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MCBM Exam 5 Kat > Translation > Flashcards

Translation Flashcards

0
Q

What are the stop codons?

A

UAA
UGA
UAG

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1
Q

What is the start codon and what does it code for?

A

It is AUG and it codes for methionine.

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2
Q

What is a pneumonic for UAA?

A

You are angry

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3
Q

What is a pneumonic for UGA?

A

You go away

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4
Q

What is a pneumonic for UAG?

A

You are gone

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5
Q

What does UUU code for?

A

Phenylalanine

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6
Q

What does CCC code for?

A

Proline

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7
Q

What does GGG code for?

A

Glycine

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8
Q

What does AAA code for?

A

Lysine

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9
Q

What is the in-frame sequence between the initiation codon and the termination codon called?

A

The open reading frame (ORF)

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10
Q

What does the N-terminal of protein correspond to on mRNA?

A

The 5’ end

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11
Q

What does the C-terminal of protein correspond to on mRNA?

A

The 3’ end

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12
Q

What did Dintzis do in 1961?

A

Used radioisotopes to follow globin synthesis in reticulocytes (immature erythrocytes)

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13
Q

Can RNA interact directly with amino acids to specify their order?

A

Nope, tRNAs serve as adapters specific for each amino acid that bind to specific codons on RNA templates

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14
Q

What happens to aa’s prior to their incorporation into protein?

A

They are enzymatically linked to tRNA molecules

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15
Q

Tell me 4 basic things about tRNA.

A

Small RNA molecules (73-93 bases)
Mitochondria have their own
All cells have at least 32 tRNAs
Some tRNAs can recognize more than one codon

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16
Q

What do most tRNAs have at their 5’ end?

A

G

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17
Q

How many bases are often modified by methylation of a normal base in tRNAs?

A

8 or more

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18
Q

What does the D arm of tRNA contain?

A

Dihydrouride

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19
Q

What is the anticodon of tRNA structure?

A

A 3 base structure in the anticodon loop on the anticodon arm

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20
Q

What does the anticodon of tRNA do?

A

Pairs with the codon in the mRNA

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21
Q

What is the first base of the anticodon called?

A

The wobble position

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22
Q

What are the 4 relationships between codons and anticodons as outlined by the wobble hypothesis?

A

1) First two bases of codon always form strong standard base pairs
2) The first base of some anticodons determines the number of codons read by a given tRNA
3) Different tRNAs are required when codons differ in either of the first two bases
4) A minimum of 32 different tRNAs to translate all 61 codons

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23
Q

What is an example of the wobble hypothesis?

A

Yeast arginine tRNA

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24
Q

What are ribosomes composed of?

A

Two subunits one small one large

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25
Q

Are ribosomes large or small?

A

Large! Largest at 23nm

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26
Q

What do both subunits of ribosomes form?

A

Peptidyl (P) site
Aminoacyl (A) site
Exit (E) site

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27
Q

What are the ribosome sizes in prokaryotes?

A

Large: 50s, small: 30s, ribosome: 70s

28
Q

What RNA are used in prokaryotes?

A

Large uses 23s and 5s RNA. Small uses 16s RNA

29
Q

What are the 5 major stages of protein synthesis?

A 
Activation of amino acids
Initiation
Elongation
Termination and ribosome recycling
Folding and post translational processing
30
Q

How are tRNAs charged/activated?

A

Amino acids are attached via ester bonds to the 3’OH of the corresponding tRNA (aminoacylation)

31
Q

What catalyzes the charging of tRNA?

A

Aminoacyl-tRNA synthetases (specific to aa’s and tRNAs)

32
Q

What are the two steps in the enzyme active site for tRNA charging?

A

1) An enzyme bound intermediate is formed by the reaction of ATP and amino acid (hydrolysis of ppi)
2) Aminoacyl group transferred to corresponding specific tRNA

33
Q

What makes tRNA charging irreversible?

A

The hydrolysis of ppi because two energy rich bonds are used

34
Q

Is the identity of the aa attached to the tRNA checked by the ribosome?

A

No, but some aa-tRNA synthetases proofread

35
Q

What are some ways that Aminoacyl-tRNA synthetases proofread?

A

Some recognize anticodon itself
Some recognize 10 or more bases in tRNA
Some recognize one specific base pair

36
Q

What makes the tRNA ready to bind to the ribosome a site?

A

Aminoacyl-tRNA form a complex with EF-Tu that also binds one GTP molecule.

37
Q

How many tRNAs for methionine do all organisms have?

