crick  double helix structure of DNA using X-ray diffraction data
• DNA sugar-phosphate backbone – held together by phosphodiester bonds. DNA is negatively
charged due to presence of PO43- in backbone
• 2H-bonds between A&T, 3H-bonds between C&G
- Amount of C/G and A/T varies across organisms. In all organisms [A]=[T], [C]=[G]
- DNA w/ a high G/C content has a higher stability compared to DNA w/ a high A/T
content due to diff. no of H-bonds
• DNA strands are anti-parallel  one strand runs 5’3’, other strand runs 3’5’

• DNA strands are complementary  during DNA replication, the new strand synthesised is
anti-parallel with respect to the template strand
For example:
Template: 5’-ATG GTA TAT CTC-3’
Complement: 3’-TAC CAT ATA GAG-5’  written as 5’-GAG ATA TAC CAT-3’

Template: 5’-UGA CUU ACC GAU-3’

Complement: 3’-ACU GAA UGG CUA-5’  written as 5’-AUC GGU AAG UCA-3’
LO4 List some examples of members belonging to each of the four major classes of
macromolecules.
Carbohydrates
• Starch – stored in plant cells.
- There are two types:
1. Amylose – linear structure and
2. Amylopectin – branched structure
• Glycogen – branched structure
• Cellulose – found in cell wall of plant  glucose forms a matrix with cross-links to provide
rigidity to the structure
• Chitin – found in cell wall of fungi and exoskeleton of arthropods

Lipids
• Phospholipids – contain a hydrophilic (polar) phosphate head and a hydrophobic (non-polar)
lipid tail
- Similar structure to TAG, except phosphate and a polar group (e.g., choline) replace one
of the three fatty acid chain
- Make up cell membrane  necessary for cell structure

• Steroids – lipid consisting of four carbon rings

fused together with chemical groups
attached
- Cholesterol – type of steroid that is found
in animal cell membranes and acts as a
precursor for the synthesis of other
steroids e.g., hormones
Proteins
• Structural – collagen (tendons and ligaments), keratin (hair and nails), fibroin (spider silk),
fibrin (blood clots)
• Enzymatic – sucrase, lactase, amylase
• Defensive – antibodies
• Transport – haemoglobin (O2 transport), albumin (substance transport e.g., vitamins)
• Hormones – insulin, cortisol
• Motor – actin, myosin
• Storage – casein (found in milk, source of amino acids for baby mammals), ovalbumin (found
in egg white, amino acid source for developing embryo)
• Receptor – photoreceptors (help with vision)
LO5 Describe some of the key functions of members belonging to each of the four major
classes of macromolecules.
Carbohydrates
• Storage polysaccharides  stored energy that can be later accessed via hydrolysis
For example:
- Starch – polymer of glucose  stored by plants as granules in cellular structures; stored
energy can be accessed when needed via hydrolysis
- Glycogen – branched polymer of glucose  stored by animals primarily in liver and
muscle cells; hydrolysis of glycogen releases glucose during ↑ demand for energy- not
sustainable energy source; quickly depleted
• Structural polysaccharides  carbohydrates that provide structure for cells
For example:
- Cellulose – polymer of glucose – major component of plant cell walls
- Chitin – polymer of glucose w/ nitrogen groups – found in exoskeleton of arthropods
(e.g., insects, spiders, crustaceans etc.), found in cell wall of fungi
Lipids
• Energy storage and transport – fats e.g., triacylglycerols (TAGs/ triglycerides) – main form of
fat in human diet.
- In excess, fats are broken down, resynthesised, and stored in adipose tissue – can be
used for energy in the future
• Structure – phospholipids (make up the cell membrane), sterols
• Chemical messengers – steroids (type of hormone derived from cholesterol), glycolipids
(lipid with CHO portion)
• Photoreceptors e.g., carotenoids – lipid soluble vitamins that are necessary for
photoreceptors to function
• Coverings – waxes e.g., the waxy outer layer on leaves
Proteins
• Structural – support
• Enzymatic – selective acceleration of chemical rxns
• Defensive – protection against disease
• Transport – carry substances around the body
• Hormones – coordination of organism’s activities
• Motor – movement
• Storage – amino acid storage
• Receptor – allow cells to respond to chemical stimuli
Nucleic Acids
• DNA = primary form of genetic material that can be inherited – comprised of chromosomes
and is mostly contained in the nuclei
- DNA can also be found in the mitochondria and chloroplast – organelles contain their
own genome
- Mitochondrial DNA – only inherited from mother as mitochondria is inherited from ova
• DNA – encodes for proteins – polypeptides synthesised from genes
• DNA is organised intro chromosomes – each chromosome = 1 DNA molecule. DNA in nuclei
exists in the form of chromatin  chromatin = DNA-protein complex
- Nucleosomes - DNA double helix is coiled around histones  ‘beads on string’
appearance – initial condensation of DNA
- Chromatin fibre – nucleosomes are organised into a series of loops
- Chromatids – further compaction of chromatin fibre into a dense structure around non-
histone scaffold proteins
- Chromosome – chromatin (2x chromatids) loops are wrapped around each other

