Prok & Euk Part 2: Control

Question 1

What is heterochromatin?

Answer 1

It is a highly compacted DNA where DNA winds more tightly around histones, this results in the silencing of genes as it limits access of RNA polymerase and general transcription factors to promoters of genes and thus prevent formation of transcription initiation complex

Question 2

What is euchromatin?

Answer 2

It is a less compacted DNA where DNA winds less tightly around histones. it allows access of RNA polymerase and general transcription factors to promoters of genes, allowing formation of transcription initiation complex.

Question 3

What is the chromatin remodeling complex?

Answer 3

They are protein complexes that alter structure of nucleosomes temporarily, resulting in either DNA being less tightly bound to histones or DNA being more tightly coiled around histones.

Question 4

What is DNA Methylation

Answer 4

DNA methylation involves the addition of methyl group to nucleotides in CG sequences.

Question 5

How does DNA Methylation prevent transcription?

Answer 5

• It blocks the binding of general transcription factors and thus assembly of transcription initiation complex at promoter
• It recruits DNA-binding proteins to the methylated DNA to condense chromatin, resulting in gene silencing

Question 6

What is histone acetylation or disacetylation?

Answer 6

Acetylation and disacetylation of histones allows chromatin to decondense and condense respectively, alternating between loose and tightly condensed states.

Question 7

What enzyme catalyses histone acetylation?

Answer 7

Histone Acetyl Transferase

Question 8

Describe the process of histone acetylation.

Answer 8

Addition of acetyl groups to lysine residues removes positive charges on histones. Tight binding between DNA and histones is loosened making promoter region more accessible to RNA polymerase and general transcription factors. This works in concert with chromatin remodeling complex, allowing formation of the transcription initiation complex

Question 9

What enzyme catalyses histone deacetylation?

Answer 9

Histone Deacetylase

Question 10

Describe the process of histone deacetylation.

Answer 10

it involves the removal of the acetyl groups, restoring a tighter interaction between DNA and histones, inhibiting transcription

Question 11

Describe gene amplification.

Answer 11

It refers to the replication of a specific gene multiple times to create more copies of that gene. Thus, during transcription and translation, more copies of mRNA and required proteins will be obtained.

Question 12

Describe the initiation of transcription.

Answer 12

The general transcription factors assemble at the TATA box in the promoter region. Transcription factors recruits RNA polymerase and positions it correctly at the promoter. Whole complex of GTFs and RNA polymerase is called a transcription initiation complex.

Question 13

What can control elements be divided into?

Answer 13

Proximal control elements (e.g. promoters) and distal control elements (e.g. enhancers and silencers)

Question 14

How does activators binding to enhancers increase frequency of transcription?

Answer 14

• Upon binding of activators to enhancers, spacer DNA (regions of non-transcribed DNA between genes) bends. Bending of spacer DNA allows direct interaction of activators with RNA polymerase and general transcription factors at the promoter, promoting assembly of transcription initiation complex.
• Bound activator may recruit histone acetyl transferase and chromtin remodeling complex to decondense chromatin, allowing greater accessibility of general transcription factors and RNA polymerase to the promoter

Question 15

How does repressors binding to silencers decrease frequency of transcription?

Answer 15

• Interferance with action of activators by masking DNA activation site, competitive DNA binding or direct interaction with general transcription factors.
• Bound repressors may recruit histone disacetylase and repressible chromatin remodeling complex to condense chromatin, reducing accessibility of general transcription factors and RNA polymerase to the promoter

Question 16

What enzyme is involved in the splicing of pre-mRNA?

Answer 16

Spliceosome or a snRNA (small nuclear RNA) -protein complex

Question 17

What is the importance of poly-A tail at the 3’ end of mRNA

Answer 17

• Enhances half-life/stability of mRNA by slowing down its degradation by ribonucleases
• serves as a signal to direct export of mature mRNA from nucleus to cytoplasm
• interacts with initiation factors to form translation initiation complex

Question 18

Describe the initiation of translation

Answer 18

Small ribosomal subunit, eukarotic translation initiation factors and initiator-tRNA form a complex. The complex binds to the 5’ cap and poly-A tail causing the mRNA to circularise. The complex then moves in the 5’ to 3’ direction along the mRNA to scan for and locate the start codon, AUG. Bind of the large ribosomal subunit completes the translation initiation complex.

Question 19

What are the controls at translational level?

Answer 19

• mRNA stabilty/half-life
• Anti-sense RNAs
• Binding of translation repressors
• Initiation factors

Question 20

What are the controls at transcriptional level?

Answer 20

• Promoter
• Enhancers and silencers

Question 21

What are the controls at genomic level?

Answer 21

• Chromatin remodeling complex
• DNA methylation
• Histone acetylation/disacetylation

Question 22

What are the controls at post-transcriptional level?

Answer 22

• Capping at 5’ end of mRNA
• Splicing of pre-mRNA
• Adding of poly-A tail to 3’ end

Question 23

What are the controls at the post-translational level?

Answer 23

• Covalent modifiations to form functional proteins
• Phosphorylation - dephosphorylation to regulate protein activity
• Protein degradation

Question 24

Describe the function of anti-sense RNA.

Answer 24

Under certain conditions, anti-sense RNA which is complementary to part of the mRNA to be degraded will be synthesised. It will complementary base pair with mRNA to form double stranded RNA. The double stranded RNA will be targeted for degradation by ribonucleases and will block translation of the mRNA

Question 25

Describe the function of translation repressors.

Answer 25

Translation initiation can be blocked by preventing formation of translation initiation complex. This can be achieved when small ribosomal subunit cannot bind and is blocked by a translational repressor protein that bind to:
(a) 5’ cap and/or its vicinity
(b) 3’ untranslated region to interfere with interaction between 3’ poly-A tail, initiation factors and 5’ cap needed for translation

Question 26

How does covalent modifications control proteins?

Answer 26

Covalent modifications in the form of glycosylation, disulfide bond formation and attachment of prosthetic groups may be necessary for protein activation.

Question 27

How does phosphorylation and dephosphorylation regulate protein activity?

Answer 27

Addition of phosphate group to protein can render it active or inactive, while dephosphorylation has the opposite effects.

Question 28

Describe the process of protein degradation.

Answer 28

Ubiquitin ligase tags a protein for degradation by catalysing the addition of protein, ubiquitin to target protein. The ubiquitin-tagged protein is then recognised by a proteasome which cleaves this protein into smaller peptides which can be further degraded by enzymes in cytoplasm.