Amino Acids Biochemistry

Arginine

Serine

Threonine

isoleucine

Alanine

Leucine

Methionine

Glutamine

Cysteine

glycine

Asparagine

Aspartic Acid

Glutamic Acid

Histidine

Lysine

phenylalanine

Proline

Tryptophan

Tyrosine

Valine

Arginine 1 letter code

R

Arginine 3 letter code

Arg

Serine 1 letter code

S

Serine 3 letter code

Ser

Alanine 3 letter code

Ala

Alanine 1 letter code

A

Asparagine 3 letter code

Asn

Asparagine 1 letter code

N

Aspartic Acid 3 letter code

Asp

Aspartic Acid 1 letter code

D

Cysteine 3 letter code

Cys

Cysteine 1 letter code

C

glutamic acid 3 letter code

Glu

Glutamic acid 1 letter code

E

Glutamine 3 letter code

Gln

Glutamine 1 letter code

Q

Glycine 3 letter code

Gly

Glycine 1 letter code

G

Histidine 3 letter code

His

Histidine 1 letter code

H

Isoleucine 3 letter code

Ile

isoleucine 1 letter code

I

Leucine 3 letter code

Leu

Leucine 1 letter code

L

Lysine 3 letter code

Lys

Lysine 1 letter code

K

Methionine 3 letter code

Met

Methionine 1 letter code

M

Phenylalanine 3 letter code

Phe

Phenylalanine 1 letter code

F

Proline 3 letter code

Pro

Proline 1 letter code

P

Threonine 3 letter code

Thr

Threonine 1 letter code

T

Tryptophan 3 letter code

Trp

Tryptophan 1 letter code

W

Tyrosine 3 letter code

Tyr

Tyrosine 1 letter code

Y

Valine 3 letter code

Val

Valine 1 letter code

V

aspartic acid sidechain pKa

3.9

glutamic acid sidechain pka

4.3

Histidine sidechain pka

6

Arginine sidechain pka

12

Lysine sidechain pka

10.7

What is the one amino acid that is achiral

Glycine because its R-group is just a H

What is the one amino acid that is a R-stereoisomer

Cysteine because it has a high priority sulfur atom

Are most amino acids L or D stereoisomers

L, NH3+ is on the left.

Are most amino acids R or S stereoisomers

S. If H is in the back it would go COO-, R-group, NH3+ (CO-R-N Rule)

What three amino acids have aromatic R-groups

Phenylalanine(F), Tryptophan(Y), Tyrosine(W)
Remember: WYF (“wife)

Which amino acids have nonpolar aliphatic R-groups

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, Methionine

Which amino acids have polar uncharged R-groups

Serine, Threonine, Cysteine, Asparagine, Glutamine

Which amino acids have positively charge R-groups

Histidine, Arginine, Lysine

Which amino acids have negatively charged R-groups

Aspartate(aspartic acid) and Glutamate (glutamic acid)

What is the ΔG(hydration) of the nonpolar aliphatic sidechains(Valine, Alanine, Isoleucine, Leucine (VAIL))

+10kJ/mol

What is the ΔG(hydration) of the S-containing and aromatic sidechains( Methionine, Cysteine, Phenylalanine)

-5kJ/mol

What is the ΔG(hydration) of the Hydrogen-bonding sidechains(Tryptophan, Tyrosine, Serine, Threonine, Asparagine, Glutamine)

-20 to -40kJ/mol

What is the ΔG(hydration) of the charged sidechains(Histidine, Lysine, Arginine, Aspartate and Glutamate)

-300kJ/mol

In what order do the aromatic sidechain amino acids absorb light from strongest to weakest

Tryptophan, Tyrosine, Phenylalanine (WYF)

What kind of bonds do peptide bonds behave like?

Double Bonds.

What is the barrier of rotation for peptide bonds?

70kJ/mol

What configuration are almost all peptide bonds in?

Trans. It is the best way to get rid of any steric hinderance.

How many rotatable backbones are there in a residue?

Two
Phi bond (Nitrogen connected to alpha carbon)
Psi bond (Alpha carbon to carbonyl carbon)

What does a Ramachandran Map represent?

It represents the number of possible conformations that an amino acid can take on. Dark blue means more common, light blue, less common, white is not possible

Which conformation does the orange box represent on the Ramachandran map?

Antiparallel β-sheet

For how many of the amino acids is this Ramachandran map standard? Which ones are not included in that group?

18. The ones that are no included are Proline and Glycine

Which conformation does the orange box represent on the Ramachandran map?

Parallel β-sheet

Which conformation does the orange box represent on the Ramachandran map?

Collagen triple-helix

Which conformation does the orange box represent on the Ramachandran map?

Left-handed α-helix

Which conformation does the orange box represent on the Ramachandran map?

Right-handed  α-helix

How might a glycine Ramachandran map differ? Why

It will have a larger blue area since its side chain is only hydrogen, allowing for more conformations without any hindrance.

How might a proline Ramachandran map differ? Why?

It will have less blue area because its side chain is so bulky that it would have less possible conformations

What is primary structure of protein?

The primary structure of a protein is the unique linear sequence of amino acids in a polypeptide chain

What is secondary structure of protein?

The secondary structure of a protein is the local folding of the polypeptide backbone into regular patterns, such as α-helices and β-sheets, stabilized by hydrogen bonds between backbone atoms.

What is tertiary structure of a protein?

The tertiary structure of a protein is its overall three-dimensional shape, formed by the folding of secondary structures and stabilized by interactions among side chains, including hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bonds.

What is quaternary structure?

The quaternary structure of a protein is the arrangement and interaction of multiple polypeptide subunits in a multi-subunit protein complex, stabilized by the same forces as tertiary structure

What is the most common form of secondary structure?

α-helix

Where do the hydrogen bonds occur between in an α-helix?

Between residues i and i+4 (ie: residue 2 and 6)

Do the R-groups face outward or inward in a α-helix

Outward

How many amino acids are there per turn in an α-helix

3.6