Lecture 12

Question 1

What is the charge of Lysine at pH 7?

Answer 1

It is positively charged because of the amino group in the side chain

Question 2

What does the side chain of Lysine contain?

Answer 2

A positively charged side chain

Question 3

What kind of H bonds is the side chain of Lysine capable of forming?

Answer 3

It is an H-bond donor through its amino group at neutral pH’s

Question 4

What is the Polarity of Lysine?

Answer 4

It is very polar

Question 5

What is the pKa of the amino group in the R group of Lysine?

Answer 5

It has a pKa of 10

Question 6

What charge does Lysine have at pH 7?

Answer 6

A positive charge

Question 7

Why does Lysine have a positive charge at pH 7?

Answer 7

Because it has an NH3 group

Question 8

Why is Lysine know as a basic amino acid?

Answer 8

Because it exists as a base at neutral pH through it amino group

Question 9

What is the charge of Arginine at pH 7?

Answer 9

It is positively charged

Question 10

What is a Guanido group?

Answer 10

The end part of the R group of arginine

Question 11

What is the pKa of the NH2 of Arginine?

Answer 11

12.5

Question 12

Why is it difficult to deprotonate the functional group of Arginine?

Answer 12

Because it is very stable due to resonance

Question 13

Why can Arginine be described as a basic amino acid?

Answer 13

Because the side chain is neutral when it is in the base form

Question 14

What is the polarity of arginine?

Answer 14

It is very polar

Question 15

What is the H-bond capability of Arginine?

Answer 15

It is an H-bond donor

Question 16

What are the exceptions for the amino acid abbreviation rules?

Answer 16

• Asparagine (Asn)
• Glutamine (Gln)
• Isoleucine (Ile)
• Tryptophan (Trp)

Question 17

Where are Polar side chains usually found?

Answer 17

In proteins on the surface where they can interact with water

Question 18

Where are non-polar side chains usually found?

Answer 18

Buried in the protein core to minimize interaction with water

Question 19

Which parts of the amino acid is a peptide bond between?

Answer 19

The carboxyl of one amino acid and the amino group of another amino acid

Question 20

What is removed in the formation of a peptide bond?

Answer 20

Two H’s from the amino group and one O from the carboxyl group to form a water

Question 21

What is the symmetry of the bond that connects amino acids together?

Answer 21

It is asymmetrical

Question 22

What does the N-terminal describe?

Answer 22

The presence of a free amino group

Question 23

What does the C-terminal describe?

Answer 23

The presence of a C terminal on one end

Question 24

What is a Dipeptide, Tripeptide, Tetrapeptide, Pentapeptide?

Answer 24

Two amino acids, three amino acids, four amino acids, five amino acids

Question 25

What is an Oligopeptide?

Answer 25

The general term for a larger number of amino acids, often refers to synthetic. peptides

Question 26

What is a Polypeptide?

Answer 26

A long chain of amino acids, usually produced naturally

Question 27

What is a Protein?

Answer 27

A large polypeptide a with a biological function

Question 28

What retains their charge in a peptide?

Answer 28

* Terminal amino group (+1) * Carboxylate group (-1) * Side chains (if they have one)

Question 29

How are the number of connected amino acids related to the peptide bond?

Answer 29

There will always be one less peptide bond than amino acids

Question 30

What is the Primary Structure?

Answer 30

The sequence of amino acids in a polypeptide

Question 31

What joins each amino acid to the next?

Answer 31

A covalent peptide bond

Question 32

From which terminus do we read polypeptide chains?

Answer 32

From N-terminus to C-terminus

Question 33

Where is no rotation permitted in peptide bonds?

Answer 33

Rotation is not permitted around the C-N bond because of the double bond character

Question 34

In a peptide bond, which atoms are found in the same plane?

Answer 34

* Two Alpha carbons * Carbonyl carbon * Oxygen * Nitrogen * Hydrogen on the nitrogen

Question 35

What are the three kinds of bonds in a peptide bond?

Answer 35

* N - Calpha * Calpha - carbonyl carbon * Carbonyl carbon - nitrogen

Question 36

Which bonds in a peptide bond allow for rotation?

Answer 36

N - Calpha and C-alpha to Carbon of the carbonyl

Question 37

What does the Primary structure determine?

Answer 37

The 3D structure

Question 38

Why is the folding conformations of polypeptides limited?

Answer 38

Due to steric hindrance

Question 39

What is the hydrogen bonding potential of a peptide bond?

Answer 39

The carbonyl and N-H can hydrogen bond with each other