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BMSC 220 > Topic 6 > Flashcards

Topic 6 Flashcards

1
Q

Regulating ____________ is one of the fundamental ways in which cells can modify their activities

A

gene expression

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2
Q

changes in gene expression are involved in…

A
  • response of cells to their environment
  • regulation of cell cycle
  • distinct activities and coordination of different cell types
  • cell differentiation and development
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3
Q

RNA polymerases

A

the principal enzyme responsible for RNA synthesis

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4
Q

Unlike DNA polymerase, RNA polymerase do not require ….

A

a primer sequence to initiate RNA synthesis

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5
Q

genes are regulated by….

A

“dimmer switches” known as promoters

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6
Q

promoters

A

DNA sequence with which RNA polymerase and other proteins interact to initiate and regulate rate of transcription

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7
Q

transcription

A

RNA synthesis using a DNA template (a copy)

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8
Q

translation

A

protein synthesis using an mRNA template (translating)

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9
Q

mRNA

A

RNA molecules that serve as templates for protein synthesis (RNA polymerase II)

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10
Q

rRNA

A

a component of ribosomes (RNA polymerase I, Polymerase III)

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11
Q

tRNA

A

serves as adaptor molecules that align amino acids along the mRNA template (RNA polymerase III)

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12
Q

make up well over 90% of total RNA by mass in any cell

A

rRNA and tRNA

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13
Q

regulatory mechanisms

A

ensure correct gene is transcribed in the correct cell type at the correct time and in correct amount

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14
Q

DNA sequence element

A

term used to denote a specific short sequence of DNA base pairs within a gene promoter

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15
Q

Cis-acting DNA sequences

A

aka promoter and enhancer elements; regulate expression of genes

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16
Q

basal or core promoter

A

ex. TATA box, initiator (Ing) DNA sequence

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17
Q

upstream promoter and enhancers

A

same functionally; transcriptional regulatory sequences that can be located at a significant distance from promoter; binding sites for gene specific transcription factors

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18
Q

enhancers can be…

A

upstream and downstream

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19
Q

usually only one _______, but could be multiple _________________

A

TATA box, CAT and GC boxes

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20
Q

SV40 enhancer

A

can function in any orientation and in any position relative to core promoter

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21
Q

plasmid DNA

A

a method by which to introduce recombinant DNA into a cell

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22
Q

reporter gene

A

a gene that encodes an easily assayed enzyme or other protein and can be used to replace the normal gene sequence adjacent to a gene promoter

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23
Q

Other methods of incorporating altered DNA sequences into a genome:

A

retrovirus/lentivirus and CRISPR/Cas9

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24
Q

transcription factors

A

proteins that are required for RNA polymerase II to initiate transcription

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25
Q

general transcription factors

A

involved in initiation of transcriptionand are part of general transcription machinery

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26
Q

gene specific transcription factors

A

not part of general machinery; proteins that exhibit DNA sequence-specific binding properties, direct activity of the general transcription factors and modulate activity of basal transcription complex

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27
Q

general transcription factors and RNA polymerase II are thought to assemble in…

A

a step-wise manner around the basal promoter region

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28
Q

the complex formed from a general transcription factor and RNA polymerase II

A

transcription initiation complex aka pre initiation complex aka basal transcription complex

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29
Q

TATA box

A

a regulatory DNA sequence found in promoters transcribed by RNA pol. II

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30
Q

TATA-binding protein or TBP

A

a basal transcription factor that binds directly to the TATA box

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31
Q

TBP-associated factors or TAFs

A

proteins associated with TBP in the general transcription factor (TFIID)

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32
Q

TFIIB associates with TFIID at the…… followed by recruitment of ………… and TFIIF

A

core promoter, RNA polymerase

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33
Q

After polymerase II joins promoter, ….. and ….. complete formation of initiation complex

A

TFIIE and TFIIH

34
Q

How do gene-specific transcription factors work?

