Chapter 4: Protein Structure

Question 1

Primary Structure

Answer 1

the sequence of amino acids that make up the polypeptide chain in a protein; usually between 100-1000 amino acid residues

Question 2

R Group

Answer 2

the variable side chain portion of an amino acid can be non polar aliphatic, polar uncharged, polar charged, non polar aromatic

Question 3

Amino Acid Structure

Answer 3

central carbon atom (alpha C) bonded to hydrogen, amino group, carboxyl group, and side chain

Question 4

Nonpolar Aliphatic R Groups

Answer 4

composed only of hydrocarbon chains, hydrophobic, plus Methionine which has thioether (S) group; ten to cluster inside proteins and stabilize structure; Proline’s rigid structure limits possible conformations

Question 5

Polar Uncharged R Groups

Answer 5

interact extensively with water and other side chains through hydrogen bonds

Question 6

Disulfide Bond

Answer 6

occurs through oxidation between the cysteine residues brought into close proximity

Question 7

Polar Charged R Groups

Answer 7

can form hydrogen bonds and ionic interactions with amino acids of opposite charge

Question 8

Nonpolar Aromatic R Groups

Answer 8

hydrophobic, especially phenylalanine; tyrosine and tryptophan can be somewhat polar

Question 9

Peptide Bond

Answer 9

covalent link between two adjacent amino acids; condensation of N-terminus of one amino acid to C-terminus of another

Question 10

Polypeptide Chain

Answer 10

many amino acids linked together by peptide bonds

Question 11

N-terminus

Answer 11

amino end of a polypeptide chain

Question 12

C-terminus

Answer 12

carboxyl end of a polypeptide chain

Question 13

Chromatography

Answer 13

a method of separating proteins

Question 14

Column Chromatography

Answer 14

a powerful chromatographic technique in which a protein mixture is applied to a column containing a matrix that interacts differently with various proteins; buffers are used to make different proteins dissociate at different times

Question 15

Ion Exchange Chromatography

Answer 15

proteins separated by charge

Question 16

Gel Exclusion Chromatography

Answer 16

proteins separated by size

Question 17

Affinity Chromatography

Answer 17

proteins sorted by the type of ligand they bind or by antibodies

Question 18

SDS-PAGE

Answer 18

a method of visualizing proteins using a polyacrimide gel; small proteins move faster; after separation, gel is treated with a dye that binds to proteins

Question 19

Secondary Structure

Answer 19

regularly repeating elements within a protein in which hydrogen bonds form between polar atoms in the backbone chain; mainly alpha helix and beta sheet; allow intrinsically polar polypeptides to traverse non polar interior of a protein

Question 20

Alpha Helix

Answer 20

formed by hydrogen bonds between backbone amide and carbonyl groups; R-groups protrude outward from the helix; right hand spiral; aromatic side chains 4 residues apart can stabilize the helix

Question 21

Beta Sheet

Answer 21

at least two segments of peptides in the beta conformation; formed by hydrogen bonds between backbone amide and carbonyl groups of two different beta strands; zigzag geometry prevents interaction of of adjacent R groups

Question 22

Antiparallel Beta Sheet

Answer 22

when beta strands are oriented in opposite N-C terminal directions

Question 23

Parallel Beta Sheet

Answer 23

when beta strands are oriented in the same N-C terminal directions

Question 24

Protein Folding

Answer 24

the process in which a polypeptide backbone folds to adopt a particular conformation

Question 25

Hierarchical Model

Answer 25

folding model that proposes that local regions of secondary structure form first, followed by longer range interactions

Question 26

Molten Globule Model

Answer 26

hydrophobic residues of a polypeptide chain rapidly group together and collapse the chain into a condensed, partially ordered molten voluble state

Question 27

Chaperones

Answer 27

specialized proteins that bind improperly folded polypeptides and facilitate correct folding pathways or provide microenvironment in which folding can occur