Grade 12 (Biology, 2024)

CHAPTER 2
MOLECULAR BIOLOGY

2.1 INTRODUCTION TO BIOLOGY

1. Define the term molecular biology and explain the nucleic acid. (5 marks)
✓ Molecular biology is the branch of biology that seeks to understand the molecular
basis of biological activity in and between cells, including biomolecular synthesis,
modification, mechanisms, and interactions. The study of chemical, physical
structures, and functions of biological macromolecules is known as molecular biology.
✓ Nucleic acids are the main information-carrying molecules of the cell which direct the
process of protein synthesis by determining the inherited characteristics of every
living thing. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). DNA is the master blueprint for life and constitutes the genetic
material in all free-living organisms and most viruses. RNA is the genetic material of
certain viruses, but it is also found in all living cells, where it plays an important role in
certain processes such as the making of proteins.

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2. Briefly explain the DNA structure together with sugar-phosphate backbone, nucleotides
and complementary base pair. (10 marks)
➢ The structure of DNA
✓ DNA is a double helix structure consisting of two polynucleotide strands twine around
each other.
✓ Each polynucleotide strand is made up of many nucleotide molecules.
✓ Each nucleotide in DNA is composed of a five-carbon deoxyribose sugar, a phosphate
group and a nitrogen containing base, all linked together by covalent bonds.
✓ Four different nitrogenous bases in DNA that can be categorized into two different
forms: purines and pyrimidines.
✓ The purine bases are adenine (A) and guanine (G). They have two fused rings in their
chemical structures.
✓ The pyrimidine bases are cytosine (C) and thymine (T). They have a single ring in their
chemical structure.

✓ Each strand forms a backbone of alternating phosphate groups and sugars.

✓ The bases of each nucleotide are attached to each sugar and protrude inward at
regular intervals along each strand.
✓ There is a constant total distance between the sugar-phosphate backbones.
✓ The two strands of a DNA molecule are not identical but are, instead, complementary
to each other.
✓ This means that a purine molecule is always paired with a pyrimidine molecule.

✓ Specifically, adenine (A) always pairs with thymine (T) and guanine (G) always pairs
with cytosine (C).
✓ This pairing is called complementary base pairing.
✓ As the same bases always complement each other, the base sequence of one strand
can be determined from the base sequence of the other strand.
✓ Hydrogen bonds link each complementary base pair.
✓ A and T are joined by two hydrogen bonds, while C and G with three hydrogen bonds.

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3. Describe the nature of antiparallel strands of DNA molecules. (5 marks)

✓ The two strands of DNA molecule are antiparallel.
✓ So, the sugar molecules are oriented differently.
✓ Therefore, each strand has directionality, or a specific orientation.
✓ One strand lies in 5’to 3’direction and another in 3’to 5’direction.
✓ The 5’ and 3’come from the numbering of the carbons on the deoxyribose sugar.
✓ The phosphate group is on the 5’carbon, and the OH group is on the 3’carbon.
✓ Therefore, the end with phosphate group is always referred as 5’end and the opposite
end of it will be 3’end.
✓ By convention, the sequence of a DNA strand is always written in the 5’to 3’direction.

4. Describe the role of DNA in molecular biology as far as you can. (10 marks)
✓ DNA is the hereditary material responsible for passing genetic information from cell
to cell and generation to generation.
✓ In total, there are around 3.2 billion base pairs in the DNA of a typical mammalian
cell.
✓ This vast number means that there are an almost infinite variety of sequences or
bases along the length of a DNA molecule.
✓ It is this variety that provides the genetic diversity within living organisms.
✓ The DNA molecule is adapted to carry out its functions in a number of ways:
✓ It is a very stable structure which normally passes from generation to generation
without change. Only rarely does it mutate.
✓ Its two separate strands are joined only with hydrogen bonds, which allow them to
separate during DNA replication and protein synthesis.
✓ It is an extremely large molecule and therefore carries a large amount of genetic
information.
✓ By having the base pairs within the helical structure of deoxyribose-phosphate
backbone, the genetic information is to some extent protected from being corrupted
by outside chemical and physical forces.
✓ Base pairing leads to DNA being able to replicate and to transfer information to
mRNA (transcription).
✓ The function of the remarkable molecule, DNA depends on the sequence of base
pairs that it possesses.
✓ This sequence is important to everything it does and, indeed, to life itself.

