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lecture 27 Flashcards

regulation of gene expression

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1
Q

what determines a cell’s function?

A

gene expression

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2
Q

what do prokaryotic organisms lack?

A

defined nucleus

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3
Q

how is dna stored in a prokaryotic cell?

A

it is free floating and circular

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4
Q

in what order to transcription, translation, and protein formation occur in a prokaryotic cell?

A

simultaneously

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5
Q

what happens to transcription when the protein is no longer needed in a prokaryotic cell?

A

it stops

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6
Q

what is the primary method of controlling gene expression in prokaryotic cells?

A

controlling transcription

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7
Q

what are the two major protein classes that regulate chromatin remodeling?

A

ATP-dependent protein remodeling complexes and histone modifying complexes

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8
Q

what is the name of the complex that regulates expression by moving, ejecting, or restructuring nucleosomes?

A

ATP-dependent protein remodeling complex

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9
Q

what happens to the chromatin structure once the ATP-dependent chromatin remodeling complex binds to DNA around the nucleosome?

A

it is loosened which allows for the histone core octomer to move

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10
Q

if a histone is acetylated, what happens to the gene?

A

it is expressed

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11
Q

if a histone is de-acetylated, what happens to the gene?

A

it is silenced

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12
Q

what is the name of the complex that enzymatically modifies N-terminal histone tails?

A

histone/DNA modifying complex

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13
Q

if DNA is methylated, what happens to the gene?

A

it is silenced

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14
Q

if DNA is de-methylated, what happens to the gene?

A

it is expressed

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15
Q

what is the histone code hypothesis?

A

transcription of DNA is regulated, in part, by specific chemical modifications to histone proteins.

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16
Q

acetylases, methylases, and phosphorylases are involved in what type of histone modification?

A

writing (uses HAT, HMT, and kinases)

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17
Q

deacetylases, demthylases, and phosphatases are involved in what type of histone modification?

A

erasing (uses HDAT, HDM, and phosphotase)

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18
Q

brodomain(Ac-K), chromodomain(Meth-K), PHD finger(H3K4me3), and WD40 repeat(scaffold) are involved in what type of histone modification?

A

reading (protein-protein interactions)

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19
Q

what does modifying the histone proteins themselves do?

A

it recruits other proteins to the modified histone

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20
Q

what are the SIX things that must happen for a gene to be expressed(turned on)?

A
  1. initiating signal
  2. signaling pathway cascade
  3. activation of transcription factor
  4. recruits other member of transcription complex
  5. transcriptional complex recruits rna polymerase ii
  6. promotor site initiates transcription
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21
Q

what is a molecule that is produced in one cellular location but its effects are seen in another?

A

hormone

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22
Q

what does a hormone require in a target cell?

A

receptors specific to that hormone

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23
Q

how do transcription factors control the rate of gene transcription?

A

they help or hinder RNA polymerase II binding to DNA, interact with other proteins to build a transcription complex, contain binding domains, multiple binding sites for distinct transcription factors

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24
Q

what structural level do transcription factors contain DNA binding domains?

A

tertiary

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25
Q

what do DNA binding domains do?

A

attach to specific DNA sequences

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26
Q

what does multiple binding sites for distinct transcription factors signify?

A

multiple transcription factors can affect expression of a single gene

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27
Q

what type of transcriptional regulation is found in the DNA itself?

A

cis-activating factor

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28
Q

what type of transcriptional regulation acts on the DNA?

A

trans-activating factor

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29
Q

where is the TATA box found?

A

promotor region

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30
Q

where do transcription factor complex proteins bind?

A

TATA box

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31
Q

what region of DNA initiates transcription?

A

promotor

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32
Q

where is the promotor located?

A

upstream but near the transcription start site of a particular gene

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33
Q

what region of DNA binds to activator proteins to activate the transcription process?

A

enhancer

34
Q

what region of DNA binds to repressor proteins to prevent binding of RNA polymerase II to the promotor?

A

repressor

35
Q

what region of DNA prevents the interaction of enhancers with promotors?

A

insulator

36
Q

what is responsible for basal level of expression and is the site of basal factor binding?

A

core promotor region

37
Q

what is responsible for the induced/repressed level of expression and is the site of activator protein binding?

A

promotor-proximal elements

38
Q

where do tissue specific transcription factors bind?

