Cellular Functions

Content

• Detailed structure of typical animal and plant cells, as seen under the electron microscope
• Outline functions of organelles in plant and animal cells
• The fluid mosaic model of membrane structure
• The structure of carbohydrates, lipids and proteins and their roles in living organisms
• Mode of action of enzymes
• Replication and division of nuclei and cells
• Understanding of chromosome number and variation
• Effect of meiosis on chromosome number and variation

Learning Outcomes

Candidates should be able to:

(a) Describe and interpret drawings and photographs of typical animal and plant cells as seen under
the electron microscope, recognising the following membrane systems and organelles: rough and
smooth endoplasmic reticulum, Golgi body, mitochondria, ribosomes, lysosomes, chloroplasts, cell
surface membrane, nuclear envelope, centrioles, nucleus and nucleolus. (Knowledge of the
principles of TEM and SEM are not required.) (For practical assessment, students may be required to
operate a light microscope, mount slides and use a graticule.)

(b) Outline the functions of the membrane systems and organelles listed in (a).

(c) Describe and explain the fluid mosaic model of membrane structure, including an outline of the
roles of phospholipids, cholesterol, glycolipids, proteins and glycoproteins.

(d) Outline the roles and functions of membranes within cells and at the surface of cells. (Knowledge
of osmosis, facilitated diffusion, active transport, endocytosis and exocytosis is required.)

(e) Describe the formation and breakage of a glycosidic bond.

(f) Analyse the molecular structure of a triglyceride and a phospholipid, and relate these structures
to their functions in living organisms.

(g) Describe the structure of an amino acid and the formation and breakage of a peptide bond.

(h) Explain the meaning of the terms primary structure, secondary structure, tertiary structure and
quaternary structure of proteins, and describe the types of bonding (hydrogen, ionic, disulfide and
hydrophobic interactions) which hold the molecule in shape.

(i) Analyse the molecular structure of a protein with a quaternary structure e.g. haemoglobin, as an
example of a globular protein, and of collagen as an example of a fibrous protein, and relate these
structures to their functions.

(j) Explain the mode of action of enzymes in terms of an active site, enzyme/substrate complex,
lowering of activation energy and enzyme specificity.

(k) Follow the time course of an enzyme-catalysed reaction by measuring rates of formation of
products (e.g. using catalase) or rate of disappearance of substrate (e.g. using amylase).
(l) Investigate and explain the effects of temperature, pH, enzyme concentration and substrate
concentration on the rate of enzyme catalysed reactions, and explain these effects.

(m) Explain the effects of competitive and non-competitive inhibitors (including allosteric inhibitors)
on the rate of enzyme activity.

(n) Explain the importance of mitosis in growth, repair and asexual reproduction.

(o) Explain the need for the production of genetically identical cells and fine control of replication.

(p) Explain how uncontrolled cell division can result in cancer, and identify causative factors (e.g.
genetic, chemical carcinogens, radiation, loss of immunity) which can increase the chances of
cancerous growth. (Knowledge that dysregulation of checkpoints of cell division can result in
uncontrolled cell division and cancer is required, but detail of the mechanism is not required.)

(q) Describe with the aid of diagrams, the behaviour of chromosomes during the mitotic cell cycle
and the associated behaviour of the nuclear envelope, cell membrane and centrioles. (Names of the
main stages are expected)

(r) Explain what is meant by homologous pairs of chromosomes.

(s) Explain the need for reduction division (meiosis) prior to fertilisation in sexual reproduction.

(t) Explain how meiosis and random fertilisation can lead to variation.

(u) Describe, with the aid of diagrams, the behaviour of chromosomes during meiosis, and the
associated behaviour of the nuclear envelope, cell membrane and centrioles. (Names of the main
stages are expected, but not the sub-divisions of prophase)
 (a), (b) Describe the main structural features and outline the roles of the following organelles:
 Nucleus
 Endoplasmic Reticulum
 Golgi apparatus
 Mitochondria
 Chloroplasts
 Ribosomes
 Centrioles
 Lysosomes
 Vesicles/ Vacuoles
 Cytoskeleton
 Cilia and Flagella
 Microvilli
 Cell Walls (Plant Cells only)

