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BMS 525 > FINAL! > Flashcards

FINAL! Flashcards

1
Q

Where does transcription occur?

A

Nucleus

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2
Q

Where does translation occur?

A

on ribosomes in the cell cytoplasm

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3
Q

Translation

A

-“decoding” a messenger RNA (mRNA) and using its information to build polypeptide
-Process by which ribosomes read genetic message in mRNA and produce a protein product according to the message.

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4
Q

What does translation involve?

A

Non-coding RNA:
-rRNA: makes up ribosomes, the protein factories
-snoRNA: facilitates necessary mods to rRNA (and other RNA)
tRNA: adaptors that bind amino acid at one end and interact with mRNA at the other end.

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5
Q

Expression

A

Production of a final product
i.e. for a protein-coding gene expression= protein produced

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6
Q

Open reading frame or coding region

A

Region of the mRNA from start codon to stop codon that codes for a protein
ALWAYS made up of exons*

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7
Q

What are the untranslated regions?

A

5’ UTR and 3’ UTR
Also exons, bud do not code for protein; regulatory in nature

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8
Q

Ribosome

A

-The large subunit ineracts with the aminoacylated end of the tRNA
-Small subunit interacts with mRNA and anticodon loop of the tRNA

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9
Q

Two subunits of E. coli and its coefficient?

A

70S ; Small 30S and decodes mRNA; 50s Large links amino acids together through peptide bonds

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10
Q

E. coli 50S SU contains

A

55 rRNA, 23S rRNA, 34 proteins (L1-L34), and a catalytic subunit

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11
Q

E. coli 30S SU contains

A

16S rRNA, 21 proteins, ensures proper tRNA/mRNA base pairing

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12
Q

Eukaryotic cytoplasmic ribosomes are

A

Larger and contain more RNAs and proteins

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13
Q

Ribozyme

A

Ribosome capable of acting as an enzyme
RNA only ribosome still catalyzes peptide bond formation
Henry Noller

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14
Q

What are the characteristics of rRNA?

A

-Highly structured
-Contain many types of modified ribonucleotides that allow complex structure

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15
Q

Translation Steps and order

A

Initiation (beginning), Elongation (middle), and Termination (end)

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16
Q

Initiation

A

Ribosome gets together with the mRNA and the first tRNA so translation can begin
-Small subunit on mRNA binding site is joined by large subunit and aminoacyl-tRNA binds

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17
Q

Elongation

A

Amino acids brought to the ribosome by tRNAs and linked together to form a chain
-Ribosome moves along mRNA, extending protein by transfer from peptidyl-tRNA to aminoacyl-tRNA

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18
Q

Termination

A

The finished polypeptide is released to go and do its job in the cell
-Polypeptide chain is released from tRNA, and ribosome dissociates from mRNA

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19
Q

What are the key ingredients of initiation?

A

-A ribosome (which comes in two pieces, large and small)
-An mRNA with instructions for the protein we’ll build
-An “initiator” tRNA carrying the first amino acid in the protein, which is almost ALWAYS methionine (Met)

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20
Q

What happens to the key ingredients during initiation?

A

The pieces must come together to form initiation complex

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21
Q

Initiation complex

A

Ribosome, mRNA, and “initiatior” tRNA
Molecular setup needed to start making a new protein

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22
Q

What two important events must occur before translation initiation can take place?

A

1) Generate supply of aminoacyl-tRNAs
-AAs must be covalently bound to tRNAs
-Process of bonding tRNA to AAs is called tRNA charging
2) Dissociation of Ribosomes into their subunits
-Cell assembles the initiation complex on the small ribosomal subunit
-Two SUs must separate to make assembly possible

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23
Q

tRNA structure

A

-All share common secondary structure represented by cloverleaf
-Four base-paired stems define three stem-loops: D loop, Anticodon loop, T loop
-Acceptor stem is site to which AAs are added in the charging step

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24
Q

Specificity of tRNA

A

All tRNA have similar structure, but sequence and modification within the tRNA allow for specificity in:
-AA charging
-Anticodon loop binding mRNA
-Acceptance into ribosome

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25
Q

What does the shape of tRNA do?

