Chapter 3 - Amino Acids, Peptides And Proteins

Question 1

What is a primary sequence ?

Answer 1

Primary sequence is the simple amino acid sequence

Question 2

What is a secondary sequence?

Answer 2

Secondary sequence is the initial folding of the primary sequence into alpha helixes and beta sheets

Question 3

What is a homodimer?

Answer 3

A functional protein made up of 2 or more polypeptides (covalently linked AA sequences) that come together to form a full enzyme.
Quarternary structure of a protein - diner with 2 identical subunits

Question 4

What are prosthetic groups?

Answer 4

Non protein attachments to protein compounds

Question 5

What are the four functions of proteins ?

Answer 5

1. Catalysis
2. Transport
3. Structure
4. Motion

Question 6

In chirality, what are L and D in relations to each other? What do they mean? In nature, a vast majority of compounds take which configuration?

Answer 6

Enantiomers.
L - when the lowest priority is going away from you, the system wheels to the left from the highest to lowest priority of the remaining 3 substituents
D - when the lowest priority group is going away from you, the system wheels to the right from highest to lowest priority of the remaining 3 substituents

Question 7

How many groups can amino acids be classified in based on the attached “R” group? What are these groups and how many are in each?

Answer 7

5 groups. 
Nonpolar aliphatic (7)
Aromatic (3)
Polar uncharged (5)
Positively charged (3)
Negatively charged (2)

Question 8

Name the amino acids in the nonpolar aliphatic group

Answer 8

Glycine-GLY-G
Alanine-ALA-A
Proline-PRO-P
Valine-VAL-V
Leucine-LEU-L
isoleucine-ILE-I
Methionine-MET-M

Question 9

Amino acids in the aromatic group (3)

Answer 9

1.
Phenylalanine-PHE-F
2. Tyrosine-TYR-Y
3. Tryptophan-TRP-W

Question 10

Amino acids in the polar, unchanged group (5)

Answer 10

1. Serine-SER-S
2. Threonine-THR-T
3. Cysteine-CYS-C
4. Asparagine-ASN-N
5. Glutamine-GLN-Q

Question 11

Amino acids in positively charged group (3)

Answer 11

1. Lysine-LYS-K
2. Arginine-ARG-R
3. Histidine-HIS-H

Question 12

Amino acids in the negatively charged group (acidic) (2)

Answer 12

1. Aspartate-ASP-D

2. Glutamate-GLU-E

Question 13

Which 3 amino acids are usually phosphorylated? What happens here?

Answer 13

Serine, Threonine and Tyrosine. Phosphoryl group is added and the charge introduced causes massive confirmation change. The 4th O is a nucleophile from the amino acid

Question 14

What other three post translational modifications are common?

Answer 14

Methylation
Acetylation
Adenylylation

Question 15

Ionization wise, what happened to amino acids at acidic, neutral and alkaline pH levels?

Answer 15

At acidic levels: the carboxyl group is protonated and the amino acid is in cationic form (NH3 with a + charge)
At neutral pH: the carboxyl group is deprotonated (taking a - charge) but the amino group is still protonated with a + charge, so the net charge is zero and it exists as a zwitterion
At alkaline pH: the amino group is neutral (with only 2 Hs) and the AA is in an ionic form since the carboxyl is existing as COO-

Question 16

Where are non polar components of proteins found in the structure? Why? What drives this?

Answer 16

Due to the hydrophobic effect, nonpolar parts are usually on the inside because they are hydrophobic. This format is driven by entropy

Question 17

How does a peptide bond form? What is the result? What is the Orgo name for peptide bonds?

Answer 17

Neucleophilic attack on the Carbonyl Carbon on one AA by the lone pair of electrons on the amino group on the other AA, causing one of
the C=O dbl bonds to break, thereby pushing electrons from the other double bond on the OH and kicking it off. This results in the
formation of:
– -O=C- NH– - formation between the two amino acids. Also called “Amide” bond in Orgo.

Question 18

What are Cofactors? Coenzymes? & Prosthetic Groups? Give examples.

Answer 18

Cofactors are functional non-amino acid components of proteins (metal ions or organic molecules).
Coenzymes are organic cofactors (NAD+ in lactate dehydrogenase)
Prosthetic Groups are covalently attached cofactors (Heme in Hemoglobin). Since they’re covalent, they are hard-fixed which
differentiates them from cofactors and coenzymes.