Translation

Question 1

whats a codon. How many?

Answer 1

triplet of DNA that encodes a specific aa. 64. 3 dont encode a specific aa. 20 aa encoded in our genetic code.

Question 2

Some aa have more than one codon which is referred to as _____

Answer 2

degeneracy; doesnt mean its inaccurate

Question 3

Codons DO NOT

Answer 3

overlap; no spaces bet them. Have to be in frame in order to produce protein with right aa sequence.

Question 4

What are the stop codons?

Answer 4

UAA, UGA, UAG

Question 5

Whats AUG, UUU, CCC, GGG, AAA,

Answer 5

AUG; Met: start codon
UUU; Phe
CCC; Pro
GGG; Gly
AAA; Lys

Question 6

whats the ORF

Answer 6

open reading frame; the inframe seq bet the initiation codon and the termination codon thats building the protein.

Question 7

What does 5’ end of mRNA correspond to? What about 3’ end?

Answer 7

N terminal of the protein. 3’ end of mRNA corresponds to the C terminal of the protein.

Question 8

Protein synthesis begins at the amino terminal end of the nascent proteins.How did they figure out which way proteins get synthesized?

Answer 8

Used radioactive leucine in reticulocytes (immature RBC) and followed globin synthesis. THey would add in leucine and extract the protein at diff time points after they added radio label and see what part of newly made proteins was being labeled. Early carboxy terminus was being labeled which means amino terminus was already being made. The longer they left label in thre the more of protein was being radio labeled.

Question 9

RNA cannot interact directly with __ ___ to specify their order

Answer 9

amino acids; tRNA does this via tRNA amino acyl synthases; serve as adaptor molecules specific for each aa that bind to specific codons on RNA templates.

Question 10

Replication has the most proofreading properties associated with it bc:

Answer 10

only have 1 DNA genome which gets transferred to daughter cells. Want it to stay constant

Question 11

what are features of tRNA

Answer 11

1. at least 32 tRNA
2. all diff for 20 aa
3. some can recognize more than 1 codon. (wobble rules of genetic code)
4. mitochondria has own set of tRNAs
5. Always have G at 5’ end
6. Always have ACC at 3’ end
7. 8 or more bases chemically modiefied

Question 12

In tRNA, the D arm contains_____. The T psudo C arm contains the ___,___,____. The anticodon arm contains the _____. The amino arm contains the ____ and binds the aa.

Answer 12

dihydrouridine; ribothymidine, psuedouridine, and cytosine.
Anticodon.
CCA

Question 13

The anticodon bp’s with the ____ in the mRNA. The tRNA and the mRNA bp ____ to each other. The first base of the codon is paired with the ____ base of the ___

Answer 13

codon; antiparralel; third; anticodon.

Question 14

Whats the wobble hypothesis

Answer 14

1. First two bases of a codon always form strong strandard (W-C) bp’s with the corresponding bases of tRNA & confer most of the specificity.
2. The first base of some anticodons det the number of codons read by a given tRNA.
3. When an aa is specified by sev diff codons, those codons that differ in either of the first two bases req diff tRNAs
4. a min of 32 diff tRNAs are req to translate all 61 codons

Question 15

If there is a U it can bind to ___ or G. If there is a G it can bind with C or ___IF there is an I (which means base is hypoxanthine) it can bind to ____ ____ or C

Answer 15

A. U

A, U

Question 16

What are the 3 sites on ribosome

Answer 16

1. Peptidyl site
2. Aminoacyl (A) site
3. Exit (E) site

Question 17

Diff in eukaryotic and prokaryotic ribosome is in their ____ value. But their S values do not add up!

Answer 17

sedimentation and density

Question 18

what are the 5 stages of protein synthesis

Answer 18

1. Activation of aa
2. initiation
3. elongationn
4. termination and ribosome recycling
5. folding and postranslational processing

Question 19

what is stage 1. what catalyzes this reaction?

Answer 19

AA are attached via ester bonds to the 3’ OH of the corresponding tRNA; this process is called CHARGING the tRNA via amino acyl-tRNA synthethase. This step is energy needy and is irreversible!

Question 20

what is the enzyme bound intermediate formed by reaction of ATP and aa? what gets transferred to corresponding specific tRNA?

Answer 20

aminoacyl adenylate (aminoacyl AMP); aminoacyl group

Question 21

how do aminoacyl tRNA synthestases recognize correct tRNAs?

Answer 21

1. some rec. anticodon itself
2. some rec. 10/more bases in tRNA
3. some rec one specific base pair!
4. structural features seem to be impt

Question 22

What does the aminoactyl tRNA form a complex with?

Answer 22

molecule called EF-Tu (elongation factor) that binds one GTP molecule

Question 23

what is stage 2?

