TOPIC 2: MOLECULAR BIOLOGY

2.1 Molecules to Metabolism

 2.1.U1: Molecular biology explains living processes in terms of the chemical substances involved
Molecular biology is a field of study that focuses on investigating biological activity at a molecular level
 This includes elucidating the structure and function of chemical substances and determining their interactions as
parts of living processes

Biological processes are tightly regulated by enzymes, whose expression is controlled by gene activation (DNA)
 Changes in activity are typically determined by signalling molecules (either endogenous or exogenous in origin)
Organic Compounds
An organic compound is a compound that contains carbon and is found in living things
 Exceptions include carbides (e.g. CaC2), carbonates (CO32–), oxides of carbon (CO, CO2) and cyanides (CN–)

 2.1.U2: Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist

Carbon
Carbon forms the basis of organic life due to its ability to form large and complex molecules via covalent
bonding
Carbon atoms can form four covalent bonds, with bonds between carbon atoms being particularly stable
(catenation)
 These properties allows carbon to form a wide variety of organic compounds that are chemically stable

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 2.1.U3: Life is based on carbon compounds including carbohydrates, lipids proteins and nucleic acids

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 Main Classes of Carbon Compounds
There are four principle groups of organic compounds that contribute to much of the structure and function of a
cell

Carbohydrates
 Most abundant organic compound found in nature, composed primarily of C,H and O atoms in a common ratio –
(CH2O)n
 Principally function as a source of energy (and as a short-term energy storage option)
 Also important as a recognition molecule (e.g. glycoproteins) and as a structural component (part of DNA / RNA)
TYPES OF CARBOHYDRATES
1. MONOSACCHARIDE

2. OLIGOSACHARIDE – 2 TO 9 MONOSACCHARIDE(EG. DISACCHARIDE)

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1. POLYSACCHARIDE

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 Lipids
 Non-polar, hydrophobic molecules which may come in a variety of forms (simple, complex or derived)
 Lipids serve as a major component of cell membranes (phospholipids and cholesterol)
 They may be utilised as a long-term energy storage molecule (fats and oils)
 Also may function as a signalling molecule (steroids)
 GLYCEROL

FATTY ACID

Draw triglyceride-

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 Nucleic Acids
 Genetic material of all cells and determines the inherited features of an organism
 DNA functions as a master code for protein assembly, while RNA plays an active role in the manufacturing of
proteins

Proteins
 Make over 50% of the dry weight of cells; are composed of C, H, O and N atoms (some may include S)
 Major regulatory molecules involved in catalysis (all enzymes are proteins)
 May also function as structural molecules or play a role in cellular signaling (transduction pathways)

Proteins are comprised of long chains of recurring monomers called amino acids
Amino acids all share a common basic structure, with a central carbon atom bound to:
 An amine group (NH2)
 A carboxylic acid group (COOH)
 A hydrogen atom (H)
 A variable side chain (R)

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

 2.1.U5: Anabolism is the synthesis of complex molecules from simpler molecules including the formation
of macromolecules from monomers by condensation reactions

2.1.U6: Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules into monomers

 2.1.A1: Urea as an example of a compound that is produced by living organisms but can also be
artificially synthesized

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  2.1.S1: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino
acid

 2.1.S2: Identification of biochemical such as sugars, lipids, or amino acids from molecular drawings

 2.1.NOS: Falsification of theories; the artificial synthesis of urea helped to falsify vitalism

2.2 Water
 2.2.U1: Water molecules are polar and hydrogen bonds form between them .

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  2.2.U2: Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties
of water

OUTLINE OF PROPERTY USE IN LIVING ORGANISMS

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 2.2.U3: Substances can be hydrophilic or hydrophobic

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  2.2.A1: Comparison of the thermal properties of water with those of methane

PROPERY WATER METHANE

MELTING POINT
BOILING POINT
SPECIFIC HEAT CAPACITY
HEAT OF VAPOURISATION

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 2.2.A2: Use of water as a coolant in sweat

 2.2.A3: Modes of transport of glucose, amino acids, cholesterol, fats, oxygen, and sodium in blood in
relation to their solubility in water

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  2.2.NOS: Use of theories to explain natural phenomena- the theory that hydrogen bonds form between
water molecules explain the properties of water

