Midterm 2.4.2

Question 1

where are peptide bonds in a protein

Answer 1

between the carboxylic acid group of one amino acid and the amino group of the next amino acid

Question 2

proteins are directional. how do they run?

Answer 2

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

Question 3

the chain of AAs in a proteins is referred to as

Answer 3

1 structure

Question 4

what’s in secondary structure proteins and how are they formed

Answer 4

⍺-helices & β-sheets

Formed
by hydrogen bonding in peptide backbone (amide H & carbonyl O)

Question 5

Quaternary structure is made of

Answer 5

multimeric proteins. multiple different polypeptides, protein complexes

Question 6

individual polypeptide chains in a multimeric protein are _____
____ can be _____ or ______

Answer 6

subunits
subunits, identical (homomeric) or different (heteromeric)

Question 7

what do ribosomes use to convert the mRNA sequence into a protein sequence?

Answer 7

tRNA

Question 8

tRNAS contain

Answer 8

modified based (residues that are chemically altered after transcription)

anticodon that binds a particular three base codon

carry specific AA (cognate AA) that correspond to that codon

Question 9

what are tRNA synthetases

Answer 9

enzymes that
“charge” tRNAs – add the amino
acid to the CCA at the 3’ end.

Question 10

what is the CAA end of an AA?

Answer 10

acceptor end

Question 11

same tRNA for 2 different codons occur when there is a single mismatch in

Answer 11

3rd position wobbe

Question 12

each codon corresponds to

Answer 12

a specific AA

Question 13

the start codon encodes the first amino acid of a

Answer 13

particular ORF (N terminal amino acid of a protein) - where translation begins

AUG (ATG in DNA sequences (for all three domains of life)

Question 14

In bacteria, start codon is translated to

Answer 14

N-formylmethionine (fMet) (chemically modified version of methionine) using a special tRNA

AUG encountered during normal translation encodes a standard
methionine. fMet often removed from proteins after translation.

Question 15

Prokaryotic ribosome is the….made up of two subunits….each subunit comprised of….

Answer 15

70S ribosome
30S (small subunit) and 50S (large subunit)
rRNA and ribosomal proteins.

Question 16

RNA has many “AUG”s. To locate bona fide start codons, bacterial mRNAs
use a ribosome binding site (RBS)

Answer 16

RBS is an RNA sequence (some variation in exact sequence)that is recognized
by ribosome - must be appropriately spaced from a start codon (e.g. AUG).

Question 17

16S rRNA component of a free 30S ribosomal subunit (not bound to 50S)
binds to….to initiate translation

then … binds to …..

once bound….

Answer 17

RBS/start codon

Initiator (fMet) tRNA then binds the start codon

Once bound, energy from
GTP is used to recruit 50S subunit & full 70S ribosome forms

Question 18

the ribosome has 3 tRNA binding sites

Answer 18

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

Question 19

A (aminoacyl) site

Answer 19

Where new charged tRNAs enter and recognize the
codon being translated. Once in place, the growing peptide from P site is
transferred its amino acid & peptide bond forms.

Question 20

P (peptidyl) site

Answer 20

After peptide bond formation, translocation occurs –
RNA moves 3 bases (one codon). The tRNA from A site moves to P site.
This tRNA transfers growing amino acid chain to the new charged tRNA
that has entered the A site. P site tRNA now lacks amino acid (uncharged)

Question 21

E (exit) site

Answer 21

Uncharged tRNAs exit here

Question 22

during translation, APE repeats until…

once this occurs,

resulting in

then

Answer 22

ribosome encounters a stop codon UAA, UGA & UAG

a protein called a release factor binds

ribosome releasing the mRNA & the completed
polypeptide

30S/50S subunits dissociate. Ribosome is free to begin a new round
of translation

Question 23

in translation, … is used as an energy source

Answer 23

GTP

Question 24

chaperones are

functions are:

Answer 24

proteins that help other proteins adopt their properly
folded and fully active state - all 3 domains in life require chaperones.

initial folding, re-folding denatured proteins, helping
subunits in multimeric proteins come together, etc.

Question 25

what is the sec system

Answer 25

Protein secretion

recognizes a signal sequence in the first ~20
amino acids of protein - translocates unfolded protein before it folds

Question 26

Tat pathway

Answer 26

secretes pre-folded proteins across membrane

Question 27

In Sec pathway, proteins are either:

Answer 27

1) Passed across cytoplasmic membrane (SecA pathway)
2) Recognized by RNA/protein complex – signal recognition particle - and
inserted into the cytoplasmic membrane (SRP pathway).

Question 28

Both pathways: (sec and tat)

Answer 28

1) Pass the unfolded protein through a membrane channel - Sec YEG
translocon
2) Require ATP for energy
3) Signal sequence is cleaved following translocation