• Some viruses contain RNA as genetic material – can be single or double stranded
• Several types of RNA exist with different functions:
- mRNA – interacts with ribosomes to ensure a specific protein is translated
- tRNA – ensures a specific amino acid is incorporated into a protein by the ribosome
- Other RNA molecules modulate gene expression and can have catalytic activity
4: Cell integrity and transport
LO1 To describe the structure of cell membranes and their function in cell integrity.
• Cell integrity – defined by integrity of the cell membrane
• Cell membrane – encapsulates cell and creates a division between the intracellular and
extracellular environment  selectively-permeable – lets some molecules but not other
across the membrane
• Structure of cell membrane  phospholipid bilayer with a hydrophobic head and
hydrophobic table

• Most membranes contain amphipathic proteins – hydrophilic portion protrudes out of

membrane, hydrophobic portion contained in cell membrane
• Fluid mosaic model – describes how molecules are spatially arranged in the membrane
- Proteins are not randomly located e.g., they may group together
- Fluidity – rapid movement of lipids and proteins laterally in the plane of the membrane
• Membrane has sidedness – asymmetrical distribution of proteins, CHO, and lipids on each
side
- The position of the protein domains relative to the membrane is fixed after protein is
inserted in the membrane
- Membrane has a distinct cytoplasmic and extracellular face
- Extracellular face is topologically equivalent to the inside face of the cell, ER, Golgi,
lysosome and vesicle membranes
- Proteins can move laterally but cannot flip between sides of the membrane 
energetically unfavourable due to interaction of hydrophilic/hydrophobic regions
o Experimental evidence for lateral movement  proteins are tagged with
fluorescent green dye and are photobleached by a laser (lose colour) – recovery of
colour in photobleached regions indicates movement of proteins
o Lateral movement of proteins is slower in lipid rafts (small, concentrated regions of
cholesterol in membrane)  reduced movement is necessary for proteins to
transmit signals from the intra to extracellular space, hence lipid rafts are also
called signalling platforms)
o Lateral movement of proteins can be stopped by anchorage to the cytoskeleton
LO2 To describe the different components of the cell membrane that are important in
maintaining cell integrity.
• Membrane components:
- Proteins: integral
membrane proteins,
peripheral membrane
proteins
- Lipids: cholesterol,
phospholipids
- CHO: glycoproteins,
glycolipids  allows
cells to be recognised
by other cells/proteins
- Cytoskeleton
• Phospholipid bilayer is a permeability barrier to most molecules  some molecules can pass
through the membrane with ease, others cannot  membrane maintains the integrity of
the cell by controlling molecular ‘traffic’
- Hydrophobic molecules dissolve in hydrophobic core and diffuse across membrane
- Small molecules e.g., O2, CO2, and H2O will cross the membrane via diffusion
- Ionised, polar, and large molecules will not cross membranes unless a transporter is
present
• Membrane proteins maintain cell integrity  help maintain the mechanical flexibility and
durability of cells e.g., RBCs can sustain substantial mechanical forces as the proteins in the
membrane make the cell flexible, deformable, and durable.
LO3 To explain the non-selective diffusion of some small molecules across cell membranes
and osmosis.
Diffusion – movement of a solute from an area of high to low concentration  passive as no energy
is required & non-specific
• A difference in concentration between the two sides of a cell means that particles will move
down a concentration gradient until equilibrium is reached
Osmosis – special type of diffusion involving the movement of water down a concentration gradient
• Hypotonic solution – [solute] in cell > [solute]
outside cell  water moves into cell
- Animals have no cell wall, so an increase in
volume can result in lysis
- Plant cells have a cell wall, and require a
hypotonic environment
• Isotonic solution – [solute] in cell = [solute]
outside cell  no movement of water
- Animals have no cell wall, so they require
an isotonic environment to maintain a
stable cell volume
- Plant cells can become flaccid in an isotonic
environment – unfavourable
• Hypertonic solution – [solute] in cell < [solute] outside cell  water moves out of cell
- Animal and plant cells may shrivel/plasmolyse in a hypertonic solutions(dehydrate) –
may be fatal
LO4 To explain the mechanisms by which small molecules may be selectively transported in
and out of cells.
Facilitated diffusion
• Transport proteins facilitate the diffusion of molecules across the membrane – driven by a
concentration gradient
• Channels – allow for direct passage from one side of the membrane to the other  allows
cell to take up and retain the molecules it wants and exclude what is unwanted  integral
membrane proteins
- Corridor for specific ions or molecules to cross the membrane
- Water can only slowly diffuse across the membrane, due to its polarity  aquaporins
are the specific channel proteins for water
- Gated channels – may be opened or closed in response to a stimulus e.g., the binding of
a specific molecule  seen in neurotransmitter receptors in the brain

