Lecture 4

Question 1

What is the common structure properties of nucleotides like RNA and DNA?

Answer 1

➢ One to three phosphate group(s)
➢ a pentose (5-carbon atom) sugar,
➢ a nitrogenous base (a pyrimidine or purine)

Question 2

What bases are purines? structure difference?

Answer 2

Adenine & Guanine
- have two cylical shapes (pentagon and hexagon)

Question 3

What bases are pyrimidines?
structure diff?

Answer 3

Thymine, Uracil and Cytosine
- have ONLY ONE cyclical shape

Question 4

What sugar and base is ONLY in RNA?

Answer 4

-Ribose (containing two OH group)
- Uracil instead of thymine

Question 5

What sugar and base is ONLY in DNA?

Answer 5

• Deoxyribose (containing one OH and one H)
  -Thymine instead of Uracil

Question 6

What are nucleotide functions as monomers?

Answer 6

• Building Blocks of Nucleic Acids (DNA & RNA)
  -Energy carriers (cell energy currency), carrying high-energy
  bonds between phosphate groups (e.g. ATP, GTP)
  -Form coenzymes (essential for enzymatic activity)
  -Intracellular signalling molecules (e.g. cyclic AMP)

Question 7

What is the structure of the DNA/RNA strand/ backbone?

Answer 7

In DNA/RNA, nucleotides are covalently linked to form polynucleotide strand (backbone)
▪ via phosphodiester bonds, linking 5’ phosphate of one nucleotide to the 3’ OH of the next
▪ Creating a 5’-to-3’ directionality
▪ Nucleic acids of human cells has a 5’ end and a 3’ end
➢ (e.g., 5’-TCG-3’)

Question 8

What is the structure of B DNA?

Answer 8

DNA (in B form) has two helical grooves of different widths, providing binding sites
for proteins/drugs
➢ major - wider
➢ minor - narrower

Question 9

What is the advantage to RNA being single stranded?

Answer 9

▪ dsRNA (double stranded) is possible in nature. Many viruses contain dsRNA genomes.
▪ Immune cells recognise dsRNA as a viral signature, triggering antiviral responses.

Question 10

What is DNA denaturation?

Answer 10

DNA Denaturation → separation of the DNA double strands into single strands
* DNA renaturation → When conditions are reversed, H bonds can be reformed →

▪ High temperatures (90-100°C) break H-bonds between complementary nucleotides
▪ Higher G-C content increases DNA stability than A-T. (3 H-bonds vs 2) thus more energy needed
▪ Principles of the PCR technique to amplify specific regions of DNA

Question 11

What is a gene?

Answer 11

A DNA segment that encode specific, inheritable traits.
* Nucleotide sequence in genes determine the specific amino acid sequence of certain
proteins through the GENETIC CODE (DNA → RNA → PROTEINS)– Lec. 4
* Human genome has ≈ 25,000 genes (<1.5% of DNA)

Question 12

Where is DNA found in eukaryotic cells?

Answer 12

Nuclear DNA in the nucleus
Mitochondrial DNA in the mitochondria

Question 13

What is DNA replication?

Answer 13

DNA replication is the process by which DNA makes a copy of itself, before cell divisions
▪ Each chromosome will result in 2 identical DNA (sister chromatids)
▪ Copied DNA is segregated into daughter cells
▪ Occurs in the nucleus during the S phase of interphase

Question 14

What type of process is DNA replication?

Answer 14

DNA replication is a SEMI-conservative process

Question 15

What are the four stages to DNA Rep?

Answer 15

1. Replication Fork Formation
2. Initiation
3. Polymerase elongation
   4.Termination

Question 16

Describe Replication Fork Formation

Answer 16

• DNA replication starts at a sequences called
  origin of replication (rich in A - T)
• At each, DNA is denatured by initiator proteins
• Helicase enzymes unwind/unzip the DNA
  double strands bidirectionally, by breaking H-
  bonds, creating two Y-shaped replication forks

Question 17

Describe initiation

Answer 17

• DNA polymerase requires an RNA primer, created
  by primase enzyme, to initiate synthesis
• DNA polymerase attaches to the 3’ end of the primer
  and synthesises new DNA strand in the 5’->3’
  direction, using the parental strand as a template
• DNA polymerase forms phosphodiester bonds
  between nucleotides, extending the new DNA strands
• The process requires deoxynucleotide triphosphates
  (dNTPs) to drive the reaction

Question 18

Describe elongation

Answer 18

Replication of leading strand is continuous
▪ Same direction as the growing replication forkReplication of the lagging strand is discontinuous
▪ It requires many RNA primers
▪ Synthesis in short DNA fragments (Okazaki
fragments), each initiated by a new RNA primer

Question 19

Describe termination

Answer 19

A nuclease degrades RNA primers
➢ The gaps are filled by DNA polymerase
➢ The enzyme DNA ligase joins adjacent Okazaki
fragments → DNA Replication is complete

Question 20

What is a benefit of DNA Polymerase?

Answer 20

DNA polymerase has proofreading activity to check &
correct base-pairing errors
▪ When a mismatch occurs, DNA polymerase removes the
incorrect nucleotide and replaces it with the correct one.

Question 21

What does DNA helicase do?

Answer 21

Unwinds parental double helix

Question 22

What does DNA ligase do?

Answer 22

Joins Okazaki fragments and seals other breaks in sugar-phosphate backbone

Question 23

What does primease do?

Answer 23

Synthesise RNA primers for DNA polymerase to start the polymerisation process

Question 24

What does DNA topoisomerase do?

Answer 24

Unravel twists in DNA that occur as a result of DNA replication