Proteins 1

Question 1

What is a peptide bond

Answer 1

The bond between the COO of one AA and NH3+ of another

Links amino acid residues

Make them into C=O and NH

Lose H2O in the reaction

Question 2

Peptide bond is also known as

Answer 2

Amide bond

Question 3

Peptide bond is what type of stable

Answer 3

Kinetically stable

Not thermodynamically

Question 4

What are amino acid residues

Answer 4

What left after the amino acids link together with peptide bonds

Question 5

What is a pentapeptide

Answer 5

Five amino acids linked together

Question 6

Polypeptide are always written from

Answer 6

Amino to carboxy

Question 7

If there is a polypeptide with a small number of AA residues it it called

Answer 7

Oligopeptide

Question 8

If a polypeptide had 50 or more AA residues it’s called

Answer 8

Protien

Question 9

What is the avg wieght of an AA residue

Answer 9

110g/mol

Question 10

How do you find the mass in Da (daltons) in a protein with 50 aA residues

Answer 10

Mass is the same as the molecular wieght of the protien

110x50

Question 11

What is the primary structure

Answer 11

A linear polymer made by linking AA residues with peptide bonds

It’s the amino acid sequence of the protien

Question 12

Between two amino acid residues bonded together, what part of the peptide bond is in the same plane?

Answer 12

From the c alpha of the first aA to the h on the n of the second aa to the c alpha of the second aa then back to the o on the c of the first aa then back to c alpha

Anything inside that box is in the same plane

Question 13

What are the types of resonces structures that can be make with peptide bonds

Answer 13

1. The c=o on one aa can turn into c-o and the double bond goes between c=nH+ because of the lone pair on N

This gives planarity, and stops free rotation around the peptide bond since it has become a double bond

2. R groups Can be in trans or cis conformations, trans if more favourable meaning all peptide bonds a in trans conf. See slide 17 for pic

Question 14

In the planar region of a peptide bond, what is the bond distance between the first aa c alpha and c=o

Answer 14

1.51 Angstroms

Question 15

In the planar region of a peptide bond, what is the bond distance between the first aa c and double bonded o

Answer 15

1.24 A

Question 16

In the planar region of a peptide bond, what is the bond distance between the first aa c and the second aa n (the peptide bond)

Answer 16

1.32 A

Question 17

In the planar region of a peptide bond, what is the bond distance between the second aa nh bond

Answer 17

1.0 A

Question 18

In the planar region of a peptide bond, what is the bond distance between the second aa n and c alpha bond

Answer 18

1.45 A

Question 19

In a peptide bond what are the bond angles in the planar region of the aa residues

Answer 19

120 degrees

Question 20

What is phi

What is psi

What is omega (w)

Answer 20

Phi is rotation about the n and c alpha that are next each other in the bond

Psi is the rotation about the c alpha and the c=o that are next each other in the bond

Omega is the rotation about the peptide bond

Question 21

What is omega if the bond is cis

Trans?

Answer 21

0 degrees

Trans 180 degrees

Question 22

What is phi if your looking down the N c alpha bond in a poly peptinde chain

Answer 22

-80 (counterclockwise)

Comparing co angles

Question 23

What is psi if your looking down the c alpha and co bond

Comparing nh angles

Answer 23

+ 100 cw

Question 24

On a Ramachandran plot what does dark yellow mean

Light yellow

White

Answer 24

Dark means very favourable

Lighter is less favourable

White is not favourable

Question 25

What is the most disfavoured conformations on a ramachandran plot

Answer 25

90,90 degrees

Phi, psi

Causes steric clash between the r group and the c=o

Question 26

Which amino acid has the most restricting n-c alpha bond conformation

Answer 26

Proline because it is in a puckered conformation

Question 27

What is a disulfide bond

Answer 27

What two cysteine amino acids undergoes oxidation to make a bond between the two S

2H

AND 2e

This forms cystine which is two linked cysteines