Amino Acids

Question 1

Answer 1

Glycine (G, gly)

Nonpolar

properties: achiral, good if you need a small side chain tends to destabilize proteins, flexible.

Question 2

Answer 2

Alanine (A, ala)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

Question 3

Answer 3

Leucine (L, leu)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

Question 4

Answer 4

Isoleucine (I, ile)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins)

Question 5

Answer 5

Methionine (M, met)

Nonpolar

properties: tetris AA (packs nicely in interior of proteins), S is inert

Question 6

Answer 6

Tryptophan (W, trp)

Nonpolar

Question 7

Answer 7

Phenylalanine (F, phe)

Nonpolar

Question 8

Answer 8

Proline (P, pro)

Nonpolar

properties: imino acid, 15% in cis, stabilizing effect on protein

Question 9

Answer 9

Serine (S, ser)

Uncharged polar

properties: Hydrogen binding, can be phosphorylated, O-linked glycosylation

Question 10

Answer 10

Threonine (T, thr)

Uncharged polar

properties: can be phosphorylated, H bonding, )-linked glycosylation

Question 11

Answer 11

Tyrosine (Y, tyr)

Uncharged polar

properties: H bonding, phosphorylation

Question 12

Answer 12

Asparagine (N, asn)

Uncharged polar

properties: amide, good for H bonding, N-linking glycosylation

*(think N for everything!)*

Question 13

Answer 13

Glutamine (Q, gln)

Uncharged polar

properties: good N donor, high concentraion in cells for N donating

*too long for other properties*

Question 14

Answer 14

Cysteine (Y, cys)

Uncharged polar

properties: sulfhydryl, able to form cross-links via disulfide bonds

disulfide bonds- only occurs in oxidizing environments (typically outside cells) or lysosomes, stabilize the structure, requires specific orientations and distances, can be intrachain or interchain

Question 15

Answer 15

Glutamic acid (E, glu)

Acidic

pKa: 4

properties: N donor

Question 16

Answer 16

Aspartic Acid (D, asp)

Acidic

pKa: 4

properties: H bonds, catalyzes reactions, nucleophile

Question 17

Answer 17

Histidine (H, his)

Basic

pKa: 6

properties: imidazole

Question 18

Answer 18

Lysine (K, lys)

Basic

pKa: 10

properties: guanidinium, planar, good H bonding

Question 19

Properties of Amino Acids

Answer 19

Free AA exists in this form

stereochem: L-Configuration in proteins (“CORN” looking from H down to C)

pKa amino group: 9

pKa carboxyl group: 2

Question 20

Properties of the Peptide Bond

Answer 20

N terminus –> C terminus

2 amino acids comes together, lose a water, and form a C-N bond

The two alpha carbons form a planar backbone

peptide bond is polar (neutralize polarity via H bonds on the insideof proteins)

sp2 hybrid orbitals (π bond)

Question 21

Configurations of Peptide Bonds

Answer 21

mostly in trans (except for 15% prolines in cis)

backbone in a plane with C alphas in the corners

angles to allow planes to rotate relative to eachother:

• Φ: C alpha (@ point in both planes) to N
• Ψ C alpha (@ point in both planes) to C’

Question 22

Primary Structure

Answer 22

amino acid sequence, defined by covalent bonds including disulfide bridges (between cysteine)

Question 23

Secondary Structure

Answer 23

Local arrangements of the peptide backbone, often defined by H-bonds

if repeated phi psi angles:

Alpha helix & beta sheet

if non repeating phi psi angles:

loops & turns

Question 24

Tertiary Structure

Answer 24

Arrangement of secondary structure elements into compact domain…i.e. a globular unit

Question 25

Quaternary Structure

Answer 25

arrangement of multiple polypeptide chains in a multisubunit protein (oligomers like hemoglobin)

Question 26

Alpha Helix H bonding, polarity, and dimensions

Answer 26

right handed C=O points to C terminus (dipole) residues separated by 3 positions for H bonds between backbone atoms \* (bonds are formed bw C=O of residue I to H of residue i+4) dimensions: 3.6 residues/turn, 5.4 A/turn, **1.5 A rise/ residue**

Question 27

Classification of Helices

Answer 27

can be hyrophobic (buried) or polar (exposed) but most are amphipathic...meaning half polar half hydrophobic when this protein packs, the nonpolar residues will be buried on the inside and the polar residues will be exposed on the surface of the protein

Question 28

Beta Sheets directions and dimensions

Answer 28

come together via H bonding in parallel or antiparallel strands to form sheets directions: strands in one plane with side chains above and below the sheet dimensions: 3.5 A / residue

Question 29

Beta sheets characteristics of parallel sheets

Answer 29

**hydrophobic** residues above and below plane.. so typically buried wrapping with amphipathic helices from the N terminus to the C terminus called "Beta bends"

Question 30

Beta sheets characteristics of anti-parallel sheets

Answer 30

**amphipathic** (hydrophobic residues above, hydrophilic residues below), so exposed ons urface of proteins easy to connect N with C (sm amino acid chane, dont have to cross over the plain like in parallel sheets)

Question 31

Turns and Loops characteristics

Answer 31

non-repetitive secondary structure make up 50% of proteins **FUNCTIONAL** residues: occur on surfaces of proteins (exposed to solvents/binding sites)

Question 32

Motifs | (supersecondary structures)

Answer 32

A: helix-loop-helix B: B-hairpin C: Greek Key D: B-a-B

Question 33

Average molecular weight of an amino acid residue

Answer 33

110 Da

Question 34

Fibrous proteins

Answer 34

structural proteins elongated and LARGE in mass ex) used in tissue formation (collagen, elastin)

Question 35

Globular proteins

Answer 35

dynamin functions spherical examples) used in transport, immune system, metabolism, catalysis (enzymes), gene expression, muscle contraction

Question 36

Forces that stabilize proteins

Answer 36

Hyrdrophobic: side chains pack to form core Van der Waals: weak but numerous Hydrogen bonds: stabilize and neutralize backbone Ionic interactions: charged residues (amino + carbox) Disulfide bridges: cysteine covalently binds two chains together

Question 37

Answer 37

primarily alpha proteins can be parallel or perpendicular

Question 38

Answer 38

primarily B proteins form a barrel to bury hyrdophobic residues top: anti-parallel and contiguous bottom: anti-parallel and two greek keys that join at a face

Question 39

Answer 39

alpha/beta proteins (most common for proteins) top: alpha helix are all parallel, beta sheets forming a barrel bottom: domain 2