• Carrier – bind the solute on one side of the membrane, which produces a conformational
change in the protein, and moves the solute across the membrane  integral membrane
proteins
- Alternates between two shapes  carries solute across membrane during shape change
- Transports solute in direction depending on concentration gradient
- Carriers have specificity – like binding sites in enzymes
- Transport through carriers (transporters) is slower than through channels
- E.g., glucose transport in mammalian epithelial cells

• The ion concentrations inside and outside a cell can differ  concentration gradients
disappear with time if they are not maintained  conc. gradients are maintained by active
transport against the gradient
• Active transport – pump a solute across a membrane against its concentration gradient 
requires energy  carried out by specific transporters
 • Transport across a membrane is directional  in active transport energy released by ATP
hydrolysis allows transport against a concentration gradient
• Different types of active transport exist:
1. Active transport – transport molecule in one direction e.g., proton pump in animals
- Proton pump actively transports H+ from intra to extracellular space
- ATP is used to power the translocation of H+
- Energy is stored by generating voltage across the membrane  the voltage and [H+] can
be used to drive other processes

2. Active cotransport – transport two molecules in one direction e.g., proton pump in
plants
- Proton pump actively transports H+ molecules across the cell membrane into
extracellular space
- H+ returns to the cytosol of the cell down a concentration gradient through the sucrose-
H+ cotransporter
- The return of H+ to the cytosol promotes sucrose uptake  indirect active transport of
sucrose

3. Active exchange transport – transport two molecules in opposite directions

**In higher animals, macromolecules are hydrolysed into monomers by enzymes in the digestive
tract  monomers (e.g., glucose) are taken up by cells in the lining of the small intestine  uses a
variety of passive and active transport mechanisms
LO5 To describe the concept of a membrane potential arising from ionic imbalances across
cell membranes.
• Membrane potential – voltage different across a membrane  voltage is created by
differences in the distribution of positive and negative ions
• All cells have a voltage difference across their plasma membrane due to an uneven
distribution of cations and anions
• Cytoplasm is -ve compared to extracellular fluid  membrane potential  favours passive
transport of cations into the cell and anions out of the cell
• Diffusion of ions is influenced by an electrochemical gradient – electrical forces (membrane
potential) and chemical forces (ion concentration)
• Electrochemical potential can drive other processes – affects trafficking of all charged
molecules across the membrane
• Neurons transmit signals over long-distances to activate other cells  done by de-polarising
their membrane using the Na+-K+ pump
Example: Sodium-Potassium Pump
• Electrogenic pump  generates concentration gradients of K+ and Na+ - contributes to
membrane potential in animal cells
1. Na+ from cytoplasm binds to pump
2. Na+ binding causes ATP to phosphorylate the pump
3. Phosphorylation produces a conformational change in pump  expels Na+ into
extracellular space
4. Extracellular K+ binds to pump
5. Phosphate unbinds from pump
6. Conformational change in expels K+ into intracellular space

