Amino Acids and Protein Structure

Question 1

2 categories of functional roles of proteins

Answer 1

dynamic; structural

Question 2

Amino Acid backbone pKas

Answer 2

Amino group: 9

Carboxyl Group: 2

Question 3

pKa

Answer 3

pH at which the number of protonated and deprotonated species are equal

Question 4

Post-translational modifications

Answer 4

phosphorylation, glycosylation, methylation, etc

Question 5

Proteins are designed for

Answer 5

maximum functionality NOT maximum stability

Question 6

Proline

Answer 6

Nonpolar

- creates turns and loops

Question 7

Pheylalanine

Answer 7

Nonpolar

- flat and planar

Question 8

Glycine

Answer 8

Nonpolar; achiral
- great for flexibility
small and easy to fill in places

Question 9

Tryptophan

Answer 9

Nonpolar

- H bonding potential; can be on surface of proteins

Question 10

Amino Acids with phosphorylation potential

Answer 10

Ser, Thr, Tyr

Question 11

Amino Acids with glycosylation potential

Answer 11

O-linked: Ser, Thr

N-linked: Asn

Question 12

Amino Acid with disulfide bonding

Answer 12

Cys

Question 13

Disulfide bond crosslinking

Answer 13

crosslinks cysteine side chains in oxidizing environments

- helps stabilize folded proteins

Question 14

Amino Acids with Acidic Side Chains

Answer 14

Aspartic Acid; Glutamic Acid
pKa: 4
NEGATIVELY CHARGED as physiological pH

Question 15

Amino Acids with Basic Side Chains

Answer 15

Histidine: pKa 6 (protonation state varies in physiological pH range; rarest AA; there for a reason)
Lysine: pKa 10
Arginine: pKa 12
- LYS and ARG: positively charged at physiological pH

Question 16

Nonpolar AA

Answer 16

Glycine
Alanine
Valine
Leucine
Isoleucine
Phenylalanine
Tryptophan
Methionine
Proline

Question 17

Uncharged Polar Side Chain AA

Answer 17

Serine
Threonine
Tyrosine
Asparagine
Glutamine
Cysteine

Question 18

Histidine

Answer 18

Rarest AA; important for pH dependent regulation

- pKa 6

Question 19

Peptide Bond

Answer 19

Planar; Polar
2 AA - H20 = Peptide Bond
- most peptide bonds trans
- 15% proline are cis, creating a turn

Question 20

Cis Peptide Bonds

Answer 20

Steric hinderance!

Proline creates a turn

Question 21

Trans Peptide Bond

Answer 21

limited configuration without steric hinderance

• only two sets of angles avoid steric collisions
• these generate repetitive secondary structures (alpha helix, beta sheet)

Question 22

Alpha Helix

Answer 22

• right handed
• C=O point to C-terminus (dipole)
• H-bonds (-C=O—H-N-) (residue n — residue n+4)

Question 23

Dimensions of Alpha Helix

Answer 23

• 3.6 residues/turn
• 5.4 A/turn
• 1.5 A rise/residue

Question 24

All backbone H bonds satisfied

Answer 24

neutralizes polarity

* exists well in hydrophobic interior*

Question 25

Classification of Helicies

Answer 25

• polar/nonpolar residues arranged to create polar and nonpolar faces
• residues are placed at 100 degree intervals around the 360 degree wheel

polar: exposed to solvent
nonpolar: transmembrane domains
amphipathic: majority of proteins

Question 26

Beta Sheet (anti-parallel)

Answer 26

3 perpendicular directions
- direction of polypeptide chain
-H-bonds between strands (central strands H bonds all satisfied)
- side chains above and below plane of sheet
Dimensions
- 3.5 A/residue
- amphipathic: exposed on surface

Question 27

Parallel sheet

Answer 27

• hydrophobic

- buried in protein interior

Question 28

Turns and Loops

Answer 28

• non-repetitive secondary structure (less regular/complex)
• ~50% of residues in globular proteins (globular=spherical)
• usually located at protein surface (binding surfaces; active sites)

Question 29

Forces that Stabilize Proteins

Answer 29

• Hydrophobic Interactions
• van der Waals Interactions
• H bonds
• Ionic Interactions
• Disulfide Bridges

Question 30

Domains

Answer 30

• structural/functional units of 100-300 AA
• 10-30 kDa
• often contiguous (not always; can be inserted btw or w/in a domain)