A

2; one exclusively for initiation, the other for methionines within the polypeptide chain

38
Q

What is the starting amino acid in prokaryotes?

A

N-formylmethionine

39
Q

What are the 7 components required for initiation in bacteria?

A 
30S ribosomal subunit
mRNA
Initiation fmet-tRNA^fmet
Three initiation factors
GTP
50S ribosomal subunit
Mg2+
40
Q

How does the small 30S subunit position itself on mRNA template in step 1 of bacterial translation initiation?

A

Codon is bound in a region of 30S subunit that is part of the P site
The initiation codon is distinguished by proximity to Shine-Dalgarno sequence

41
Q

What does IF-1 block?

A

The A site

42
Q

What does IF-3 do?

A

Prevents the 30S and 50S subunits from combining prematurely

43
Q

How does the initiator tRNA bind to the P site in step 2 of bacterial translation initiation?

A

The 30S subunit, mRNA, IF-1, IF-3 complex is joined by IF-2 (itself bound to GTP) and fmet-trna^fmet

44
Q

Where does the anticodon of the initiator tRNA pair with the initiation codon?

A

Only in the P site (fmet-trna^fmet will only bind to the P site)

45
Q

How does the large 50S subunit bind to the complex in step 3 or bacterial translation initiation?

A

The large complex binds the 50S ribosomal subunit resulting in GTP bound by IF-2 hydrolyzed to GDP which is then released and all intrinsic factors leave the complex

46
Q

What are the components of the final initiation complex?

A

Charged initiator tRNA in complete P site and an empty A site

47
Q

How is initiation in eukaryotes different?

A

At least 9 initiation factors involved
One binds to 5’ cap and complex formed with 40S subunit
Kozak sequence found at many initiation sites
If ORF is short, translation will begin again at next AUG
Complete 80S ribosome assembled using other IFs and initiating Met-trna^met

48
Q

What is elongation?

A

The stepwise addition of aa’s to polypeptide chain by formation of peptide bonds.

49
Q

In both prokaryotes and eukaryotes how many ribosomes are found bound to each mRNA molecule?

A

10-100 ribosomes

50
Q

How does elongation allow efficient use if mRNA?

A

Many polypeptides can be synthesized simultaneously using just one molecules worth of genetic information.

51
Q

What does elongation require in bacteria?

A 
Initiation complex (for first peptide bond)
Next Aminoacyl-tRNA (specified by next codon)
Elongation factors (EF-Tu, EF-Ts, EF-G)
52
Q

What are the 3 steps of elongation in bacterial translation?

A

1) Bind next Aminoacyl-tRNA
2) Peptide bond formation
3) Translocation

53
Q

What enzyme catalyzes peptide bond formation in elongation in bacterial translation?

A

Peptides transferase which is a ribozyme

54
Q

Where does the energy for bacterial translation elongation come from?

A

From the high energy ester bond between aa and tRNA

55
Q

Where do the spent tRNAs shift to?

A

They shift from the P site on the 30S to the E

56
Q

After the spent tRNA move what happens?

A

The A site is now empty, ready for the next aa-tRNA

57
Q

Can the A and E sites be occupied simultaneously?

A

Nope

58
Q

Why are two steps used to move tRNAs?

A

Anchors one end of tRNA while other moves during peptide bond formation and translocation
Prevents premature release of peptidyl-tRNA (waste of energy) and enhances processivity

59
Q

What is proof reading on chromosome limited to?

A

Codon-anticodon interactions

While GTP and GDP are bound base pairing is checked, incorrect base pairs are dissociated

60
Q

What is elongation proof reading optimized for?

A

Speed and fidelity: slower speeds=higher fidelity and vice versa

61
Q

How many termination factors are there?

A

3 in prokaryotes (RF1, RF2, RF3)

1 in eukaryotes (eRF)

62
Q

What stop codons bind to RF1?

A

UAG UAA

63
Q

What stop codons bind to RF2?

A

UGA UAA

64
Q

How are transcription and translation tightly coupled in bacteria?

A

Protein synthesis actually takes place before mRNA completed or degraded

65
Q

How expensive is protein synthesis?

A

At least 4 high energy bonds expended per peptide bond

122 kj/mol for one 21kj/mol peptide bond

66
Q

Why is protein synthesis so energy costly?

A

To maintain proper alignment of codon, tRNA and growing end of polypeptide chain

67
Q

What percent of large proteins (1000aa) are synthesized correctly?

A

90%

68
Q

At what rate are smaller proteins synthesized correctly?

A

99%

MCBM Exam 5 Kat (15 decks)

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