2.3 Carbohydrates and Lipids

 2.3.U1: Monosaccharide monomers are linked together by condensation reactions to form disaccharides
and polysaccharide polymers
 2.3.U2: Fatty acids can be saturated, monounsaturated and polyunsaturated

 2.3.U3: Unsaturated fatty acids can be cis or trans isomers

 2.3.U4: Triglycerides are formed by condensation from three fatty acids and one glycerol
 2.3.A1: Structure and function of cellulose and starch in plants and glycogen in humans

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 2.3.A2: Scientific evidence for health risks of trans fat and saturated fatty acid

 2.3.A3: Lipids are more suitable for long term energy storage in humans than carbohydrates

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 2.3.A4: Evaluation of evidence and the methods used to obtain the evidence for health claims made
about lipids

 2.3.S1: Use of molecular visualization software to compare cellulose, starch and glycogen

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 2.3.S2: Determination of body mass index by calculation or use of a nomogram

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  2.3.NOS: Evaluating claims- health claims made about lipids in diets need to be assessed

2.4 Proteins

Ques Explain the Primary, secondary, tertiary and quaternary levels of protein structure.

1. Primary structure involves the sequence of amino acids that are bonded together by
peptide bond to form a polypeptide
2. secondary structure:
folding / pleating of polypeptides to form - pleated sheets / coiling of
polypeptides to form -helix;held in place by hydrogen bonds;make structure
stable;contributes to strength of fibrous proteins;provide structural role in organisms;eg -
helix is keratin / -sheet is silk;
3. tertiary structure:
3-D shape;due to bonding between amino R-groups / residues;hydrogen bonds / disulphide
bridges / sulphur bonds / ionic bonds;form globular proteins;which are soluble;eg
lysozyme / enzymes;

4. quaternary - linking together of polypeptides to form a single protein;

using the same bonding as for tertiary structure;linking of a non-polypeptide structure /
prosthetic group;named example of quaternary structure eg hemoglobin (has four
polypeptides);
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 2.5 Enzymes
Ques

Ques. Define the term active site of an enzyme.

Ans. the site (on the surface of an enzyme) to which substrate(s) bind / the site (on the
enzyme) where it catalyzes a chemical reaction.

Ques. Outline how enzymes catalyze biochemical reactions.

Ans. bring substrates close together in active site / in correct orientation;
forms enzyme-substrate complex / substrate(s) bind to active site;
lowers the activation energy for the reaction;
weakens bonds in the substrate;

2.5.2 Collision Frequency

The rate of enzyme catalysis can be increased by improving the frequency of collisions via:
 Increasing the molecular motion of the particles (thermal energy can be introduced to increase kinetic energy)
 Increasing the concentration of particles (either substrate or enzyme concentrations)
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2.5.3

Ques. Explain the effects of temperature, pH and substrate concentration on enzyme activity.
ans. enzymes have an active site;
that fits the substrate precisely;
changes in the chemical environment of the enzyme can lead to a
shape / conformational change in the protein;
leading to a change in the shape of the active site;
may interfere with the binding of the substrate with the active site;
altering pH can alter intermolecular interactions within the protein;
or within the active site;
enzymes have an optimum pH;
increase in temperature can increase molecular motion leading to
disruption of intermolecular interactions;
increases chance of enzyme substrate collisions so enzyme activity increases;
optimal temperature;
temperature changes / pH changes can denature the protein;
the more substrate, the more product / more enzyme-substrate complex forms;
after a point, all active sites are bound to substrate / all active sites occupied;
additional substrate will not lead to a greater rate of product formation at
this point;

Ques. Outline enzyme-substrate specificity.