Organelles Structure Function

Nucleus  Largest organelle  Control of cellular activities by regulating
 10 – 20 µm in diameter protein and enzyme synthesis
 Spherical/ ovoid in shape  Nuclear division is the basis of cell replication
 Surrounded by a double membrane: nuclear  Nucleolus is responsible for the synthesis and
envelope partial assembly of ribosomes
o Outer membrane is continuous with
endoplasmic reticulum
o Inner membrane is in contact with the
nucleoplasm
 Nuclear envelope perforated with nuclear
pores
 Contains nearly all the cell’s DNA (organised
into chromosomes)
 One or more nucleolus found within the
nucleoplasm
 Proteins present:
o Histone
o Chromosomal scaffold
o Enzymes involved in protein synthesis
Endoplasmic  Consists of a network of membranous  Rough ER: Site where proteins are made and
Reticulum tubules and sacs known as cisternae transported (through the cisternae or
 Originates from outer membrane of nuclear packaged in membraneous vesicles)
envelope  Smooth ER: Synthesis of lipids (including
 Consists of: membrane phospholipid) and steroid
o Rough ER – has ribosomes lining its hormones
surface
o Smooth ER – lacks ribosomes, more
tubular
Golgi  Consists of a stack of flattened membrane-  Chemically modify, sort and transport
Apparatus bound sacs (also known as cisternae) molecules within it for secretion across the
 It is continually being formed at one end (cis cell membrane or for delivery to other parts
face) by fusion of a vesicle from the ER and of the cell
continually being bud off at the other end  Examples of modification: glycosylation
(trans face) where vesicles are pinched off. (adding of CHO group) and phosphorylation
 Middle region is known as the medial region (adding of phosphate group)
 Lysosome formation
Lysosomes  Small, spherical vesicles  Digestion of materials taken in by endocytosis
 0.2 – 0.5 µm in diameter (larger in plants)  Autophagy (unwanted substances are
 Surrounded by a single membrane engulfed and digested within the lysosomes)
  Contains digestive enzymes (e.g. proteases,  Release of enzymes outside the cell by
nucleases, lipases which breaks down exocytosis of the vesicle
proteins, nucleic acids and lipids respectively)  Autolysis (self-digestion of a cell by release of
 Formed from the pinching off of the GA lysosomal contents within the cell)
Mitochondrio  Rod-shaped/ cylindrical shaped  Involved in cellular respiration to release
n  0.5 – 1.5 µm wide, 3-10 µ long energy (usually occur in large numbers,
 Bounded by a double membrane (outer and possibly >1000 in a metabolically active cell)
inner membrane is separated by the inter-  Presence of own ribosomes and DNA/ RNA
membrane space) suggests that it is capable of producing its
 Outer membrane is smooth and continuous own protein/ enzymes required in respiration
 Inner membrane is extensively folded to form
cristae, which projects into the interior
(matrix)
 Hereditary materials (DNA and RNA) and
ribosomes are also found in the matrix
Chloroplasts  Specialised members of plastids  Site of photosynthesis
(Plant cells)  Large organelles, Rod-shaped, only smaller
than the nucleus
 Few µm in diameter and 5 – 10 µm long
 Bounded by a double membrane
 Outer membrane is smooth and continuous
 Inner membrane give rise to lamellae/
thylakoids, which extend throughout the
interior (stroma)
 Within the stroma, thylakoids are stacked to
form grana, which are joined to other grana
by the intergranal lamellae
 Grana and intergranal lamellae contains
photosynthetic pigments which make
chloroplast appear green
 Also contains hereditary materials and
ribosomes
Ribosomes  About 20 nm in diameter  Site of protein synthesis
 Composed of about equal amount of proteins
and RNA (rRNA)
 2 subunits: a large (60S) and a small (40S)
subunit
 May be attached to the rough ER or as a free
ribosome
 Usually occur in clusters as polyribosomes
Centrioles of  In animal cells only  Involved in cell replication
the  Centrosome consists of 2 hollow cylindrical
centrosome bodies (centrioles), lying at right angles to
each other, beside the nucleus
 Each centriole is made up of 9 triplets of
microtubules arranged in a ring
Vacuoles  Fluid-filled sac  Animal Vacuole: temporary food storage
 Bounded by single membrane  Plant vacuoles:
 In animal cells: usually small and less o Entry of water by osmosis is important
permanent, e.g. food vacuoles in cell expansion during cell growth as
 In plant cells: large central vacuole well as normal water relations of plants
surrounded by membrane (tonoplast), (vacuoles are highly concentrated)
containing cell sap that is concentrated with o May contains pigment and waste
ions, sugars, waster product, pigment, etc product
o May contain hydrolytic enzymes
o Food reserve (contains dissolved
sucrose and mineral salts)
Cytoskeleton  Collective network of fibrous protein  A variety of mechanical and transport
 structure functions to move vesicles from one part of
 Fibres consists of microtubules (very fine the cell to another
unbranched, hollow tubes with walls made  Aid in endocytosis and exocytosis
up of tubulin protein) and other types of
filaments
Cilia and  Structurally identical organelles, but flagella  For locomotion of single cells or to move
flagella are longer fluids over the cell surface
 Outgrowths from cells
 Cilia beat in one direction, while flagella beat
like a wave
 Contains a ‘9 + 2’ arrangement: 9 pairs of
microtubules in a ring, with 2 single
microtubules at the centre of the ring
Microvilli  Finger-like extensions of cell surface  Increase surface area to volume ratio to aid in
membrane of some animal cells absorption
Cell walls  Surround plant cells, external to plasma  Mechanical support
(Plant cells) membrane  Protective layer
 Relatively rigid, secreted by living cell
(protoplast) within
 Primary wall – laid down during cell division
in plants, consisting primarily of cellulose
fibrils running through a matrix of other
polysaccharides
 Secondary wall formed by the thickening of
the primary wall
(c) Describe and explain the fluid mosaic model of membrane structure, including an outline of the
roles of phospholipids, cholesterol, glycolipids, proteins and glycoproteins.

(d) Outline the roles and functions of membranes within cells and at the surface of cells.
(Knowledge of osmosis, facilitated diffusion, active transport, endocytosis and exocytosis is
required.)

The Fluid Mosaic Model:

It is described as a fluid as both proteins and lipids

component move rapidly in the plane of the
membrane unless anchored or restricted in some
ways.
It is described as a mosaic as protein molecules are
scattered among the phospholipids molecules,
resembling a mosaic.

What are the functions of cell membranes?

a) Compartmentalization
 Ensures maintenance of a constant internal environment
 Prevents mixing of reagents
 Maintain high concentration of reactants at specific sites
b) Regulation of passage of substance into and out of the cell
 Due to the selective permeability of membranes, it only allow certain substance to enter the cell while
keeping out harmful ones
c) Transport of solutes
d) Communication with the external environment
 Receptor proteins that receive chemical messenger molecules.
 Important for signal transduction
e) Intercellular Communication
 Animal cells: intercellular junctions
 Plant cells: plasmodesmata
f) Attachment of membrane-bound enzymes

Explain how the structure of phospholipids allows it to be suitable as the basic building material of
the cell membrane.

Phospholipids contain 2 regions, a hydrophilic phosphate head and a hydrophobic hydrocarbon tail. The
hydrophilic head faces outwards into the aqueous medium on both side of the cell membrane and the
hydrophobic tails are able to gather together to form a hydrophobic interior. Thus, the membrane is able to be
a bilayer, consisting of 2 layers of phospholipids, with the outer hydrophilic region and the inner hydrophobic
region which acts as a boundary, regulating the movement of substance into and out of the cell.

Explain how proteins are held in the membrane.

