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MFM > Regulation of Transcription and Translation > Flashcards

Regulation of Transcription and Translation Flashcards

1
Q

what are the prokaryotic elongation factors?

A

EF-tu, EF-G

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2
Q

process of tRNA being linked to appropriate AA?

A

tRNA charging, resulting in aminoacyl-tRNA (because specific nucleotides in anticodon and AA-accepting arm allow correct tRNA to be recognized by synthetase enzyme

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3
Q

prokaryotic rRNA

A

smaller, contain 3 types of rRNA instead of 4

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4
Q

why is alpha amanitin so deadly?

A

it inhibits transcription in eukaryotes by binding to rna polymerase II

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5
Q

2nd step translation

A

carboxyl end of polypeptide chain is uncoupled from tRNA at P site and joined by a peptide bond to the free amino group of the amino acid linked to the tRNA at the A site

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6
Q

size of large and small subunits in eukaryotes?

A 
large = 60S
small = 40S
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7
Q

who does ricin inhibit translation?

A

causes eukaryotic ribosome inactivation: catalytic inactivation of 28S rRNA via N-glycosidase action on A.

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8
Q

can rRNA do anything by itself

A

no it must be bound to protein to be functional

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9
Q

what is alternative splicing?

A

mRNAs can be spliced different ways to produce different protein products from the SAME gene!

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10
Q

what are introns

A

long noncoding intervening sequences that need to be spliced by spliceosomes (snRNPs)

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11
Q

what are negative regulators (gene specific transcription factors)?

A

prevent recruitment of RNA polymerase

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12
Q

mechanisms of genetic switches

A

proteins recognize and bind to specific dna sequences by activating or repressing (activators enhance binding to promoter or opening DNA helix, repressors bind to sequences upstream from promoter and prevent binding to promoter)

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13
Q

when are the poly A tail and 5’ guanosine cap added to mRNA? (aka when is mRNA processing)

A

as the mRNA primary transcript is being produced from the RNA exit channel (the factors responsible for capping, splicing and polyadenylating are bound to the back of RNA polyII)

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14
Q

what is the weight of eukaryotic ribosomes?

A

80S

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15
Q

how does streptomycin inhibit prokaryotic translation?

A

prevents initiation by preventing formation of initiation complex, hinders elongation via codon misreading/insertion of improper AA in the A binding site

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16
Q

what are exons

A

expressed sequences encoding proteins

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17
Q

which are the translation initiation factors in eukaryotes?

A

eIF (eukaryotic initiation factors), eIF2, eIF3, eIF4A, eIF4E, eIF4G, eIF5B

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18
Q

how is translation terminated?

A

release factor (RF) binds to stop codon in A site (called RF in prokaryotes, eRF in eukaryotes)

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19
Q

why does tRNA have a cloverleaf shape?

A

it is single stranded so can fold upon self

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20
Q

what is the specific function of the CAAT box and GC box?

A

improves the efficiency of transcription

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21
Q

describe the prokaryotic promoter region

A

has two sequences, -10/Pribnow box TATAAT and -35 TTGACA

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22
Q

what are positive gene specific transcription factor regulators?

A

recruit transcription factors and RNA polymerase

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23
Q

what is rho independent transcription termination

A

the polymerase requires 2 sequences in the RNA (a GC rich hairpin and 8 uridines) in order to induce release of polymerase

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24
Q

where does translation occur?

A

cytoplasm

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25
Q

4th step translation

A

small subunit moves exactly 3 nucleotides along mRNA molecule, bringing it back to its original position relative to large subunit, resetting ribosome with empty A site for step 1

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26
Q

what does the aminoacyl site of ribosome do?

A

binds appropriate aminoacyl-tRNA determined by the codon-anticodon base pairing

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27
Q

MOA of rifampin

A

binds to beta subunit on bacterial rna (SPECIFICALLY prokaryotic) and prevents rna synthesis because RNA polymerase cannot initiate

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28
Q

what specific enzyme does tRNA require to function?

A

aminoacyl-tRNA synthetases, of which each amino acid has its own version

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29
Q

what do snRNPs do

A

they are small nuclear ribonucleoproteins starting with U’s (U1,U2,U4,U5,U6) that recognize beginnnig of intron and end of introns in mRNA

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30
Q

what is the general function of rRNA?

A

is not translated, acts as a structural molecule, forming subunit of ribosome when combined

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31
Q

what is the sequence of translation initiation in prokaryotes?

A

shine dalgarno sequence, 10 bases upstream from start codon, that base pairs with 16S rRNA on the 30S subunit

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32
Q

How many types of RNA polymerase?

A

3

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33
Q

what is the shine dalgarno sequence?

A

ribosome binding site within mRNA sequence in prokaryotes that is 10 bases upstream from start, it base pairs with 16S rRNA (30S) which allows to recognize RNA and sets up the ribosome in the right position to start translation

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34
Q

what happens when histone’s lysine tails are deaceytlated?

A

histones remain closely linked and dna transcription is repressed

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35
Q

what does the large subunit of ribosome do?