Ans. active site of enzyme binds to specific substrate;

shape of the active site and substrate fit / complement each other;
lock and key model;
chemical properties of substrate and enzyme attract / opposite charges;
enzyme / active site is not rigid and substrate can induce slight changes in shape;
allows substrates of similar structure to bind with same enzyme;
induced fit;
causes weakening of bonds in substrate to lower activation energy;

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 The Lock and Key Model
According to the lock and key model, the enzyme’s active site complements the substrate precisely
The substrate fits a particular active site like a key fits into a particular lock
This theory of enzyme-substrate interaction explains how enzymes exhibit specificity for a particular substrate

2.5.4 Enzymes can be denatured.

Denaturation- structural change in protein --- it result in loss of its biological properties.(usually permanent)
- shape change of active site, substrate cannot fit in, reaction does not proceed.
- due to temperature change, pH change

2.5.5
Immobilised enzymes have been fixed to a static surface in order to improve the efficiency of the catalysed
reaction
 Enzyme concentrations are conserved as the enzyme is not dissolved – hence it can be retained for reuse
 Separation of the product is more easily achieved as the enzyme remains attached to the static surface

Immobilised enzymes are utilised in a wide variety of industrial practices:

 Biofuels – Enzymes are used to breakdown carbohydrates to produce ethanol-based fuels
 Medicine – Enzymes are used to identify a range of conditions, including certain diseases and pregnancy
 Biotechnology – Enzymes are involved in a number of processes, including gene splicing
 Food production – Enzymes are used in the production and refinement of beers and dairy products
 Textiles – Enzymes are utilised in the processing of fibres (e.g. polishing cloth)
 Paper – Enzymes assist in the pulping of wood for paper production

Ques. Outline two examples of the commercial application of enzymes in biotechnology.

Ans. the name of the enzyme and the substrate;
the name(s) of the product(s);
a statement as to why the application is useful commercially;

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 Award [3 max] per example,
eg pectinase acts on (soluble) pectin;
produces smaller, more soluble carbohydrates;
used in fruit juice clarification / to increase yield;

eg endonuclease DNA acts on DNA;

produces DNA fragments;
used in genetic engineering;

eg protease acts on (insoluble) proteins;

produces amino acids;
washing powders - stain removal;

ques. Outline one industrial use of lactose.

Ans. lactose intolerance high in some human populations / Asian / African / native
American and Australian aboriginal populations;
lactase used to produce lactose-free / low-lactose milk;
lactase breaks down lactose to glucose and galactose;
source of lactase is usually yeast / many sources such as bacteria, moulds;
milk passed over immobilized lactase / lactase bound to inert substance;
increase sweetness of milk;
no need to add extra sugar in manufacture of flavoured milk drinks /
frozen desserts;
can add (harmless) bacterium such as L.acidophilus which has same effect on
lactose as in yoghurt;

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2.6 DNA and RNA

QUES. Outline the structure of DNA.

ANS. double helix;

two chains of nucleotides / composed of nucleotides;
nucleotides consist of base, deoxyribose (sugar)and phosphate;
bases are adenine, cytosine, guanine and thymine;
anti-parallel / strands;
3  5 links between nucleotides;
hydrogen bonds between base pairs / purine and pyrimidine on opposite
chains;
only A-T and G-C / complementary base pairs are A-T and G-C;
two bonds between A-T and 3 between G-C;

 2.6.U1: The nucleic acids DNA and RNA are polymers of nucleotides

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 2.6.U2: DNA differs from RNA in the number of strands present, the base composition and the type of
pentose

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 2.6.U3: DNA is double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding
between complementary base pairs

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 2.6.A1: Crick and Watson’s elucidation of the structure of DNA using model making

 2.6.S1: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles,
pentagons, and rectangles to represent phosphates, pentoses and base

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  2.6.NOS: Using models as representation of the real world- Crick and Watson used model making to
discover the structure of DNA
Making DNA Models
Using trial and error, Watson and Crick were able to assemble a DNA model that demonstrated the following:

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 DNA strands are antiparallel and form a double helix
 DNA strands pair via complementary base pairing (A = T ; C Ξ G)
 Outer edges of bases remain exposed (allows access to replicative and transcriptional proteins)

As Watson and Crick’s model building was based on trial and error, a number of early models possessed faults:
 The first model generated was a triple helix
 Early models had bases on the outside and sugar-phosphate residues in the centre
 Nitrogenous bases were not initially configured correctly and hence did not demonstrate complementarity

2.7 DNA Replication, Transcription and Translation

QUES. Living organisms use DNA as their genetic material. Explain how DNA is replicated within the cells of
living organisms.