Proteins stay in the membrane because they have regions of hydrophobic R groups of amino acids which
interact with the fatty acid tails. The rest of the proteins contains hydrophilic R groups of amino acids and faces
the aqueous environment on either side of the membrane.
Describe how the structure of the cell membrane is related to its selective permeability. [3]

 Phospholipids bilayer acts as a barrier to polar/ charged/ water-soluble molecules

 Proteins form channels through the membrane
 Size/ shape/ hydrophilic groups of channel determine selectivity/ channels open or close in response to
certain signals such as change in voltage or the binding of another molecule
 Facilitated diffusion occurs through these channels
 Allow binding of certain molecules on one side of the membrane and transformation/ change shape to
release them on the other side
 Carrier proteins may also be involved in active transport/ phosphorylated with the use of ATP
 Cholesterol affects permeability/ fluidity/ Short-chained/ unsaturated fatty acids increase permeability.

Explain how membrane composition affects membrane integrity at low temperature.

 Plasma membrane is made of phospholipid bilayers

 Presence of double bonds causes a kink in fatty acid chain of unsaturated fatty acids
 This prevents close packing of fatty acid tails of phospholipids
 Thus, a lower temperature is required for phase transition

OR
 Membrane containing a high proportion of saturated fatty acid has a higher temperature of phase
transition.
 Thus, it freezes readily at low temperature and hence do not maintain membrane integrity
 Therefore, membrane with higher ratio of unsaturated to saturated fatty acids tend to maintain
membrane integrity at low temperature
 Cholesterol present disrupts close packing of phospholipids and helps to maintain fluidity
 Longer fatty acid tails increases hydrophobic interaction and hence reduces fluidity

Describe the roles of biological molecules in the cell membrane structure. [8]

 The cell membrane is a phospholipid bilayer [1/2]

Phospholipids
 The hydrophilic phosphate heads of the phospholipids face outwards into the aqueous environment on
either side of the membrane. [1/2]
 The hydrocarbon tails face inwards [1/2] and create a hydrophobic interior OR
 The role of phospholipids in the plasma membrane is to form a hydrophobic boundary in an aqueous
medium [1/2] between the interior and exterior of a cell or an organelle.
 Some fatty acid tails are saturated and some are unsaturated. Unsaturated tails are bent and fit together
more loosely. The unsaturated fatty acids form kinks [1/2] so that the membrane is more fluid.

Cholesterol
 Membrane also contains cholesterol. [1/2]
 Disturbs close packing of phospholipids and important for maintaining fluidity of cell membranes. [1/2]

Proteins
 Most protein molecules float about in the phospholipid bilayer, forming a fluid mosaic pattern.
 They have regions of hydrophobic amino acids which interact with the fatty acid tails [1/2]
 The rest of the protein is hydrophilic and faces the aqueous environment on either side of the
membrane [1/2]
 Integral/ intrinsic proteins are embedded in the phospholipid bilayer [1/2]
 Peripheral/ extrinsic proteins are embedded in the phospholipid bilayer [1/2]
 Functions as [any two]:
o Transport proteins: Provide a hydrophilic channel across the membrane that is selective for a
particular solute or for active transport of substances.
 o Enzymes: A protein built into the membrane may be an enzyme with its active site exposed to
substances in the adjacent solution.
o Receptor sites: Portion exposed to the outside may have a binding site for a chemical messenger
(e.g. hormone)
o Cell adhesion: Membrane proteins of adjacent cells may be attached together in various kinds of
intercellular junctions.

Carbohydrates
 Some proteins and lipids have short branching carbohydrate chains, forming glycoproteins and
Glycolipids respectively [1/2]
 These may act as receptors or recognition sites and are involved in cell recognition [1/2]

Discuss the role of proteins in the function of cellular membranes, with reference to three named
examples. [12]

 Proteins embedded in fluid matrix of phospholipid bilayer of membranes.

 Unique set of proteins determine specific function of membrane
 Integral membrane/ transmembrane proteins span membrane bilayer

Attachment of protein to membrane

 Hydrophobic regions of protein associates with hydrophobic core of membrane
 Hydrophilic regions exposed to aqueous environment on either side of the membrane

Integral proteins may have roles such as:

(A) Transport proteins/ Carrier proteins

 Providing hydrophilic channels/ pores
 For transport of polar solutes
 Via facilitated diffusion; down concentration gradient
 Carrier proteins shuffle substances by changing shape
 Certain proteins coupled to ATPase; for active transport/ pumping substances against concentration
gradient
 Specificity for translocation of certain substances
 Important fro selective permeability of membrane
o E.g. aquaporins facilitating water passage; glucose transporters
o E.g. Sodium-Potassium ATPase pump is important to maintain membrane potential
 Pumps 3Na+ out for every 2K+ pumped into cell
 Membrane potential favors passive transport of cations into cells and anions out
 Setting up of electrochemical gradient
 Important for propagation of nerve impulses along axonal membrane

(B) Signal Transduction

 As receptors for Extracellular signal molecules/ ligands
o E.g. GPCRs
o Ligand binding cause conformational change in receptor
o Required to relay message to interior of cell

(C) Cell-Cell Recognition

 Glycoproteins and/ or Glycolipids
 Specifically recognized by other molecules on other cells

(D) Cell-Cell Adhesion

 Formation of gap junctions/ tight junctions
(E) Attachment to cytoskeleton/ Extracellular matrix elements
 Helps maintain cell shape
 Provides animal cells with stronger structural framework
 Localizes certain membrane proteins
 Coordinating Extracellular and intracellular changes

(F) Enzymatic Activity

 Active site in membrane protein exposed to substances in adjacent solution
o E.g. Tyrosine kinase receptors (Receptor dimerisation and autophosphorylation upon ligand
binding)
o E.g. ATPase synthase (ADP phosphorylation coupled to flow of protons through enzyme complex)
 Some membrane bound enzymes organized together for metabolic pathway
o E.g. ETC components in mitochondria/ chloroplast

(G) Other Functions

 Receptor-mediated endocytosis
o Proteins involved – specific membrane protein receptors exposed to Extracellular fluid, coat pins
on cytoplasmic side (of same region on membrane)
o Upon ligand binding, vesicles form to enclose ligands
o Cell acquires in bulk substances in ECF
(e) Describe the formation and breakage of a glycosidic bond.

