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M2M wk 1 > test1 cards week1b > Flashcards

test1 cards week1b Flashcards

1
Q

reverse transcriptase

A

catalyzes the synthesis of DNA from RNA template

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2
Q

retroviral genetic material

A

is RNA, they use reverse transcriptase to make DNA from their RNA

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3
Q

Telomerase

A

maintains ends of chromosomes (telomeres), uses an RNA template to do this, so it has reverse transcriptase activity

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4
Q

end of replication problem

A

leading strand can be synthesized until the very end, but the lagging strand cannot (read the end of the DNA replication handout)

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5
Q

telomere lengthening

A

cancer cells can do this to make cells immortal

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6
Q

DNA is the only macromolecule that is repaired

A

DNA is irreplaceable, so 100’s of genes are required for DNA repair

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7
Q

base los s (depurination, depyrimidination) repair

A

BER

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8
Q

deamination of A, C, or G

A

BER

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9
Q

UV 2+2 dimers

A

direct reversal or NER

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10
Q

base alkylation repair

A

direct reversal, BER or MMR

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11
Q

base oxidation by ROS repair

A

BER or MMR

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12
Q

bulges in helix caused by insertion or deletion of nucleotides repair

A

NER

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13
Q

Bulky chemical adducts causing bulges repair

A

NER

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14
Q

mismatch errors repair

A

MMR

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15
Q

closslinking repair

A

SSBR or NER

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16
Q

Strand break repair

A

direct reversal, SSBR or DSBR

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17
Q

Staller DNA replication forks

A

DSBR

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18
Q

deamination

A

can cause pt mutation: eg 5-methylcytosine loses NH3 to make thymine

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19
Q

base alkylation

A

can cause pt mutation; due to H-bond changes will replicate differently

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20
Q

reversal of a specific single stranded DNA break

A

direct reversal by DNA ligase

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21
Q

reversal of UV T-T or T-C dimers

A

direct reversal (photolyase)

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22
Q

reversal of base alkylation

A

direct reversal: O6-meG methyltransferase (MGMT)

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23
Q

repairs base damage that does not distort DNA

A

Base Excision repair

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24
Q

repairs base damage that does distort the DNA

A

Nucleotide excision repair

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25
Q

nucleotide excision repair

A

distorded DNA is recognized by protein endonuclease also cleaves phosphodiester bonds; helicase unwinds; exonuclease removes nucleotide; polymerase installs complimentary nucleotide; ligase closes the gap

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26
Q

Global genome NER

A

recognizes distorting genome lesions in any region

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27
Q

transcription coupled NER

A

recognizes lesions in regions that are being transcribed

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28
Q

mutations in genes that mediate NER

A

lead to diseases such as Cockayne synd, xeroderma pigmentosum, trichothiodystrophy

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29
Q

base excision repair

A

altered base specific glycosylases recognize and remove; DNA pol replaces; ligase fixes nicks

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30
Q

mismatch repair

A

MutS and MutH (MSH and MLH in mammals) recognize mismatches, endonuclease cleaves phosphodiester bonds, exonuclease removes nucleotide, helicase unwinds, DNA Pol replaces, ligase fixes nicks

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31
Q

MMR detection of new strands

A

nascient lagging strand has transient 5’ DNA ends from okazaki frags; nascient leading strand is marked by transient ribonucleotides

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32
Q

mutations in MMR

A

cause hereditary non-polyposis colorectal cancer

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33
Q

lesion bypass

A

used when too much DNA damage for NER, BER, or MMR to handle. Allows for bypass or error prone pol’s with loosened specificity to continue thru damaged region. They lack a proofreading 3’ to 5’ exonuclease. HIGHLY MUTAGENIC

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34
Q

Double strand breaks

A

repaired by non-homologous end joining or homologous recombination

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35
Q

non-homologous end joining

A

often innacurate, can result in insertion or deletion

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36
Q

homologous recombination

A

used homologous template DNA; very accurate

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37
Q

single strand breaks

A

caused by: collapsed DNA replication, stalled transcription, and PARP (poly(ADP-ribosylation)

38
Q

DNA DAMAGE CHECKPOINT

A

pauses cell cycle to allow for DNA repair; signalling pathways using protein kinases ATM and ATR. Or can lead to apoptosis

39
Q

deficiencies in DNA damage checkpoint

A

genomic instability and malignant conversion

40
Q

DNA control elements

A

TATA box, promoter, proximal elements, enhancers

41
Q

TATA box

A

initiator sequence usually 25-35 bps upstream of the start site, determines site of transcription initiation and directs binding ofRNA polII

42
Q

promotor proximal elements

A

200 bps upstream of TSS, ~20bps long, help regulate transcription, and can be bound by factors in a celltype specific manner

