Genomic Regulation

Question 1

What are the 3 roles of the nucleus?

Answer 1

Cell regulation
Proliferation
DNA transcription

Question 2

Describe the central dogma of genetics.

Answer 2

DNA -> RNA -> Protein

DNA –> RNA (transcription)
RNA –> Protein (translation)

Question 3

Which part of the central dogma does RNA virus such as HIV affect? What is the enzyme this virus utilizes?

Answer 3

DNA –> RNA (Transcription)

Reverse Transcriptase

Question 4

Why are mitotic chromosomes condensed 500 times more than interphase chromosomes?

Answer 4

To prevent physical damage to the DNA as chromosomes are separated and passed on to daughter cells.

Question 5

How is DNA packaged? (Hint: What kinds of bonds are used, there are 3 of them)

Answer 5

DNA hydrogen bonds with the histone octamer in each nucleosome.

2 other bonds include hydrophobic interactions and Salt linkages

Question 6

______ _____ are highly conserved across species.

Answer 6

Histone proteins

Theres only a 2 amino acid difference between a pea and a cow histone H4

Question 7

What is the charge of histones? Why is this important?

Answer 7

Positive, this is important because DNA is negative and therefore binds to positively charged histones

Histones have many Lysine and Arginine Amino acids

Question 8

Which part of the histone is targeted for post-translational modifications?

Answer 8

Lysine residues

Question 9

____ are the basic unit of chromosome packing

Answer 9

Nucleosomes

Question 10

Proteins that bind to DNA are made up of what two classes?

Answer 10

Histones

Non-histone chromosomal proteins (transcription factors)

Question 11

Each nucleosome core particle consists of a complex of ____ ____ ____

Answer 11

Eight histone proteins

Question 12

What are the 2 components of a chromatin? What does this form?

Answer 12

Protein and DNA

This forms beads on a string

Question 13

TF Euchromatin is often under active transcription

Answer 13

True

Question 14

What two places of the chromosome are heterochromatins concentrated?

Answer 14

At the centromeres and telomeres

Question 15

Long Terminal Repeats (LTRs) are formed by what enzyme?

What are they used for?

Answer 15

Reverse Transcriptase of retroviral RNA

Used by viruses to insert their genetic material into the hosts genomes

Question 16

What does DNA polymerase require to begin the replication process?

Answer 16

DNA Polymerase requires a free 3’ -OH group to begin the replication process

Question 17

During replication, which strand is synthesized continuously and which in segments?

Answer 17

Leading strand is synthesized continuously

Lagging strand is synthesized in segments

Question 18

What is the function of Single-Stranded DNA Binding Proteins (SSBP)? What does this prevent the formation of?

Answer 18

They bind cooperatively to exposed ssDNA and stabilize them. This prevents the formation of hairpins.

Question 19

During DNA replication, the replication fork creates an un-winding problem for the parental helix. What enzyme is utilized to relieve this stress?

what enzyme is this called in bacteria?

Answer 19

Topoisomerase relieves this supercoil

AKA as DNA Gyrase in bacteria

Question 20

How can Topoisomerase Inhibitors be used to prevent cancers?

What does do Topoisomerase Inhibitors lead to?

Answer 20

Without Topoisomerases activity, the cell cycle is blocked and generates single and double stranded breaks, which harms the integrity of the genome.

This leads to apoptosis and death of the cancer cell

Question 21

Does DNA Polymerase have the ability to proofread DNA?

Answer 21

Yes

Question 22

Differentiate between Germ cells and Somatic cells in terms of mutation rates and how this affects the organism.

Answer 22

Germ cells have low mutation rates in order to maintain the species

Somatic cells have low mutations rates to avoid cancer

Question 23

What is the function of Histone Deacetylase (HDAC)?

What is the function of Histone Acetylase (HAT)?

Answer 23

Histone Deacetylase (HDAC) is used to repress gene expression by compacting the chromatin

Histone Acetylase is used to activate gene expression by opening the chromatin and making it transcriptionally active

Question 24

What kinds of modifications do histone proteins undergo?

Answer 24

Post-Translational Modifications

Question 25

What are the 4 components of a histone?

Answer 25

H2A H2B H3 H4

Question 26

Which 2 components of the histone protein have long tails protruding from the nucleosome?

Answer 26

H3 and H4

Question 27

What are the 7 types of Post-Translational Modifications?