Carbohydrates are polymers made up of many monosaccharides molecules joining together. The bond
between each monosaccharide is known as a glycosidic bond. And the process is known as condensation.
Water is removed from this process.

During the condensation, a glycosidic bond is formed usually between carbon atoms 1 and 4 of the adjacent
monosaccharide. This is known as a 1 – 4 glycosidic bond. (The only exception is during the branch point of
polymers such as amylopectin, where it exists as a 1 – 6 glycosidic bond.)

Other variations of a glycosidic bond:

If a α glucose is used and the bond is formed between C1 and

C4, it is known as a α (1-4) glycosidic bond.
Similarly, a β glucose will form a β (1-4) glycosidic bond.

Occurrence of the various bonds:

α (1-4) glycosidic bond: Amylose, straight chain portion of amylopectin

α (1-6) glycosidic bond: Amylopectin (branching point)
β (1-4) glycosidic bond: Cellulose

The reverse reaction whereby a disaccharide or a polysaccharide is being broken down into its constituent
monomer is known as hydrolysis. Water is required for this reaction.
Structure-Function Relationship

1. Starch

(a) Large Molecule

Being large, starch is insoluble in water, making it a suitable storage polysaccharide as it does not affect the
water potential of the cell or diffuse out of plant cells.

(b) Folded into a compact shape

This allows large amounts of starch to be stored within a fixed volume

2. Glycogen

(a) Large Molecule

Being large, glycogen is insoluble in water, making it a suitable storage polysaccharide as it does not affect the
water potential of the cell or diffuse out of plant cells.

3. Cellulose

(a) Hydroxyl groups projects outwards from each chain in all directions, forming hydrogen bonds with
neighboring regions
Such cross-linking between adjacent β-glucose chains helps confer high tensile strength to the molecule,
allowing cellulose to act as a good structural polysaccharide and a good cell wall material.

(b) Presence of large inter-molecular space

This allows the molecule to be permeable to water

(c) Large Molecule

As such, cellulose is insoluble to water, making it a suitable structural polysaccharide.

(d) Made up of β-glucose molecules, resulting in the formation of β (1,4) glycosidic bonds between β-glucose
residues, resulting in the formation of straight chains
This allows the chains to associate into groups to form microfibrils which then combine to form macrofibrils,
which have high tensile strength.
(f) Analyse the molecular structure of a triglyceride and a phospholipid, and relate these structures
to their functions in living organism.

Triglycerides

(A) Good source of energy

 Triglycerides have a high ratio of energy storing C-H bonds to carbon atoms, thus triglycerides
function as a good source of energy [1] in living organisms. / Effective store of energy for hibernating
animals [1]

(B) Source of metabolic water

 Hydrogen atoms in triglyceride molecules yield metabolic water on oxidation, thus triglycerides are a
good source of metabolic water when oxidized during respiration. [1]
 Metabolic water is particularly important to desert animals [1] such as camels

(C) Thermal Insulator

 Triglycerides are poor conductors of heat. Triglycerides therefore function as good thermal
insulators, preventing excessive heat loss. [1]
 This is especially important for mammals living in cold climates (e.g. polar bear and whales). [1]

(D) Good/ Suitable storage molecule

 Triglycerides possess low mass thus can be stored in a small volume. [1]
 This makes them especially useful for animals where locomotion [1] requires mass to be kept to a
minimum.
 In plants, it is useful in seeds where dispersal by wind or insects [1] makes small mass a necessity
 Triglycerides are large and uncharged, thus they are insoluble in water. [1]
 They can be stored in large amounts without having any effect on the water potential of cells. [1]

(E) Buoyancy in aquatic mammals

 Triglycerides are less dense than water, hence providing aquatic mammals, e.g. whales, with
buoyancy. [1]

 Phospholipids

(A) Biological Molecules

 Each phospholipid molecule consists of a hydrophilic phosphate head and two hydrophobic fatty
acid tails. In aqueous environment, phospholipid molecules form a bilayer in biological membranes.
[1]
 The phosphate heads face outwards and interact with the aqueous medium, while the hydrocarbon
tails face inwards and are shielded from the aqueous medium. This allows the formation of a
hydrophobic barrier to exist between the aqueous interior and exterior of the cell. [1]
 C=C bonds at fatty acid chains causes a kink and results in greater separation between molecules/
membrane fluidity. [1]
 Hydrophobic interactions occur between the lipid layer and hydrophobic portions of membrane
proteins, holding membrane proteins of various functions in place. [1]
 Hydrophilic heads interact with hydrophilic portions of peripheral proteins, loosely holding them at
the surface of the membrane. [1]
 Phospholipids associate covalently with membrane carbohydrates to form Glycolipids, which
function in cell-cell adhesion/ cell-cell recognition. [1]
(g) Describe the structure of an amino acid and the formation of a peptide bond.

Basic structure of an amino acid:

An amino acid molecule consists of 3 groups:

 Amino group (-NH2)
 Carboxyl group (-COOH)
 R group that consist of one of various
chemical structures that determines
the properties of the different amino
acid

Due to the amino and carboxyl group, amino acids are

amphoteric, meaning that they have both acidic as well
as basic properties.

They are also water soluble and able to form

zwitterions, i.e. ions that are dipolar.

Most amino acids are neutral. Depending on the

different R groups, they might be acidic or basic.

Formation of a peptide bond:

A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule
reacts with the amino group of the other molecule, releasing a molecule of water (H2O).

Type of reaction: Condensation Reaction

When many amino acids are linked together by

peptide bonds, they form a polypeptide chain.

The reaction is reversible and peptide bonds can be

hydrolysed back to its constituent amino acids
through hydrolysis.
(h) Explain the meaning of the terms primary structure, secondary structure, tertiary structure and quaternary structure of proteins, and describe the types of
bonding (hydrogen, ionic, disulfide and hydrophobic interactions) which hold the molecule in shape.

