Functions and Dysfunctions of Genomic Regulation

Question 1

What effect does acetylation have on chromatin?

Answer 1

It opens the chromatin and transcriptionally activates it.

Question 2

What residues of histone proteins are targets for post translational modification?

Answer 2

Lysine residues

Question 3

How many histones are in each nucleosome core particle?

Answer 3

8 histone proteins

Question 4

What does DNA polymerase require to begin processing?

Answer 4

A free 3’-OH

Question 5

What is miRNA?

Answer 5

A biological process in which RNA molecules inhibit gene expression, or translation.

Question 6

What is the significance of long terminal repeats (LTRs)?

Answer 6

Formed by reverse transcription of retroviral RNA. Used by viruses to insert their genetic material into the host genomes.

Question 7

What are topoisomerase and what is its clinical significance?

Answer 7

Breaks phosphodiester bond in DNA to relieve supercoiling created my replication. Drugs that target topoisomerase are used as anti-cancer drugs.

Question 8

What are nucleoside analogue inhibitors and how do they work?

Answer 8

They are nucleoside analogues that lack the 3’-OH. Because of this, they arrest DNA synthesis by acting as chain terminators. Can be used to treat cancers and viral infections.

Question 9

Describe the effect of UV radiation (non-ionizing radiation) on DNA.

Answer 9

Can produce a covalent linkage between two adjacent pyrimidines (T-T or C-T), creating pyrimidine dimers.

Question 10

Describe the effect of ionizing radiation on DNA.

Answer 10

It can lead to double strand breaks, chemical modification of bases, and DNA-protein cross-links.

Question 11

What are the two main types of spontaneous DNA damage?

Answer 11

Depurination and deamination

Question 12

What are the different types of deamination?

Answer 12

Adenine to Hypoxanthine
Guanine to Xanthine
Cytosine to Uracil

Question 13

Where are CpG Islands found and what is its role in gene expression?

Answer 13

They are found in the promotor regions of DNA. Methylation of CpG islands stably silences genes.

Question 14

What carcinogen is a metabolism product following the consumption of well done meat? What is its pro-carcinogen?

Answer 14

Carcinogen: BPDE

Pro-carcinogen: benzo[a]pyrene

Question 15

What are the different types of chemical agents that can cause DNA damage?

Answer 15

Cross-linking agents, alkylating agents, and intercalating agents.

Question 16

What is Thalidomide?

Answer 16

An intercalating agent. Initially used as an anti-anxiety medication, but later found to cause birth defects.

Question 17

What are the symptoms of Xerderma pigmentosum (XP) and what repair pathway is affected by it?

Answer 17

UV sensitivity and increased rate of skin cancer. Defect in nucleotide excision repair.

Question 18

What are the symptoms of hereditary nonpolyposis colorectal cancer (HNPCC) and what repair pathway is affected by it?

Answer 18

Increased rate of colon cancer. Defect in mismatch excision repair.

Question 19

What are the symptoms of Cockayne syndrome and what repair pathway is affected by it?

Answer 19

Neurodegenerative disorder characterized by growth failure, photosensitivity, and premature aging. Defect in transcription coupled nucleotide excision repair.

Question 20

How is HNPCC inherited?

Answer 20

In an autosomal dominant manner.

Question 21

A mutation in what enzyme and repair mechanism can cause breast cancer?

Answer 21

BRCA2, repair by homologous recombination

Question 22

Describe nucleotide excision repair.

Answer 22

Used to repair chemical adducts that distort DNA. NER complex removes stretch of DNA and DNA polymerase fills in the gap. Ligase seals nicks.

Question 23

Describe mismatch excision repair.

Answer 23

Used to repair incorrect base in newly synthesized daughter strand. MER complex binds DNA with mismatch and removes region. DNA polymerase fills in the gap. Ligase seals nicks.

Question 24

What is the consequence of non-homologous end joining following a double strand break?

Answer 24

One or more nucleotides will be lost in the process

Question 25

What is rifampicin?

Answer 25

An antibiotic that inhibits bacterial RNA synthesis. It has a side effect of increasing the metabolism of other drugs.

Question 26

What is the significance of DNA methylation occurring at gene promoter CpG islands?

Answer 26

It blocks transcription and can be inherited by daughter cells following cell division.

Question 27

What is the significance of ubiquitin in protein degradation?

Answer 27

When bound to a protein, it signals a proteasome to digest the protein into peptides.

Question 28

Describe SUMO-Targeted Ubiquitin Ligases (STUbLs).

Answer 28

Contains a RING domain that puts ubiquitin on proteins. Also contains SUMO-interacting Motifs (SIMs) that interact with SUMO.