Lecture 5 - 3-D Structure of Proteins

Question 1

What is responsible for hydrogen bonding within proteins?

Answer 1

-Amino groups (NH3) -Carbonyl groups (COOH)

Question 2

The carbons of an AA that lie on either side of the chiral carbon

Answer 2

alpha-Carbon

Question 3

Alpha-carbons are on same side of the amino acid

Answer 3

Cis

Question 4

Alpha-carbons on opposite side of the amino acid

Answer 4

Trans

Question 5

Bond between Nitrogen and chiral carbon

Answer 5

phi

Question 6

Bond between chiral carbon and carboxylic acid group

Answer 6

psi

Question 7

Linear arrangement of AA residues

Answer 7

primary structure

Question 8

Coiling and/or pleating of amino acid chain

Answer 8

secondary structure

Question 9

Alpha helices work to stabilize proteins by _____

Answer 9

Hydrogen bonds

Question 10

Number of amino acids per turn in alpha helix

Answer 10

3.6

Question 11

In beta strands, when one AA hydrogen bonds with only one other AA, it is a (parallel/anti-parallel).

Answer 11

Anti-parallel

Question 12

In beta strands, when one AA residue hydrogen bonds to two other AA residues, it is (parallel/anti-parallel)

Answer 12

parallel

Question 13

Specific 3-D configuration of a peptide chain

Answer 13

Tertiary structure

Question 14

Bonding between cystiene residues, works to stabilize proteins by covalent linkage

Answer 14

Di-sulfide bonds

Question 15

The structure of most “structural proteins”

Answer 15

Filamentous (F-proteins)

Question 16

The structure of most enzymes

Answer 16

Globular (G-proteins)

Question 17

Multiple subunit proteins coming together, often after post-translational modification

Answer 17

Quaternary structure

Question 18

How are subunits held together in quaternary structure???

Answer 18

NON-covalent linkages!!!!

Question 19

What is the repeating motif in collagen?

Answer 19

-Gly-X-Y-Gly-X-Y-

Question 20

Why is repeating Gly in collagen important?

Answer 20

Allow for small, tight protein turns; it can be compacted

Question 21

Clinical correlation: what is the mechanism behind “scurvy?”

Answer 21

A defective Proline hydroxylase prevents -OH from being added to Proline, this produces the inability to form collagen, which results in poor wound healing/destroyed connective tissue

Question 22

Breaking of disulfide bonds

Answer 22

protein denaturation

Question 23

What are the steps of protein denaturation?

Answer 23

Increased heat produces most of the denaturation; chemical denaturation breaks di-sulfide bonds

Question 24

What are the three main denaturing agents?

Answer 24

• Urea - Beta-mercaptoethanol - Guanidinium chloride

Question 25

The ____ of a protein is formed by the amino/carbonyl connection, with side chains projecting off.

Answer 25

backbone

Question 26

2* structure bonding

Answer 26

α−helix and β−turn/β−sheets

Question 27

3* structure bonding

Answer 27

-S-S- bonding

H-bonding

metal binding

hydrophobic interaction