Primary Secondary Structure: Secondary Structure: Secondary Structure: Tertiary Structure

Structure α-helix β-pleated sheets Triple helix
Definition This structure This structure refers to the twisting of the polypeptide chain into α-helix (e.g. keratin) or a β-pleated sheet (e.g. fibroin) This structure refers to the folding an
refers to the due to hydrogen bonds between the hydrogen and oxygen atoms. bending of the polypeptide on itse
sequence of into a compact globule due to
amino acids in combination of hydrogen bonds, ion
a polypeptide. bonds, disulphide bonds an
hydrophobic interactions.
Bonds None – not Hydrogen bonds between peptide Hydrogen bonds between peptide None – not applicable Disulphide bonds, hydrogen bond
within applicable linkages of polypeptide backbone linkages of polypeptide backbone hold ionic bonds and hydrophob
chains (which stabilizes the helix) adjacent part in parallel regions interactions between the R group
together. amino acids.

Amino and carboxyl group involved

peptide bond formation that are no
part of the R group and not involved
ionic bonds.
Bonds None – not None – not applicable None – not applicable Hydrogen bonds between peptide None – not applicable
between applicable linkages of polypeptide back bond
chains holds 3 polypeptide chains together
General Polypeptide Polypeptide chain forming an Zig zag sheets of parallel-lying 3 polypeptide chains wound into a Globular
Structure chain with extended spiral spring polypeptide chains triple helix (which are held by H
specific bonds) Compact
number, 3.6 amino acid residues found in 1 Exists as parallel β-pleated sheets or
sequence and complete turn of α-helix structure anti-parallel β-pleated sheets 3-Dimensional shape
variety of
amino acid
residues
Examples All proteins Keratin Fibroin Collagen Peptide hormones
have primary Enzymes
structure
(i) Analyse the molecular structure of a protein with a quaternary structure e.g. haemoglobin, as
an example of a globular protein, and of collagen as an example of a fibrous protein, and relate
these structures to their functions.

Collagen

Structure: Frequent recurrence of glycine-proline-hydroxyproline:

(a) Small size of glycine residue
(b) Proline and hydroxyproline had large hydrophobic R groups that face the outside of the
triple helix
Function: Glycine is the only residue that fits into the triple helix:
(a) Ensures that the polypeptide chains that form the triple helix is closely held, which
confers high tensile strength to the collagen molecule
(b) High tensile strength is crucial for function of collagen as connective tissue

(c) Hydrophobic interaction results in collagen being insoluble, which makes it a suitable
structural protein

Structure: Presence of hydrogen bonds formed between –NH groups of glycine residues in one chain
and –CO groups of other residues in an adjacent chain
Function: Further stabilizes the triple helix structure

Haemoglobin

Structure: (a) Hydrophobic amino acid residues of each subunit are buried in the interior of the folded
structure
(b) Hydrophilic amino acid residues of each subunit are facing the exterior aqueous medium
Function: Allows haemoglobin to be soluble in water, which makes it suitable as a transport protein

Structure: Each subunit comprise of a protein component (globin) and a non-protein component (haem
group):
(a) Haem group consists of a porphyrin ring and an iron ion (Fe 2+)
(b) Fe2+ forms strong bonds with oxygen and is important for oxygen binding
Function: Allows O2 to be transported efficiently

Structure: Haemoglobin is a conjugate protein consisting of 4 subunits (2 α-chains and 2 β-chains), each
with their respective haem group (hence a total of 4 haem groups)
Function: Allows allostery to occur, where binding of O 2 with the Fe2+ of a single haem unit results in
faster uptake of O2 by subsequent haem groups.

HIV Protease

Structure: (a) Globular protein with quaternary structure consisting of 2 monomer subunit folded into a
3-D shape
(b) Hydrophilic amino acid faces exterior of molecule and hydrophobic amino acid faces the
interior
Function: Enables the protease to act in aqueous medium as the enzyme is soluble in water

Structure: (a) Amino and carboxyl terminal of each monomer interdigitates

(b) Presence of α-helix and β-pleated sheets in each monomer, stabilized by hydrogen bonds
(c) Core domain present in each monomer
Function: Stabilisation of homodimer so that configuration of enzyme is maintained and catalytic site is
stabilized.
Structure: Active site at the centre of the homodimer contains the conserved catalytic triad made up of
aspartic acid-theorine-glycine from each monomer, stabilized by hydrogen bonds
Function: Active site is complementary to substrate, allowing the formation of the enzyme-substrate
complex

Structure: Each identical monomer consists of 99 amino acids which is folded and interacts to form a
symmetrical 3D shape
Function: Formation of active site, which is complementary to shape of substrate

Structure: (a) Flap domain, which covers the active site, consists of anti-parallel β-hairpin loop
(b) Flap domain is glycine rich and is highly flexible
Function: Confers an open and close conformation for substrate binding and product release.

Explain how the overall structure of the HIV Protease is maintained.

(a) Hydrogen bonds, ionic bonds and hydrophobic interactions formed between R-groups of amino acids
residues between polypeptide chains/ subunits holds the various polypeptide subunits together

(b) Hydrogen bonds, ionic bonds, hydrophobic interactions and disulphide bonds formed between R-groups of
amino acid residues within same polypeptide chain/ subunits allows each subunit to fold into a precise,
compact, globular 3-D structure.

***Similar concept applies for other protein structure: bonds inside each chain and within different chains.

Explain how the different properties of the R-groups are important in the structure and
functioning of proteins.

Structure:
R-groups are involved in determining the tertiary structure of proteins
(a) Interactions between the R groups enable the primary structure to fold into a compact 3 dimensional
shape unique to the protein
(b) Bonds between the R-groups maintain the tertiary structure

Functions:
(a) Maintenance of tertiary structure is important for enzymatic function – conformation of active site is
essential to enzyme specificity
(b) Presence of polar R groups increases solubility of proteins, allowing globular protein to function in
solution e.g. haemoglobin
(c) Presence of hydrophobic R groups renders the protein insoluble. This is important for structural
functions
(j) Explain the mode of action of enzymes in terms of an active site, enzyme/substrate complex,
lowering of activation energy and enzyme specificity.

