Amino Acids

Question 1

Primary Structure

Answer 1

Amino Acid Sequence

Question 2

Central Dogma

Answer 2

DNA to mRNA to Protein

Question 3

Enantiomers

Answer 3

Chirality isomers, D and L

Question 4

Chirality of Mammalian Amino Acids

Answer 4

L-configuration

Question 5

Alipathic Amino Acids

Answer 5

Gly, Ala, Val Leu, Ile, Met, Pro

Question 6

Special Group on Proline

Answer 6

Imino

Question 7

Aromatic Amino Acids

Answer 7

Phe, Tyr, Trp

Question 8

Uncharged Polar Amino Acids

Answer 8

Ser, Thr, Asn, Gln, Cys

Question 9

Charged Polar Amino Acids

Answer 9

Lys, Arg, His, Asp, Glu

Question 10

pH with 50% protonation of an amino acid

Answer 10

pKa

Question 11

Henderson-Hasselbach Equation

Answer 11

pH = pKa + log(A/HA)

Question 12

pH where an amino acids has net charge of zero

Answer 12

Isoelectric point

Question 13

Region where the pH does not respond to large additions of H or OH

Answer 13

Buffering

Question 14

Leading Amino Acid at N-terminus

Answer 14

Met

Question 15

Covalent bonds formed by the oxidation of cysteine

Answer 15

Disulfide linkage

Question 16

5’ End

Answer 16

N-Terminus

Question 17

3’ End

Answer 17

C-Terminus

Question 18

Orientation of Amide Bond

Answer 18

Planar due to resonance, Trans due to steric interference

Question 19

Phi Bond

Answer 19

N to Alpha-C

Question 20

Psi Bond

Answer 20

Alpha-C to Carbonyl

Question 21

Amide Bond

Answer 21

Carbonyl to N

Question 22

Driving force for protein folding

Answer 22

Hydrophobic Interactions

Question 23

Reason proteins have very few structures with low Gibbs free energy and usually only one native structure (Exponential Descent Down the Funnel)

Answer 23

Cooperativty

Question 24

Length of Turns in Alpha Helix

Answer 24

3.6 Residues, 5.4 A

Question 25

Order of H-bonds from 5’ to 3’

Answer 25

C=O to H-N, Parallel to Helical Axis

Question 26

Polarity of Alpha Helix

Answer 26

Amphipathic

Question 27

Beta Pleated Sheet Orientation

Answer 27

Parallel 5’ to 3’ same direction
Antiparallel alternating 5’ to 3’ and 3’ to 5’
Mixed combination of parallel and antiparallel

Question 28

Amino acids for hairpin turns

Answer 28

Type I use Proline

Type II use Glycine

Question 29

Amino acid used for end of alpha helices and beta sheets

Answer 29

Proline

Question 30

Tertiary Structure

Answer 30

Domains due to R group interactions

Question 31

Quaternary Structure

Answer 31

Subunits interacting together

Question 32

Metamorphic Proteins

Answer 32

Multiple stable structures for a single protein

Question 33

Alpha-Keratin Structure

Answer 33

Two right handed alpha-helices who form a left handed alpha coiled coil.

Question 34

Alpha-Keratin Coil Bonding

Answer 34

Both non-covalent and covalent disulfide bonds

Question 35

Collagen Structure

Answer 35

Three left-handed helices called alpha-chain with -Gly-X-Y- sequences where X is proline and Y is often either hydroxyproline or hydroxylysine

Question 36

Collagen Abundance

Answer 36

20-25% of total body protein

Question 37

Importance of Ascorbate and disease caused by its deficiency

Answer 37

Required by enzymes for the formation of hydroxyproline and hydroxylysine.
Scurvy which is marked by weakness of collagen in body (i.e. bleeding gums)

Question 38

Synthesis of Collagen

Answer 38

Left handed helices have residues hydroxylated and begin forming the right handed super helix in the ER
Procollagen shuttled out of cell
Tropocollagen formed by terminating excess N and C terminal peptides allowing the tropocollagen super helices to self-assemble

Question 39

Structure of Elastin

Answer 39

Connective tissue protein with rubber properties in lungs, arterial walls, and elastic ligaments. Mainly nonpolar amino acids and proline and lysine

Question 40

Synthesis of Elastin

Answer 40

Tropoelastin released into ECM where it interacts with glycoprotein microfibrils
Some lysyls will be converted to allysine which cross-link lysine to form the matrix of elastin

Question 41

Degradation of Elastin and Pathology

Answer 41

Alpha-Antitrypsin (alpha-AT) inhibits elastase which degrades elastin.
Genetic deficiency in alpha-AT due to S and Z alleles
Cigarette smoke oxidizes a Met residue which causes alpha-AT not be able to bind to elastin