43
Q

enhancers

A

contain multible control elements each 8-20 bps long, thus an enhancer can be 100-200 bps long; usually 200 to 10’s of kilo bases upstream OR downstream from the promoter

44
Q

b-thalassemia

A

an inherited anemia due to deficient production of b-globin proteinby erythroid cells. Occurs due to different types of mutations one of which can be in the b-globin promoter, thus reducing the amount of b-globin mRNA produced

45
Q

Hemophilia B Leyden

A

X-linked clotting disorder, affected males have 1% of normal factor IX until puberty. The factor IX gene has mutations in the promoter - preventing binding of the approriate transcriptional activators. At puberty, androgen receptors can bind to the active site and increase transcription

46
Q

Fragile X syndrome

A

FMR1 gene facilitates methylation of cytosine residues in CpG islands. FMR1 gene normally has 6-50 CGG repeats in the 5’ region, affected males (1 in ~1500) have >200 CGG repeats and leads to increased silencing of the FMR1 gene. This results in mental retardation, dysmorphic facial features and post pubertal macroorchidism

47
Q

transcription activators and repressors

A

Proteins encoded by one gene that act on other genes to regulate their transcription. Can therefore diffuse around the nucleus and affect transcription of numerous genes. Can either activate or repress transcription.

48
Q

two classes of transcription activators and repressors

A

Sequence-specific DNA binding proteins and Co-factors

49
Q

Sequence-specific DNA binding proteins

A

bind to promoter or enhancer elements (DNA control elements) in their target genes to regulate transcription. The elements they bind to are usually 6-8 base pairs long. Usually bind DNA by inserting their _-helices into the major groove of DNA, making contacts between the amino acid side chains of the protein and the bases in the DNA

50
Q

co-factors

A

Do not bind directly to the DNA elements but rather bind to sequence-specific DNA binding proteins and affect transcription through this contact.

51
Q

two major domains of ss DNA binding proteins

A

DNA binding domains - confer sequence specificity; activation domain - very unstructured, medaite protein-protein interactions that recruis general transcription machinery and/or co-activators that modify chromatin

52
Q

classification of sequence specific transcription factors

A

classified by their DNA binding domains: homeodomain proteins (helix-turn-helix); Zinc-finger proteins; basic leucine zipper proteins; basic helix-loop-helix (bHLH)

53
Q

Craniosynostosis

A

characterized by the premature closure of one or more sutures in the skull and affects 1/3000 infant; one varient is causes by a mutation of the homeodomain protein MSX2

54
Q

Androgen insensitivity syndrome (AIS)-

A

AIS includes feminization or undermasculinization of the external genitalia at birth, abnormal secondary sexual development in puberty, and infertility. Caused by mutations in either the DNA binding domain or the ligand binding domain of the androgen receptor (a zinc finger DNA binding protein)

55
Q

Waardenburg Syndrome type II

A

characterized by deafness, pigmentation anomalies of the eyes, and other pigmentation defects (hair, skin). Mutations in the microphthalmia-associated transcription factor (MITF) gene (which encodes a bHLH DNA binding protein) are observed in 15-20% of the patients.

56
Q

dimerization of seq specific DNA binding factors

A

The Zinc finger, bZIP, and bHLH can all form heterodimers. If each monomer of the heterodimer has a different DNA binding specificity, the formation of heterodimers will increase the number of potential sequences to which that family of sequence specific transcription factors can bind. Combinatorial Control

57
Q

How do transcriptional activators or repressors, once bound to DNA control elements, stimulate transcription?

A
  1. Activators and Repressors regulate assembly of initiation complexes and rate of initiation of transcription 2.Activators and Repressors regulate changes in chromatin structure influencing the ability of general transcription factors to bind promoters
58
Q

what are the two classes of chromatin remodeling factors?

A
  1. DNA-dependent ATPases (SWI/SNF)- disrupt histone octamers and DNA. 2. Factors that reversibly modify histones through acetylation (HATs and HDACs)
59
Q

nucleasome

A

a core of histone proteins around which DNA is wound

60
Q

histone N- termini

A

rich with lysine residues, which can be reversibly modified by acetylation, phosphorylation, methylation, and ubiquitination. Acetylation is associated with gene control.

61
Q

Activators and Repressors can recruit:

A

either histone acetyltransferases (HATS) or deacetylases (HDACs).