A

Maximizes stability

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26
Q

What does the anticodon base-pair with in tRNA?

A

The corresponding codon in mRNA

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27
Q

What unique base-pairing does tRNA utilize?

A

Wobble Base-pairing
-3rd position have the least influence – wobble position
-Same tRNA can base pair with multiple codons via nonWatson-Crick base pairs

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28
Q

Wobble Hypothesis

A

-Codon-Anticodon recognition involves wobbling
-Multiple codons that encode the same AA most often differ at the third base position
-Pairing between first base of anticodon and third base of codon can vary from standard Watson-Crick base pairing according to specific wobble rules

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29
Q

Most of the time, existing nts in tRNA are what instead of replaced? What does this do for the structure of tRNA?

A

-Modified
-Regulate stability and recognition by proteins and rRNA

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30
Q

tRNA Charging

A

AA attached by ester bond between its carboxyl group and 2’ or 3’ hydroxyl group of terminal adenosine of tRNA

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31
Q

Aminoacyle-tRNA synthetases

A

-Join AAs to their cognate tRNAs
-Differences in tRNAs recognized by synthetases to charge with proper AA
- i.e. D loop nt seq or mods may be unique enough to allow only one synthetase to recognize it
- i.e nt adjacent to acceptor stem allow only that tRNA to fit into the synthetase

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32
Q

Initiator tRNA

A

-All initiation begins with AUG codon, but not ALL AUGs are initiation codons
- 2 Different tRNA recognize intiatior AUGs and internal AUGs

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33
Q

Initiator tRNA

A

-All initiation begins with AUG codon, but not ALL AUGs are initiation codons
- 2 Different tRNA recognize intiatior AUGs and internal AUGs-

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34
Q

N-formyl-methionyl-tRNA (tRNAfMet)

A

The aminoacyl-tRNA that initiates bacterial polypeptide translation
-Amino group of the methionine is formylated
-Met-tRNA = internal AUG

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35
Q

Initiation in simplified terms

A

-elongating ribosome (bacteria) = 70S
-At termination, the 2 SUs separate
-SUs reassociate to 70S during initiation

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36
Q

Ribosome: “Where do I start?”

A

-Prokaryotes: based on sequence
-Eukaryotes: Based on structure

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37
Q

Determining Ribosome Binding Site on mRNA in Prokaryotes

A

-Start codon AUG on an mRNA is chosen as initiation codon due to presence of SHINE DALGARNO SEQUENCE upstream of translation site (prokaryotes only)

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38
Q

Shine Dalgarno Sequence

A
  • Ribosome binding site
    -Base pairs with 16S rRNA ( in small subunit)
    -Upstream of the translation site (in prokaryotes only)
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39
Q

Why use Shine-Dalgarno sequences?

A

-Many AUG sequences in mRNA
-Bacterial RNAs are often polycistronic (cistron is coding region), so one bacterial mRNA can contain the coding sequence for several genes
- SD sequence marks start of each coding sequence, letting the ribosome find the right start codon for each gene.

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40
Q

What does initiation in bacteria need?

A

30S subunits and Accessory factors
-Initiation of translation requires separate 30S and 50S ribosome SUs
-Initiation also requires INITIATION FACTORS which bind to 30S SUs

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41
Q

Initiation factors

A

IF-1, IF-2, and IF-3

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42
Q

Bacterial IF-3

A

-Binds to free 30S SU to inhibit binding of 30S to 50S
-30S SU carrying initiation factors binds to an initiation site on mRNA to form an initiation complex
-IF-3 MUST be released to allow 50S SUs to join the 30S-mRNA complex

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43
Q

What is use of fMet-tRNA controlled by?