Answer 27

``` Methylation Acetylation Phosphorylation Ubiquitination SUMOylation Citrullination ADP-ribosylation ```

Question 28

Differentiate between the 2 types of spontaneous DNA damage, Depurination and Deamination?

Answer 28

Depurination- losing a Guanine or an Adenine Deamination- oxidizing an amino side chain. Can be Adenine -> Hypoxanthine, Guanine to Xanthine, or Cytosine to Uracil** (main one)

Question 29

What are the repercussions following depurination and deamination?

Answer 29

Depurination- If an adenine is removed, after DNA replication the mutated strand will cut out the Thymine therefore causing an A-T nucleotide pair to be deleted and shortening the sequence by 1bp. The conserved sequence will fix the damage by adding another adenine. Deamination- If a cytosine is changed to a uracil, after DNA replication occurs the mutated strand will have a Uracil bound to an Adenine when the proper pair should be Cytosine bound to Guanine.

Question 30

What is the problem with methylated cytosine residues in Cytosine-phosphate-Guanine (CpG) islands? How is this fixed and what nucleotide is the methylated cytosine converted into?

Answer 30

Methylation of CpG islands stably silences genes (whether they be cancer or DNA repair genes) Methylated Cytosine is deaminated to produce Thymine that is mismatched with Guanine. DNA glycosylase removes the Thymine.

Question 31

Define the type of damage that is repaired by the process Direct Repair.

Answer 31

Pyrimidine dimers are repaired through this process.

Question 32

Define the type of damage that is repaired by the process Base Excision Repair.

Answer 32

Single-base mismatches Non-distorting Alterations (Ex. Depurination)

Question 33

Define the type of damage that is repaired by the process Nucleotide Excision Repair. What disease does this cause?

Answer 33

Removing the entire nucleotide Xeroderma Pigmentosum

Question 34

Define the type of damage that is repaired by the process Mismatch Excision Repair. What are the enzymes involved? What disease does this cause?

Answer 34

Mismatched daughter strand MutS and MutL, DNA Polymerase, and DNA Ligase Hereditary Nonpolyposis Colorectal Cancers

Question 35

Define the type of damage that is repaired by the process Recombination Repair (Both non-homologous and homologous recombination). What disease does this cause?

Answer 35

Double stranded breaks and interstrand cross-linking Leads to BRCA1/2 breast cancer (Homologous Recombination only)

Question 36

Define the type of damage that is repaired by the process Transcription-Coupled Repair. What disease does this lead to?

Answer 36

Stalled RNA polymerase during transcription (Note-not during replication***) Causes Cockayne Syndrome

Question 37

What does Xeroderma Pigmentosum cause? What process is affected?

Answer 37

Skin cancer and UV sensitivity Nucleotide Excision Repair is affected

Question 38

What does Ataxia Telangiectasia cause? What is defective in patients suffering from this?

Answer 38

Causes Leukemia, Lymphoma, gamma-ray sensitivity ATM protein (a protein kinse activated by double strand breaks) is mutated ATM stands for Ataxia Telangiectasia Mutated protein

Question 39

What does BCRA2 cause? What is the repair process defective?

Answer 39

Breast, Ovarian, and Prostate Cancer Repaired by homologous recombination

Question 40

What does Fanconi Anemia cause? What is the repair process affected?

Answer 40

Congenital abnormalities, Leukemia DNA interstrand cross-link repair (remember that this is from both non-homologous and homologous combination)

Question 41

Describe the process of Direct repair to correct Thymine Dimers.

Answer 41

Thymine dimer occurs on DNA strand Photolyase excises the dimer

Question 42

Describe the Base Excision Repair process. Be sure to note key enzymes.

Answer 42

Deaminated Cytosine is converted to a Uracil, which is wrongly base paired to Guanine Uracil DNA Glycosylase removes the Uracil base AP Endonuclease and Phosphodiesterase remove the Sugar Phosphate DNA Polymerase adds the new, correct nucleotide DNA Ligase seals the nick in the double helix

Question 43

Describe the Nucleotide Excision Repair process. Be sure to note key enzymes.

Answer 43

Pyrimidine Dimer forms on one side of the DNA strand Excision Nuclease creates a nick on either side of the Pyrimidine Dimer (note that this incorporates a few nucleotides on either end to ensure the whole dimer is removed) DNA Helicase unzips the pyrimidine dimer and extra nucleotides and removes it from the DNA strand DNA Polymerase and DNA Ligase lay down the correct nucleotides and fill in the gaps *Note that this is similar to Direct Repair, but this process does not act directly on the Pyrimidine Dimer, but instead on the DNA strand surrounding the dimer

Question 44

Describe the Mismatch Excision Repair (MER) process. Be sure to note key enzymes.

Answer 44

DNA-Dependent DNA Polymerase proofreads the DNA and removes (almost all) errors missed MutS binds with MutL and scans for nicks within the DNA strand and if one is found it triggers degradation of the nicked strand DNA Polymerase and DNA Ligase lay the correct nucleotides and fills in the gaps Note that MER only occurs for incorrectly paired bases for the newly synthesized daughter strand

Question 45

What are the 3 causes of double stranded breaks?

Answer 45

Ionizing radiation Replication errors Oxidizing agents

Question 46

What are the 2 mechanisms used to repair double stranded breaks?

Answer 46

Non-homologous End Joining- Nick in the ds leads to nucleotides being lost in both directions from each nick and then these nucleotides are ligated together. This leads to a deletion in the DNA sequence. Homologous Recombination- Nicks in the ds lead to the loss of nucleotides due to degradation from both ends of the each nick. The sister chromatic is then used to provide the information to correctly repair the missing nucleotide pieces. End result is a completely repaired chromosome.

Question 47

Describe the Transcription-Coupled Repair process. What 2 types of repair process utilizes this? What disease is associated with this repair process?

Answer 47

If there is an issue with the DNA strand, cells can direct RNA Polymerases to stall at the issue and repair the machinery there. The two process that utilize this type of repair is: Base Excision Repair Nucleotide Excision Repair Cockaynes Syndrome is associated with this repair process- due to RNA Polymerase permanently being stalled at sites of damage in important genes

Question 48

What are the 3 checkpoints of the cell cycle?

Answer 48

G1 to S Phase S Phase G2 to M Phase

Question 49

What is the function of Histone Deacetylases (HDACs)?

Answer 49

Enzymes that remove acetyl groups from the lysines on core histones

Question 50

How does DNA Methylation affect gene transctription? Where do they typically occur? Hint: What kind of sites?

Answer 50

It represses gene transcription when at the gene promoter Usually occurs within CpG sites, which are typically proximal to the start of transcription

Question 51

What amino acid residue does Ubiquitin attach to on target proteins?

Answer 51

Lysine

Question 52

What are the 3 types of chemical agents that cause DNA damage?

Answer 52

Cross-linking agents Alkylating agents Intercalating agents (Ex. Thalidomide)- found in the major groove of DNA