Each nucleotide is made up of:

1. Pentose sugar
2. Nitrogenous bases
3. Phosphate group

Pentose sugar:
1. A 5 carbon sugar that occurs in a ring form
2. Two types of pentose found in nucleic acids: ribose in RNA and deoxyribose in DNA
3. Main difference between ribose and deoxyribose:
The hydroxyl group attached to carbon 2 in ribose is replaced with a hydrogen atom

Nitrogenous bases:
1. Heterocyclic ring composed of carbon and nitrogen atoms
2. Each nucleic acids consists of 4 different types of nitrogenous bases, which can be categorised
into:
a. Purines, a six membered ring attached to a five membered ring: adenine and guanine
b. Pyrimidines, a five membered ring: cytosine, thymine and uracil

The three components; nitrogenous bases, pentose sugar and phosphoric acid are joined together to
form a nucleotide via condensation reaction.
1. Carbon 1 of pentose is linked via glycosidic bonds to the nitrogenous bases
2. Carbon 5 of pentose is linked via phosphoester bonds to the phosphate group

1. DNA is a long thin molecule, diameter of 2nm

2. Consists of 2 strands
3. Coiled to form a double helix, with the helix making one complete turn every 3.4nm
4. Has 10 nitrogenous bases to each complete turn of the helix
5. Molar amount of pyrimidines is equal to the molar amount of purines: A+G = C+T
6. A:T ⇒ 1:1, C:G ⇒ 1:1

1. DNA consists of 2 polynucleotide strands

2. Each strand forms a right handed helical spiral, and the two strands are coiled around each other
to form a double helix
3. DNA has a diameter of 2nm.
4. The two polynucleotide strands are antiparallel, with one oriented in the 5’ to 3’ direction and
the other oriented in the 3’ to 5’ direction
5. Each strand has its own sugar phosphate backbone with phosphate groups projecting outwards
from the double helix and nitrogenous bases orienting inwards
6. Specific complementary base pairing occurs between adenine and thymine, and cytosine and
guanine
7. The bases on opposite strands are held together by relatively weak hydrogen bonds:
- A-T base pair is held by 2 hydrogen bonds
 - C-G base pair is held by 3 hydrogen bonds
8. Ratio of A:T is 1:1 and ratio of C:G is 1:1
9. Along the central axis of the DNA molecule, the base pairs are stacked 0.34nm apart. One
complete turn of the double helix has 10 base pairs and spans a distance of 3.4nm.
10. Each DNA strand has many thousands of kilobases.
11. Because of the way the bases are bonded to each other, the two sugar phosphate backbones are
unequally spaced along the central axis resulting in grooves of unequal sizes known as major
grooves and minor grooves.

Replication:
Semi-conservative replication involves the separation of 2 parental DNA strands with each parental
strand serving as a template for the daughter strand. The new daughter molecule is made of one
daughter DNA strand and a parental strand.

1. Replication begins at specific sites known as origins of replication.

2. The two polynucleotide strands separate and form a replication bubble. At the end of the
replication bubble is a replication fork.
3. Replication proceeds in both directions until the entire molecule is copied.

1. Helicase catalyses the breakage of hydrogen bonds, thus separating the 2 parental DNA strands.
2. Single stranded binding proteins bind to the single stranded regions of DNA, helping to maintain
the stability of the replication fork.
3. Topoisomerase creates a transient break by nicking a strand of DNA. This unwinds the DNA
double helix ahead of the replication fork for initiation of replication.

1. Each portion of the parental DNA strand serves as a template for making RNA primer with
complementary base sequence.
2. Primase catalyses the synthesis of RNA primer in 5’ to 3’ direction
3. DNA polymerase (III) can now elongate the strand by adding the next dNTPs to the free 3’
hydroxyl end of the primer
4. DNA polymerase (I) will later replace RNA nucleotides of the primers with DNA nucleotides.