A

promotor-proximal elements

39
Q

what can lie far away from the gene of interest and can retain its function even when it’s reversed?

A

promotor-proximal elements

40
Q

what allows promotor-proximal elements, specifically enhancer, to work?

A

looping of DNA - it brings transcription factors and trans-activating factors together

41
Q

what leads to higher efficiency transcription of gene of interest?

A

enhancer

42
Q

what is the primary role of insulators?

A

prevent transcription of NON-TARGET genes

43
Q

what are the FIVE steps of RNA processing?

A
  1. 5’ capping
  2. 3’ tail poly-adenylation
  3. RNA splicing
  4. RNA transport
  5. miRNA
44
Q

what does the 5’ guanine cap do?

A

it protects the RNA chain from degradation by nucleases

45
Q

when does 5’ capping occur?

A

it happens co-transcriptionally, once the RNA chain is ~30 nucleotides long

46
Q

what is the poly A signal?

A

AAUAAA

47
Q

is the poly A signal conserved or unconserved?

A

conserved

48
Q

what is the name of the enzyme that cleaves nascent RNA DOWNSTREAM of the AAUAAA site?

A

ribonuclease

49
Q

what is the name of the enzyme that adds adenine ribonucleotides to the 3’ end?

A

poly(A) polymerase

50
Q

what are the two major functions of 3’ polyadenylation?

A
  1. enhances stability of RNA molecule
  2. regulates transport to the cytoplasm
51
Q

what are INtervening sequences of RNA NOT expressed in proteins?

A

introns

52
Q

what is the mechanism by which introns are removed?

A

splicing

53
Q

what are sequences of RNA that are RETAINED in mRNA and ARE expressed in proteins?

A

exons

54
Q

what is the protein/RNA complex that directs and ensures proper RNA splicing?

A

spliceosome

55
Q

what is the process that exports mature mRNA from the nucleus into the cytoplasm?

A

RNA transport

56
Q

what protein controls RNA transport?

A

messenger ribonucleo-proteins

57
Q

through what is mRNA transported?

A

large multi-protein pore complexes

58
Q

what is a class of naturally occurring, small non-coding RNA molecules whose main function is to down-regulate gene expression?

A

miRNA (mature micro RNA)

59
Q

what structure does miRNA have?

A

stem-loop, hairpin structure

60
Q

how does miRNA down-regulate gene expression?

A

it blocks translation by the ribosome and speeds up deadenylation(breakdown of the poly-A tail)

61
Q

during which stage does most translational regulation occur?

A

initiation

62
Q

ribosomal subunit proteins and initiation proteins for a complex to recognize what part of mRNA?

A

5’ guanine cap

63
Q

the complex scans down the RNA sequences until it finds what?

A

the start codon (AUG)

64
Q

to which large subunit(60S) part is the initiation codon lined up with by the initiation complex?

A

P site

65
Q

what are the subunits of a ribosome and what do they make when combined?

A

40S, 60S, 80S

66
Q

what is the process wherein ribosomes are stacked on an mRNA molecule?

A

ribosomal pausing

67
Q

what are the effects of ribosomal pausing?

A

the ribosome can release and the incomplete polypeptide may prematurely degrade

68
Q

what happens once the ribosome reaches a STOP codon?

A

release factors bind to the ribosome

69
Q

by what process is the protein released from the ribosome?

A

hydrolysis

70
Q

what are the TWO types of structural post-translational modifications?

A
  1. disulfide bonds
  2. proteolytic cleavage
71
Q

between what do disulfide bonds form?

A

cysteine residues

72
Q

what does proteolytic cleavage cleave and what does it result in?

A

it cleaves a pre-protein, resulting in a mature, functional protein

73
Q

what are the TWO functional groups of post-translational modification?

A

myristolation and phosphorylation

74
Q

what type of functional group is characterized by the attachment of lipid chains resulting in membrane localization of a protein?

A

myristolation

75
Q

what type of functional group is characterized by the attachment of phosphate group to specific amino acids resulting in regulation of enzymatic activity?

A

phosphorylation

76
Q

what is added to a protein in myristolation?

A

lipid chains

77
Q

what is added to a specific amino acids in phosphorylation?

A

phosphate group

78
Q

what is the result of myristolation?

A

membrane localization of a protein

79
Q

what is the result of phosphorylation?

A

regulation of enzymatic activity

80
Q
A

genetics (30 decks)

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