Lecture 6 - RNA Translation Flashcards Preview

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Flashcards in Lecture 6 - RNA Translation Deck (59):
1

Are AA codes distributed equally?

NOPE

2

How many possible reading frames are there in protein synthesis?

3

3

What is usually the proper reading frame?

The longest one

4

What do codons for the same AA have in common?

Tend to contain the same nucleotides at the first and second positions, and vary at the third position (Wobble position)

5

Do stop codons code for an AA?

NOPE

6

Describe the structure of tRNA.

Clover leaf shape made of alpha helices:

5' => D loop => anticodon loop => T loop => acceptor stem => 3' end with attached AA

7

What 3 unusual bases does tRNA contain? What are they derived from?

1. Pseudouridine (weird greek W)
2. Dihydrouridine (D)
3. Inosine (I)

Derived from Uracil

8

If the anticodon is GUA, what is the mRNA sequence?

UAC

9

How is inosine in tRNA formed? When?

Deamination of guanine on a nucleotide
Post-transcription

10

How many tRNA genes in humans? How many anticodons does this represent?

500 genes = 48 codons

11

Which base-pairing during translation is more wobbly: prokaryotes or eukaryotes?

Prokaryotes

12

Which base-pairing during translation is more wobbly: prokaryotes or eukaryotes?

Prokaryotes

13

What is the difference between inosine and hypoxanthine?

Inosine is a nucleotide, hypoxanthine is its base

14

PROKARYOTES: what anticodon bases can C on the mRNA base-pair with?

1. G
2. I

15

PROKARYOTES: what anticodon bases can A on the mRNA base-pair with?

1. U
2. I

16

PROKARYOTES: what anticodon bases can U on the mRNA base-pair with?

1. A
2. G
3. I

17

PROKARYOTES: what anticodon bases can G on the mRNA base-pair with?

1. C
2. U

18

EUKARYOTES: what anticodon bases can U on the mRNA base-pair with?

1. A
2. G
3. I

19

EUKARYOTES: what anticodon bases can C on the mRNA base-pair with?

1. G
2. I

20

EUKARYOTES: what anticodon bases can A on the mRNA base-pair with?

U ONLY

21

EUKARYOTES: what anticodon bases can G on the mRNA base-pair with?

C ONLY

22

EUKARYOTES: what anticodon bases can G on the mRNA base-pair with?

C ONLY

23

In wobble-pair pairing, how does the nonstandard base pairing compare to normal ones?

Not as strong

24

What do the differences in wobble base-pairing interactions between bacteria and eucaryotes presumably result from?

Subtle structural differences between bacterial and eucaryotic ribosomes

25

Do all tRNAs get used in almost all organisms?

YUP

26

How is an AA activated for protein synthesis? 1 enzyme and 2 steps?

Enzyme: aminoacyl-tRNA synthetase

1. AA + ATP = adenylated AA (at carboxyl C) + 2 Pi
2. Adenylated AA + tRNA = aminoacyl-tRNA (AA added on OH group at 3') + AMP

27

What does it mean for an AA do be adenylated?

It has AMP added on it

28

How many aminoacyl-tRNA synthetase types are there? Do they have similar structures?

20: 1 for each AA

NOPE not really

29

Why is the AA bound to tRNA said to be activated?

Because the hydrolysis of the ester bond between the carboxyl end of the amino acid and the ribose is associated with a large favorable change in free energy

30

What is the tRNA(Cys) to tRNA(Ala) experiment? What did it demonstrate?

1. Charged a cysteine tRNA with Cys and then converted it to Ala by removing the thiol group.
2. Then performed in vitro translation, and Ala was incorporated into the protein instead of Cys

This demonstrated that translation is not checking whether or not the correct AA is attached to the tRNA

31

What are the 2 adaptors of the genetic code translation?

1. The aminoacyl-tRNA synthetase which couples a particular amino acid to its corresponding tRNA
2. The tRNA molecule whose anticodon forms base pairs with the appropriate codon on the mRNA

32

What is hydrolytic editing?

Aminoacyl-tRNA synthetases remove their own coupling errors by hydrolysis of the incorrectly attached AA at their editing site (proofreading site)

33

What 2 parts if the aminoacyl-tRNA synthetase are able to recognize its tRNA molecule?

1. Anticodon region
2. AA-accepting arm

34

Describe the formation of the peptide bond during protein synthesis. ]

Peptidyl tRNA is attached to the C terminus of the growing polypeptide chain and the amino group of the AA on the aminoacyl-tRNA attacks the carboxyl at the C-terminus to form the peptide bond.

35

Where does the peptide bond formation during protein synthesis happen?

Ribosomes

36

What are the 2 classes of ribosomes/polyribosomes? Do they differ?

