Topic 6-L2- Translation

Question 1

Proteins are _________. They are comprised of polymers of amino
acids connected by __________

Answer 1

polypeptides. peptide bonds.

Question 2

Amino acids have an

Answer 2

amino group on one side, an ⍺–carbon in the middle (has “R group”) and a carboxyl group on the other side.

Question 3

Peptide bonds are between the

Answer 3

carboxylic acid group of one amino

acid and the amino group of the next amino acid.

Question 4

proteins are directional based on how

polymers are assembled

Answer 4

from N-terminus (free amino terminus) to C-terminus (free carboxylic acid terminus

Question 5

There are 20 different amino acids that make up proteins. They have the

Answer 5

same backbone, but different R groups.

Question 6

primary structure

Answer 6

The chain (sequence) of amino acids in a protein

Question 7

secondary structure.

Answer 7

Small segments of protein adopt simple local structures (local in 3D space, not necessarily in sequence)

Question 8

Most common secondary structure elements are

Answer 8

⍺-helices & β-sheets. Formed by hydrogen bonding in peptide backbone (amide H & carbonyl O)

Question 9

Tertiary structure.

Answer 9

The full 3D structure of a protein

Will typically include multiple secondary structure elements arranged in different ways & other structural features as well

Question 10

Quaternary structure is the result of

Answer 10

multiple different polypeptides

coming together – multimeric proteins (or protein complexes).

Question 11

The individual polypeptide chains in a multimeric protein are

Answer 11

subunits. Can be:

• identical (homomeric)
• different (heteromeric)

Question 12

Proteins contain “domains” - these are

Answer 12

structural and/or functional
segments. Can be small or large - most proteins contain a few (or more)
different domains

Question 13

A given domain is defined as having a particular

Answer 13

structure and/or carrying out a particular function. Typically, a given domain will be found in a number of different proteins.

Question 14

Common domain example

Answer 14

“helix-turn-helix” (HTH) domains

Question 15

HTH domains bind DNA – found in

Answer 15

> 200 different proteins in any given Salmonella genome…mostly DNA-binding regulatory binding proteins.

Question 16

The ribosome uses tRNAs to

Answer 16

convert (“translate”) the mRNA sequence into a protein sequence

Question 17

Each tRNA has a specific

Answer 17

anticodon that binds a particular three base codon.

Question 18

At other end, tRNAs carry the specific

Answer 18

amino acid (cognate amino acid) that
corresponds to that codon.

Question 19

tRNA synthetases are the enzymes that

Answer 19

“charge” tRNAs – add the amino

acid to the CCA at the 3’ end.

Question 20

“wobble” –

Answer 20

same tRNA for 2 different codons

Question 21

start codons – mostly

Answer 21

AUG, GUG, UUG.

In E. coli:
83% AUG, 14% GUG, 3% UUG.

Question 22

In bacteria, start codon is translated to

Answer 22

N-formylmethionine (fMet)

(chemically modified version of methionine) using a special tRNA.

Question 23

AUG encountered during normal translation encodes a standard

Answer 23

methionine. fMet often removed from proteins after translation.

Question 24

In Archaea/Eukarya, __________ is used

Answer 24

methionine (unmodified)

Question 25

The three stop codons are

Answer 25

UAA , UGA & UAG

Question 26

Prokaryotic ribosome is the 70S ribosome -- is made up of two subunits

Answer 26

– 30S (small subunit) and 50S (large subunit). Each subunit is comprised of rRNA and ribosomal proteins.

Question 27

30S & 50S interact dynamically

Answer 27

associate/dissociate during translation

Question 28

E. coli has ribosomes like

Answer 28

- 30S ribosome containing 16S rRNA And 21 proteins. | - 50S containing 5S/23S rRNA and 31 proteins.

Question 29

rRNA carries out much of the main function of ribosome – including

Answer 29

catalyzing peptide bond formation.

Question 30

For each ORF, bacterial mRNAs contain a

Answer 30

ribosome binding site (RBS) also known as a Shine-Dalgarno sequences (with 5’ UTR).