• For every 3 Na+ expelled from cell, 2 K+ are imported into the cell
• Extracellular fluid becomes more +ve, cytoplasm becomes more -ve
LO6 To describe the different types of endocytosis.
• Exocytosis and endocytosis allow for bulk transport of molecules across the plasma
membrane
• Large molecules are transported across the membrane via vesicles
• Endocytosis – cells import molecules by forming vesicles from the plasma membrane
1. Phagocytosis – cell-eating  cell engulfs a particle by wrapping pseudopodia around it
and packaging it into a large vesicle/vacuole  vesicle then travels across membrane
- Used by macrophages in higher animals to destroy bacteria – involves recognition of
‘foreign’ particles
2. Pinocytosis – cell-drinking  new vesicles are formed by random invaginations of the
plasma membrane  any and all solutes are taken into the cell
- No specificity
3. Receptor-mediated cytosis  receptor proteins on the cell surface recognise and bind to
specific molecules
- Receptors are clustered in regions called ‘coat pits’
- Vesicles are formed in which the receptors and their bound molecules are concentrated
- Highly selective, specific uptake process

Transport External energy Driving force Membrane Specificity

Mechanism required protein required
Simple diffusion/ No Concentration No Non-specific
osmosis Gradient
Facilitated diffusion No Concentration Yes Specific
– channels and Gradient
carriers
Active transport Yes ATP hydrolysis - Yes Specific
energy
Phagocytosis / Yes ATP hydrolysis Cell membrane Specific
receptor-mediated
endocytosis
Pinocytosis Yes ATP hydrolysis Cell membrane No, although
specific
molecules can
trigger
pinocytosis
5: Metabolism
LO1 Explain the terms metabolism, catabolism and anabolism.
• Metabolism – biochemical reactions that occur in a cell/organism  metabolic pathways
involve a series of enzyme catalysed reactions
• Catabolism – reactions that release energy by breaking complex molecules into smaller ones
polymer  monomer + energy
- Humans oxidise macromolecules to provide energy required for work:
1. Digestion  polymers to monomers
2. Uptake by epithelial cells
3. Transport around body
4. Uptake by cells
5. Catabolism / storage in cells
• Anabolism – reactions that consume energy by synthesising large molecules from smaller
ones  biosynthesis
monomer + energy  polymer

LO2 Explain the basic model for enzyme catalysis

• Enzymes – biological catalyst, most enzymes are proteins, enzyme activity is regulated
• Enzymes are specific to substrate – determined by active site of enzyme
• Enzymes lower EA of chemical rxns
• Temp, pH level, cofactors, inhibitors, allosteric regulation & feedback inhibition influence
enzyme activity
1. Cofactors  non-protein factors required for catalysis
- Inorganic e.g. metal ions such as Iron
- Organic/ coenzymes e.g., vitamins
2. Inhibition
- Competitive inhibitors – bind at active site, prevent substrate binding – can be overcome
by ↑ amount of substrate
- Non-competitive inhibitors – bind to different part of enzyme – induces conformational
change that prevents enzyme catalysis
3. Allosteric regulation – may inhibit or stimulate enzyme activity  binding of a molecule
at one site of the enzyme changes the function at another site
- Allosteric activation – cooperativity – binding of substrate to one complex enhances the
binding of a substrate at another site, which enhances binding at another site and
another and so on
4. Feedback inhibition – end product of a reaction interferes with the enzyme that helped
produce it  enzyme is deactivated using the product of the reaction the enzyme
catalysed at the start
- Regulates the amount of a substance made  helps to not overproduce/underproduce

LO3 Describe the structure and function of ATP

• ATP – adenosine triphosphate
• Hydrolysis of ATP to form ADP (adenosine diphosphate) releases energy
 • Energy in ADP + Pi  ATP; when work is done ATP  ADP + Pi

- Work can be chemical (enzyme rxns, polymer synthesis etc), mechanical (movement of
muscles – ATP drives movement of motor proteins), and transport (active transport)

LO4 Describe the terms respiration and fermentation.

• Fermentation – partial degradation of sugars without the need for oxygen  occurs
sometimes in skeletal muscles (e.g. during intense exercise) and always in red blood cells
- Conversion of glucose to lactic acid
- Rapid production of ATP
• Respiration – complex oxidation of sugars  requires oxygen
• Amino acids and fats can only be broken down by aerobic respiration
• CHOs can be broken down via both fermentation and respiration
• Respiration produces more ATP than fermentation

LO5 Describe the importance of redox reactions in metabolism, including the common
cofactors.
LO1 Describe the catabolism of different macromolecules.
LO2 Describe the central features of glycolysis, the TCA cycle and oxidative phosphorylation.
LO3 Explain the process of chemiosmosis.
LO4 Compare the advantages and disadvantages of fermentation and aerobic respiration.
LO5 Explain the control of cellular respiration via feedback.