(l) Investigate and explain the effects of temperature, pH, enzyme concentration and substrate
concentration on the rate of enzyme catalysed reactions, and explain these effects.

Enzymes

Enzymes are biological catalysts made up of proteins that help to speed up the rate of biochemical reactions
by lowering the activation energy required for the reaction, without being chemically changed at the end of
the reaction.

Properties of enzymes

1. Usually globular proteins

2. Required in small amount
3. Reversibility
4. Extremely efficient: small amount is required to catalyse a reaction
5. Highly specific in action: active site is complementary to the substrate only
6. Activity is affected by: pH change, temperature, substrate and enzyme concentration, inhibitors or activators

Mode of action:

Enzymes have an active site, where the shape is complementary to the shape of the substrate it works on,
allowing the substrate to fit accurately – just like a lock and key.

Upon binding of the 2 molecule, they form a temporary structure called the enzyme-substrate complex.
Following product formation, the product(s) are no longer to fit into the enzyme and thus are released, freeing
the enzyme to bind to another substrate molecule – enzyme remains unchanged and free to catalyse another
reaction. Thus, a small amount is required for a relatively larger amount of substrate.

Induced fit hypothesis: Upon binding of substrate, the enzyme undergoes a slight conformational change to its
active site to allow it to bind more effectively with the substrate to catalyse the reaction.

Suggest how the substrate may be held in the active site of an enzyme while it carries out
its catalytic activities.

 The shape of the active site is complementary to that of the substrate.

 Upon binding, this induces a small conformational change in the enzyme active site, allowing the substrate
to fit more snugly into the active site.
 Substrate is held in place by hydrogen bonds, ionic or hydrophobic interactions.

Explain how 2 amino acids are brought close together to form the active site.

 Enzymes are globular protein.

 Folding of the polypeptide chain to form the tertiary structure would enable the two amino acids to be
brought close together.
 Tertiary structure is then maintained by hydrogen bonds, ionic bonds, disulphide bonds and hydrophobic
interactions which occur between the R groups of amino acids.
Describe the ways in which an enzyme interacts with its substrate.

1. Maintaining precise substrate orientation

Enzymes hold their substrates in an arrangement that forces them together in the proper orientation for the
reaction to occur. This is done by forming temporary interactions with the substrate.

2. Through physical stress

Once a substrate binds to the active site of the enzyme, certain bonds may be placed under physical stress,
thus increasing the likelihood of a bond being broken.

3. Change in substrate reactivity

When the R groups of the amino acids of the enzymes are in close proximity with the substrate, they can:
(a) Change the charge of the substrate
(b) Alter the distribution of the electrons within the bonds
(c) Cause other change which serves to increase the reactivity of the substrate

Factors affecting rate of enzymatic reaction

1. Temperature

 As temperature increases, the rate of reaction increases until the optimum temperature is reached.
Beyond which, rate of reaction decreases rapidly
 Optimum temperature – point where enzymes are functioning at its maximum level
 As temperature increases, there will be an increase in kinetic energy of enzyme and substrate.
 This increase the frequency of successful collision and thus, more enzyme-substrate complex is formed.
 Q10 is a reflection of the rate of reaction affected by temperature
 Beyond the optimum, rate of reaction decreases rapidly as enzymes are being denatured
 Excessive heat disrupts the intramolecular force stabilizing the secondary and tertiary structure
 Thereby disrupting the precise nature of the active site, as the secondary and tertiary structure is broken
down, leaving only the primary structure unaffected.
 Hence, the enzyme is denatured and unable to perform its catalytic function.

2. pH

 At the optimum pH, the enzyme active site is most ideal for substrate binding
 Thus, rate of reaction is at its maximum rate
 At pH lower or higher, the rate of reaction would decrease due to the denaturation of enzyme
 At lower pH, there is a higher concentration of H +. These H+ would connect with the negative ions on the
enzymes, disrupting the shape and hence denaturing the enzyme
 At higher pH, the high proportion of OH - will cause enzymes to lose H+, causing a change in the ionic
bonding holding the enzymes together, resulting in enzyme denaturation
3. Substrate Concentration

 Generally, the higher the substrate concentration, the higher the rate of reaction
 An increase in the substrate concentration would lead to an increase in the frequency of successful
collisions between the substrate and enzyme, thus more enzyme-substrate is formed and rate is
increased.
 This is until Vmax is reached, when any further increase in substrate concentration would no longer lead to
an increase in the rate of reaction
 This is because all the active site of the enzymes are used up and any free substrate would have to wait
until the enzyme-substrate complex has released its product
 Rate of reaction is now limited by enzyme concentration
 Km: measurement of the rate of reaction. It is the substrate concentration at which the rate of reaction is
half its maximum.
 Km determines the affinity of the enzyme with the substrate. Low K m means that the enzyme has a high
affinity with the substrate while a high Km means that the enzyme have a low affinity with the substrate.

4. Enzyme Concentration

 An increase in enzyme concentration will lead to an increase in the rate of reaction

 As enzyme concentration increases, the frequency of successful collisions between enzyme and substrate
increases
 Thus, more enzyme-substrate complex is formed and more products are released
 This is until Vmax is reached
 Then, rate of reaction is limited by substrate concentration.
 (m) Explain the effects of competitive and non-competitive inhibitors (including allosteric
inhibitors) on the rate of enzyme activity.

Competitive Inhibition Non-competitive Inhibition

Graph - -
Site of binding of At the active site of the enzyme At a region other than the active site of the
inhibitor enzyme
Structure of inhibitor Structurally similar to substrate No structural resemblance with substrate
Mode of action Compete with the substrate for active sites of Alter the shape of the enzyme molecule so
enzyme – temporary effect that the active shape is no longer able to bind
to substrate molecule – permanent effect
Effects of increasing At high [substrate], effects of inhibitors are At high [substrate], inhibitory effects are still
[substrate] on rate of not observed observed
reaction
Maximum rate of Can be attained if [substrate] is sufficiently Can never be reached regardless of how high
reaction high [substrate] is
Examples Malonic acid: Cyanide:
Competes with succinate for the active sites Attaches itself to the copper prosthetic group
of the enzyme succinic dehydrogenase in the of the enzyme cytochrome oxidase, thereby
Kerbs cycle inhibiting respiration

Allosteric Regulation:

Certain enzymes have 2 different active sites for the binding. In which case, the activity of one site is
dependent on the binding of a regulatory molecule on the other site.