Question 31

The RBS binds to

Answer 31

16S rRNA in a free 30S ribosomal subunit (no 50S) – helps ribosome locate bona fide start (typically AUG) codons.

Question 32

Free 30S subunit binds RBS, fMet tRNA binds AUG. Using GTP for energy, 50S subunit recruited – _________ forms.

Answer 32

full 70S ribosome

Question 33

The ribosome has 3 tRNA binding sites:

Answer 33

* A (aminoacyl) site * P (peptidyl) site * E (exit) site

Question 34

A (aminoacyl) site:

Answer 34

Where new charged tRNAs enter and recognize the codon being translated. Growing peptide from P site is transferred to the amino acid carried by the tRNA. Translocation occurs – RNA moves 3 bases (one codon).

Question 35

P (peptidyl) site:

Answer 35

Second position - tRNA moves to P site. Now this tRNA transfers growing amino acid chain to new charged tRNA that has entered the A site. Once complete, tRNA lacks amino acids (uncharged)

Question 36

E (exit) site:

Answer 36

Uncharged tRNAs exit here

Question 37

During translation, going through the three RBS repeats until ribosome encounters a stop codon. Once this occurs, a protein called a

Answer 37

release factor binds – releases peptide and mRNA – 30S/50S dissociate. Ribosome free to begin again.

Question 38

The same mRNA can be simultaneously translated by multiple different ribosomes – multiple ribosomes on a single transcript called

Answer 38

polysomes

Question 39

transcription and translation are often

Answer 39

coupled in prokaryotes – RNA being translated while transcription still going on (RNA polymerase and ribosomes both attached to transcript)

Question 40

Each eukaryotic mRNA encodes

Answer 40

one gene – contrasted prokaryotic | transcripts encode 2+ ORFs (ribosomes re-initiate on same transcript)

Question 41

Main mechanistic differences in the initiation step. 5’ cap recognized by

Answer 41

initiation complex in eukaryotes (ribosome binding site). More regulation/complexity at this step.

Question 42

Eukaryotic ribosomes are larger and a bit more complex then prokaryotes -

Answer 42

40S (small subunit) 60S (large subunit) 80S complete ribosome

Question 43

Chaperones are proteins that help

Answer 43

other proteins adopt their properly | folded and fully active state

Question 44

Do all three domains use chaperons?

Answer 44

Yes

Question 45

Chaperones functions:

Answer 45

initial folding, re-folding denatured proteins, helping subunits in multimeric proteins come together, preventing aggregation, incorporating cofactors into enzymes…there are even RNA chaperones

Question 46

How do chaperones gain energy?

Answer 46

ATP hydrolysis

Question 47

Special chaperones are activated in response to

Answer 47

high or low temperatures (heat shock / cold shock proteins) to assist with protein/RNA folding

Question 48

In E. coli major chaperones include

Answer 48

DnaJ/DnaK, GroEL and GroES.

Question 49

NarJ is a different sort of chaperone. It inserts an

Answer 49

essential cofactor – Moco (contains molybdenum) - in the enzyme nitrate reductase

Question 50

All proteins are synthesized by

Answer 50

ribosomes in the cytoplasm

Question 51

All prokaryotes use

Answer 51

translocase systems that transport proteins across (and into) the cytoplasmic membrane.

Question 52

Most translocated proteins contain a signal sequence at the

Answer 52

N-terminus that targets the protein to a particular secretion system – often removed after translocation.

Question 53

The Sec secretion system & twin arginine translocase (Tat) are

Answer 53

ubiquitous in prokaryotes – others are more specialized

Question 54

The Sec secretion system recognizes a signal sequence in the first ~20 amino acids of protein -

Answer 54

translocates unfolded protein before it folds

Question 55

Protein either passed across

Answer 55

- cytoplasmic membrane (SecA pathway) Or - recognized by RNA/protein complex – signal recognition particle - and inserted into membrane (SRP pathway). Both pathways pass the unfolded protein through a membrane channel - Sec YEG translocon

Question 56

Both pathways for transporting proteins require

Answer 56

ATP

Question 57

Tat pathway

Answer 57

secretes folded proteins – proteins that | must fold in cytoplasm