A

catalyzes the formation of peptide bonds that covalently link AA together into a polypeptide chain

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36
Q

what is the main function of DNA methylation?

A

covalent attachment of methyl group to cytosine bases (that are located 5’ to guanosine) in the promoter region of DNA represses genes

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37
Q

what does mRNA generally look like?

A

5’ guanosine cap, untranslated region (UTR), start codon AUG, coding region , stop codon, and the trailer aka polyA tail

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38
Q

what is different about the prokaryotic genome?

A

is organized in a polycistronic way, meaning many of their genes are found in operons in which multiple genes are encoded by one transcriptional unit

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39
Q

what if microRNA is not an exact match to mRNA?

A

mRNA is stored and eventually degraded

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40
Q

what is the function of the 5’ cap?

A

7-methyl guanosine seals 5’ end and decreases the rate of degradation and serves as recognition site for the binding of the mature mRNA to a ribosome at protein synthesis initiation

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41
Q

which drugs are translation inhibitors?

A

streptomycin, tetracycline, clindamycin, erythromycin, ricin

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42
Q

what are the eukaryotic elongation factors?

A

eEF-1, eEF-2

43
Q

what if the microRNA is an exact match to the mRNA?

A

if complementary to mRNA, then the mRNA is degraded and RISC is released

44
Q

what is rho dependent transcription termination?

A

the rho protein binds a cytosine rich region in new mRNA, travels in a 5-3’ direction so when rho comes into contact with the rna polymerase it physically knocks off the rna polymerase

45
Q

main difference between prokaryotic and eukaryotic gene structure?

A

prokaryotic genes have operons and polycystonic genes

46
Q

what are the prokaryotic initiation factors?

A

IF-1, IF-3, IF-2

47
Q

how many eIF?

A

12 +

48
Q

size of large and small subunits in prokaryotes>

A 
large = 50S
small = 30S
49
Q

general mechanism of ribosome?

A

bring tRNA and mRNA together and coordinates translation

50
Q

3rd step translation

A

shift of large subunit relative to small subunit moves the 2 tRNAs into the E and P sites of the large subunit

51
Q

biggest differences between eukaryotic and prokaryotic translation?

A
  1. binding of mRNA to small ribosomal subunit
  2. first AA
  3. initiation factors
  4. ribosome size
52
Q

what enzymes regulate gene transcription through histone modification?

A 
histone acetyltransferase (HAT)
histone deacetyltransferase (HDAC)
53
Q

what happens when histone’s lysine tails are acetylated?

A

chromatin is relaxed and loosely associated with histone, DNA is available for transcription

54
Q

what occurs when iron is low in cells?

A

iron response protein binds to IRE in transferrin mRNA and stabilizes it to allow for translation (on 3’ end) to increase expression of transferrin; it also binds to the IRE on the 5’ end of ferritin mRNA to shut down expression of ferritin

55
Q

what are microRNAs?

A

short, noncoding RNAs that bind mRNA in 3’ UTR, they are transcribed from the genome in a large form that requires cleavage and binding to RISC to be active

56
Q

general mechanism of tRNA?

A

links mRNA sequence to corresponding amino acid -physical link between nucleotide sequence of RNA and amino acid sequence of proteins

57
Q

MOA of interchangable RNA polymerase subunits in gene regulation

A

the RNA polymerase associates with different versions of sigma subunit which gives specificity to specific gene promoters

58
Q

what does the small subunit of ribosome do?

A

matches tRNA to codons of mRNA

59
Q

describe the prokaryotic RNA polymerase

A

the functional unit consists of the 5 subunit core enzyme and a sigma factor (sigma 70)

60
Q

tRNA processing occurs where?

A

in nucleus, transcribed by RNApolymerase III with introns first, then spliced, then CCA added to 3’ end

61
Q

what type of RNA polymerase transcribes mRNA or protein coding genes?

A

RNA polymerase II

62
Q

what causes binding of mRNA to small ribosomal subunit in prokaryotes?

A

the shine delgarno sequence upstream of AUG binds to complementary sequnce in 16S rRNA

63
Q

what does the ejection site do?

A

binds free tRNA (AA free) before it leaves the ribosome

64
Q

where is rRNA synthesis and processing occur? and how?

A

nucleolous by rna pol I, 45S transcript made which is then cleaved into 3 mature rRNA (5.8S, 18S, 28S) then 5S is transcribed by rna polIII

65
Q

how many IF?

A

3

66
Q

2 translation factors?

A

translation initiation factors and translation elongation factors

67
Q

how does diptheria toxin inhibit translation?

A

inactivates eukaryotic eEF-2 through ADP-ribosylation

68
Q

what do the TFII’s do in transcription?

A

form the pre-initiation complex for RNA polymerase II during eukaryotic transcription, help bind, recruit, helicase, bridge

69
Q

binding sites for tRNA on ribosome?

A

aminoacyl site (A), peptidyl site (P), ejection site (E)

70
Q

how does clindamycin inhibit prokaryotic translation?

A

binds to 50S subunit, overlapping A and P sites to block peptidyl transferase activity (peptide bond formation)

71
Q

2 means of gene regulation in prokaryotes?