A

IF-2 and the ribosome

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44
Q

IF-2

A

Control use of fMet-tRNA
-Binds initiatior fMet-tRNAf and allows it to associate with the 30S SU

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45
Q

Prokaryotic Initiation Steps

A

1) Dissociation of 70S into 50S and 30S
2) IF1, IF2, and IF3 bind cooperatively to 30S SU
3) IFs direct binding of mRNA (at SD) and initiator tRNA, forming 30S initiation complex
4) IF1 and IF3 leave
5) IF2 hydrolyzes GTP and then leaves
6) 50S associates with 30S– forms active 70S complex

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46
Q

Eukaryotic Translation

A
  • No SD sequences to indicate the start codon
    -The ribosome recognizes the 5’ cap
    -Transcripts are largely monocistronic
    -5’ UTR is short
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47
Q

Scanning Model of Initiation

A

-Eukaryotic 40S ribosomal SUs locate start codon by BINDING 5’ CAP and scanning downstream to find the 1st AUG in a favorable context
-Kozak’s Observations (Rules) not always correct
- 5-10% of the time, most ribosomal SUs bypass 1st AUG scanning for a more favorable one - Leaky Scanning

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48
Q

Kozak’s Observations

A

-Internal AUGS not used
-Initiation does not occur. ata fixed distance from 5’ end (5’UTR varying length)
-Most of the time, first AUG downstream from cap is initiator
-Cap promotes translation

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49
Q

Gist of Eukaryotic Initiation

A

1) tRNA carrying methionine attaches to the small ribosomal subunit
2) Together, they bind to the 5’ end of the mRNA by recognizing the 5’ GTP cap
3) They “walk” along the mRNA in the 3’ direction, stopping when they reach the start codon (often but not always the first AUG)

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50
Q

Leaky Scanning

A

-When Kozak’s rules don’t apply
-5-10% of the time, most ribosomal SUs bypass 1st AUG scanning for a more favorable one

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51
Q

What allows the right AUG to be chosen in leaky scanning?

A

AUG needs to be in CONTEXT

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52
Q

AUG in CONTEXT

A

-A of AUG as -1 position
- Purine in -3 position
-G in +4 position

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53
Q

Effects of mRNA secondary structure

A

-Secondary structure near the 5’-end of an mRNA can have either positive or negative effects on start codon selection
-Hairpin just past AUG can force a pause by ribosomal SU and stimulate translation
-Very stable stem loop between cap and initiation site can block scanning and inhibit translation

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54
Q

What can “hiding” a start codon in a STABLE hairpin do?

A

Prevent recognition of THAT AUG, leading to a more downstream AUG being used

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55
Q

What does selecting different start sites make?

A

Different isoforms

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56
Q

eIFs

A

Eukaryotic initiation factors ; similar to prokaryotes

57
Q

Eukaryotic Initiation factors

A

-Initiator tRNA and specific initiation codon
– Met on initiator tRNA is NOT formylated
-tRNAi-Met

58
Q

What is required for ALL stages of initiation, including binding the initiator tRNA, attachment of the 40S SU to mRNA, joining of 60S SU, and movement of the ribosome?

A

Initiation factors

59
Q

43S preinitiation complex

A

eIF2, eIF3, Met-tRNAi, eIF1, eIF1A

60
Q

eIF2

A

Binds Met-tRNA to ribosomes (similar to prokaryotic IF2)

61
Q

eIF1 and eIF1A

A

Aid in scanning to initiation codon

62
Q

eIF3

A

Binds to 40S ribosomal subunit, inhibits reassociation with 60S SU (similar to prokaryotic IF3)

63
Q

eIF4

A

Cap-binding protein allowing 40S SU to bind 5’-end of mRNA

64
Q

eIF5

A

Encourages association between 60S ribosome SU and 48S complex

65
Q

eIF6

A

Binds to 60S SU, blocks reassociation with 40S SU

66
Q

Three parts of the eIF4F Cap-Binding Complex

A

1) eIF4E, has actual cap-binding activity
2) eIF4A: RNA helicase, ATP-dependent unwinding of hairpins found in the 5’-leaders of eukaryotic mRNA
3) eIF4B: has RNA-binding domain, can stimulate binding of eIF4A to mRNA

67
Q

eIF4G

A

-Scaffold protein capable of binding to other proteins including: eIF4E, eIF3, and PAB1
- Recruits 40S SUs to mRNA and stimulates translation

68
Q

Viral RNAs do what to eukaryotic initiation factors ?

