Ch 1 Amino acids, peptides, and proteins

no; GABA doesn’t

Do amino acids have to have the amino and carboxyl groups bonded to the same carbon?

proteinogenic amino acids

the collective name for the amino acids that the AAMC will test on; there are 20 of them and they all have their amino groups and carboxyl groups bonded to the same carbon

glycine (it has two hydrogens attached to its alpha carbon)

All amino acids are chiral except for which one?

S (L-amino acids, so the amino group is drawn to the left in a Fischer projection)

All amino acids, except for glycine and cysteine, have what type of absolute configuration?

R

What type of absolute configuration does cysteine have?

L amino acids have the amino group on the left, D amino acids have it on the right

What is the difference between how D and L amino acids are drawn in a Fischer projection?

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline (Great Athletes Very Likely Improve Muscle Power)

What are the amino acids with nonpolar, nonaromatic side chains?

tryptophan, phenylalanine, tyrosine (Why Fight Yoda?)

What are the amino acids with aromatic side chains?

Serine, threonine, asparagine, glutamine, cysteine, thiol (Smart Teachers Need Quick Coffee)

What are the amino acids with polar side chains?

Aspartic acid (aspartate) and glutamic acid (glutamate)

What are the amino acids with negatively charged (acidic) side chains?

lysine, arginine, and histidine (Kings Rule Honorably)

What are the amino acids with positively charged (basic) side chains?

-The ones with long alkyl side chains (alanine, isoleucine, leucine, valine, phenylalanine)

What are the hydrophobic amino acids?

histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine

What are the hydrophilic amino acids?

mutagenesis

the process by which mutations are deliberately introduced into a DNA sequence in order to produce a mutant gene or protein

Example: S46A says that the 46th amino acid in a chain was originally a serine (S), but was mutated to an alanine (A)

What is shorthand to denote a single amino acid mutation?

the carboxylic acid group

What group on the general structure of an amino acid is considered acidic?

the amino group

What group on the generic structure of an amino acid is basic?

protonated

At low pH, do ionizable groups tend to be protonated or deprotonated?

deprotonated

At high pH, do ionizable groups tend to be protonated or deprotonated?

zwitterions

What we call amino acids that have both a negative and positive charge (positive charge on amino, negative charge on carboxyl)

carboxyl

say you are titrating 1 M glycine solution. At low pH, glycine exists as +NH3CH2COOH. When you slowly add NaOH, does it lose the proton on the amino group or the carboxyl group first?

isoelectric point (pI)

When every molecule in an amino acid titration exists as a zwitterion (everything is electrically neutral)

low

Do amino acids with acidic side chains have low or high values for pI?

high

Do amino acids with basic side chains have low or high values for pI?

residues

another name for amino acid subunits

oligopeptides

the name for small peptides, up to about 20 residues

polypeptides

the name for long chains of peptides, past 20 of them

dehydration synthesis

What type of reaction is peptide bond formation?

yes; because of the carbonyl close to it

Does the C-N bond after a peptide bond formation have resonance? Why?

They are drawn in the same order that it is synthesized by ribosomes: from N-terminus to C-terminus

How are peptides drawn in relation to their N and C terminuses?

N-terminus

when a peptide bond forms, the free amino end is known as the ___________

C-terminus

the free carboxyl end of a peptide after peptide bond formation

trypsin and chymotrypsin

What are the two hydrolytic enzymes that facilitate hydrolysis of peptides?

The H goes to the amide nitrogen of one amino acid and the OH goes to the carbonyl carbon of the other

During peptide bond hydrolysis, where does the H go and where does the OH go?

True or False: A single amino acid on its own is considered an oligopeptide

sequencing

a lab technique that determines the primary structure of a protein

keratin (human hair, skin, and fingernails)

What is a classic example of a protein that has alpha helices?

3.6

How many amino acids does one turn of an alpha helix have?

the oxygen atom in the carbonyl of one amino acid and the hydrogen atom next to the nitrogen in another amino acid

Between what atoms does a hydrogen bond form in secondary structure of proteins?

away

Do the R group in alpha helices point away or toward the helix core?

fibroin (silk fibers)

What is a classic example of a protein that uses beta pleated sheets?

NOTE: Review what “turns” are in Chapter 1.4 bc I have no idea it made no sense

fibrous proteins

proteins that look like sheets or long strands

globular proteins

proteins that are spherical

tertiary structure

level of structure that is caused by hydrophilic and hydrophobic interactions between R groups of amino acids

proline’s R group includes a ring, so it introduces kinks in alpha helices and creates turns in beta pleated sheets

What is special about proline’s role in secondary structure?

salt bridge

when an interaction consists of both a hydrogen bond and an ionic bond

disulfide bond

the bond that forms when two cysteine molecules become oxidized to form cystine

molten globules

the intermediate states a protein goes through when molding into its 3D shape

denaturation

when a protein loses its tertiary structure so it thus loses its function

solvation layer

when a solute dissolves in a solvent, the layer that nearby solvent molecules form this around that solute

cooperativity (allosteric effects)

during quaternary structure, when one subunit undergoes a conformational change that either enhances or reduces the activity of other subunits

conjugated proteins

proteins that require a covalently attached molecule (prosthetic group) to function

prosthetic groups

groups attached to conjugated proteins in order for them to function

heme

the name for the prosthetic group on hemoglobin and myoglobin

pyrrole rings

the name for the four rings that are found on the prosthetic group for hemoglobin and myoglobin

lipoproteins

proteins with lipid prosthetic groups

glycoproteins

proteins with carbohydrate prosthetic groups

nucleoproteins

proteins with nucleic acid prosthetic groups

No; they interfere with non-covalent interactions like hydrogen bonds and side chain interactions

When urea and SDS denature proteins, are they interfering with covalent bonds?

melting point (T_m)

When there are equal amounts of folded and unfolded proteins in a denaturation curve caused by temperature

midpoint concentration (C_m)

When there are equal amounts of folded and unfolded proteins in a denaturation curve caused by chemical denaturation