A
  1. interchangable rna polymerase subunits

2. genetic switches

72
Q

what causes the binding of mRNA to the small ribosomal subunit in eukaryotes?

A

the cap at the 5’ end binds the eIF’s and the 40S subunit containing the tRNA at the start codon

73
Q

what is the difference between pre-mrna and mature mrna?

A

pre- has introns and exons, no cap or tail

74
Q

1st step translation

A

tRNA carrying next amino acid in chain binds to the vacant A site on the ribosome by forming base pair with the codon that is exposed there

75
Q

what are the 4 functional units of RNA polymerase?

A
  1. Jaws - to clamp around DNA template and hold into place
  2. ribonucleoside triphosphate tunnel - to allow free ribonucleoside triphosphates into the active site
  3. active site - enzymatic activity adding nucleotides to 3’ end
  4. RNA exit channel - point of exit for newly formed mRNA
76
Q

is tRNA translated?

A

no, but is an important part of mRNA translation, 20 different tRNAs one for each AA

77
Q

how does tetracycline inhibit prokaryotic translation?

A

inhibits aminoacyl-tRNA binding at A site during elongation

78
Q

weight of prokaryotic ribosomes?

A

70S

79
Q

first AA in eukaryotes?

A

Met

80
Q

what happens if cytosine is methylated?

A

gene is not transcribed

81
Q

example of gene specific transcription factors?

A

myo-D in myogenesis, binds to promoter region that are important to myogenic process

82
Q

what does the peptidyl site of ribosome do?

A

binds to peptidyl-tRNA (tRNA bound to the peptide being syntheized)

83
Q

what 4 things are needed for translation?

A

processed mRNA molecule, tRNA, ribosomes, translation factors

84
Q

what are the 3 general components of a eukaryotic gene?

A

promoter, regulatory sequences, coding region

85
Q

what occurs if the anticodon and amino acid accepting arm both allow correct tRNA to be recognized by synthetase?

A

an aminoacyl-tRNA is formed

86
Q

3 types of RNA?

A 
mRNA = messenger rna, encodes a protein
rRNA = ribosomal rna, component of the ribosome
tRNA = tranfer rna, translates the information encoded on mRNA into AA sequence
87
Q

eukaryotic rRNA

A

contain 4 types of rRNA = 18S, 28S, 5S and 5.8S,

88
Q

what is the function of the polyA tail?

A

prevents degradation of mRNA until it is translated

89
Q

what is the specific function of TFIID?

A

the TATA binding protein

90
Q

what occurs when iron is high in cells?

A

iron binds to IRP (iron response protein) and releases it from the transferrin receptor in mRNA and causes it to degrade to decrease cellular uptake of iron, iron also binds to IRP of ferritin mRNA and allows for its translation to increase iron storage

91
Q

7 steps of prokaryote transcription

A
  1. holoenzyme binds to promotor site
  2. rna polymerase unwinds dna
  3. transcription starts
  4. after first 10 bases, sigma factor is released
  5. rna polymerase changes form slightly and continues
  6. rna polymerase reaches termination sequence
  7. hairpin structure disrupts polymerase and dissociates with DNA
92
Q

function of polyribosomes

A

more protein molecules made in a given amt of time due to a large cytoplasmic assembly of several ribosomes spaced apart along a single mRNA molecule

93
Q

3 types of eukaryotic regulation of transcription

A

OVERALL: promotion or prevention of transcription initiation complex assembly

  1. histone modification
  2. DNA methylation
  3. gene specific transcription factors
94
Q

what is the function of sigma70 in RNA polymerase?

A

has a high affinity for DNA and binds specifically to the -35 and -10 sequences of the promoter - important to recruit core enzyme for initiating transcription

95
Q

what is the first step of transcription in eukaryotes?

A

TFIID binds to the TATA box
TFIID recruits TFIIB
then TFIIE, TFIIF, TFIIH and the associated RNA polymerase bind to TFIID/B complex and begin

96
Q

what is the promoter region in eukaryotes comprised of?

A

TATA box at -25, CAAT box and GC box at -40 to -110

97
Q

what is the unique characteristic of prokaryotic gene replication?

A

transcription and translation can occur simultaneously because prokaryotes do not have a nuclear envelope or have to ship their DNA to the cytoplasm

98
Q

how do mRNA molecules leave the nucleus?

A

the exon junction complex (EJC) associates with mRNA, associates with nuclear pore complex and escorts it out of the nuclear pore

99
Q

How does release factor work for termination?

A

peptidyl transferase adds water molecule to peptidyl-tRNA instead of an amino acid which frees the carboxyl end of the polypeptide chain from its attachment to tRNA molecule

100
Q

what is the weight of mitochondrial ribosomes?

A

55S

101
Q

2 functional domains on tRNA

A

1anticodon region = recognizes speciifc codon in mRNA

2 amino acid attachment site on opposite side

102
Q

what is the first amino acid in prokaryotes?

A

formyl-methionine

103
Q

what happens if cytosine/promoter is demethylated?

A

gene is transcribed

MFM (39 decks)

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