A

Hijack them to facilitate translation of viral RNA

69
Q

Internal Ribosome Entry Site (IRES)

A

A eukaryotic mRNA sequence that allows a ribosome to initiate polypeptide translation WITHOUT migrating from the 5’ end

70
Q

What does a dicistronic assay indicate with PV?

A

That internal ribosome entry site (IRES) activity is present in the PDCD8 5’ UTR

71
Q

What does Polio virus do to translation?

A

Shuts down host mRNA translation, but translated its own RNA using IRES

72
Q

Why control initiation on a translational level given the amount of control at transcriptional and post-transcriptional level?

A

SPEED
New gene products can be produced quickly
Simply turn on translation of pre-existing mRNA
-Valuable in eukaryotes, transcripts relatively long, and take correspondingly long time to make
Most control of translation happens at the initiation step

73
Q

Translation Elongation

A

-similar in bacteria and eukaryotes
- Three Sites of the Ribosome: E site, P site, and A site

74
Q

In what direction is a polypeptide synthesized?

A

3’ to 5’

75
Q

In what direction does the ribosome read the RNA?

A

5’ to 3’

76
Q

What is the nature of the genetic code that dictates which amino acids will be incorporated in response to the mRNA?

A

The anticodon sequence

77
Q

E Site

A

-Elongation site on ribosome
- Exit site
-Where tRNAs leave the ribosome

78
Q

P site

A

Elongation site on ribosome
-Pepidyl-tRNA site
-Holds the tRNA carrying the growing polypeptide chain

79
Q

A site

A

-Elongation site on ribosome
-Aminoacyl-tRNA site
-Where incoming tRNA binds

80
Q

Elongation Cycle (three steps)

A

1) Aminoacyl-tRNA to the ribosomal A site (Ef-Tu)
2) Peptide bond between peptide in P site and newly arrived aminoacyl-tRNA in the A site (peptidyl transferase); Lengthens peptide by one amino acid and shifts it to the A site
3) Translocates the growing polypeptidyl-tRNA with its mRNA codon to the P Site ( EF-G)

81
Q

EF-Ts are involved in what?

A

The first elongation step
-T = transfer
-Transfers aminoacyl-tRNAs to the ribosome
-Actually TWO different proteins: Tu, u = unstable and Ts, s= stable

82
Q

EF-G

A

Participates in the third step of elongation;
G, GTPase activity

83
Q

EF-Tu

A

*elongation factor
-Monomeric G protein whose active form (bound to GTP) binds to aminoacyl-tRNA

84
Q

EF-Tu-GTP-aminoacyl-tRNA Complex

A

Binds to the ribosome’s A site

85
Q

What triggers Ef-Tu to hydrolyze GTP and what happens after that?

A

tRNA hydrogen binding to mRNA triggers Ef-Tu and after hydrolyzation, shifts tRNA in the ribosome so it can accept the amino acids chain

86
Q

Ef-Tu bound to GDP is what?

A

Released from ribosome

87
Q

EF-Ts does what?

A

Regenerates GTP to allow recycling of EF-Tu to EF-Tu-GTP

88
Q

Elongation Step 1:

A

Codon Recognition
-Incoming aatRNA to A Site
-H bonds from between the mRNA codon and tRNA anticodon
-Energy required

89
Q

When does proofreading for translation occur?

A

In the first step of elongation

90
Q

Ef-TU-GTP hydrolysis and release are what?

A

slow; peptide bond formation is slow.

91
Q

What does the slowness of EF-TU-GTP hydrolysis allow?

A

Proofreading; time for incorrect tRNAs to leave the A site before incorporation of the wrong AA into the polypeptide

92
Q

Weakness of incorrect codon-anticodon base pairing ensures what?

A

That Dissociation of tRNA from mRNA/ribosome complex occurs more rapidly than peptide bond formation

93
Q

How is speed of translation related to accuracy?