Answer 23

Initiation: all organisms have two tRNAs for methionine (initiation and within polypeptide chain)

Question 24

What is the starting aa in bacteria

Answer 24

N - formylmethionine

Question 25

In bacteria, initiation req 7 components:

Answer 25

1. 30s ribosomal subunit 2. mRNA 3. initiating fMet tRNA 4. 3 initiation factors: IF-1, 2, &3 5. GTP 6. 50s ribosomal subunit 7. Mg++

Question 26

What does the Shine Dalgarno seq in bacteria do?

Answer 26

Places P site of ribosome complex right over the AUG of the start site.

Question 27

What do IF-1 and 3 in bacteria do?

Answer 27

IF-1 binds and blocks the A site. IF-3 helps with positioning 30s ribosome on Shine Dalgarno seq.

Question 28

what is step 2 of initiation in bacteria

Answer 28

30s ribosomal subunit, mRNA, IF-1, and 3 is joined by IF-2 and fMet-tRNA. the tRNA binds to P site, NOT a site.

Question 29

what is step 3 of initiation in bacteria

Answer 29

30s subunit binds to 50s ribosomal unit. GTP bound by IF-2 gets hydrolyzed to GDP. The other IF leave. The complete ribosome has charged initiatior tRNA in complete P site and an empty A site. This complex is officially called the initiation complex.

Question 30

In eukaryotes there are ___ initiation factors. We have a ____sequence rec by 40s subunit. Complete ___ribosome assembled using the other IFs and initiating Met-tRNA

Answer 30

9. One binds to 5' cap of mRNA and complex formed with 40s subunit. Kozak; has AUG embedded in it. 80s

Question 31

what is stage 3 of protein synthesis for eukaryotes? how does it work?

Answer 31

Elongation: stepwise addition of aa to polypeptide chain by formation of peptide bonds. In both pro and eukaryotes there are 10-100 ribosomes found bound to each mRNA molecule.

Question 32

In bacteria elongation requires 3 steps:

Answer 32

1. Initiation complex (for first peptide bond) 2. Next aminoacyl -tRNA specified by next codon 3. Elongation factors EF-Tu, EF-Ts, EF-G

Question 33

what is the enzyme that catalyzed peptide bond formation between the aa's

Answer 33

peptidyl transferase; this enzyme is a ribozyme (23s rRNA) which gets its energy by the high energy ester bond bet aa and tRNA

Question 34

In elongation stage in bacteria the initiating fMet is transferred from its ____ to the amino group of the second aa in the ____ site. A dipeptidyl tRNA is now base paired to the second codon in the ___ sit of the 30s subunit. The spent initiation tRNA is base paired to the AUG in the P site on the 30s subunit

Answer 34

tRNA; A; A;

Question 35

Once peptide bond forms it changes conformation with the ___s but not the 30s. The deacylated inititiation tRNA moves into the E site of 50s and new dipeptidyl trNA moves to P site on 50s.

Answer 35

50

Question 36

In translocation of elongation, the ribosome moves along the mRNA one codon towards the 3' end. Movement is mediated by elongation factor___. Ribsome movement shifts the ____tRNA from the ___ site on the 30s subunit to the P site. The spent tRNA shifts from the ___ site on the 30s to the E site. The ___ site is now empty and ready for next aa -tRNA

Answer 36

EF-G. GTP. dipeptidyl | A. P. A.

Question 37

T/F A and E sites cannot be occupied simultaneously.

Answer 37

True

Question 38

Why use two steps to move tRNA?

Answer 38

Prevents premature release of peptidyl tRNA and enhances processivity.

Question 39

Bacteria have ___releasing factors to terminate protein synthesis. RF 1 is for ___ and UAA. RF 2 is for ___ and UAA. No one know what the third one is for. They induce peptidyl transferase to transfer _____ to water resulting in release of peptide chain from ribosome. In eukaryotes there is only ___ releasing factor

Answer 39

3; UAG; UGA; peptide chain. 1

Question 40

Transcription and translation are tightly coupled in bacteria. This allows protein synthesis to take place before ___ is completed and degraded

Answer 40

mRNA

Question 41

Protein synthesis is expensive. There are at least __ high energy bonds expended per peptide bond. Energy is used for ____. Used to maintain proper alignment of codon, tRNA and growing end of polypeptide chain

Answer 41

4. specificity

Question 42

Overall error rate for protein synthesis is:

Answer 42

1:10,000 aa

Question 43

what are inhibitors of translation

Answer 43

antibiotics and toxins: 1. tetracycline; bind procaryote A site; block aa tRNa binding which is useful for treating periodontal disease 2. chloramphenicol: blocks peptidyl transfer in prokaryotes and mitochondria; useful for treating rickettsial infections 3. streptomycin: binds s12 of 30s ribosome. 4. aminoglycosides: block 50s ribosome binding to initiation complex 5. cycloheximide: blocks eukaryote 80s peptidyl transferase 6. diptheria toxin: catalyzes ADP-ribosylation of eEF2, inactivating it 7. ricin: extremely toxic protein from castor bean; inactivates eukaryote 60s subunit by depurinating A residue of 28S rRNA.