ANS. helix is unwound;

two strands are separated;
helicase (is the enzyme that unwinds the helix separating the two strands);
by breaking hydrogen bonds between bases;
new strands formed on each of the two single strands;
nucleotides added to form new strands;
complementary base pairing;
A to T and G to C;
DNA polymerase forms the new complementary strands;
replication is semi-conservative;
each of the DNA molecules formed has one old and one new strand;

QUES. The following diagram represents replication in DNA.

A B

Electronically reproduced by permission of Pearson Education,

Inc.,
Upper Saddle River, New Jersey]

(a) State the name and describe the function for the enzymes labelled A and B on the diagram.

(i) A: Name: ..........................................................................................

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 Function: ..........................................................................................

(ii) B: Name: ..........................................................................................

Function: ..........................................................................................
(2)

(b) Identify the cellular location of DNA replication in eukaryotic cells.

....................................................................................................................................
(1)

(c) State at which period during the cell cycle DNA replication occurs.

....................................................................................................................................
(1)

(d) Explain the significance of complementary base pairing during DNA replication.

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(2)

 2.7.U1: The replication of DNA is semiconservative and depends on complementary base pairing

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 2.7.U2: Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds

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 2.7.U3: DNA polymerase links nucleotides together to form a new strand, using a pre-existing strand as a
template

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 2.7.A1: Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain
reaction (PCR)

2.7.S2: Analysis of Meselson and Stahl’s results to obtain support for the theory of semi-conservative
replication of DNA

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 2.7.NOS: Obtaining of evidence for scientific theories- Meselson and Stahl obtained evidence for the
semi-conservative replication of DNA

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 2.7.4 PROTEIN SYNTHESIS
TRANSCRIPTION

QUES. Explain the process of transcription in eukaryotes.

ANS. RNA polymerase controls transcription / is the enzyme used in transcription;

DNA is unwound by RNA polymerase;
DNA is split into two strands;
mRNA is made by transcription;
promoter region (by start of gene) causes RNA polymerase to bind;
anti-sense / template strand of DNA is transcribed;
direction of transcription is 5  3 ;
free nucleotide triphosphates used;
complementary base pairing between template strand and RNA
nucleotides / bases;
Accept this marking point if illustrated using a diagram
RNA contains uracil instead of thymine;
terminator (sequence) stops RNA polymerase / transcription;
mRNA is released / RNA polymerase released;

QUES. Describe the genetic code.

ANS. composed of mRNA base triplets;

called codons;
64 different codons;
each codes for the addition of an amino acid to a growing polypeptide chain;
the genetic code is degenerate;
meaning more than one codon can code for a particular amino acid;
the genetic code is universal;
meaning it is the same in almost all organisms;
(AUG is the) start codon;
some (nonsense) codons code for the end of translation;

Ques.

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QUES. The process of translation involves the use of transfer RNA (tRNA) and amino acids. Outline the
structure of tRNA.

ANS. tRNA is composed of one chain of (RNA) nucleotides;

tRNA has a position / end / site attaching an amino acid;
(Reject tRNA contains an amino acid.)
at the 3' terminal / consisting of CCA / ACC;
tRNA has an anticodon;
anticodon of three bases which are not base paired /
single stranded / forming part of a loop;
tRNA has double stranded sections formed by base pairing;
double stranded sections can be helical;
tRNA has (three) loops (sometimes with an extra small loop);
tRNA has a distinctive three dimensional / clover leaf shape;

The information needed to make polypeptides is carried in the mRNA from the nucleus to the ribosomes
of eukaryotic cells. This information is decoded during translation. The diagram below represents the
process of translation.

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 (a) Annotate the diagram to show the direction in which the ribosome moves during translation.
(1)

(b) State the name of the next amino acid which will attach to the polypeptide.

....................................................................................................................................
(1)

(c) Explain how the amino acid was attached to the tRNA.

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(3)

(d) Identify two locations within a eukaryotic cell where translation occurs.

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 ....................................................................................................................................