Binding of activator: stimulates enzyme action

Binding of inhibitor: inhibits enzyme action

The presence of such regulator causes a slight conformational change to the active site of the enzyme, thereby
stabilizing the active or inactive enzyme configuration respectively.
e.g. presence of inhibitor causes the change in the active site and prevents substrate from binding with the
enzyme.
(n) Explain the importance of mitosis in growth, repair and asexual reproduction.

The significance of mitosis is in its ability to maintain the genetic stability of an organism – this means that the
2 daughter cells formed:
(a) Contains the same chromosome number
(b) Are genetically identical to the parent cell

Importance of mitosis:

(a) Mitosis occurs during the growth and development of a multicellular organism, e.g. in the development of a
fertilized egg into an adult human being
(b) Mitosis occurs during the replacement of worn-out parts of the body
(c) Mitosis is the basis of asexual reproduction
 If a species is successful in colonizing a particular habitat, there is little advantage in the short term in
producing offspring that are different from their parents
 This is because if the offspring is different, it may not be able to adapt to the habitat and soon die off.
It is therefore better to quickly establish a colony of individuals, which are identical to the parents.
E.g. animals (hydra) and plants (e.g. ferns and potato) propagate by asexual means through mitosis.

Explain how mitosis provides for genetic stability

In mitosis, the daughter cells receive precisely the same number and types of chromosomes as the original
parent cell. This means that the diploid constitution is maintained from one generation of cells to another.

Features of mitosis that ensures genetic stability:

(a) DNA is replicated before mitosis begins

 This results in chromosomes having 2 identical sister chromatids bound by the centromere
 No genetic variation: no association of homologous pairs of chromosomes and no formation of chiasmata
 no crossing over occurs
 The amount of DNA is doubled at Interphase and then halved at Anaphase

(b) Arrangement of chromosomes on the spindle

 At Anaphase, identical sister chromatids of each chromosome separate and move towards their respective
poles
 This ensures that the chromosomes are distributed evenly between the 2 daughter cells

(r) Explain what is meant by homologous pair of chromosomes

A diploid organism has 2 sets of chromosomes, one derived from each parent. Any 2 (a pair of) chromosomes
which determine the same characteristics are called homologous chromosomes.

Homologous chromosomes have:

 Same length
 Same centromere position
 Same staining pattern
 Genes coding for the same characteristics at corresponding loci
 Pair with each other during prophase I of meiosis

Although homologous chromosomes determine the same characteristic, they need not be identical. If both
sets of chromosomes are found in a cell, it is said to be in a diploid condition.
 (q) Describe with the aid of diagrams, the behaviour of chromosomes during the mitotic cell cycle
and the associated behaviour of the nuclear envelope, cell membrane and centrioles. (Names of
the main stages are expected)

(u) Describe, with the aid of diagrams, the behaviour of chromosomes during meiosis, and the
associated behaviour of the nuclear envelope, cell membrane and centrioles. (Names of the main
stages are expected, but not the sub-divisions of prophase)

Prior to nuclear division: Interphase

The cell cycle consists of interphase, nuclear division and cytokinesis. Interphase is the phase where the cell is
deemed to be in its resting and active state. There are 3 stages in this phase:

G1 phase (1st growth phase) – cell forms new cell organelles for daughter cells
S phase (synthesis phase) – DNA replicates
G2 phase (2nd growth phase) – cell builds up its energy store for nuclear division

Describe what happens to DNA in Interphase

 DNA replication occurs

 DNA double helix unwinds/ hydrogen bonds between the bases are broken
 Each strand acts as a template for replication (semi-conservative replication)
 DNA Polymerase adds nucleotides to 3’ end of growing polynucleotide chain
 Specific base pairing (A with T, C with G)
 One strand is synthesized continuously
 Other strand is synthesized in short fragments/ Okazaki fragment
 Resulting in the formation of 2 daughter DNA molecule

Describe the events that occur during each phase of meiosis and the significance of each
event.

Stage Event Significance

Prophase I Disintegration of nuclear membrane Allows spindle formation between opposite
poles of cell
Centrioles migrate to the opposite poles of the Allows the movement of chromosomes to poles
cell and from the microtubules within it forms in Anaphase I
the spindle fibre
Disintegration of nucleoli and condensation of Facilitates travel of genetic material without
chromosome entanglement
Pairing of homologous chromosomes to form Alignment of genes on chromosomes in
bivalents preparation for crossing over of homologous
sections of non-sister chromatids
Formation of chiasmata Allows crossing over to occur. Changes
combination of alleles on chromosomes,
allowing variation in gametes
Metaphase I Random alignment of homologous Preparation for the independent assortment of
chromosomes at equator; one on each side of homologous chromosomes
the equatorial plate
Anaphase I Non-sister pair of chromatids pulled to opposite 1. Separation of homologous chromosomes
poles by the shortening of centromere-to-poles 2. Independent assortment results in variation in
spindle combination of paternal and maternal
chromosomes
3. Each cell obtains haploid set of chromosomes
Telophase I Formation of nuclear envelope and nucleolus; 1. Produces 2 daughter haploid nucleus and
spindle fibre disintegrates later, cells (by cytokinesis)
2. Prepares cells for meiosis II
Prophase II 1. Disintegration of nuclear envelope; Similar to Prophase I
2. Formation of spindle fibres;
3. Disintegration of nucleoli and
4. Condensation of chromosomes
Metaphase II 1. Chromosomes align on metaphase plate Allows random distribution of non-sister
2. 2 non-sister chromatids (result of crossing chromatids
over) held by centromere
Anaphase II 1. Centromere divides Produces 2 sets of chromosomes to ensure each
2. Chromatids move to opposite poles daughter cell receive one set of genetic material
Telophase II 1. Spindle fibre disintegrates Produces 4 unique haploid daughter cell
2. Uncoiling of chromosomes and reformation of
nuclear envelope and nucleolus

For mitosis, the significance is similar, except no crossing over occurs and 2 cells obtained is genetically
identical to parent cell.