1. On RER membrane
2. Free soluble

Not at all, except for the kinds of proteins they synthesize

37

How do eukaryotic and prokaryotic ribosomes differ overall?

Eukaryotic ones have more subunits and factors

38

What are the 2 subunits of eukaryotic ribosomes? What is the total called?

60S + 40S = 80S

39

What are the 2 subunits of prokaryotic ribosomes?

50S + 30S = 70S

40

List all of the ribosomal binding sites.

LARGE SUBUNIT:
1. A-site: aminoacyl-t-RNA binding site
2. P-site: peptidyl-t-RNA binding site
3. E-site: t-RNA binding site for exit

SMALL SUBUNIT:
1. mRNA binding site

41

Are all t-RNA binding sites of a ribosome always bound during protein synthesis?

Never more than 2 are occupied

42

In which site of the ribosome is the tRNA with the new AA when the peptide bond is formed?

A site

43

Describe the 4 steps of translation.

1. Aminoacyl-tRNA molecule binds to a vacant A-site along with EF-Tu-GTP/EF1-GTP and a spent tRNA molecule dissociates from the E-site
2. New peptide bond is formed by the peptidyl transferase activity of the ribozyme
3. Binding of EFG-GTP/EF2-GTP at A site causes a lean forward, leaving the two tRNAs in hybrid sites: P on the large subunit and A on the small for the newly bound tRNA; E on the large subunit and P on the small for the t-RNA about to exit
4. GTP hydrolysis on EFG/EF2 causes movement of tRNAs to E and P sites which carries the mRNA a distance of three nucleotides through the ribosome. This “resets” the ribosome with a fully empty A-site, ready for the next aminoacyl-tRNA molecule to bind

44

In what direction is mRNA translated?

5- => 3'

45

Which end of the protein is made first?

N-terminal

46

What are 3 mechanisms to proofread RNA translation?

1. EF-Tu/EF1 protein: brings the tRNA to the A site and pauses to see if it's the right one. If correctly paired there is GTP hydrolysis (+ Pi) following by dissociation of the whole EF-Tu-GDP. If incorrectly paired, it will take tRNA away (this can happen twice so 2 proofreading opps)

2. EF-G/EF2: right after peptide bond formation, EFG-GTP/EF2-GTP binds in the A site of the large subunit. If correctly paired there is GTP hydrolysis (+ Pi) following by dissociation of the whole EFG-GDP/EF2-GDP. If incorrectly paired, it will take tRNA away.

3. Small ribosome subunit is able to recognize correct codon-anticodon matches by H-bonding

47

What are EF-Tu and EF-G?

Elongation factors in prokaryotes

48

What are the elongation factors in eukaryotes?

EF1 and EF2

49

What signals the end of translation of each codon?

GTP hydrolysis on EF-G/EF2

50

Describe the 4 steps of translation initiation in eukaryotes.

1. Small subunit of the ribosome which is already bound by initiator tRNA bound to Met in the P site which is also bound by initiation factor 2 + GTP ALL bind as a complex to initiation factors bound to the 5' cap of mRNA

2. Initiator tRNA, powered by ATP-helicases for scanning, moves along the mRNA searching for the RIGHT AUG sequence (release of ADP and Pi)

3. GTP on eIF2 is hydrolyzed and Pi + eIF2-GDP are released

4. Large ribosomal unit binds to small subunit

51

How does the ribosome ensure that both ends of the mRNA are intact prior to translation?

Translation initiation requires the poly-A tail of the mRNA bound by eIF4G which, in turn, interact with eIF4E bound to 5' cap

52

How are translation and transcription upregulated?

Initiation is made more favorable

53

What does eukaryotic initiation factor 2 (eIF2) bind to?

tRNA bound to Met

54

What does eIF4E bind to?

The 5' cap of the mRNA

55

What is the first AA of all proteins in eukaryotes? What tRNA binds it?

Always Met bound by the initiator tRNA

56

Does the initiator tRNA always stop at the first AUG it encounters?

Not always, because it is looking for an AUG in the proper context: situated among other nucleotides that label it as an initiation codon (Kozak sequence)

57

Describe the 3 steps of translation termination for eukaryotes.

1. Release factor recognizes the termination codon on the mRNA and binds it in the A site
2. Binding triggers movement of release factor to P site and tRNA to E site (large subunit only) + release of completed polypeptide with the final addition of water to finalize the C-terminus
3. Series of reactions that requires additional proteins and GTP hydrolysis for dissociation of elongation complex and the ribosome to dissociate into its two separate subunits

58

What is the binding of the release factor to the A site during translation termination an example of? Explain

Molecular mimicry because the release factor resemble tRNA even though one is made of AAs and the other of nucleotides

59

What is a polyribosome?

Series of ribosomes that simultaneously translate the same eukaryotic mRNA molecule in a circular process to produce many proteins in a shorter amount of time