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(1)

ANS. (a) 5 3 1
Award the mark only if a single headed arrow is shown.
(b) Alanine / Ala 1
(c) an activating enzyme attaches amino acid to the tRNA;
specific enzyme for specific tRNA;
recognizes tRNA by its shape / chemical properties;
energy (ATP) is needed;
amino acid attached at 3 end;
amino acid attached at CCA; 3 max
(d) rough ER;
cytoplasm;
chloroplast (stroma of) / mitochondria (matrix of); 1 max

QUES. The diagram below shows the structure of a ribosome during protein synthesis.

II polypeptide

I III

IV

(b) State the names of the structures labelled above.

I. ..........................................................................................................................

II. ..........................................................................................................................

III. ..........................................................................................................................

IV. ..........................................................................................................................
(2)

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 (c) State the name of a structure shown on the diagram that has an anticodon.

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(1)

(d) Explain why the process used during protein synthesis in cells is called translation.

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(2)

(e) Explain briefly how termination of translation occurs.

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(2)
ANS. (b) Award [2] for four correct and [1] for three or two correct.
I. small (sub)unit (of ribosome);
II: large (sub)unit (of ribosome);
III: transfer RNA / tRNA;
IV: messenger RNA / mRNA; 2 max
(c) transfer RNA / tRNA 1
(d) codon / triplet of bases to amino acid;
nucleic acid / base sequence / (m)RNA to polypeptide / protein / amino acid
sequence;
genetic code has to be translated; 2 max
(e) stop / terminator / nonsense codon (is reached);
polypeptide is released;
mRNA detaches from ribosome;
subunits of ribosome separate;

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2.8 Cell Respiration

QUES. Explain the similarities and differences in anaerobic and aerobic cellular respiration.
ANS. similarities: 3 max
both can start with glucose;
both use glycolysis;
both produce ATP / energy (heat);
both produce pyruvate;
carbon dioxide is produced;
(both start with glycolysis) aerobic leads to Krebs’ cycle and anaerobic
leads to fermentation;

differences: 5 max
anaerobic:
(fermentation) produces lactic acid in humans;
(fermentation) produces ethanol and CO2 in yeast;
occurs in cytoplasm of the cell;
recycles NADH (NAD+);

aerobic cellular respiration:

pyruvate transported to mitochondria;
further oxidized to CO2 and water (in Krebs’ cycle);
produce a larger amount of ATP (36–38 ATP) / anaerobic produces less ATP (2);
can use other compounds / lipids / amino acids for energy;

QUES. Anaerobic respiration occurs in the absence of oxygen while aerobic respiration requires oxygen.

(a) State one final product of anaerobic respiration.

.....................................................................................................................................
(1)

(b) Complete the table showing the differences between oxidation and reduction.

Oxidation Reduction
Electrons gained or
lost
Oxygen or hydrogen
gained or lost
(2)

(c) The structure of a mitochondrion is shown in the electron micrograph below.

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 Name the parts labelled A, B and C and state the function of each.

Part A: Name: ..........................................................................................................

Function: ......................................................................................................

Part B: Name: ...........................................................................................................

Function: ......................................................................................................

Part C: Name: ...........................................................................................................

Function: ......................................................................................................
(3)

ANS. (a) ATP;

CO2;
ethanol;
lactic acid;
heat energy; 1
(b)
Reaction Oxidation Reduction
Electrons gained or loss of electrons gain of electrons;
lost
Oxygen or hydrogen gain of oxygen / loss of oxygen /
gained or lost loss of H+ / gain of H+ /
hydrogen hydrogen;

Award [2] for four correct and [1] for two correct. 2
(c) A – matrix: site for Krebs’ cycle / link reaction / ATP synthesis;
B – inner membrane / cristae: site of oxidative phosphorylation / e– transport
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 chain / increase surface area / ATP synthesis;
C – inter membrane : H+ / proton build up;
or
C – outer membrane: determines which substances enter the mitochondrion;

QUES. Explain the process of aerobic cellular respiration.

ANS. glucose is broken down to pyruvate in the cytoplasm;

with a small yield of ATP / net yield of 2 ATP;
and NADH + H+ / NADH;
aerobic respiration in the presence of oxygen;
pyruvate converted to acetyl CoA;
acetyl CoA enters Krebs cycle;
Krebs cycle yields a small amount of ATP / one ATP per cycle;
and FADH2 / FADH + H+ / NADH / NADH + H+ /
reduced compounds / electron collecting molecules;
these molecules pass electrons to electron transport chain;
oxygen is final electron acceptor / water produced;
electron transport chain linked to creation of an electrochemical gradient;
electrochemical gradient / chemiosmosis powers creation of ATP;
through ATPase;
[8]

QUES. Explain the production of energy during aerobic respiration from pyruvate that has been
produced by glycolysis.