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5. Explain the structure of RNA molecule, together with different types and their functions.
(5 marks)
The structure of RNA
✓ Like DNA, RNA is a polymer of nucleotides.
✓ RNA contains four nucleotides with the bases; Adenine (A), Uracil (U), Cytosine (C),
Guanine (G).
✓ Unlike DNA, RNA is single stranded.
✓ However, tRNA can fold back on itself, and complementary base paring within the
same molecule stabilizes the looped structure.
✓ Since all are produced from a DNA template, all are synthesized in the nucleus.
✓ There are several types of RNA molecules.
✓ Only three different RNA molecules that involved in protein synthesis and their
functions are listed in Table.

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6. Explain a replication bubble of DNA replication and replication fork. (5 marks)

✓ Proteins and enzymes assist in replication of DNA.
✓ Replication begins at special sites called origins of replication, the replication bubbles
form.
✓ Helicase enzymes unwind the double helix and unzip the two parental strands by
breaking hydrogen bonds.
✓ The separated two parental strands act as templates.
✓ Single-stranded binding proteins act as scaffolding, holding the two strands apart.
✓ Topoisomerase lessens the tension on the tight helix.
✓ At each end of the replication bubble is a replication fork, a Y-shaped region where
the new strands of DNA are elongating.

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7. What do you understand about “Leading and Lagging strands” and role of DNA
polymerase I, during DNA replication? (5 marks)
✓ DNA polymerase replicates the two original strands differently.
✓ Although it builds both new strands in the 5’ to 3’ direction, one strand is formed
towards the replication fork in continuous and linear fashion. This is called the leading
strand.
✓ The other strand, the lagging strand, forms in direction away from the replication fork,
in a series of segments called Okazaki fragments.
✓ Each Okazaki fragment is about 100-200 nucleotides long and then they are joined
into one continuous strand by the enzyme DNA ligase.
✓ DNA polymerase I carry out mismatch repair, a kind of proofreading that corrects
errors.
✓ Damaged regions of DNA are excised out by DNA nuclease.

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8. Clarify the transcription stage of protein synthesis and explain the any two stages.
(10 marks)
✓ Transcription occurs in the nucleus of the cell.
✓ It is the process of copying sequence of DNA to mRNA.
✓ There are three defined stages in the transcription;
initiation, elongation, and termination
Initiation:
✓ For each gene, only one strand of the double-stranded DNA molecule is
transcribed.
✓ This strand is called the antisense strand or template strand.
✓ The other strand, which is not transcribed, is called the sense strand or coding
strand.
✓ It has the same sequence as the product mRNA, with thymine instead of uracil.
Elongation:
➢ During the elongation phase shown, the RNA polymerase complex works its way along
the DNA molecule, synthesizing a strand of mRNA that is complementary to the
template strand of DNA in 5’ to 3’ direction.
Termination:
➢ When the RNA polymerase complexes reach the termination signal, they detach from
the DNA strand.
➢ The new mRNA strand is released from the transcription assembly.

9. Describe the modification of mRNA. (5 marks)

2.1.1 Modification of mRNA
- The newly synthesized mRNA is called precursor mRNA or pre-mRNA.
- Before moving out from the nucleus to the cytoplasm, the following modifications
convert pre-mRNA to mature mRNA.
1. Addition of a 5’cap at 5’end
2. Addition of a 3’poly-A tail at 3’end
3. Removal of introns (non-coding regions) with specific enzyme and the remaining
exons (coding regions) are joined.