1. The two separated parental DNA strand can form a template along which deoxyribonucleoside
triphosphate can align themselves according to complementary base pairing
2. DNA polymerase (III) catalyses the formation of a phosphoester bond between the 3’ hydroxyl
group of the last nucleotide of the growing strand and 5’ phosphate group of the incoming dNTP
3. DNA polymerase (III) catalyses the polymerisation of new DNA strand in 5’ to 3’ direction
4. The growing new DNA strand is antiparallel to its parental template strand
5. The leading strand is synthesized continuously as a single polymer along the template strand
- The leading strand is polymerised in the mandatory 5’ to 3’ manner towards the
replication fork
 6. The lagging strand is synthesized discontinuously as a series of short fragments known as okazaki
fragments along the template strand
- Each okazaki fragment requires an RNA primer for strand initiation
- Each okazaki fragment is polymerised in the mandatory 5’ to 3’ manner against the
overall direction of replication fork
7. DNA ligase catalyzes the formation of phosphoester bonds between the 3’ end of okazaki
fragments and 5’ end of growing strand
8. Each daughter DNA molecule now consists of a newly synthesized strand and parental strand.

End replication problem:

1. The end replication problem arises due to the specificity of DNA polymerase. Both the 3’
hydroxyl group and 5’ phosphate group are required to fit into the enzyme active site for
reaction to occur. Without 3’ hydroxyl group at the 5’ ends of the newly strands, addition of
DNA nucleotides is impossible, resulting in a gap
2. This shortening of the DNA strand at the end of each replication decreases the number of times
a cell can divide, resulting in apoptosis of the cell.
3. Telomeres which are found at the ends of the DNA molecules are used to buffer the loss of
important genetic information as a result of this end replication loss.

Transcription:
Definition: synthesis of RNA molecule with base sequence complementary to a section of DNA, ie. the
gene

The gene is defined as:

1. An unit of inheritance with a unique base sequence that encodes information specific for the
construction of a particular RNA molecule/ polypeptide chain.
2. A unit of inheritance specifically for a particular type of biological function - phenotype. This unit
of inheritance is located at a fixed position on the chromosome.

1. RNA polymerase recognises and attaches to the promoter of the gene of DNA.
2. RNA polymerase breaks the hydrogen bonds between complementary base pairing for the DNA
double helix.
3. The DNA double helix unwinds and DNA strands separate.
4. One of them serves as a template for making mRNA.

1. Free ribonucleoside triphosphates align themselves along the DNA template strand according to
complementary base pairing.
2. RNA polymerase catalyses the linkages of ribonucleotides by phosphoester bond.
3. RNA polymerase causes the elongation of RNA in the 5’ to 3’ direction by adding ribonucleotides
to the free 3’OH end of the growing RNA.
4. The separated DNA strands rewind into a double helix behind RNA polymerase.
 1. Transcription proceeds until after RNA polymerase transcribes a termination sequence in DNA.
2. RNA polymerase detaches from DNA. mRNA is released.

Features of mRNA:
1. A RNA polynucleotide strand corresponding to a given segment of DNA, which codes for
polypeptide chain
2. Relatively unstable - is continually synthesised and degraded
3. The minimum length of mRNA molecule is set by the length of the polypeptide chain it codes for.
4. The molecule exists as a fairly linear-stranded structure.
5. After transcription, an enzyme from the eukaryotic nucleus modies the primary transcript in
various ways before it leaves the nucleus via nuclear pores.

Post transcriptional modifications:

1. Each end of a pre-mRNA molecule is modified in a particular way
- The 5’ end is immediately capped with a modified form of guanine nucleotide. This 5’
cap has at least 2 important functions:
→ helps protect mRNA from degradation by hydrolytic enzymes
→ after mRNA reaches the cytoplasm, the 5’ cap acts as an “attach” here sign for
ribosomes
- At the 3’ end, an enzyme makes a poly(A) tail consisting of some 50-250 adenine
nucleotides
→ serves to inhibit degradation and probably helps ribosomes to attach to it
→ facilitate export of mRNA from nucleus
2. Spliceosome cuts the introns and joins all the exons together to form a single continuous strand
via a process called splicing.

