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MCM Quiz2 > Functions and Dysfunction in Genomic Regulation > Flashcards

Functions and Dysfunction in Genomic Regulation Flashcards

1
Q

Central dogma of biology?

A

DNA to RNA to Protein

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2
Q

How can RNA become DNA?

A

reverse transcriptase, such as in HIV

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3
Q

How is DNA organized?

A

into chromosomes

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4
Q

How is DNA structured?

A

Helix due to hydrogen bonding

Anti Parallel due to hydrogen bonding

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5
Q

Purines?

A

A and G

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6
Q

Pyramidines?

A

C, T ,U

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7
Q

How much of the DNA genome is used for coding? For how many proteins?

A

1.5%, 100000

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8
Q

What form are mitotic chromosomes in during interphase?

A

Condensed, avoid damage to chromosomes

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9
Q

What is the Histone octamer and what does it make?

A

-basic unit of chromosome packing

“beads on a string”

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10
Q

Whats so significant about AA that make up histone?

A
  • 20% Lysine or Arginine
  • Attracted to negatively charged DNA backbone
  • Targets of post-translational modifications (PTMs)
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11
Q

what is Histone deacetylase?

A

represses gene expression by compacting (winding) the chromatin

activated by nuclear receptors

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12
Q

what is Histone Acetyltransferase?

A

activates gene expression by acetylating and unwinding chromatin

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13
Q

What is euchromatin?

A

lightly packed DNA

Often but not always under active transcription

92% of human genome is euchromatic

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14
Q

what is Heterochromatin?

A

Contains few active genes

tightly bound

Position effect: activity of a gene depends on relative position of chromosome

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15
Q

Where do acetylation / methylation /ubiquitination occur?

A

N-terminus of Histone proteins

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16
Q

What is methylation? what and how does it do it? what is the significance?

A

Represses gene transcription when at gene promoter

Uses cytosine and adenine via methyl transferase enzyme

Associated with: genomic imprinting, X-chromosome inactivation, repression of transposable elements, Aging, carcinogenesis

Altering DNA methylation -> important component of cancer development

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17
Q

What is the significance of CpG Islands?

A

Gene promoter regions

can acquire abnormal hypermethylation leading to transcriptional silencing

this can be inherited by daughter cells following cell division, if in germ cells

can give rise to oncogene suppressor silencing, might be a target for epigenetic therapy

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18
Q

What is hypomethylation?

A

chromosomal instability, loss of imprinting

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19
Q

Phosphorylation, what is it and what does it do?

A 
negative phosphate on 
positively charged histones would 
decrease the affinity histones have 
for negatively charged DNA, allowing 
for increased expression.
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20
Q

What does DNA replication need to occur? How is it replicated?

A

DNA polymerase requires a primer with a free 3’ -OH to begin processing

Replication is Semiconservative

Bi-directional replication

Synthesized 5’ to 3’

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21
Q

Helicase?

A

Unzips DNA Helix

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22
Q

Topoisomerase? what does it do

A

Relieves overwound supercoils

Breaks phosphodiester bond

Blocks cell cycle

Generate single/double stranded breaks

Harms integrity of genome

Leads to apoptosis and cancer cell death

Targeted in cancer therapy

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23
Q

What are the inhibitor of topoisomerase?

A

Topoisomerase I inhibitor:
Irinotecan is inhibited
Used for colorectal cancer

TOPOisomerase- II Inhibitor
Etoposide & Anthracyclines are inhibited

Anthracyclines cause cardiotoxicity

  • Doxorubicin
  • Daunorubicin

Etoposide causes secondary Leukemias.

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24
Q

DNA ligase?

A

Seals nicks

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25
Q

DNA polymerases?

A

Synthesize new DNA chain in the 5’ -> 3’ direction

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26
Q

Single-stranded binding protein?

A

Binds the single-stranded DNA that

has been separated

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27
Q

What Nucleoside analog inhibitors? what do they do? whats their significance?

A

LACK 3’-OH GROUP, inhibit DNA replication

Nucleosides analogs need to be converted to dNTPs before they can act as inhibitors of DNA polymerase

Examples: ara-C, Acyclovir, AZT

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28
Q

what is ara-C?

A

Treatment of leukemia

Ara-C contains the sugar arabinose, which is converted to ara-CTP by animal cells

Potent competitive inhibitor of DNA polymerase

29
Q

What is Acyclovir?

A

Treatment of herpes/shingles lesions

A Herpesvirus-encoded thymidine kinase phosphorylates Acyclovir and the host’s enzymes convert the monophosphate to triphosphate

30
Q

What is AZT?

A

treatment for HIV

Drug is taken up by HIV-infected cells and uses the viral RVTase to arrest viral DNA synthesis by acting as chain terminators.

31
Q

What does Ionizing radiation do?

A

causes strand breaks

causes DNA protein cross links

40 to 60 chemically distinct base damages

32
Q

What does non ionizing radiation do?

A

produces a covalent link between two adjacent pyrimidines (T-T or C-T)

makes pyramidine dimers

causes Basal and squamous cell carcinoma

33
Q

what/how do spontaneous mutations in DNA happen?

A

spontaneously

DNA replication errors, base deletion or substitution

34
Q

What is depurination?

A

(A or G) is removed from the nucleotide via hydrolysis of N-glycosidic bond between the base and the deoxyribose group

make an apurinic (AP) or abasic site

35
Q

What is deamination? how and what happens?