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10. Enumerate the translation stage of protein synthesis. (5 marks)

Translation
✓ The second stage of protein synthesis involves translation which occurs in the
cytoplasm.
✓ It is the conversion of a sequence of nucleotides into a sequence of amino acid in the
polypeptide chain.
✓ There are two subunits in the ribosome.
✓ At the small subunits, mature mRNA is attached.
✓ There are three binding sites for tRNA on the large subunit of ribosome: A site, P site,
and E site.
✓ Each tRNA carries the specific amino acid at time at its acceptor stem.
✓ Opposite to the acceptor stem is the anticodon which connects to the specific codon
on the mRNA.

11. Explain the nature of initiation and termination stages of translation process.
(10 marks)
Initiation
✓ Translation occurs in the cytoplasm.
✓ In the initiation phase, all the translation components come together.
✓ The small ribosomal sub-unit attaches to the mRNA near the start codon (AUG).
✓ The first tRNA that binds to the codon is the initiator tRNA with its UAC anticodon,
which joins with the AUG codon of mRNA.
✓ Then, a large ribosomal sub-unit joins to form the active ribosome.
Termination
✓ The termination phase begins when a stop codon on the mRNA is reached.
✓ The polypeptide and the components of the translation machinery are separated.
✓ A protein, called a release factor, cleaves (cuts) the polypeptide from the last tRNA.
✓ The polypeptide is released and will eventually fold into its three-dimensional shape
as protein, ready to carry out its cellular activities.

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12. Explain the nature of elongation stages of translation process. (5 marks)

Elongation phase
✓ The polypeptide becomes longer, adding one amino acid at a time.
✓ During elongation, a cycle of four steps is rapidly repeated.
✓ First, a tRNA with an attached polypeptide is in the P site, then, peptide bond is formed
and tRNA carrying the next amino acid enters the A site.
✓ Next, the polypeptide chain is transferred to the amino acid of the tRNA in the A site.
✓ This makes the polypeptide chain one amino acid longer than before.
✓ Last, the mRNA moves forward by one codon, and the polypeptide-bearing tRNA is
now at the ribosome P site.
✓ The uncharged tRNA exits. The new codon is at the A site and can receive the next
complementary tRNA carrying the next amino acid of the polypeptide.

13. Mention the three important characteristics of genetic code. (10 marks)
✓ The genetic code has three important characteristics.
1. The genetic code is redundant.
✓ This means that more than one codon can code for the same amino acid.
✓ There are only three codons that do not code for any amino acid.
✓ These codons serves as “stop” signals to end protein synthesis.
2. The genetic code is continuous.
✓ a series of three-letter codons without spaces, punctuation, or overlap.
✓ Knowing exactly where to start and stop protein synthesis is essential.
✓ A shift of one or two nucleotides in either direction can alter the codon groupings and
result in an incorrect amino acid sequence.
3. The genetic code is nearly universal.
✓ Almost all organisms build proteins with the genetic code.
✓ The universality of the genetic code means that a codon in the fruit fly codes for the
same amino acids as in a human.
✓ This has important implication for gene technology, such as cloning.
✓ A gene that is taken from one kind of organism and inserted into another kind of
organism will produce the same protein.

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14. Describe the method of recombinant DNA with appropriate illustration. (5 marks)
2.1.2 Recombinant DNA
✓ It is a method of transferring a gene from one organism into the genome of another
organism of different species.
✓ In order to insert the recombinant gene into a target cell, a vector is needed, which
may be plasmid of bacteria, harmless virus, liposome or gene gun.