A

by either modifying the rate of transcription initiation by the basal transcription complex and/or rate of basal transcription complex assembly

35
Q

Similar to TBP, recognition and binding sites of most transcription factors consist of……

A

short DNA sequences

36
Q

which transcription factor recognizes the DNA sequence GGGCGG (GC box)

A

SP1

37
Q

which transcription factor recognizes the DNA sequence CCAAT(CAT box)

A

CBTF

38
Q

What specifies the amount of transcriptional initiation by RNA pol. II

A

combo of transcription factors interacting at a specific gene’s promoter/enhancer sequence at one point in time

39
Q

immunoglobin heavy chain enhancer

A

contains nine functional sequence elements

40
Q

DNA-affinity chromatography

A

a method used to isolate transcription factors based on their binding to specific DNA sequences in order to study them further

41
Q

steroid hormone receptors

A

transcription factors that regulate gene transcription in response to hormones

42
Q

homeodomain proteins

A

contains a helix-turn-helix DNA binding domain and play critical roles in regulation of gene expression during embryonic development

43
Q

transcription factors can function as either…

A

transcriptional activators and transcriptional repressors

44
Q

2 general mechanisms of action of transcriptional activators

A
  • interact with mediators and general transcription factors

- interact with coactivators, which modify chromatin structure

45
Q

mediator

A

a large protein complex that binds to pre initiation complex and plays a key role in linking general transcription factors to gene specific transcription factors that regulate gene expression

46
Q

How do transcription factors bound to distant enhancers interact with proteins in the RNA pol/mediator complex at the core promoter?

A

DNA looping

47
Q

Release of RNA pol from basal complex to initiate transcription requires what….

A

phosphorylation and helices activities of TFIIH

48
Q

gene expression is regulated by…

A

repressors and transcriptional activators

49
Q

transcriptional repressors function by

A
  • blocking binding of transcription activator to DNA sequence element
  • repress mediator activity
  • interaction with co-repressors
50
Q

co-repressors

A

modify chromatin structure into a non-permissive state

51
Q

example of gene activation and repression

A

control of lac operon

52
Q

chromatin

A

decondensed state

53
Q

chromatin remodeling

A

moving, removal and/or addition of histones

54
Q

histone code

A
  • histone tail acetylation and deacetylation

- other histone modification

55
Q

histone modification can be stably inherited through…

A

epigenetic mechanisms

56
Q

Chromatin remodelling factors

A
  • slide nucleosomes along DNA
  • change conformation of the nucleosomes
  • eject the histone from DNA
57
Q

histone acetylation

A

modification of histones by addition of acetyl groups to specific lysine residues in histone tails; result in transcriptionally permissive chromatin

58
Q

histone deacetylation

A

gives rise to non-permissive chromatin state

59
Q

DNA methylation

A
  • prevent movement of transposon

- inactivate genes involved in development and differentiation

60
Q

methylation patterns

A

-can be reversed but also passed to daughter cells as epigenetic inheritance

61
Q

genomic imprinting

A

only of of two parental alleles of some genes is expresses during embryonic development

62
Q

polyadenylation

A

adding a poly-A tail to pre-mRNA

63
Q

what is added to 5’ end in the beginning

A

7-methylguanosine cap

64
Q

spliceosomes

A

large complexes composed of proteins and RNAs; multiple snRNP complexes

65
Q

snRNAs

A

small nuclear RNAs that range in size to form the RNA component of spliceosome

66
Q

types of snRNAs

A

U1, U2, U4, U5, U6

67
Q

snRNPs

A

small nuclear ribonucleoprotein particles; complexes of snRNAs with proteins that play central roles in splicing process

68
Q

types of snRNPs

A

U1, U2, U3, U5, U4/U6

69
Q

actual splicing reaction is catalyzed by..

A

U6

70
Q

alternative splicing

A

generation of different mRNAs by varying the pattern of pre-mRNA splicing to create multiple different, but related, proteins from same gene; some exons are removed with the introns

71
Q

Each human gene yields and average show many alternatively spliced mRNAs?

A

6; but some can produce thousands

72
Q

SR splicing factors

A

SR proteins; bind to exon sequence to direct where a spliceosome forms; make final choice of exons that will appear in any one cell type for alternatively spliced mRNA

73
Q

DSCAM gene

A

contains four sets of alternative exons, each being incorporated into the spliced mRNA

74
Q

Why is DSCAM mRNA important to neurons during embryonic development?

A

cell surface adhesion molecule important in allowing neurons to find their target cells

75
Q

alternative splicing of DSCAMmeans…

A

different forms of a cell surface

76
Q

pre-rRNA

A

primary transcript cleaved to form individual ribosomal RNAs (28S, 18S, 5.8S)

77
Q

Extensive processing of pre-rRNA takes place…

A

before they can be assembled for use in protein synthesis

78
Q

pre-tRNAs

A

transcribed as a group and are cleaved into individual tRNA molecules

79
Q

5’ end of eukaryotic tRNA is cleaved by…

A

RNase P

80
Q

3’ end of eukaryotic tRNAis cleaved by…

A

conventional RNase and has the sequence CCA added to end to facilitate binding to amino acids

BMSC 220 (12 decks)

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