Describe the behaviour of chromosomes during mitosis and meiosis.

Mitosis
Prophase 1. Condensation of chromosomes occurs
2. Each chromosomes occurs as 2 sister chromatids joined at a point called the centromere
Metaphase Chromosomes arrange themselves at the equator of the spindle and becomes attached to the
spindle fibres at the centromeres
Anaphase 1. Centromere of each chromosome divides
2. Sister chromatids of each chromosomes separates and move, centromere first to opposite poles
of the spindle, this is due to the shortening of the centromere-to-pole spindle fibres
Telophase 1. Chromatids reach their respective poles of the spindle
2. Chromatids becomes the chromosomes of the daughter cells
3. Chromosomes uncoil and return to their original threadlike form

Meiosis
Prophase I 1. Condensation of chromosomes occur
2. Each chromosomes occur as 2 sister chromatids joined at a point called the centromere
3. Homologous chromosomes pair up to form bivalents
4. Crossing over occurs at chiasmata, where non-sister chromatids of homologous chromosomes
break and rejoin, exchanging a portion of one non-sister chromatids with an equivalent portion of
another
Metaphase I 1. Random arrangement of bivalents at the equator of the spindle
2. Centromeres become attached to the individual spindle fibres
Anaphase I Homologous chromosomes separate due to the shortening of centromere-to-pole spindle fibres
Telophase I Chromosome reach their respective poles of the spindle
Prophase II 1. Condensation of chromosomes occurs
2. Each chromosomes occurs as 2 non-sister chromatids joined at a point called the centromere
Metaphase II Chromosomes arrange themselves at the equator of the new spindle and become attached to the
spindle fibres at the centromeres
Anaphase II 1. Centromere of each chromosome divides
2. Non-sister chromatids of each chromosomes separate and move, centromere first to opposite
poles of the spindle; this is due to the shortening of the centromere-to-pole spindle fibres
Telophase II 1. Chromatids reach their respective poles of the spindle
2. The chromatids become the chromosomes of the daughter cells
3. Chromosomes uncoil and return to their original threadlike form
Describe the roles of spindle fibres in meiosis

 Pulls sister chromatids/ homologous chromosomes to opposite poles at anaphase

 Help align chromosome at equatorial plate
 Other (non-kinetochore) spindle fibres lengthen to elongate the cell in preparation for cytokinesis

(s) Explain the need for reduction division (meiosis) prior to fertilisation in sexual reproduction.

(t) Explain how meiosis and random fertilisation can lead to variation.

Discuss the role of meiosis in sexual reproduction and promoting genetic variation.

Role in sexual reproduction

 Meiosis produces haploid gametes for sexual reproduction
 Meiosis results in the formation of 4 gametes, each with half the number of chromosomes of the parent
cell
 During fertilization, the nuclei of the male and female gametes fuse to produce a zygote, which has a fixed
number of chromosomes for each species  diploid condition (2n)
 If meiosis did not occur, fusion of gametes would result in a doubling of chromosomes for each successive
sexually reproduced generation
 Thus, as meiosis produces haploid gametes, doubling is prevented.

Role in genetic variation

 This is essential for the process of evolution
 By providing a varied stock of individuals, it permits the natural selection of those best suited to the
existing conditions and so ensures that the species constantly change and adapt when these conditions
alter
 Cause of genetic variation by meiosis:

1. Crossing over during Prophase I

a. Due to association of homologous chromosomes, chiasmata are able to form
b. Non-sister chromatids of homologous chromosomes break and rejoin
c. Leading to an exchange of corresponding gene loci between non-sister chromatids
d. This leads to new combinations of alleles on the chromosomes in the resulting gametes

2. Random assortment and independent separation of homologous chromosomes during metaphase I

and anaphase I
a. Number of possible combinations: 2n

3. Random assortment of chromosomes and independent separation of chromatids during metaphase II

and anaphase II respectively
a. If crossing over has occurred, “sister” chromatids would no longer be identical
b. Upon separation during Anaphase II, the resulting daughter cells therefore will have different
combination of alleles

Outline how meiosis leads to the formation of 4 haploid nuclei

Meiosis occurs in 2 stages: meiosis I and meiosis II

During meiosis I, each parent cell divides to form 2 daughter cell with haploid nuclei, with the division of
nuclear material (DNA). During meiosis II, each haploid daughter cell divides again to form another daughter
cell, with the division of chromatids.

Thus, 4 haploid nuclei is formed.

 State precisely what crossing over involves

Involves exchange of corresponding gene loci between non-sister chromatids of homologous chromosomes.

Result: New combination of alleles on chromosomes of daughter nuclei

No. of sets of chromosomes vs amount of DNA in a cell

Diploid cell End of Interphase End of Mitosis End of Meiosis I End of Meiosis II
before S-phase of
interphase
No. of sets of 2n 2n 2n n n
chromosomes
Homologous
chromosomes
separated
Amount of DNA X 2X X X X/2
DNA replicated, Sister chromatids Homologous Sister chromatids
amount of DNA separated chromosome separated
doubled separated

Source of Genetic Variation

Source of Genetic Variation Remarks

Crossing over during Prophase I Sources of genetic variation are Source of genetic variation are inherent
Random assortment and independent inherent to Meiosis to sexual reproduction
separation of homologous
chromosomes during metaphase I and
anaphase I
Random assortment of chromosomes
and independent separation of
chromatids during metaphase II and
anaphase II respectively
Random fusion of gametes
Chromosomal mutation
Gene mutation Introduces new alleles into gene pool