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MCM II > Let 1 Genomic Regulations > Flashcards

Let 1 Genomic Regulations Flashcards

1
Q

How much volume does the nucleus take up

A

6%

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2
Q

Roles of the Nucleus

A

Cell regulation proliferation DNA transcription

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3
Q

What is the central Dogma

A

1.DNA to RNA to Protein 2.DNA replication 3. transfer of genetic info from parent to offspring 4. transcription vrsus tranlsation 5. mRNA exclusive carrier of info DNA to protein 6. RNA can go to DNA (RNA virus)

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4
Q

DNA is both ______ and _______

A

double stranded and anti- parallel

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5
Q

how many bonds between A and T

A

2 hydrogen bonds

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6
Q

how many bonds between G and C

A

3 hydrogen bonds

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7
Q

What are the grooves of DNA

A
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8
Q

What needs to happen to allow DNA to fit all 3.2 billion Base pairs?

A

An incredible amount of condensation is needed throughout cell cycle (condensed 500 times) compared with interphase chromosomes

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9
Q

What is DNA wound around?

A

Histone Proteins

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10
Q

There are 142 H bonds between DNA and what?

A

histone octamer in each nuclesomes

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11
Q

T/F histone protein are highly conserved across species?

A

T

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12
Q

What makes up 20% of histone protein?

A

Lysine(Lys) or K Arginine(Arg) or R

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13
Q

Do histones have a charge?

A

Positive charges which attracts them to negatively charged DNA backbone

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14
Q

Two types of proteins that bind DNA

A
  1. Histone proteins
  2. non-histone chromosomal proteins (TFs) transcription factors
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15
Q

Nucleosome core particle consists of a complex of ______?

A

eight histone proteins (octomer)

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16
Q

DNA+protein=________

A

chromatin

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17
Q

What is Euchromatin?

A

LIGHTLY PACK FORM OF chromatin.

most active portion of genome

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18
Q

What is Heterochromatin

A

very condensed chromatin (stains dark)

late replicating and genetically inactive

Near centromeres and telomeres

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19
Q

What happened in Feb, 2001

A

sequence of human genome was announced

(90%)

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20
Q

Percentage of DNA sequence in exons?

A

1.5% (this is low)

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21
Q

what are CGH arrays?

A

comparative genome hybridization

Probe human genome CHIP with DNA from one person and with DNA from a normal reference ( detecs copy number variation.)

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22
Q

what is RNAi

A

bio process in which RNA miRNA molecules inhibit gene expression or translation

Neutralize targeted mRNA molecules

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23
Q

What are Long Terminal Repeats?

A
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24
Q

What do 99% of introns begin and end with?

A

begin with […GT] and end with [AG…]

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25
Q

What deacetylates Histones?

A

Histone Deacetylase (HDAC)

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26
Q

What acetylates histones?

A

Histone Acetyl Transferase (HAT)

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27
Q

what does acetylation and deacetylation do?

A

Deacetylation keeps beads wound tight on string wich represses gene expression

Acetylation actively promotes gene expression. ( beads are wound loosely)

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28
Q

Where do post-translational modifications (PTM) occur in histones?

A

on the histone tails

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29
Q

Types of PTM to histones

A
30
Q

what is DNA Methylation

A

MEthyl groups added to DNA molecule (Cytosine and Adenine). This changes activity (represses gene transcription when at gene promoter)

(Genomic imprinting, x-chrom inact, aging, carcinogens)

31
Q

What does DNA polymerase require in a primer ?

A

a free 3’ -OH to begin processing

32
Q

DNA polymerase moves in what direction

A

5’ to 3’

33
Q

What does semi-conservative mean with DNA

A
34
Q

What part of DNA continuous vs. discontinuous?

A
35
Q

What unwinds DNA

A

DNA helicase ATP used

36
Q

What do Single stranded DNA binding proteins do (SSBP)

A

binds cooperatively to exposed ssDNA

(stabilizes unwound DNA)no haripins

(Bases remain exposed)

37
Q

Topoisomerase role and name in bacteria?

A

relieves overwound supercoils (DNA Gyrase in bacteria)

by breaking phosphodiester bond.

38
Q

What is the pharmaceutical significance of DNA topoisomerase?

A

Used as anti-cancer agents (topoisomerase inhibitors)

  • block the cell cycle
  • generate single and double stranded breaks
  • harms integrity of genome
  • leads to apoptosis and cancer cell death
39
Q

What synthesizes RNA-DNA primer?

