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Biochemistry 2 > protein synthesis > Flashcards

protein synthesis Flashcards

1
Q

protein synthesis components

A

The mRNA
tRNAs
Ribosome
Additional proteins

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2
Q

genetic code rules

A

triplet code
3 bases code for 1 aa (codon)
It is non-overlapping
There is start and stop, but no other punctuation
It is degenerate
All codons have meaning (some mean same thing, synonymous)
1 start codon, 3 stop codons

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3
Q

tRNAs

A

decode the sequence
tRNAs recognize codons in mRNA and carry the appropriate amino acid
Anti-codon in tRNA hybridizes with the codons in mRNA

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4
Q

aminoacyl tRNA synthetases roles

A

attach the correct amino acid to its cognate tRNA
Cells have 20 different aminoacyl tRNA synthetases
Each synthetase must recognize the specific tRNA and the specific amino acid

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5
Q

aminoacyl-tRNA steps (2)

A

First activate the amino acid

Transfer activated amino acid to tRNA

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6
Q

2 classes of aminoacyl-tRNA synthetases

A

Class 1: glutaminyl-tRNA synthetase

Class 2: threonyl-tRNA synthetase

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7
Q

Discrimination of various tRNAs by aminoacyl-tRNA synthetases

A

No universal rules
Some, but not all, use the anticodon
Bases in the acceptor stem can be important
Base at position 73 can be important (“discriminator base”)
The glutaminyl-tRNAGln synthetase makes extensive contacts with its cognate tRNAGln

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8
Q

Codon : anticodon pairing

A

But polyU mRNA can interact with all Phe-tRNAPhe

So there must be more to codon-anticodon recognition

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9
Q

wobble hypothesis

A

First 2 bases have stringent specificity, while third base pair is more flexible
Inosine, a base often found in the third position of the anti-codon, can form base pairs with cytosine, uracil, or adenine

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10
Q

prokaryotic ribosomes composition

A

Ribosomes are proteins + RNAs

Ribosomes bring together the mRNA and amino acid-bound tRNAs and catalyze polypeptide synthesis

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11
Q

30s rRNA precursor

A

includes rRNAs and tRNAs

RNaseIII and other nucleases release rRNAs and tRNAs

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12
Q

tertiary structure of 16S rRNA

A

Folds into scaffold upon which proteins of 30S subunit can assemble
23S and 5S rRNAs establish the form of the 50S subunit
Each subunit can self-assemble after combining the individual proteins and rRNAs under appropriate conditions

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13
Q

ribosomal subunit decoding center

A

is responsible for reading the mRNA by mediating codon-anticodon interactions
This is in small subunit

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14
Q

ribosomal large subunit

A

Large subunit contains the peptidyl transferase activity needed to synthesize a new peptide bond

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15
Q

both ribosomal subunits (large and small) are involved in…

A

translocation

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16
Q

ribosome’s 3 binding sites for tRNAs…

A

A: acceptor site (binds incoming tRNA)
P: peptidyl site (binds growing polypeptide chain)
E: exit site (binds uncharged tRNA)

17
Q

translation overview

A

1) initiation
2) elongation
3) termination

18
Q

Initiation in bacteria

A

Proks use special initiator tRNA bound to formylated methionine
This tRNA can only be used for the first amino acid: can’t be used for internally coded methionine

19
Q

Formylation of methionyl-tRNAfMeti

A

The same aminoacyl-tRNA synthetase adds methionine to the Met-tRNAfMeti and the Met-tRNAMet
Formyl transferase recognizes the Met-tRNAfMeti
Formulation of Met blocks the 5’ amino group

20
Q

Identification of start codon in bacteria

A

5’ UTR of the transcript contains “Shine-Dalgarno” sequence, recognized by 3’ end of the 16S rRNA
Internal Shine-Dalgarno sequences may also be identified

21
Q

Initiation of protein translation (bacteria)

A

Requires initiation factors (IFs)

22
Q

elongation steps

A

1)Decoding: codon-directed binding of an incoming aminoacyl-tRNA in the A site
- Elongation factor EF-Tu-GTP facilitates recognition and binding of the incoming charged tRNA
- EF-Ts is a guanine exchange factor needed to recycle EF-Tu-GDP back to the EF-Tu-GTP form
2) Peptidyl-transfer: peptide bond formation in the A site
3) Translocation: The ribosome moves to the next codon in the mRNA
Elongation factor EF-G-GTP facilitates translocation

23
Q

decoding

A

Specific nucleotides in the 16S rRNA undergo conformational changes only when correct base-pairing occurs
If the appropriate conformational changes do not occur, the charged tRNA is ejected without hydrolysis of GTP

24
Q

peptidyl-transferase active site

A

Located in large subunit

Addition energy input is NOT needed for peptide bond formation

25
Q

peptide bond formation occurs where

A

on A site

26
Q

translocation sites

A

1) Deacetylated tRNA is moved from P-site to E-site
2) peptidyl-tRNA in A-site must be moved to P-site
This opens A-site for next charged tRNA
3) Translocation is a 2-step process
The acceptor stems in the 50S subunit move before the anticodon stems in the 30S subunit move
Hydrolysis of EF-G-GTP is needed for second step

27
Q

termination

A

Elongation continues until a stop codon is reached
RF-1 binds UAA and UAG
RF-2 binds UAA and UGA
RF-3 is recruited
Binding triggers hydrolysis of nascent peptide
RRF triggers release of mRNA from the ribosome

28
Q

role of GTP hydrolysis in protein synthesis

A

Energy of GTP hydrolysis fuels conformational changes in ribosome that drives the steps of protein synthesis
During elongation, 2 GTP are hydrolyzed for each amino acid incorporated into the growing polypeptide chain
1 GTP is also needed during initiation, plus 2 GTPs needed for termination

29
Q

release factors

A

mimic structure of elongation factors

IF-2, EF-Tu, EF-G, and RF-3 all bind the same place on the ribosome

30
Q

protein synthesis in euks

A

Euk mRNA: 5’ cap, 5’ UTR, coding sequence, 3’ UTR, polyA tail
5’ cap is needed for recognition by the ribosome (no Shine-Dalgarno sequence)
Only one coding sequence can be read per mRNA (monocistronic)

31
Q

euk translation initiation (3 stages)

A

1) 43S preinitiation complex
2) 48S initiation complex
3) 80S initiation complex

32
Q

mRNAs do what prior to translation

A

circularize

33
Q

peptide chain elongation and translation in euks

A

Similar to elongation in proks, just different names
eEF1 is made of eEF1A (~EF-Tu) and eEF1B (~EF-Ts)
eEF2 (~EF-G)
Euk cells have a single release factor (RF)

34
Q

When is controlling protein synthesis important?

A

If there is a backlog of normal protein folding, protein translation slows
Many antibiotics preferentially inhibit protein translation in bacteria

35
Q

Controlling translation initiation

A

Phosphorylation of eIF2 prevents eIF2B from exchanging GDP for GTP
This slows translation by inhibiting initiation
There are several eIF2alpha kinases that become active under specific cellular conditions

Biochemistry 2 (32 decks)

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