62
Q

Histone acetyltransferases (HATS)-

A

a co-activator; acetylates lysine; allows for binding of specific transcription factors - thus serves as a ‘code’ to recruit different factors that will then affect the transcriptional site

63
Q

Histone deacetylases (HDACs)-

A

a co repressor; de-acetylates

64
Q

trans-acting transcription factors

A

can switch from repressors or activators by recruiting HAT’s or HDAC’s

65
Q

activators

A

eg. CBP or p300; recruit HATs

66
Q

repressors

A

recruit HDACs

67
Q

some diseases involved in histone acetylation

A

Leukemia, epithelial cancers, Rubenstein-taybi synd, polysomy X, Fragile X syndrome

68
Q

Rubinstein-Taybi Syndrome

A

rare genetic multisystem disorder (affects 1/125,000); Characterized by growth retardation, mental retardation, craniofacial dysmorphism, abnormally broad thumbs and great toes. Results from mutations in one copy of the CREB binding protein (CBP) gene. CBP is an essential transcriptional coactivator for many different transcription factors and is a histone acetyltransferase.

69
Q

Leukemia-

A

A hematopoietic malignancy. Are generally the result of chromosomal translocations leading to gain of function fusion proteins- some of which involve fusions of transcriptional regulators with HATs or HDACs, altering the activity of the regulators .

70
Q

euchromatin

A

where genes reside; more accessible form of chromatin

71
Q

heterochromatin

A

always repressed because inaccessible found near centromeres, telomeres, and internal chromosome positions, so inaccessible

72
Q

Constitutive Heterochromatin

A

is always heterochromatin and contains satellite DNA. Example - centromeric DNA

73
Q

Facultative Heterochromatin

A

can change to euchromatin, depending on the cell type or developmental stage, and is enriched in LINE sequences. Example - X-inactivation

74
Q

How are the sequence-specific DNA binding proteins regulated?

A
  1. The conformation of the DNA-binding protein can be altered by ligand binding 2. Entry into the nucleus can be regulated 3. The amount of transcription factor in the cell can be regulated 4. DNA binding can be regulated 5. Phosphorylation of the DNA-binding protein can alter various properties including protein degradation, recruitment of co-activators, and DNA binding
75
Q

Overview of Basic Principles of Transcriptional Regulation

A

see slide 54 - FORD

76
Q

The nuclear receptor family of Zinc finger transcription factors work by binding to:

A

Steroid hormones

77
Q

ligang binding can affect:

A

dimerization of receptor, recruitment of coactivators/repressors, and translocation into the nucleus. Examples include estrogen receptor activation and glucocorticoid receptor activation

78
Q

Estrogen receptor binds DNA as a homodimer

A

through a pair of Zn fingers

79
Q

estrogen binds to estrogen receptor which causes

A

its dimerization

80
Q

tamoxifen

A

estrogen agonist: competitively binds to ER and prevents recruitment of HAT co-factors

81
Q

regulating entry into the nucleus example

A

NF-kB is normally in the cytoplasm when bound to IkB.In response to a variety of stimuli, I_B can be phosphorylated, targeting it for degradation. NF_B is then released and moves to the nucleus, where it turns on a number of target genes, including those involved in inflammation

82
Q

aspirin

A

works in part by inhibiting the phosphorylation, and thus degradation of IkB. This prevents the translocation of NFkB to the nucleus, thus inhibiting the transcription of genes involved in the inflammatory response.

83
Q

dephosphorylation of cytoplasmic NF-AT:

A

High intracellular calcium activates calcineuin’s phosphatase activity

84
Q

activated calcineurian phosphatase:

A

dephosphorylates cytoplasmic NF-AT. This exposes the nuclear localization sequence, allowing NF-AT to enter the nucleus where it affects transcription of genes involved in the immune response and in heart function.

85
Q

immunosuppresants cyclosporin and FK506 mode of action

A

inhibit calcineurin, thereby inhibiting NF-AT action.

86
Q

Extracellular regulators stimulate Wnt to:

A

ultimately destibilize the Axin-APC-GSK3 complex which is needed to phosphorylate beta catenin for degradation. The resulting increase in beta catenin allows for some to move to the nucleus, where it interacts with the TCF family of transcription factors and promotes the expression of Wnt responsive genes.

87
Q

APC mutations

A

increase cellular beta catenin - has implications in colon cancer

88
Q

p53 downregulation

A

p53- is downregulated by binding to the MDM2 protein which not only masks its activation domain, but also targets it for destruction by the ubiquitin-proteasome pathway. *Note importance of p53 in human cancers.

89
Q

Example of regulating DNA binding:

A

Id proteins- The Id family members negatively regulate DNA binding by heterodimerizing with other HLH proteins through their HLH domains, but preventing DNA binding due to their lack of a basic domain.

90
Q

Example of how phosphorylation affects activity of trans-acting factors:

A

phosphorylation of CREB (cyclic AMP response element-binding protein) promotes transcription be allowing recruit ment of CBP/PolII - leading to transcriptional activation of the gene

M2M wk 1 (2 decks)

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