Chapter 3 - Protein Primary Structure

Question 1

Proteins are _______ composed of __ amino acids (AAs).

Answer 1

polymers; 20

Question 2

Describe the structure of a protein.

Answer 2

All are alpha AAs, an -NH2 & a -COOH attached to the same alpha carbon, and an R group

Question 3

At physiological pH (_____): The -NH2 is _______ (pKa ~_), The -COOH is ________ (pKa ___)

Answer 3

7.1-7.4; protonated; 9; deprotonated; < 3

Question 4

At pH 6.8-7.4, most AAs are _______(dipolar ions) and the molecule has a net charge of ____.

Answer 4

zwitterions; 0

Question 5

Why do chemists rarely use R/S nomenclature to describe AAs?
In nature __-AAs are used to construct proteins, __-AAs are rare in nature.

Answer 5

Because priorities change due to
differences in sidechain structure; L; D

Question 6

What are the different types of AAs classified by R groups?

Answer 6

Aliphatic (hydrophobic), Aromatic (hydrophobic), Sulfur-containing, Alcohol-containing, Basic, Acidic

Question 7

Glycine is the only AA without…

Answer 7

a chiral carbon.

Question 8

Each of the aliphatic AAs, contains…

Answer 8

hydrophobic sidechains (glycine is not very hydrophobic)

Question 9

L-Tyr and L-Trp absorb _______ at ___ nm, can be used to determine the ______ in solution.

Answer 9

UV-light; 280; protein

Question 10

List the sulfur-containing AAs.

Answer 10

L-Methionine and L-Cysteine

Question 11

Describe L-Methionine.

Answer 11

Has a nonpolar methyl thioether, fairly hydrophobic, often is the 1st
AA in a polypeptide chain.

Question 12

Describe L-Cysteine.

Answer 12

Has a Beta thiol, ionizable at physiological pH
(pKa = 8.4), form weak H-bonds with N, O, 2 sulfhydryl can form a
disulfide bond (e.g., cystine)

Question 13

List the alcohol-containing AAs and describe them.

Answer 13

L-Serine and L-threonine; β-OH groups on side chains, weakly ionizable sidechains (pKa ~16), nucleophilic, have 2 chiral centers, L-Threonine has a second chiral center

Question 14

Why does salt have a high melting point?

Answer 14

Bc for non-covalent interactions, whole (+) charge to (-) charge interactions are strongest.

Question 15

Is H-bonds stronger than whole charge/charge interactions? What about Van der Waals interactions?

Answer 15

Weaker than whole charge/charge, stronger than Van der Waals interactions

Question 16

Describe basic AAs.

Answer 16

Sidechain has basic N atom, polar, at physiological pH: protonated

Question 17

Describe acidic AAs & amide derivatives. Give ex.s

Answer 17

Acidic : L-Aspartate & L-glutamate have carboxylic acids in sidechains,
deprotonated at physiological pH, negatively charged
Amide: L-Asparagine & L-glutamine are primary amide derivatives
of L-Asp and L-Glu, highly polar, but uncharged

Question 18

Define hydropathy.
Quantitative hydropathy scales rely on… and is based on…
It heavily influences what?

Answer 18

the relative hydrophobicity/hydrophilicity of an AA; hydrophobic/hydrophilic environments; based on ΔG for
transfer of an AA from a lipid bilayer to water; protein folding

Question 19

Each AA has at least __pKa
values (α-_____ & α-____)…more if __ contains _____ functional
group.

Answer 19

2; carboxy; amino; R; ionizable

Question 20

Ionization of AAs influences…

Answer 20

3D shape of proteins and enzyme catalysis

Question 21

The isoelectric point (pI) is the
pH when…

Answer 21

the AA exists in dipolar
form, electronically neutral, net
charge is ‘0’ (‘zwitterion’).

Question 22

How are peptide bonds formed?

Answer 22

α-Carboxyl of 1st AA reacts
with α-amino of 2nd AA
forms peptide bond

Question 23

For peptide bonds, there is a partial __________. ______________ decreases steric hinderance of __ groups.

Answer 23

double bond; Trans configuration; R

Question 24

How to name peptides?

Answer 24

Change -ine or -ate to -yl

Question 25

How do you classify peptides?

Answer 25

Based on the # of amino acids: Oligopeptides have 2~20 AA, Polypeptides have > 20 AAs
Based on the shape of the molecule: chain, cyclic

Question 26

Define proteins and how they are classified (6).

Answer 26

biopolymers of amino acids (>50)
Polypeptide, long, continuous and unbranched;
Monomeric: 1 peptide chain.
Multimeric: more than 1 subunits.
Simple: hydrolyze to amino acids only.
Conjugated: bonded to a prosthetic group (sugar, nucleic acid, lipid…) Fibrous: long/stringy filaments, water insoluble, function
Globular: folded into spherical shape, most are functional (enzymes, hormones, transport proteins…)

Question 27

Describe the overview protein structure for primary, secondary, tertiary and quaternary structures.

Answer 27

1: Linear sequence of amino acids (N-terminus to C-terminus)
2: Polypeptides form regular arrangements w/regional motifs based on H-bonding –> α-helix / β-sheets/bends
3: Most proteins form complex 3D structure stabilized by cumulative
effects of large # weak chemical interactions and others
4: Interactions among complex proteins: multiple subunits

Question 28

What forces normal protein folding? What happens when proteins are misfolded?

Answer 28

Hydrophobic effects; result in incorrect function, lead to disease

Question 29

List the steps of protein purification.

Answer 29

1. Extraction of protein from whole cells
2. Use of salting/dialysis to remove some impurities
3. Use chromatography methods to isolate proteins

Question 30

Explain salting and dialysis.

Answer 30

Salting: Increasing [salt] to precipitate proteins based on solubility
Dialysis: Salted protein solution is placed in a bag with a semi-impermeable membrane, soaks in buffer

Question 31

AAs that are more hydrophobic have larger or smaller free energy charge transfer numbers?

Answer 31

Higher numbers.

Question 32

List the AAs of the aromatic group.

Answer 32

Phenylalanine, tryosine, tryptophan

Question 33

List the AAs of the aliphatic group.

Answer 33

Glycine, alanine, valine, leucine, isoleucine, proline