BICH 440 Exam 2

Pka Arg

12.5

Pka Asp

4

Pka Cys

8.5

Pka Glu

4

Pka His

6.0

Pka Lys

10.5

Pka Ser

13

Pka Thr

13

Pka Trp

16

Pka Tyr

10.5

Glycine

Alanine

Valine

Leucine

Isoleucine

Methionine

Proline

Phenylalanine

Tryptophan

Lysine

Arginine

Histidine

Aspartic acid

Glutamic acid

Serine

Threonine

Asparagine

Glutamine

Tyrosine

Cysteine

A =

Alanine, Ala

C =

Cysteine, Cys

D =

Aspartic acid, Asp

E =

Glutamic acid, Glu

F =

Phenylalanine, Phe

G =

Glycine, Gly

H =

Histidine, His

I =

Isoleucine, Ile

K =

Lysine, Lys

L =

Leucine, Leu

M =

Methionine, Met

N =

Asparagine, Asn

P =

Proline, Pro

Q =

Glutamine, Glu

R =

Arginine, Arg

S =

Serine, Ser

T =

Threonine, Thr

V =

Valine, Val

W =

Tryptophan, Trp

Y =

Tyrosine, Tyr

Hydrophobic amino acids:

GAMP FLIWV (Glycine, Alanine, Methionine, Proline, Phenylalanine, Leucine, Isoleucine, Tryptophan, Valine)

Polar and charged side chains:

DREKH (Aspartic Acid, Arginine, Glutamic Acid, Lysine, Histidine)

Polar and uncharged side chains:

STQNCY (Serine, Threonine, Glutamine, Asparagine, Cysteine, Tyrosine)

PI ~ 3

Asp, Glu

PI ~ 5

Cys

PI ~ 5.5

Ser, Thr, Asn, Gln, Met, Phe, Tyr, Trp

PI ~ 6

Gly, Ala, Val, Leu, Ile,

PI ~ 6.5

Pro

PI ~ 7.5

His

PI ~ 9.5

Lys

PI ~ 11

Arg

Association constant (Ka)

$$\frac{\left\lbrack PL]\right\rbrack}{\left\lbrack P_{free}\right\rbrack\left\lbrack L_{free}\right\rbrack]}$$

Dissociation constant (Kd)

$$\frac{\left(\left\lbrack P_{total}\right\rbrack-\left\lbrack PL]\left\lbrack L_{total}\right\rbrack-\left\lbrack PL\right\rbrack\right)\right)}{\left\lbrack PL\right._{}]}$$

[L] resulting in a 0.5 saturation =

Kd

S =

$R\Sigma p_{i}\ln\left(p_{i}\right)$ pi = probability of microstate, R is 8.314 J/(K*mole)

Alpha Helix

Phi ~ -57, Sai~ -47, periodic hydrogen bonding (amide to amide), 3.6 residues per turn (5.4 Angstroms), right handed

Beta Strands

Phi ~ -120, Sai ~ 120, wavy, can be parallel or antiparallel

Green, blue, white, yellow

C, N, H, S

All free amino acids are

Polyprotic

What’s special about Cysteine?

The ability to reversibly crosslink via dehydration, forming a disulfide bond

What’s special about Proline?

Cyclized side chain making the cis conformation stable, unlike the other amino acids

IMPs

Helical bundles and beta barrels

Alpha Keratin

Coiled coil, left handed twist, smaller turn than normal

Beta keratin

Gly-X-Gly-X, X being a smaller amino acid such as Serine or Alanine

Collagen

Triple helix, 1/3 G, 15-30% Pro or hydroxyproline, repeated sequence of Gly-Pro-Hydropro