OR

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 2.9 Photosynthesis

2.9.1 QUES. Write a balanced equation of photosynthesis .

Ans.

2.9.2 Ques. Define electromagnetic spectrum, light, PAR.

Ans.

2.9.3 Ques. Finding an absorption spectrum?

Ans.
 The absorption spectrum indicates the wavelengths of light absorbed by each pigment (e.g. chlorophyll)

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 The action spectrum indicates the overall rate of photosynthesis at each wavelength of light

There is a strong correlation between the cumulative absorption spectra of all pigments and the action
spectrum
 Both display two main peaks – a larger peak at the blue region (~450 nm) and a smaller peak at the red region
(~670 nm)
 Both display a trough in the green / yellow portion of the visible spectra (~550 nm)

Ques. The absorption spectrum of chlorophyll a and chlorophyll b are shown in the graph below.

chlorophyll b

chlorophyll a

Absorbance

400 500 600 700

Wavelength / nm

On the graph above, draw the action spectrum of photosynthesis for a green plant.

Ques. Chromatography and its types-

Ans. Chromatography is an experimental technique by which mixtures can be separated
 A mixture is dissolved in a fluid (called the mobile phase) and passed through a static material (called the
stationary phase)
 The different components of the mixture travel at different speeds, causing them to separate
 A retardation factor can then be calculated (Rf value = distance component travels ÷ distance solvent travels)

Two of the most common techniques for separating photosynthetic pigments are:
 Paper chromatography – uses paper (cellulose) as the stationary bed
 Thin layer chromatography – uses a thin layer of adsorbent (e.g. silica gel) which runs faster and has better
separation

Mechanism and phases of photosynthesis-

Photosynthesis is a two step process:
 The light dependent reactions convert light energy from the Sun into chemical energy (ATP)
 The light independent reactions use the chemical energy to synthesise organic compounds (e.g. carbohydrates)

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 Step 1: Light Dependent Reactions
 Light is absorbed by chlorophyll, which results in the production of ATP (chemical energy)
 Light is also absorbed by water, which is split (photolysis) to produce oxygen and hydrogen
 The hydrogen and ATP are used in the light independent reactions, the oxygen is released from stomata as a
waste product

Step 2: Light Independent Reactions

 ATP and hydrogen (carried by NADPH) are transferred to the site of the light independent reactions
 The hydrogen is combined with carbon dioxide to form complex organic compounds (e.g. carbohydrates, amino
acids, etc.)
 The ATP provides the required energy to power these anabolic reactions and fix the carbon molecules together

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Ques. Explain the reasons for

(a) a large area of thylakoid membrane in the chloroplast.

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.....................................................................................................................................
(2)

(b) low rates of photosynthesis in plants growing beneath trees, where the light has already
passed through the trees’ leaves.

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.....................................................................................................................................
(2)

(c) large amounts of RuBP carboxylase in the chloroplast;

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 .....................................................................................................................................

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(2)
Ans. (a) more chlorophyll / photosystems;
so more light absorbed; 2

(b) insufficient light / poor absorption hence low rate of photosynthesis;

higher leaves absorb majority of red and blue wavelengths;
only green / orange / yellow wavelengths available for lower leaves; 2 max

(c) catalysis of reaction in the Calvin cycle;

RuBP carboxylase not very effective so much needed / reference
to photorespiration;
used for carbon fixation;
carbon fixation is vital to the plant / carbon dioxide needed
for photosynthesis;

Ques. Outline the effect of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.

Ans. light:
rate of photosynthesis increases as light intensity increases;
photosynthetic rate reaches plateau at high light levels;

CO2:
photosynthetic rate rises as CO2 concentration rises;
up to a maximum when rate levels off;

temperature:
rate of photosynthesis increases with increase in temperature;
up to optimal level / maximum;
high temperatures reduce the rate of photosynthesis;

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