Genomic Regulation

Question 1

Which residues in histone proteins are the target of post-translational modifications?

Answer 1

Lysine

Question 2

How many histone proteins are in each nucleosome?

Answer 2

8 histone proteins

Question 3

______ actively represses gene expression

Answer 3

Histone Deacetylation

Question 4

______ actively promotes gene expression

Answer 4

Histone Acetylation

Question 5

What kind of bonds are formed between DNA and the histone octamer?

Answer 5

Hydrogen bonds: hydrophobic interactions and salt linkages.

Question 6

Which amino acid in histone proteins is the target of post-translational modifications?

Answer 6

Lysine

Question 7

Protein+DNA=?

Answer 7

Chromatin

Question 8

What variations are the basis for our differences and for disease states?
How to detect them?

Answer 8

Copy Number Variations (CNVs)

Comparative Genome Hybridization

Question 9

almost all Introns begin with___ and end with___ nucleotide sequence

Answer 9

GT———AG

Question 10

Which histone proteins have long tails protruding from the nucleosome?

Answer 10

H3 and H4 histones

Question 11

Where are Methyl groups added to the DNA Molecules during DNA Methylation?
When does it repress gene transcription?

Answer 11

Cytosine and Adenine.

It represses gene transcription when at gene promoter.

Question 12

What energy does DNA Helicase use to unwind DNA?

Answer 12

Hydrolyzes ATP. Enzyme consists of 6 subunits.

Question 13

Which proteins help stabilize the unwound DNA and prevents the formation of hairpins during DNA Replication?

Answer 13

SSBP (Single Stranded DNA Binding Protein)

Question 14

Which enzyme synthesizes RNA-DNA primer?

Answer 14

DNA Polymerase alpha(in complex with Primase)

Question 15

Which enzyme(s) synthesize new DNA chain in the 5-3 direction? What is it called in prokaryotes?

Answer 15

DNA polymerase Gamma and e. DNA Pol III in Prokaryotes.

Question 16

Which enzyme removes DNA Primer in eukaryotes? What about in prokaryotes?

Answer 16

Flap endonuclease 1 (FEN1). DNA Pol I in Prokaryotes.

Question 17

Which enzyme fill sin gaps in Eukaryotes? Prokaryotes?

Answer 17

DNA Polymerase Gamma. DNA Pol I in prokaryotes.

Question 18

What kind of bonds do DNA Topoiomerase break during the unwinding of DNA?

Answer 18

Phosphodiester bonds.

Question 19

_______ acts as an competitive inhibitor of DNA Polymerase to stop DNA synthesis. Also used in treatment of Leukemia.

Answer 19

Arabinosylcytosine (Ara-C)

Question 20

Which nucleoside analogs lack the 3’ OH group and act as chain terminators? Which one is used in treatment of HIV?

Answer 20

AZT and Acycloguanosine (acyclovir). AZT is used in treatment of HIV.

Question 21

UV Radiation is considered a non-ionizing radiation. What kind of DNA Damage does it cause?

Answer 21

Pyrimidine dimers: example: Thymine dimers.

Question 22

What are the 2 kinds of Spontaneous DNA Damage?

Answer 22

Depurination and Deamination.

Question 23

What are the 3 nucleotides that get Deaminated? What is the final product for each one?

Answer 23

Adenine—–Hypoxanthine
Guanine—–Xanthine
Cytosine—–Uracil.

Question 24

Deamination of Methyl-C converts into____? What enzyme fixes this problem?

Answer 24

Thymine. This will be mismatches with G.

A special DNA Glycosylase recognizes and removes the T.

Question 25

Thymine Dimer is corrected by which DNA Repair mechanism?

Answer 25

Direct Repair: Photoreactivation. Used photolyase and light to remove the Thymine-Thymine bond.

Question 26

What repair mechanism fixes single-base mismatches, and non distorting alterations? What enzymes does it use?

Answer 26

Base Excision Repair: DNA Glycosylase hydrolyzes the N-glycosidic bond for the altered base.
AP endonuclease cuts phosphodiester bond. DNA Pol beta replaces excised nucleotide and DNA Ligase seals nick.

Question 27

What repair mechanism fixes chemical adduce that distort DNA (example Pyrimidine dimers)?

Answer 27

Nucleotide Excision Repair. NER complex recognizes distortions and nicks DNA on both sides of damage site.

Question 28

Xeroderma Pigmentosum have defective proteins in which complex?

Answer 28

NER complex. This is utilized in the Nucleotide Excision Repair Mechanism.

Question 29

What are the 2 enzymes in Mismatch Excision Repair and describe their function

Answer 29

MutS binds while MutL scans for the nick and triggers degradation of nicked strand.

Question 30

Which gene is mutated in the Hereditary Nonpolyposis colorectal Cancer(HNPCC)
Also, how is this inherited?

Answer 30

There is an inherited mutation in the MER gene. HNPCC is inherited in an Autosomal Dominant Manner.

Question 31

What are the 2 ways DNA is fixed during the Double Strand Break Repair?

Answer 31

Nonhomologous end joining and Homologous Recombination.

Question 32

Name the disease caused by a defect in the the Transcription-coupled Repair?

Answer 32

Cockayne’s Syndrome.

Question 33

What are the symptoms of Cockayne’s Syndrome?

Answer 33

Growth retardation, skeletal abnormalities, sensitivity to sunlight.

Question 34

Name 2 HDAC inhibitors

Answer 34

Vorinostat, Valproic Acid

Question 35

Where are CpG Islands usually found?

Answer 35

On the promoter region of the gene.

Question 36

What kind of silencing occurs during hypermethylation of CpG Islands?

Answer 36

Transcriptional Silencing

Question 37

Topoisomerase I Inhibitor

Answer 37

Irinotecan

Question 38

Topoisomerase II Inhibitor

Answer 38

Etoposisde.

Question 39

Which type of RNA molecules inhibit gene expression or translation?

Answer 39

miRNA