A

DNA polymerase alpha

40
Q

What synthesizes DNA and what direction

A

DNA polymerase delta and epsilon 5’ to 3’

41
Q

What fills in gaps in DNA

A

DNA polymerase delta

42
Q

What seals nicks in DNA

A

DNA ligase

43
Q

how are errors mainly corrected in DNA synthesis

A

proofreading (DNA polymerase) and repair

44
Q

Types of DNA damages

A
  • Ionizing radiation
  • non-iodizing radiation
  • spontaneous DNA damage (depurination/deamination)
  • chem agents
  • methylated cytosine resudes in CpG sites/ islands
45
Q

ionizing radiation

A
46
Q

Non-ionizing radiation

A
47
Q

Spontaneous (depurination)

A
48
Q

spontaneous-deamination

A
49
Q

Spontaneous DNA damage possible outcomes

A

Either a base deletion or substitution

50
Q

What happens to a methylated CpG island?

A

stable silences genes (cancer/DNA repair genes)

51
Q

How does methylated cytosine cause problems

A

deamination of Mehyl-C produces a Thymine which is now mismatched with G

52
Q

Cross-linking and its agents

A

cross links between bases in the same DNA stand or between two complementary DNA strands

Nitrogen mustard

cisplatin

mitomycin C

CArmustine

53
Q

Alkylating Agents

A

induce a wide variety of methylated base changes and alkylation of phosphodiesters into triesters

Dimethyl sulfate (DMS)

Methyl methanesulfonate (MMS)

54
Q

what are intercalating agents plus ex.?

A

insert between stacked bases of DNA double helix causing some unwinding of the helix and seperation of base pairs

Thalidomide

55
Q

how metab can produce carcinogens

A
56
Q

Double strand break repair (Recombination repair)

Nonhomologous vs Homologous

A

N-accidental break►loss of nucleotides from ends ►

end joining ► deletion of DNA sequence

H-accidental break► loss of nucleotides from ends ►

end processing and homologous recombination ► damage repaired accurately using info from sister chromatid

57
Q

Homologous or non-homologous break repair more common?

A

Non. generally okay as so little of genome is protein coding

can see scarring

58
Q

Epigenetics

A

a mechanism for regulating gene activity independent of DNA sequence that determines which genes are turned on or off

59
Q

ubiquination

A

lysine side chain residues. lysine attach to lysine ubiqinated chain signals problems. signals proteosome for degredation

cycle repeats with reuse of ubiquitin

60
Q

SUMOylation cycle

A

precursor with glycines which is activated to mature SUMO which attaches substrate

61
Q

Ubiquitination of SUMOylated protein

A

Poly SUMOnation which then gets ubiquitinated which then gets degraded (post translational modifications will work together)

62
Q

CpG islands and sites modification

A

Hypermethylation can cause stably silence these CpG islands which are in 70% of promoter regions so it will silence the gene.

63
Q

Start Codon

A

ATG (in DNA) AUG (in RNA) Methionine

64
Q

What is Direct repair

A

pyrimidine (or thymine) dimer by UV light can be separated by photolyase which is activated by light.

O6 methylguanine pairs with T rather than C. MGMT transfers methyl group from guanine to a to a cysteine on itself directly reversing damage

65
Q

What is base excision repair (BER)

A

single base mismatches or non distorting alterations

The single base can be removed and then replaced

66
Q

What is Nucleotide excision repair (NER)

A

repair adducts that distort the DNA like pyrimidine dimers. DNA unwound a nick on both sides of mistake made template guides for replacement of missing section

67
Q

Mismatch Excision Repair (MER)

A

MER finds a wrongly places nucleotide in the daughter strand. nicks the affected area and then replaces the daughter strand bases (not known how daughter stand known)

68
Q

Recombination repair

A

Homologous and non homologous end joining (double strand break repair)

69
Q

transcription coupled repair (TCR)

A

RNA polymerase stalls at a lesion during transcription which recruits ERCC 6 and 8 to recruit other repair items

70
Q

Translesion synthesis

A

incorporate A opposite T dimers uses a DNA polymerase that doesnt proofread.

71
Q

Nucleoside analogue inhibitors of DNA synthesis

A

DNA synthesis formation of 3’ to 5’ phosphodiester bonds nucleoside analogues that lack the 3’ OH group act as drugs that inhibit DNA replication (acyclovir) acts as chain terminators

MCM II (11 decks)

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