15. What do you understand the role of golden rice. (10 marks)
2.1.3 Production of golden rice
✓ Rice is a staple food in many parts of the world.
✓ Vitamin A deficiency can cause blindness.
✓ Even more importantly, lack of vitamin A can cause an immune deficiency syndrome,
and this is a significant cause of mortality in some parts of the world, particularly in
children.
✓ Children of families living in poverty often lack animal products in their diets as they
are too expensive.
✓ Even if such children have a diet containing a wide range of vegetables rich in
carotenoids, it is still difficult for them to avoid vitamin A deficiency.
✓ Further research showed that substituting the gene from daffodils plant with one from
maize gave even higher quantities of carotene, and the single transformation with
these genes is the basis of all current Golden Rice.
✓ The genetically modified rice is called Golden Rice, because it contains a lot of the
orange pigment beta-carotene which can be converted into vitamin A when it is eaten.

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16. State the production of genetically engineered organisms. (5 marks)

✓ Genetic engineering is the alteration of the genetic material of an organism in a
specific manner.
✓ Transgenic bacteria, plants, and animals are commonly referred to as genetically
modified organisms (GMOs).
✓ Transgenic describes an organism that is produced from the introduction of foreign
DNA into its genome, providing it with a new phenotype.
✓ The recombinant DNA techniques and methods of DNA analysis are integral to the
production of GMOs.

17. Enumerate the benefits of genetic engineering of crops. (5 marks)

✓ Benefits of genetic engineering of crops include:
1. Increased crop yield,
2. Increased heat and drought tolerance,
3. Increased resistance to a range of pests and pathogens,
4. Increased salt tolerance, reduction in harvesting cost and pesticide use, and
5. Enhanced nutritional value and food quality due to slower spoilage.
✓ Moreover, plants are also being engineered to produce medicinal products.
✓ Since the mid-1980s, products such as human growth hormone, clotting factors, and
antibodies have been produced in transgenic plants.
✓ For instance, one type of antibody made by corn can deliver radioisotopes to tumour
cells.
✓ Another made by soybeans can be used to treat genital herpes.

18. Enumerate the benefits of genetically modified animals. (5 marks)

✓ Benefits of GM animals are
1) Increased production of a particular product, higher milk yield in cows, greater
muscle mass in animals used for meat,
2) Increased resistance to disease
3) Manufacture of human proteins, such as antibodies, blood clotting factors or
important proteins for medicinal purposes and
4) Production of organs for transplantation (xeno-transplantation)

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(xeno

19. Describe the steps in production of genetically modified animal. (5 marks)

- Clone a human hormone gene into a plasmid vector next to a sheep beta-lactoglobulin
promoter. This promoter is functional only in mammary cells, so the protein product
is secreted into the milk.
- Inject this recombinant plasmid into a sheep oocyte.
- The plasmid DNA will integrate into the chromosomal DNA, resulting in the condition
of the hormone gene into the sheep’s genome.
- The oocyte is fertilized and implanted into a female sheep, which then gives birth to a
transgenic sheep offspring.
- Obtain milk from a female transgenic sheep. The milk contains a human hormone.
- Purify the hormone from the milk.

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20. Give an account of the production of genetically modified animals. (10 marks)
✓ The production of transgenic animals is a much more complex process than the
production of transgenic plants, and not surprisingly, it is also highly controversial.
✓ To produce transgenic animals, a foreign gene is inserted into the genome of an animal
oocyte (egg) that is then fertilized.
✓ The fertilized egg is implanted in a host female and allowed to develop.
✓ The resulting offspring are the transgenic form of the animal.
✓ The procedure has been used to produce transgenic fish, pigs, cows, rabbits, and
sheep.

✓ Transgenic animals can be used to produce pharmaceutical products such as human

