Bio/Biochem Deck 1: Amino Acids & Protein Structure

What amino acid is this?

Alanine, Ala, A

What amino acid is this?

Arginine, Arg, R

What amino acid is this?

Asparagine, Asn, N

What amino acid is this?

Aspartic acid, Asp, D

What amino acid is this?

Cystine, Cys, C

What is this amino acid

Glutamine, Gln, Q

What is this amino acid?

Glutamic acid, glu, E

What is this amino acid?

Glycine, gly, G

What is this amino acid?

Histidine, his, H

What is this amino acid?

Isoleucine, ile, I

What is this amino acid

Leucine, leu, L

What is this amino acid?

Lysine, lys, K

What is this amino acid?

Methionine, met, M

What is this amino acid?

Phenylalanine, phe, F

What is this amino acid?

Proline, pro, P

What is this amino acid?

Serine, ser, S

What is this amino acid?

Threonine, thr, T

What is this amino acid?

Tryptophan, trp, W

What is this amino acid?

Tyrosine, tyr, Y

What is this amino acid?

Valine, val, V

List the aromatic amino acids?

Phenylalanine, Tryptophan, Tyrosine

List the acidic amino acids?

Aspartic acid, glutamic acid

List the Basic amino acids?

arginine, histidine, lysine

Which amino acid is often involved in enzyme active sites because its charge changes near physiological pH?

Histidine

List the nonpolar amino acids

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

Where are hydrophobic amino acids usually found in a globular protein?

Buried in the interior

List the polar amino acids

Serine, Threonine, Asparagine, Glutamine

Which amino acids are commonly phosphorylated?

Serine, Threonine, Tyrosine

What is the pka for the amine group?

9

What is the pka for the carboxylic group?

2

What is the pka for the R-group of aspartic acid?

3.9

What is the pka for the R-group of glumatic acid?

4.3

What is the pka for the R-group of histidine?

6

What is the pka for the R-group of cystine?

8.3

What is the pka for the R-group of tyrosine?

10.1

What is the pka for the R-group of Lysine?

10.5

What is the pka for the R-group of Argenine?

12.5

If pH > pKa, is a group protonated or deprotonated?

Deprotonated.

pH > pKa → loses H⁺

pH < pKa → gains H⁺

Why is RNA less stable than DNA?

RNA has a 2'-OH group that can attack the phosphate backbone, making it susceptible to alkaline hydrolysis.

Which nucleic acid undergoes alkaline hydrolysis more easily?

RNA

Which amino acid is NOT chiral?

Glycine

Its R group is another hydrogen

Which amino acid causes bends in proteins?

Proline

Its ring structure creates kinks

What type of reaction forms a peptide bond?

Condensation (dehydration synthesis)

Water is released.

What type of reaction breaks a peptide bond?

Hydrolysis

Water is consumed

What stabilizes secondary structure?

Hydrogen bonds between backbone atoms.

What levels of protein structure are disrupted during denaturation?

Secondary, tertiary, and quaternary.

Primary structure remains intact.

What can denature proteins?

• Heat

• Extreme pH

• Organic solvents

• Urea

• Heavy metals

What is the isoelectric point (pI)?

The pH at which the amino acid has a net charge of 0

If pH is greater than the pI, is the amino acid more positive or negative?

More negative

If pH is less than the pI?

More positive

1)Why are hydrophobic amino acids buried inside proteins?

2)Why are charged amino acids usually found on the surface of globular proteins?

1) To avoid contact with water, increasing protein stability.

2) They interact favorably with water.

Which amino acid is most likely to form a disulfide bond?

Cysteine

Does denaturation break peptide bonds?

No.

It disrupts higher-order structure only