Amino Acids, Peptides, and Proteins I and II

Question 1

Identify alpha carbon, amino group, carboxylic acid group, and side chains of an amino acid.

Answer 1

Amino group - NH3+
Side chain - R
Alpha carbon - (NH3)-C-(COOH)
Carboxylic Acid Group- COOH

Question 2

What are the hydrophobic, nonpolar amino acids? (Aliphatic)

What are the aromatic amino acids?

Answer 2

Glycine (G), Valine V), Alanine (A), Leucine (L), Isoleucine (I), Methionine (M)

Phenylalanine (F), Tyrosine (Y), Tryptophan (W)

Question 3

What are the polar, uncharged and charged amino acids?

Answer 3

Uncharged: Serine (S), Threonine (T), Cysteine (C), Proline (P), Asparagine (N), Glutamine (Q)
+ Charged: Histidine (H), Lysine (K), Arginine (R)
- Charged: Aspartate(D), Glutamate(E)

Question 4

Disulfide Bond and Function

Answer 4

Covalent linkage between two sulfur atoms.
In amino acids, between thiol groups of two cysteines. Functions to connect chains and stabilize secondary and tertiary structure (has ability to make inter and intra chain linkages).

Question 5

List Major Post-Translational Covalent Modifications of Amino Side Chains.

Answer 5

1. Hydroxylation of Proline
2. Carboxylation of Glutamate
3. Glycosylation
4. Modification of Side Chains by Acetylation and Methylation
5. Reversible Phosphorylation/Dephosphorylation of Ser, Thr, and Tyr.
6. Ubiquitination

Question 6

What enzyme is responsible for hydroxylation of proline?

Answer 6

Prolyl hydroxylase.

Question 7

What creates a proline helix?

Answer 7

Multiple prolines and hydroxyprolines in a row. This is a predominant secondary structure in collagen.

Question 8

Does addition of hydroxyl groups to proline increase or decrease the stability of collagen?

Answer 8

Increase

Question 9

Prolyl hydroxylase relies on what co factor to be active?

Answer 9

Vitamin C

Question 10

What is the condition Scurvy caused by?

Answer 10

Lack in Vitamin C. Prolyl hydroxylase cannot function without this cofactor, thus cannot hydroxylate proline resulting in loss of integrity of collagen in the body.

Question 11

The addition of a carboxyl group to the side chain of glutamate is carried out by what enzyme?

Answer 11

Gamma-glutamyl carboxylase.

Question 12

What cofactor does gamma-glutamyl carboxylase acquire to function?

Answer 12

Vitamin K

Question 13

Where is carboxylation of glutamate found?

Answer 13

In clotting factors.

Question 14

Why would a Vitamin K deficiency result in hemorrhage?

Answer 14

Gamma-glutamyl carboxylase cannot carboxylate glutamate without its cofactor, thus results in clot formation.

Question 15

How does Waarfain prevent clotting?

Answer 15

Waarfin inhibits the activity of gamma-glutamyl carboxylase.

Question 16

Where does acetylation by HATs (Histone Acetyl Transferases) usually occur at?

Answer 16

Lysine residues on free tails of histones.

Question 17

Where does methylation by methyltransferases usually occur at?

Answer 17

At lysine and arginine residues. Dimethyl lysine, dimethyl arginine.

Question 18

How does acetylation and methylation modify the protein when it does?

Answer 18

They alter the charge on the amino acid, resulting in activation of transcription.

Question 19

What is Vorinostat?

Answer 19

An HDAC inhibitor used in cancer therapies. It prevents the removal of acetyl groups from histones by histone deacetylase, which is responsible for silencing tumor supressor genes.

Question 20

What is glycosylation?

Answer 20

Site specific enzymatic process that attaches glycans to proteins. Makes protein more polar.

Question 21

Why are glycans important?

Answer 21

They serve a variety of structural and functional role in membrane and secreted proteins.

Question 22

What are the five glycans that are produced?

Answer 22

N-linked: glycans to N of Asp and Arg
O-linked: glycans attached to hydroxy O
Phospho-glycans
C-linked glycans

Question 23

Functions of Glycosylation

Answer 23

Proper protein folding, increased stability of secreted glycoproteins, cell-cell adhesion, role in recognition

Question 24

What is the Congenital Disorder of Glycosylation (CDG)?

Answer 24

N-linked glycosylation is interrupted. Results in developmental delay and hypertonia.

Question 25

What is Gleevac?

Answer 25

A tyrosine kinase inhibitor used to treat chronic myelogenous leukemia (CML).

Question 26

What is Ubiquitination?

Answer 26

Targets protein for destruction by proteosome by adding ubiquitin to lysine residues.

Question 27

What is Bortezomib?

Answer 27

Proteosome inhibitor used to treat multiple myeloma.

Question 28

Where is the peptide bond in a chain of amino acids?

Answer 28

Btwn the carbonyl carbon and amide carbon.

Question 29

Why can mutation in an amino acid sequence cause disease?

Answer 29

Alter the function of the protein because protein is misfolded, unstable, truncated or extended, or no longer responding to regulation.

Question 30

Phi angle

Answer 30

angle around alpha carbon and amide nitrogen bond

Question 31

Psi angle

Answer 31

angle around alpha carbon and carbonyl carbon

Question 32

What is the general important function of proteases?

Answer 32

Break peptide bonds to ensure proteins are not active in locations where they could be destructive. (general and specific proteases)

Question 33

What is a hydrogen bond?

Answer 33

Interaction of hydrogen atom with electronegative atom, F O N.

Question 34

What is the role of hydrogen bond in alpha helices?

Answer 34

H bonds form between the carbonyl oxygen of the nth amino acid and amide nitrogen of the nth + 4 amino acid. Results in right handed helical structure and side chains pointing outward.

Question 35

What is the role of hydrogen bonds in beta sheets?

Answer 35

To link two polypetide chains, can be parallel or antiparallel.