A

Inversely; faster translation = more errors

94
Q

Elongation Step 2

A

The polypeptide chain
- 50S SU has peptidyl transferase activity, provided by rRNA ribozyme
- Nascent PP chain is transferred from peptidyl-tRNA in P site to aminoacyl-tRNA in A site
-Peptide bond synthesis generates deacylated tRNA in P site and peptidyl tRNA in A site

95
Q

Difference between ribosome and ribozyme?

A

The ribosome is a ribozyme but EACH individual SU/rRNA on its own is NOT a ribozyme

96
Q

Elongation Step 3

A

Translocation Moves the Ribosome
-Ribosomal translocation moves the mRNA through the ribosome by three nucleotides
-Translocation moves deacylated tRNA into the E site and the peptidyl-tRNA into the Psite and empties the A site
-Process requires elongation factor EF-G which hydrolyzes GTP after translocation is complete

97
Q

Elongation factors bind alternatively to Ribosome

A

-Once A site is empty, EF-Tu can bring another charged tRNA
-Ribosomes cannot bind EF-G and EF-Tu simultaneously

98
Q

Elongation Summary

A

-Translocation requires EF-G, whose structure resembles the aminoacyl-tRNA-EF-Tu-GTP complex
-Binding of EF-Tu and EF-G to the ribosome is mutually exclusive –> EF-G blocks EF-Tu
- Translocation requires GTP hydrolysis, which triggers a change in EF-G, which, in turn, triggers a change in ribosome structure

99
Q

Antibiotics and toxins often act on what that affects translation?

A

The ribosome

100
Q

Puromycin

A

Antibiotic that inhibits translation

101
Q

How does puromycin work?

A

Ribosome treats Puromycin similar to aminoacyl-tRNA and allows polypeptide to transfer from the P site to the Puromycin in the A site; once Puromycin moves to the P site it initiates translation termination

102
Q

Translational Termination

A

*elongation cycle repeats to grow polypeptide
-Eventually, ribosome encounters STOP codon

103
Q

Stop Codon

A

-Signals time for last step
-No tRNA for stop codon
-Release factor binds to A site instead

104
Q

What are termination codons recognized by?

A

Protein Release Factors
-NOT BY aminoacyl-tRNAs

105
Q

Protein Release Factors

A

-Proteins that have a conformation mimicking tRNA: bind to A site and recognize stop codon; cannot accept a polypeptide chain, so chain is released
-Prokaryotic termination factors: RF1 and RF2

106
Q

Peptide Release

A

-Prokaryotic and Eukaryotic RF involved in this step

107
Q

RF1

A

Recognizes UAA and UAG

108
Q

RF2

A

Recognizes UAA and UGA

109
Q

RF3

A

Is a GTP-binding protein facilitating binding of RF1 and RF2 to the ribosome

110
Q

RRF

A

Ribosomal Release Factor
Separates Ribosomal subunits

111
Q

eRF1

A

Recognizes all three termination factors

112
Q

eRF3

A

Ribosome-dependent GTPase helping eRF1 release the finished polypeptide

113
Q

Release of Ribosomes from mRNA

A

-Does not happen spontaneously after termination
-Recycling factors help release mRNA, tRNA, and ribosomal SUs from complex
-Prokaryotic ribosomes use RRF and EF-G
Eukaryotes use different proteins that resemble RRF

114
Q

Once ribosomal subunits are released they associate with what?

A

Initiation factors (i.e eIF1 and 3, and IF3) and are free to start another round of translation
-The same 2 SUs do not come back together (random)
-More efficient translation termination, the more efficient translation

115
Q

Aberrant Termination (euk)

A

-Pre-mature stop (nonsense-mediated decay)
-No Stop (non-step mediated decay)
-Stalled ribosome (no-go decay)

116
Q

What is quality control of mRNA translation performed by?

A

Cytoplasmic Surveillance Systems

117
Q

Exon Junction Complexes (EJCs)

A

Involved in non-mediated decay
- recognition of a termination codon as PREMATURE involves EJCs (downstream and in mammals) and 3’ UTR structure or length

118
Q

Pioneer Round of Translation

A

-First translation event for a newly synthesized and exported mRNA

119
Q

NMD Triggers what?

