Chapter 3 - proteins

Question 1

Amino acids

Answer 1

• 20 of them
• An amino group (NH₂) + carboxyl group (COOH)
• Distinguished by R group
• All except glycine are L-amino acids

Question 2

Monomer units of proteins

Answer 2

amino acids

Question 3

Glycine

Answer 3

Only amino acid not normally ocurring as “L”. It doesn’t have a chiral center, so no “L” or “D” naming.

Question 4

K

Answer 4

Lysine (lys) - basic

Question 5

R

Answer 5

Arginine (Arg) - basic

Question 6

H

Answer 6

Histidine (his) - basic

Question 7

E

Answer 7

Glutamic Acid (Glu) - acid

Question 8

D

Answer 8

Aspartic Acid (Asp) - acid

Question 9

S

Answer 9

Serine (Ser) - polar uncharged

Question 10

T

Answer 10

Threonine (Thr) - polar uncharged

Question 11

T

Answer 11

Tyrosine (Thr) - polar uncharged

Question 12

L

Answer 12

Leucine (Leu) - Nonpolar (hydrophobic)

Question 13

A

Answer 13

Alanine (Ala) - nonpolar (hydrophobic)

Question 14

Proline

Answer 14

amino acid with a twist - found in proteins where they bend at Proline (P)

Question 15

Methionine

Answer 15

Always at the start of a protein. Has a S in R group (1 of 2 amino acids).

Question 16

Cysteine

Answer 16

Links subunits of protein. Reactive amino acid that forms a disulfide covalent bond when H come off from SH.

Question 17

Dipeptide

Answer 17

2 amino acids linked together

Question 18

Peptide bond

Answer 18

Formed by dehydration synthesis. Involves 4 atoms (C-N with O “partially neg” and H “partially pos”). The assymetry makes the bond somewhat “stiff”.

Question 19

Zwitter ion

Answer 19

When both ends of molecule are ionized

Question 20

End of a peptide chain

Answer 20

amino terminus (N-terminus) and carboxy terminus (C-terminus)

Question 21

oligopeptides

Answer 21

“a bunch” of peptides

Question 22

polypeptide vs. protein

Answer 22

Used interchangably. Protein refers to complete functional unit and polypeptide to a chain of many peptides.

Question 23

Alpha helix dimensions

Answer 23

0.54 nm per coil

Question 24

beta sheet dimensions

Answer 24

0.7 nm per pleat. parallel or antiparallel

Question 25

hemoglobin structure

Answer 25

a tetramer with 4 subunits: 2 alpha polypeptide chains, 2 beta chains

Question 26

prosthetic groups

Answer 26

example is hemoglobin with an iron molecule at the center

Question 27

covalent modification

Answer 27

transformation from an inactive to active enzyme. Kinase is a in design that modifies other proteins to add a phosphate. The reverse is done by phosphatase, which removes a phosphate.

Question 28

metal cofactors

Answer 28

enzyme with site groups that hold a metal cofactor in its active site (example Zinc)

Question 29

motifs

Answer 29

identification of a structural feature of a protein

Question 30

domains

Answer 30

iidentification of a functional region of a protein

Question 31

chaperone proteins

Answer 31

facilitate holding of other proteins. 2 classes: Hsp70, chaperonins

Question 32

dimer

Answer 32

structure of 2 proteins assembled together

Question 33

x-ray crystallography

Answer 33

used to determine protein shape

Question 34

NMR spectroscopy

Answer 34

use to analyze small proteins or protein domains