MCAT Amino Acids

Which enantiomer configuration of amino acids do humans use exclusively?

L

What is the stereo configuration of all amino acids except cysteine?

S

What is the absolute configuration of the alpha carbon of Cysteine?

R

Which enantiomer configuration is this Amino Acid?

L

Which enantiomer configuration is this Amino Acid?

R

What configuration is Glycine?

Achiral

What is the typical charge of the Amino group?

positive

What is the typical charge of the Carboxylic group?

negative

What is the acronym for nonpolar, aliphatic amino acids?

GAPVLIM

What is the acronym for uncharged polar amino acids?

STCNQ

What is the acronym for nonpolar, aromatic amino acids?

KYW

What is the acronym for positively charged amino acids?

KHR

What is the acronym for negatively charged amino acids?

DE

What is different about Histidine in comparison to other positively charged amino acids?

neutral side chain at physiological ph

What is unique about Proline?

The R group forms a ring with the amino group

What do Glycine and Proline do to secondary structure?

Disrupts them

What are the two secondary structures?

alpha helices and beta sheets

Why is proline favored for beta turns?

compact

What is unique about Serine, Threonine, and Tyrosine?

They are alcohols and can be phosphorylation targets or form hydrogen bonds

What is unique about Cysteine?

Can form disulfide bonds with other Cysteines

What is unique about Tyrosine?

It contains both a nonpolar aromatic ring and a polar hydroxyl group

What is the typical pka of a terminal carboxyl group?

3.1

What is the typical pka of Aspartic Acid or Glutamic Acid?

4.1

What is Aspartic Acid or Glutamic Acid vs Aspartate or Glutamate?

Protonated or nonprotonated

What is the typical pka of Histidine?

6.0

What is the typical pka of a terminal amino group?

8.0

What is the pka of Lysine?

10.8

What is the pka of Arginine?

12.5

What is secondary protein structure held together by?

H bonds

Which amino acids can mimic the effect of a phosphorylated functional group?

Aspartate and Glutamate

What is the phosphomimetic effect?

The R group of Aspartate and Glutamate acts similar to a phosphoryl group

What are ionic interations or salt bridges?

Positive and Negative amino acids on a protein attract each other

What are the two methods of synthesizing amino acids?

Strecker and Gabriel Synthesis

What is Strecker Synthesis?

ammonia + aldehyde → imine + cyanide ion → alpha-aminonitrile + H2O → amino acid

What is the stereochemistry of Strecker Synthesis?

non-stereospecific

What is a racemic mixture?

An equal amount of enantiomers

What is Gabriel Synthesis?

phthalamide malonic ester + base catalyzed hydrolysis → product decarboxylated → amino acid

What is the stereochemistry of Gabriel Synthesis?

non-stereospecific

What breaks disulfide bonds?

acid (BME)

What is a peptide bond?

A bond between the carboxyl group of one amino acid residue and the amino group of the next

What breaks peptide bonds?

H2O

What is hydrolysis?

Addition of H2O to break a bond

Which is spontaneous? Peptide bond formation or Peptide bond hydrolysis?

Hydrolysis

Why don’t peptide bonds break all the time?

High activation energy

What is primary protein structure?

Amino acid sequence

What is secondary protein structure?

Alpha helices or beta sheets

What are the three types of beta sheets?

Parallel, antiparallel, or mixed

What is the spacing of H bonds in an alpha helix?

4 amino acids

What is tertiary structure?

The 3d folded structure of a singular protein

What is quaternary structure?

The combination of multiple peptides

How are hydrophobic residues organized in a protein’s 3D structure?

Hydrophobic residues are located towards the center of the protein.

What is the only covalent bond that influences tertiary structure?

Covalent bonds

What is a protein called when it loses its tertiary structure?

Denature

What is it called when multiple peptide subunits combine together?

Polypeptide

What are prosthetic groups?

non-protein molecules that are tightly bound to a peptide and are required for protein functionality

What is an apoprotein?

A protein without its prosthetic group

What is a holoprotein?

A protein with its prosthetic group

What helps proteins fold?

Chaperones

What helps proteins stay in their native conformation?

Entropy

What factors can affect the stability of a protein in its native conformation?

temperature, salinity, pH

What causes hydrophobic particles to clump together in an aqueous environment?

The surrounding water molecules gain entropy

What is the isoelectric point?

The pH where the net charge of a protein equals 0

How can the pI of a protein be determined experimentally?

Isoelectric focusing

What is electrophoresis?

Using a positive charge to pull proteins across a gel

What is Western Blotting?

radioactive antibodies are used to visualize the proteins on a gel

What is the difference between Native Page and SDS Page?

SDS denatures proteins so that they run based on molecular weight alone