A

amino group of purine or pyrimidine base is hydrolyzed

Adenine -> hypoxanthine
Guanine -> xanthine
Cytosine -> uracil

Forms unnatural deoxyuridine (dU)

36
Q

what are intercalcating agents?

A

A chemical that can insert itself between the stacked bases at the center of the DNA double helix, possibly causing a frameshift mutation

thalidomide!!

37
Q

What did thalidomide do!

A

Children born with short “flipper-like” appendages

horrible birth defects

38
Q

Why are methylated cytosine residues in CpG islands bad?

A

methylation of CpG islands stably silences genes (cancer/DNA repair genes)

Loss of amine of methyl-c produces T mismatched with G

39
Q

what is Benzo(a)pyrene?

A

Makes BPDE, carcinogen

40
Q

What are cross linking agents?

A

exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them

These adducts interfere with cellular metabolism, such as DNA replication and transcription, triggering cell death

Nitrogen mustard
Cisplatin
Mitomycin C
etc

41
Q

Alkylating Agents, what are they and what do they do?

A

substance that causes replacement of hydrogen by an alkyl group especially in a biologically important molecule; specifically : one with mutagenic activity that inhibits cell division and growth and is used to treat some cancers.

DDS,MMS

42
Q

What is direct repair?

A

uses DNA photolyase & methylguanine methyltransferase

enzymatic

43
Q

what is base excision repair?

A

DNA glycolases, AP endonuclease, AP lyases (of DNA polymerase), DNA polymerase Beta, DNA ligase

44
Q

Nucleotide Excision Repair, why is it significant?

A

NER protein complex, DNA polymerase Beta, DNA ligase

Similar to MER but uses different proteins in process, but outcome is the same

Deficiency in NER leads to xeroderma pigmentosum

45
Q

Mismatch Excision Repair (MER)- ?

A

MER complex, helicase/endonuclease, DNA polymerase Beta, DNA ligase

46
Q

what is recombination repair?

A

Nonhomologous end joining- Damaged ends filled in and joined; some base pairs may be missing. Multiples proteins used including DNA ligase

Homologous recombination- Exonuclease, DNA polymerase, MER system

Deficiency leads to BRCA1/2 Breast cancer risk

47
Q

Transcription-Coupled Repair (TCR)?

A

Deficiency leads to cokayne syndrome

stalling transcription

48
Q

Translation Synthesis

A

Uses DNA polymerase

49
Q

what does direct repair fix?

A

Pyrimidine Dimers & O6-methylguanine

50
Q

what does Base Excision Repair fix?

A

Single base mismatches, nondistoring alterations (depurination)

51
Q

what does Nucleotide Excision Repair fix?

A

Chemical adducts that distort DNA (pyrimidine dimers)

52
Q

what does Mismatch Excision Repair fix?

A

mismatched base in daughter strand

53
Q

what does Recombination Repair fix?

A

double-strand breaks, interstrand cross-linking

54
Q

what does Transcription-Coupled Repair fix?

A

stalled RNA polymerase during transcription

55
Q

what does Translation Synthesis fix?

A

unpaired thymine dimers or apurini AP sites

56
Q

what is Xeroderma Pigmentosum?

A

photosensitivity, prone to developing melanomas and SCC

UV light causes cyclobutane thymine dimers to form in DNA

With defective XP proteins in NER complex show disease

57
Q

Hereditary nonpolyposis colorectal cancer?

A

Inherited mutations in one of the alleles in MER complex have increased risk to HNPCC

58
Q

Cockayne syndrome?

A

Defect in transcription-coupled repair

growth retardation, skeletal abnormalities, sensitivity to sunlight

RNA polymerase is permanently stalled at sites of damage in important genes

59
Q

BRCA associated breast cancer?

A

Mutations in these genes cause 5x increase in woman’s risk in getting breast/ovarian cancer pre-menopause

Also associated with increased risk of cervical, uterine, pancreatic and colon cancer in women

*Recombination repair

60
Q

What is Epigenetics?

A

study of heritable changes in gene expression (active versus inactive genes) that do not involve changes to the underlying DNA sequence

61
Q

Histone Deacetylases (HDACs), what do they do?

A

enzymes that remove acetyl groups from lysines on core histones and Transcription factors, repressing genes

Cancer cells sensitive to inhibitors of such lysine deacetylases

62
Q

HDAC Inhibitors, what are they and what do they do?

A

Vorinostat, Entinostat, valproic acid

Anticonvulsants and anticancer drugs

63
Q

Rifampicin, what does it do?

A

inhibits bacterial RNA synthesis

Binds to B subunit of RNA polymerase,preventing it from initiating translation

Treats tuberculosis

Side Effects: upregulation of liver cytochrome p-450, which increases metabolisms of other drugs and hormones
*Red urine, sweat and tears

64
Q

What are the CpG sites?

A

Left: sites every 1/10 nucleotide, gene promoter

Right: every 1/100 nucleotides, commonly methylated

65
Q

what is the effect of methylation on gene transcription?

A

Gene suppression

66
Q

what is the effect of sumoylation on gene transcription?

A

Similar to ubiquitination

67
Q

what is the effect of Ubiquitination on gene transcription?

A

Ubiquitin attaches to lysine residues to signal to proteins for cell degradation (in proteasome; signal dependent)

68
Q

what is the effect of Histone acetylation/deacetylation on gene transcription?

A

Acetylation- gene activation

Deacetylation- gene suppression

69
Q

what is the effect of Phosphorylation on gene transcription?

A

Signals for degradation via proteasome

MCM Quiz2 (10 decks)

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