Gao 4-21, 25, 28, 30 protein synth

Question 1

How many codons for how many amino acids

Answer 1

64 codons for 20 aa’s

Question 2

Degenerate meaning

Answer 2

many aa’s coded by different codons- more than one pathway to aa addition

Question 3

evolutionary importance of wobble base of codon

Answer 3

decrease chance of functional mutation by one third

Question 4

which end of the protein is first synthesized

Answer 4

amino

Question 5

In what direction is the transcript translated

Answer 5

5’ –> 3’

Question 6

3 types of mutations that can occur to the coding sequence

Answer 6

missense (another aa is substituted), nonsense, frameshift

Question 7

Sequence for beginning of ORF

Answer 7

AUG (methyanine)

Question 8

Why create a missense mutation in a protein

Answer 8

To test activity difference: ex- phosphorylatable aa’s

Question 9

Which base of the codon is wobble?

Answer 9

3’ of the codon (5’ of the anticodon)

Question 10

2 common features of tRNA

Answer 10

1) L-shaped, 2) 75-93bps, 3) T,pseudouracyl,C Loop (Variable Arm), 4) hydroxyuracyl (D arm), 5) 3’ end CCA (acceptor arm) 6) 5’ end Phosphorylated (anticodon arm)

Question 11

what reaction must occur on the aa so that it may be charged to the tRNA

Answer 11

it must be adenylated by ATP (C-terminal attacks alpha P of ATP) – makes high energy acyl linkage

Question 12

what enzyme charges the tRNAs

Answer 12

aminoacyl tRNA synthetase (aaRSs)- one for each aa

Question 13

to Which hydroxyl group of RNA does the Class I synthetase charge tRNA

Answer 13

3’ OH, Class II synthetase does 2’OH charging

Question 14

Purpose of recognition elements in tRNA- where are most of them found?

Answer 14

to get correctly charged with synthetase/aa. Most are found in the acceptor arm

Question 15

What additional function do 8/20 aaRSs possess

Answer 15

proofreading- if intermediate tRNA is bound to the wrong aa

Question 16

What step in a gene becoming a protein has the least accuracy

Answer 16

aa-charging of tRNAs

Question 17

how if the first aa of the transcript special

Answer 17

always Met, in prok. it is formyl-Met, but it loses the formyl and/or Met in the finished product. Made from codon AUG or GUG

Question 18

Why is a special aa needed to start translation

Answer 18

because it must be able to bind in the P site and prevent elongation factor binding

Question 19

What enables initiator tRNAs to bind in the P site

Answer 19

GC repeats in the anitcodon arm

Question 20

Shine-Delgarno sequence

Answer 20

sequence of the mRNA that base-pairs with the rRNA of the small subunit’s P site to identify the first codon

Question 21

How do eukaryotes identify the first codon

Answer 21

by scanning mechanism- the Kozak sequence upstream of the AUG increases efficiency of start codon recognition- it is a tRNA-mRNA interaction- NOT an rRNA-mRNA interaction

Question 22

What is the very first step needed to synthesize a protein

Answer 22

separating the large and small ribosomal subunits

Question 23

Which proteins bind to small subunit to stabilize it for separation from the large subunit

Answer 23

eIF3

Question 24

Which proteins block the A site before the initiator Metionine can come in

Answer 24

eIF1, 1A

Question 25

eIF2

Answer 25

GTPase that binds directly to the intiator tRNA before it can bind to the P site

Question 26

what functions do the eIF4 proteins accomplish

Answer 26

helicase for secondary structure of the mRNA, scaffolding complex between the cap and the small subunit ribosome/tRNA

Question 27

The 5 steps of initiation in eukaryotic protein translation

Answer 27

1) pre-initiation complex (PIC) formation 2) mRNA prep 3)ATP-dependent scanning mRNA 4) Large ribosome attachment 5) initiation

Question 28

How are mRNA’s made circular for translation

Answer 28

the Poly-A Binding proteins interact with the eIF4F proteins to stabilize the complex, allow multiple ribsome attachment

Question 29

IRES

Answer 29

internal ribosome entry sites- mRNA elements that make complex secondary structure that allow stranslation without cap, initiation factors. Must be discovered experimentally. Chemically made circular

Question 30

What are the 3 steps of elongation?

Answer 30

Accomidation, Peptide bond synthesis, translocation

Question 31

What 2 factors are needed for accomodation step of elongation

Answer 31

eEF1A and 1B

Question 32

What function does eEF1A perform

Answer 32

protects aa from forming peptide bonds before codon:anticodon interface, gives tRNA affinity for A site, GTPase- hydrolyzes when codon aligns

Question 33

How is peptide bond synthesis catalyzed

Answer 33

by the 28S rRNA of the large subunit (amino attacks carboxyl)

Question 34

At what stage is the A site carrying the growing peptide chain

Answer 34

Peptide synthesis step

Question 35

eIF4E

Answer 35

G-cap-binding

Question 36

eIF4A

Answer 36

helicase

Question 37

eIF4F

Answer 37

complex of eIF4E, G, A

Question 38

describe translocation step of elongation

Answer 38

eEF2 pushes the peptide-bearing tRNA to the P site using GTP hydrolysis

Question 39

Which factors participate in termination

Answer 39

eRF1, eRF3, GTP

Question 40

How does the release complex terminate the chain

Answer 40

eRF1 bind the stop codon, while eRF3 uses GTP to align the whole complex and then eRF1 hydrolyzes the chain

Question 41

Signal peptide features

Answer 41

a charged amino acid followed by a stretch of hydrophobic residues

Question 42

subunits of the SRP receptor

Answer 42

peripheral alpha and transmembrane beta

Question 43

Three factors needed for conducting secretory protein-synthesizing ribosomes to membrane

Answer 43

SRP(GTP), SRP receptor(GTP), translocon (containing signal peptidase)

Question 44

Type of transmembrane protein that has C-terminal stop-transfer membrane-anchor sequence

Answer 44

type 1 single pass

Question 45

Type of transmembrane protein with N-term in cytosol

Answer 45

Type II - internal signal anchor sequence