Translation:
A process whereby a sequence of codons in mRNA is converted into a sequence of amino acids in a
polypeptide chain.

Features of genetic code:

1. T: the genetic code comprises triplets of bases of mRNA, one codon specifically codes for an
amino acid
2. U: the genetic code is universal, the same codons code for the same amino acids across all
species of organisms
3. N: the genetic code is non-overlapping, the mRNA sequence is read continuously in a series of
triplets without skipping any nucleotides
4. D: the genetic code is degenerate, >1 codon may code for the same amino acid
5. The START codon is AUG which also codes for the amino acid methionine and initiates the
synthesis of all polypeptide chains
6. The END codons are UGA, UAA, UAG which do not code for amino acids. It signals the
termination of translation.
S-F of tRNA:
Structure Function

Anticodon at one end Specifies the identity of amino acid attached at

the 3’ end

Specific sequence of bases in anticodon Formation of complementary base pairing with

mRNA codon

3’ CCA end of tRNA Attachment site of specific amino acids

tRNA adopts a compact L-shape/ clover-leaf Anticodon at one end, the point of attachment of
shape amino acid at the other end to reduce steric
hindrance during translation

tRNA has 3 loops 1 loop for forming complementary base pairing

with rRNA of ribosomes
1 loop for binding to aminoacyl-tRNA synthetase
during amino acid activation
1 loop for binding to specific mRNA codon via
complementary base pairing

rRNA:
➔ Plays enzymatic and structural role in ribosomes - site of synthesis of polypeptides
➔ Assembled with proteins imported from cytoplasm to form large and small subunits.

Ribosomes are the sites of polypeptide synthesis. Its composition is 60% rRNA and 40% proteins.

RIbosomes are made up of 2 subunits - large and small subunits.

- The small subunit has a binding site for mRNA
- The large subunit has 3 binding sites for tRNA.
❖ peptidyl-tRNA site holds the tRNA carrying the growing polypeptide.
❖ aminoacyl-tRNA site holds the tRNA carrying the next amino acid to be added to the
polypeptide
❖ Exit site allows the discharged tRNA to leave the ribosome.
- In doing so, the ribosome holds the tRNA and mRNA close together and positions the next amino
acid for addition to the carboxyl end of growing polypeptide. It then catalyses the formation of
new peptide bonds.

1. An amino acid is attached to each tRNA molecule at its 3’CCA end forming an aminoacyl-trna
complex.
2. tRNA binds to their specific amino acids as determined by their anticodons
3. The reaction is catalysed by an enzyme called aminoacyl-trna synthetase.
1. mRNA molecule binds to small ribosomal subunit.
- Initiation begins when the 5’ cap of mRNA fits into the special binding site on the small
ribosomal subunit.
- The small ribosomal subunit binds to initiator tRNA with methionine attached, and then
translocates downstream in search of AUG start codon where translation of coding
regions of mRNA must begin.
2. The anticodon of initiator tRNA binds to START codon of mRNA
3. The large ribosomal subunit binds to the small ribosomal subunit forming a ribosomal complex.

1. Anticodon of incoming tRNA carrying its amino acid pairs with mRNA codon at aminoacyl tRNA
site
2. Peptidyl transferase catalyses the peptide bond formation between the amino acid carried by
ribosome at A site with the ribosome bound by tRNA at peptidyl-tRNA site.
3. The ribosome translocates with tRNA at A site along with its attached polypeptide to the P site,
bringing the mRNA with it
4. The tRNA at P site moves to the exit site and from there, leaves the ribosome
5. The mRNA is moved through the ribosome in the 5’ to 3’ direction only on the mRNA
6. Elongation cycle is repeated until the ribosome reaches a stop codon.

1. Release factor binds directly to the codon at the A site

2. Release factor causes the addition of a water molecule
3. This reaction hydrolyses the completed polypeptide from tRNA and freeing the polypeptide from
ribosome
4. Translational complex is disassembled
5. Polypeptide chain folds into its unique 3 dimensional conformation.