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Molec and Cell > Chapter 6: Gene Expression > Flashcards

Chapter 6: Gene Expression Flashcards

1
Q

This is a consensus promoter sequence that usually occurs ~25 bps upstream from the gene it primes

A

TATA box

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2
Q

before transcription, the RNA polymerase binds – generally – to this region

A

promoter region

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3
Q

what is the combined error rate of DNA polymerase and exonuclease activity?

A

1 x 10^7

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4
Q

What is the combined error rate of RNA polymerase activity?

A

1 x 10^4 (1 in 10,000)

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5
Q

What are 3 reasons why RNA polymerase has a higher error rate than DNA polymerase?

A
  1. energy conservation
  2. RNA mutations are non-hereditary
  3. much faster
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6
Q

What is the name of the TBP transcription-associated protein?

A

TATA-binding protein

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7
Q

this transcription-associated protein identifies and binds to the TATA box sequence with high affinity

A

TBP (TATA-binding protein)

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8
Q

What is the function of TIID protein?

A

distorts DNA @ the TATA box which allows for further transcription factor assembly

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9
Q

What is the function of the TFIIH protein?

A

has both helicase and kinase activity

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10
Q

Why are there so many transcription factors required for RNA transcription initiation?

A

prevents nonsense transcriptions from hyperexpression/overproduction of non-functional protein

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11
Q

what are promoter regions (enhancers)?

A

a region of DNA (upstream) that binds activator proteins that can then bind to corresponding mediator

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12
Q

What is the function of promoter regions (enhancers)?

A

method of regulating RNA pol activity

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13
Q

What are the two binding fates of activator protein binding to promoter regions?

A
  1. activator binds to mediator
  2. addition of histone-modifying and chromatin-remodelling proteins
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14
Q

What are the two outcomes of activator protein binding to promoter regions?

A
  1. activator binds to mediator
  2. addition of histone-modifying and chromatin-remodeling proteins
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15
Q

what is the function of mediators and activators?

A

allows for various methods of RNA transcription/gene expression control; can increase/decrease transcription speed

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16
Q

what is an advantage of splicing?

A

allows for the usage of a single DNA regions for the production of multiple different proteins

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17
Q

whats the name of snRNP?

A

small nuclear ribonuclear protein

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18
Q

what is the function of snRNPs?

A

bind and replace DNA regions to splice out introns

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19
Q

where does snRNP activity occur?

A

in the nucleus

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20
Q

what happens to mRNA after splicing

A
  1. new 5’ end is capped
  2. new 3’ end is polyadenylated
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21
Q

why must capping and adenylation occur after splicing?

A

ensures that immature mRNA sequences can’t be translated before exiting the nucleus

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22
Q

in what organisms does capping and adenylation not occur?

A

prokaryotes

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23
Q

what are 3 functions of the nucleolus?

A
  1. stable environment for rRNA and subunit synth
  2. recycling and modifying rRNA proteins
  3. rRNA transcription location
24
Q

what are the 2 ribosomal subunits in eukaryotes?

A

40S and 60S

25
Q

what region of the DNA are the ribosomal subunits sourced from?

A

45S precursor rRNA

26
Q

how many nucleotides are in the 45S precursor rRNA?

A

13,000

27
Q

what are the two ribosomal subunits found in prokaryotes?

A

30 and 50S

28
Q

what is the start codon?

A

AUG

29
Q

What are the stop codons?

A
  1. UAA
  2. UAG
  3. UGA
30
Q

What is the function of tRNA synthase (tRNA ligase)?

A

pairs each tRNA complex with its corresponding amino acid for each codon

31
Q

What is the error rate of tRNA synthase?

A

1 in 40,000 AAs

32
Q

what is the rate of translation?

A

2 AA per second

33
Q

what are the 3 ribosomal sites (and their functions)?

A
  1. A –> tRNA and AA binding site
  2. P –> peptide bond formation
  3. E –> ejection site
34
Q

how many proteins are needed for 60S synthesis? 40S synthesis?

A

~49; 33

35
Q

this is an estimate of a protein’s density and molecular weight as is settles in sucrose

A

sedimentary coefficient

36
Q

what two translation factors are associated/binded with the 5’ cap of mRNA

A

elF4E and elF4G

37
Q

what transcription factor is associated with initiator tRNA when binding to the P site of the small subunit?

A

elF2 protein

38
Q

what are 7 steps of translation initiation?

A
  1. initiator tRNA binds to P site with elF2 protein
  2. 5’ cap of mRNA binds to elF4E and elF4G
  3. initiator tRNA runs along mRNA for AUG
  4. elF2 and other factors dissociate
  5. large subunit binds
  6. new aminoacyl tRNA attaches to A site
  7. P region forms peptide bond between AAs
39
Q

about what percentage of proteins will be misfolded and dysfunctional?

A

~33%

40
Q

about what percentage of proteins will be misfolded in general

A

~66%

41
Q

what are the 3 methods of protein folding?

A
  1. cotranslational protein folding
  2. chaperone-assisted protein folding
  3. chaperonin rescue
42
Q

what is cotranslational protein folding?

A

protein folding that beings spontaneously right after release from ribosome

43
Q

what proteins utilize chaperone-assisted folding?

A

proteins with sensitive R-groups that may react easily

44
Q

what machinery is required for chaperone-assisted protein folding?

A

hsp70 machienery and ATP

45
Q

what is the function of hsp70 macheinery?

A

protects sensitive R-groups (using ATP) until necessary to fold them

46
Q

how do hsp70 proteins respond to heat and stress?

A

concentrations increase to counteract unideal protein folding environment

47
Q

how does ATP help hsp70 proteins?

A

remove Pi from bound ATP

48
Q

what method of protein folding uses hsp60 proteins?

A

chaperonin rescue of misfolding

49
Q

what are the stages of chaperonin rescue?

A
  1. incorrect protein binds to hydrophobic sites
  2. GroES cap contains protein in hsp60
  3. ideal environment for refolding is created
  4. correctly folded protein is released
50
Q

these are misfolded proteins that stick together in large, stable complexes

A

protein aggregates

51
Q

what is the purpose of polyubiquitin?

A

acts as a death/digestion tag for unwanted proteins; sends to proteosome

52
Q

this is the portion of a proteosome that chops up the peptide bonds between proteins

A

protease

53
Q

this is a portion of a proteosome that interact’s the a target protein’s polyubiquitin tag

A

unfoldase

54
Q

this is a type of protein aggregate that is the result of highly abnormal protein misfolding

A

prion

55
Q

why are prions so dangerous?

A

the collect correctly folded proteins to convert them to the stable aggregate form with no function; clogs up nervous systems

56
Q

this is structure is formed when a normal protein interacts with its abnormal prion form

A

heterodimer

57
Q

this structure results when a normal protein is converted to an abnormal prion form

A

homodimer

Molec and Cell (18 decks)

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