proteins by using a recombinant plasmid vector.
✓ The vector contains the gene for the growth protein as well as the promoter that
directs the expression of the genes in mammary cells.
✓ The recombinant DNA is then injected into an oocyte.
✓ The oocyte is fertilized and implanted into a host female.
✓ The transgenic animals are the offspring produced from that implantation.
✓ The milk of female transgenic offspring contains human growth protein.
✓ Benefits of GM animals are
i. Increased production of a particular product, higher milk yield in cows, greater
muscle mass in animals used for meat,
ii. Increased resistance to disease
iii. Manufacture of human proteins, such as antibodies, blood clotting factors or
important proteins for medicinal purposes and
iv. Production of organs for transplantation (xeno-transplantation)
21. Describe the four steps in nucleotide excision repair of DNA damage. (5 marks)
- Teams of enzymes detect and repair damaged DNA, such as this thymine dimer (often
caused by ultraviolet radiation), which distorts the DNA molecule.
- A nuclease enzyme cuts the damaged DNA strand at two points, and the damaged
section is removed.
- Repair synthesis by a DNA polymerase fills in the missing nucleotides.
- DNA ligase seals the free end of the new DNA to the old DNA, making the strand
complete.

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2.1.4 DNA replication

✓ Making of an exact copy of the DNA molecule.

✓ The replication is made by a semiconservative method, which was predicted by
Watson and Crick and proven by Meselson and Stahl.
✓ It is regarded as semiconservative because each of the resulting two molecules
consists of one old strand and one new strand.

✓ DNA polymerase III cannot initiate the synthesis.

✓ The preexisting chain actually consists of RNA primer produced by an enzyme called
primase.
✓ As the two strands of DNA are antiparallel, they are oriented in opposite directions
to each other.
✓ Therefore, the formation of two new strands must also be antiparallel to their
template strands.
✓ DNA polymerase can only add complementary nucleotides,
✓ C with G and A with T, to the free 3’ end of the primer,
✓ never to the 5’ end.
✓ Thus, a new DNA strand can elongate only in the 5’ to 3’ direction.
✓ Each time the DNA replicates, some nucleotides from the chromosome are lost.
✓ To protect against the possible loss of genes at the end of the chromosomes,
eukaryotes have special nonsense nucleotide sequences (TAAGGG) at the ends of
chromosomes that repeat thousands of times.
✓ These protective ends are called telomeres, which are created and controlled by the
enzyme telomerase.
✓ So, every time DNA replicate, the telomeres get shorter.

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2.2 Genetic code

✓ for determining how genetic information in the form of a nucleotide sequence is
converted to an amino acid sequence of a protein.
✓ It defines a code specifying the relationship between a nucleotide codon and an
amino acid.
➢ There are only four nucleotides in RNA (A, U, G and C),
➢ But 20 different kinds of amino acids.
✓ If 2 nucleotides per amino acid would only provide 4x4 or 16 possible combinations,
✓ Thus, the minimum combination of the four nucleotides was a triplet code, which
could produce 4x4x4, or 64 possible combinations.
✓ From this reasoning came the triplet hypothesis, which proposed that the genetic
code consists of a combination of three nucleotides, called a codon.
✓ Between 1961 and 1965, various research groups compared artificially synthesized
RNA molecules of known nucleotide sequences with the amino acid sequences of
polypeptides.
✓ From these studies, the mRNA codons and their corresponding amino acids were
determined. These are listed in Table.

✓ By convention, the genetic code is always interrupted in terms of the mRNA codon
rather than the nucleotide sequence of the DNA.

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2.3 Protein synthesis

✓ The two steps in protein synthesis are transcription and translation.
✓ In transcription, mRNA is synthesized based on the DNA template of a gene.
✓ This is followed by translation, which involves the production of a protein with an
amino acid sequence that is based on the nucleic acid sequence of mRNA.
✓ The central dogma of molecular biology stated that genetic information flows from
DNA to RNA to Protein.
✓ The translation of nucleotide sequence to amino acid sequence uses the genetic code.

2.4 Some techniques in molecular biology

✓ There are some exciting technologies emerging from research in molecular genetics,
which has provided the ability to manipulate the genes of organisms
(microorganisms, plants, and animals).
✓ Scientists can now use genetically modified organisms (GMOs)
o to produce medication,
o to profile the DNA sequence of a cancerous tumor, and
o to treat genetic disorders
o by introducing the correct form of a disease-related gene into an individual’s
genome.
✓ Another intriguing research focus is the relationship between aging and
chromosomes.

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