Basic Molecular Biology

Question 1

What are the components of a nucleotide?

Answer 1

A 5-carbon sugar (deoxyribose or ribose), a nitrogenous base (A, T, C, G, U) and a phosphate group

Question 2

Name a difference between purines and pyrimidines

Answer 2

Purines (A and G) have a double ring and pyrimidines (C, T, U) have a single ring

Question 3

What are the three main mechanisms of epigenetic regulation of gene expression?

Answer 3

DNA methylation, histone modification and ATP-dependent chromatin remodelling

Question 4

What are gene promoters comprised of?

Answer 4

A 5’ ‘proximal’ sequence which is upstream of the ‘core’ sequence. The proximal sequence binds transcription factors that modify the affinity of the core region and for the binding of RNA polymerase. The core sequence binds the RNA polymerase and includes the transcription start site and the TATA box where the transcription bubble forms.

Question 5

What are the 3 stages of DNA replication?

Answer 5

Initiation: at an origin recognition complex (ORC), orchestrated by CDK/cyclin complexes. Involves binding of DNA polymerase.

Elongation: of the nascent strand

Termination: either at the end of the strand or when two replication forks meet

Question 6

What is the main stages in the mechanism of splicing?

Answer 6

1. The spliceosome (large RNA-protei complex comprised of small nuclear ribonucleoproteins (snRNPs) binds to an intron causing it to fold, to bring the 5’ and 3’ intron ends together (specifically, the donor site to the branchpoint).
2. The 5’ end is cleaved, forming a lariat
3. The 3’ end is cleaved and the exon ends are ligated.
4. The intron lariat is degraded

Question 7

What is NMD and what is its purpose?

Answer 7

Nonsense mediated decay: a mechanism that targets mRNA transcripts with premature termination codons for degradation to protect against dominant negative or gain of function effects of truncated proteins. It is also used to fine-tune gene expression levels.

Question 8

What is the difference between BER and NER repair pathways?

Answer 8

Base excision repair (BER) repairs non-bulky damage caused by deamination, a loss of base or oxidation. This involves the removal of the damaged base, then the removal of the nucleotide by AP endonuclease (APE1).

Nucleotide excision repair (NER) repairs bulky adducts, crosslinks and pyrimidine dimers (e.g. by UV damage). This pathway removes a number of nucleotides within the region before the sequence is replaced with new nucleotides.

Question 9

What are the main functions of tumour suppressor genes?

Answer 9

Tumour suppressor genes regulate several cellular functions. These genes can be broadly classified based on their role in cell growth/cell cycle progression, cell proliferation, DNA repair mechanisms, and other crucial cellular signalling functions such as the apoptosis induction.
Without functional tumour suppressor genes, there is a high risk of dysregulated cell growth and development of cancers.

Question 10

What type of mutation is a driver in a tumour suppressor gene?

Answer 10

Loss of function (Nonsense, frameshift, deletions, out of frame rearrangements)

Question 11

What role do proteins produced by onocogenes perform?

Answer 11

The majority of oncogene proteins function as elements of the signalling pathways that regulate cell proliferation and survival in response to growth factor stimulation

Question 12

What are the mechanisms which lead to oncogenic activation?

Answer 12

Gene amplification (duplication / overexpression)
Activation by SNVs (Missense)
In frame rearrangements