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MCM- Exam 2 > Genomic Regulation > Flashcards

Genomic Regulation Flashcards

1
Q

How does DNA run

A

Anti-parallel; double stranded

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2
Q

How is DNA synthesized

A

DNA polymerase and it adds to the 3’ end

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3
Q

Purines

A

Guanine and Adenine

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4
Q

Pyrmadines

A

Thymine, Cytosine, and Uracil

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5
Q

How many bonds are between A and T

A

two

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6
Q

How many bonds are between G and C

A

three

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7
Q

What are the two grooves in DNA

A

The Major and Minor groove

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8
Q

Mitotic DNA is condensed how many more times, compared to interphase chromosomes

A

500 times

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9
Q

Why is Mitotic DNA so much more condensed

A

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

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10
Q

How many hydrogen bonds are between DNA and the Histone Octamer

A

142

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11
Q

What is the charge on a histone

A

Positive

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12
Q

What is the charge on DNA

A

Negative; from the phosphate groups on the DNA backbone

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13
Q

What two A.A.’s are prominent on Histones to promote the Positive charge

A

Lysine and Arginine

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14
Q

How many proteins are in a histone

A

8

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15
Q

What is chromatin

A

DNA bound around Histone complex

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16
Q

What is Euchromatin

A

Lightly packed chromatin, enriched genes that are active in gene expression

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17
Q

What is Heterochromatin

A

Very condensed chromatin; contains very few active genes

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18
Q

Who described the double helix of DNA

A

Watson and Crick

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19
Q

When was the sequence of DNA genome discovered

A

February 2001

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20
Q

What do exons do

A

Encode Proteins

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21
Q

What is personalized medicine

A

Copy Number Variation testing; to be pharmo-specific

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22
Q

What is RNAi

A

RNA interference, miRNA inhibits gene expression

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23
Q

What is Long Terminal Repeats

A

Identical Sequences of DNA; formed by reverse transcription of retroviral RNA. Used by viruses to insert their genetic material into the host genome

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24
Q

How many alternatives are their in “Alternative RNA Splicing’ on average

A

2

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25
Q

What do most introns begin with

A

GT

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26
Q

What most introns end with

A

AG

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27
Q

What does Histone Deacetylase do

A

Takes the Acetyl group off of the Histone and silences gene expression

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28
Q

What does Histone Acetyl Transferase do

A

Acetyl-izes the Histone group, allowing the Chromatin to unwind

29
Q

What is the target of PTM’s for Histone proteins

A

The Histone Protein Tails

30
Q

What does DNA Methylation do

A

Represses gene transcription at gene promoter

31
Q

What happens to a CpG island when hypermethylated

A

Transcriptional silencing, which when down on a gamete, is passed on to the next generation

32
Q

What happens to a CpG Island when hypomethylated

A

Chromosomal instability, and loss of imprinting

33
Q

What are CpG’s associated with

A

Gene Promoters

34
Q

What direction is DNA synthesized

A

5’ to 3’

35
Q

What does DNA polymerase require to start replication

A

A free 3’ hydroxyl end

36
Q

Which DNA strand is continuous in synthesis

A

The leading strand

37
Q

Which DNA strand in fragmented in synthesis

A

The lagging strang, into Okazaki fragments

38
Q

What does DNA Helicase do

A

Unwinds DNA, uses ATP

39
Q

What does the Single Stranded DNA-Binding Protein do

A

Helps stabilize the unwound DNA, prevents formation of hairpins so that DNA bases remain exposed

40
Q

What does Topoisomerase do

A

Relieves overwound supercoils in the DNA, as DNA helicase unwinds it

41
Q

Anti-cancer drugs target Topoisomerase for what

A

To stop DNA synthesis. The DNA will supercoil and DNA helicase will be unable to split it.

42
Q

What can DNA polymerase do to the growing DNA strand other than make it

A

Proof Read

43
Q

What can UV radiation cause

A

Pyrmidine Dimers

44
Q

What does Ionizing Radiation do

A

Causes double stranded DNA breaks

45
Q

What does Non-Ionizing Radiation do

A

Create thymine bonds

46
Q

What is Depurination

A

Losing Purine group

47
Q

Deamination

A

Losing an amine. Example Cytosine to Uracil loses NH3

48
Q

What is the interchelating agent we need to know

A

Thalidomide

49
Q

What does Base Excision DNA Repair, repair

A

Single base matches, non-distorting alterations

50
Q

What enzymes and molecules does DNA Nucleotide Excision Repair Use

A

NER protein complex, DNA Polymerase, and DNA Ligase

51
Q

What does DNA Mismatch Excision Repair, repair

A

Mismatched base in daughter strand

52
Q

What does DNA Mismatch Excision repair use

A

MER Complex. helicase/endonuclease, DNA polymerase, and DNA ligase

53
Q

What does the Xeroderma Pigmentosum genetic defect cause and what kind of defect is it

A

Skin Cancer, UV sensitivity, neurological abnormalities; nucleotide-excision repair

54
Q

What does the BRCA2 DNA defect do and what kind of defect is it

A

Breast, Ovarian, and Prostate Cancer

Repair by homologous recombination

55
Q

What does the Fanconi Anemia Groups A-G DNA Defect cause and what cause the defect

A

Congenital abnormalities, leukemia, genome instability

DNA inter strand cross-link repair

56
Q

What role do MutL and MutS play

A

DNA Excision repair

57
Q

What is HNPCC

A

Inherited autosomal dominant DNA repair mismatch; high rate of colorectal cancer.

58
Q

What can cause double strand breaks in DNA

A

Ionizing radiation, replication errors, oxidizing agents, and other metabolites

59
Q

What would happen if double strand DNA is not repaired

A

Chromosomes would break into smaller fragments and be lost

60
Q

What does non-homologous end joining cause

A

Loss of nucleotides and DNA scars

61
Q

What causes Cockaynes Syndrome

A

Defect in transcription-coupled repair; RNA polymerase is permanently stalled at sites of damage in important genes

62
Q

How does Cockayne Syndrome present

A

Growth retardation, skeletal abnormalities and sensitivity to sunlight

63
Q

HDACS vs HATS

A

HDACS- deacetylate, causing winding

HATS- Acetylate, causing unwinding

64
Q

What are some HDAC inhibitors

A

Vorinostat and Entinostat

65
Q

What does Nuclear Receptor-Mediated Gene Activation do

A

Knocks off the HDAC and allow a HAT to bind and start

66
Q

Where does methylation of CpG Islands occur

A

At the 5 position of the pyrmidine ring off of cytosine

67
Q

What does methylation at the 5 position of the pyrmidine ring off of cytosine form and cause

A

5-methylcytosines and stably silences genes

68
Q

When you ubiquinate a protein where does it go

A

the Proteosome

MCM- Exam 2 (3 decks)

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