A

Decay of the mRNA, degradation of the nascent polypeptide, and removes the ribosome

120
Q

NMD is stimulated by what?

A

Lef-over EJC
Premature stop codons in the last exon will not be recognized by NMD*

121
Q

Non-Stop Decay (NSD)

A

Targets mRNAs lacking an in-frame termination codon

122
Q

Eukaryotic Ribosomes stalled at the end of the Poly(a) tail contain what?

A

0-3 nt of Poly(A) tail
-Stalled ribosome state is recognized by carboxyl-terminal domain of protein called Ski7p
-Ski7p associates tightly with cytoplasmic exosome
-Non-stop mRNA recruit Ski7p-exosome complex to the vacant A site
-Ski complex is recruited to the A-site

123
Q

What degrades the RNA in NSD?

A

The exosome, positioned just at the end of non-stop mRNA; aberrant PP is presumably destroyed

124
Q

No-Go Aberrant Termination

A

-When ribosomes are stalled on an mRNA (e.g. secondary structure)
-mRNA decay begins with an endonucleolytic cleavage near stalled ribosome
-Exonucleases degrade cleaved mRNA
-Provides another potential means of post-transcriptional control by selective degradation of mRNAs

125
Q

Dominant and Recessive describe what?

A

Phenotypes; the mutation contributes to the phenotype

126
Q

Recessive Phenotypes

A

-Occur with loss of function mutations
-Loss of function usually means that the protein is no longer made

127
Q

Dominant Phenotypes

A

-Occur when protein is made, but it’s presence disrupts the process
-Think about receptor that usually works as a dimer. If one SU cannot bind the ligand, it doesn’t matter if the other one can, both are now inacvtive

128
Q

Mutations of the same gene can cause?

A

Moderate or Severe phenotypes

129
Q

Maternal-Zygotic Transition

A

mRNAs present in early development derived from oocyte (maternal)
-mRNAs stored in a translationally repressed state until needed
-Upon necessity (signal), translation of specific maternal mRNA can resume
-Requires A LOT of regulation

130
Q

In the blastula, zygotes transcription ….

A

Turns on and maternal mRNAs are degraded
-This shifts gene expression responsibilities to zygote

131
Q

Repressing translation through eIF4 binding is what?

A

A point of translation regulation

132
Q

Regulating translation during the cell cycle:

A

-4E-BP production turned on at start of mitosis by growth factor stimulation
-Helps reduce protein synthesis while cells are dividing

133
Q

eIF2 alpha-SU is a target of what and how?

A

Translational control
-Phosphorylation inhibits its ability to GTP –> GDP
-Heme-starved reticulocytes activate HCR: heme -controlled repressor (HCR): phosphorylates eIF2
-Interferon and dsRNA activate DAI: dsRNA activated inhibitor: viral protection mechanism that leads to phosphorylation of eIF2

134
Q

Repression of translation from individual mRNA by mRNA-binding protein

A

-Ferritin mRNA (codes for iron storage protein) translation is subject to inductio by iron
-Only affects transcripts with an IRE – selective not global translational regulation

135
Q

let-7 miRNA

A

Shifts polysomal profile target mRNAs in human cells toward smaller polysomes (blocks translation initiation in human cells)

136
Q

What type of translation initiation is not affected by let-7 miRNA?

A

Cap-dependent due to presence of IRES, or a tethered initiation factor
-miRNA blocks binding of eIF4E to cap of target mRNAs in human cells

137
Q

What can be an indication of global translational activity?

A

A polysome profile

138
Q

NSP14: Sars-CoV-2 Viral Protein

A

-Transfection of cells with NSP14 affects global translation
-M2 mutant of NSP14 restores translation
-Other results show that NSP14 does not affect amount of mRNA present

139
Q

Post-Translational Regulation

A

-Folding is a co-translational event occurring as nascent PP is being made: proteins must fold properly, membrane proteins must be inserted into membrane; ribosome attached to ER and inserts in the membrane there; ribosomes often translate near location where protein will be used/processed
-Most newly-made PPs do not fold properly alone: require folding help from molecular chaperones

BMS 525 (2 decks)

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