7 and 8A Amino acids and Protein Secondary Structure

Question 1

How many amino acids do peptides have?

Answer 1

50 or less

Question 2

How many amino acids do polypeptides and proteins have?

Answer 2

Greater than 50

Question 3

What are zwitterions?

Answer 3

Molecules that have a positive and negative charge, and no net charge at pH 7

Question 4

What type of side chains do acidic Amino Acids have?

Answer 4

Have a side chain with a carboxylate group that ionizes at physiological pH

Question 5

How are amino acids characterized?

Answer 5

Characterized by their ability to interact with water

Question 6

The only non-chiral standard amino acid is?

Answer 6

glycine

Question 7

What is the Isoelectric Point (pI)

Answer 7

When amino acids have no net charge ue to ionization of both groups

Question 8

Peptide bonds are formed by what type of reaction?

Answer 8

Amide linkages formed by nucleophilic acyl substitution (dehydration reaction)

Question 9

How are Shiff bases formed?

Answer 9

By imine products of primary amine groups interacting with carbonyl groups, eg. in amino acid biosynthesis reactions.

Question 10

What is a Schiff base?

Answer 10

Referred to as aldimines, are intermediates formed by the reaction of an amino group with an aldehyde group

Question 11

How many standard amino acids are there?

Answer 11

20

Question 12

How are amino acids amphoteric?

Answer 12

They have a carboxyl group which can act as an acid and an amino group that can act as a base

Question 13

What are nonpolar amino acids (structurally)?

Answer 13

Contain hydrocarbon groups with no charge

Question 14

What are polar amino acids?

Answer 14

They have functional groups that can easily interact with water through hydrogen bonding.

The functional group is either a hydroxyl group (serine, threonine and tyrosine etc.), thiol group (cysteine) or an amide group (asparigine, glutamine etc.)

Question 15

What is the three and one letter abbreviation of asparigine?

Answer 15

ASN

N

Question 16

What is the three and one letter abbreviation of aspartic acid?

Answer 16

Asp

D

Question 17

What is the one letter abbreviation for arginine?

Answer 17

R

Question 18

What is the three letter abbreviation for glutamine?

Answer 18

Gln

Q

Question 19

What is the three letter abbreviation for isoleucine?

Answer 19

Ile

Question 20

What is the three letter abbreviation for tryptophan?

Answer 20

Trp

W

Question 21

What are the amino acids involved as metabolic intermediates in the urea cycle?

Answer 21

Arginine
Ornithine
Citrulline

Question 22

Which amino acids can be phosphorylated?

Answer 22

Serine
Threonine
Tyrosine

Question 23

True or false, amino acids can exist as stereoisomers. Why?

Answer 23

True, because the alpha-carbon is attached to four different groups, they can exist as stereoisomers.

(except glycine, which is the only nonchiral standard amino acid)

Question 24

What are D and L used to signify with amino acids?

Answer 24

Used to indicate the similarity of the arrangement of atoms around the molecules assymmetric carbon to the asymmetric carbon of the glyceraldehyde isomers (reference compound for optical isomers)

Only L amino acids are used in translation, D can be used after post-translational modifications

Question 25

What causes a more complex titration curve with amino acids?

Answer 25

More ionizable side chains cause a more complex titration curve, as it proceeds stepwise as each group is deprotonated by NaOH

Question 26

What are peptide bonds? How are they formed (what type of reaction?)

Answer 26

Amide linkages formed by nucleophilic acyl substitution (a dehydration reaction).

Question 27

Where is the free amino group on the peptide chain? Where is the carboxyl group found? What terminal end for each?

Answer 27

The N-terminal contains the free amino group, the C-terminal has a free carboxyl group.

Question 28

Is the peptide bond rigid and flat? Or soft and curvy? Why?

Answer 28

Rigid and flat (found by Linus Pauling) The C-N bonds between two amino acids are shorter than other C-N bonds. This gives them partial double bond characteristics (they are resonance hybrids)

Question 29

How many peptide bonds in a polypeptide cannot rotate freely due to their short double-bond-like nature?

Answer 29

One third of the bonds in a polypeptide backbone cannot rotate freely. This limits the number of conformational possibilities

Question 30

What happens when cysteine is oxidized?

Answer 30

A reversible disulphide bridge between another oxidized cysteine

Question 31

What does a cysteine-cysteine disulfide double bridge do for the polypeptide?

Answer 31

Helps stabilize it

Question 32

When do Shiff base formations occur most? (most importantly)

Answer 32

Amino acid biosynthesis reactions