Biochemistry Chapter 1: AA, Peptides & Proteins (4 Stars) Flashcards
Amino acids have four groups attached to a central (alpha) carbon: an amino group, a carboxylic acid group, ______, and an R group
hydrogen atom
The R group determines chemistry and ______ of that amino acid.
Function
______ amino acids appear in the proteins of eukaryotic organisms.
20
The stereochemistry of the alpha-carbon is ____ for all chiral amino acids in eukaryotes.
l
d-amino acids can exist in ___________.
prokaryotes.
All chiral amino acids except _____have (S) configuration.
cysteine
All amino acids are chiral except ____,
glycine, which has a hydrogen atom as its R group.
Nonpolar, nonaromatic: 7
glycine, alanine, valine, leucine, isoleucine, methionine, proline
Aromatic: 3
tryptophan, phenylalanine, tyrosine
Polar: 5
serine, threonine, asparagine, glutamine, cysteine
Negatively charged (acidic): 2
aspartate, glutamate
Positively charged (basic): 3
lysine, arginine, histidine
Amino acids with long alkyl chains are _____, and those with charges are ______many others fall somewhere in between
hydrophobic hydrophilic
Amino acids are ______; that is, they can accept or donate protons.
amphoteric
The pKa of a group is the_____ at which half of the species is deprotonated;
pH
At low (acidic) pH, the amino acid is ______.
fully protonated.
At pH near the pI of the amino acid, the amino acid is a _______.
neutral zwitterion.
At high (alkaline) pH, the amino acid is______
fully deprotonated.
The isoelectric point (pI) of an amino acid without a charged side chain can be calculated by averaging the ____# ______ values.
two pKa values.
The titration curve is nearly flat at the _____ values of the amino acid.
pKa
The titration curve is nearly ______ at the pI of the amino acid.
vertical
Amino acids with charged side chains have an additional _____ value, and their pI is calculated by averaging the _____ values that correspond to protonation and deprotonation of the zwitterion.
pKa
Amino acids without charged side chains have a pI around ____
6.
Basic amino acids have a pI well above____.
6
Dipeptides have two amino acid residues; tripeptides have three. Oligopeptides have a _______
few amino acid resides (20).
Forming a _____ bond is a condensation or dehydration reaction (releasing one molecule of water).
peptide
The nucleophilic amino group of one amino acid attacks the electrophilic ______ group of another amino acid.
carbonyl
Amide bonds are rigid because of ______
resonance.
Breaking a peptide bond is a ______ reaction.
hydrolysis
Primary structure is the
linear sequence of amino acids in a peptide and is stabilized by peptide bonds.
Secondary structure is the local structure of neighboring amino acids, and is stabilized by ______ bonding between amino groups and nonadjacent carboxyl groups.
hydrogen
alpha-helices are _____ coils around a central axis.
clockwise
Beta-pleated sheets are rippled strands that can be _____ or _____
parallel or antiparallel.
Proline can interrupt _______ structure because of its rigid cyclic structure.
secondary
Tertiary structure is the three-dimensional shape of a single polypeptide chain, and is stabilized by _______ interactions, acid–base interactions (salt bridges), hydrogen bonding, and disulfide bonds.
hydrophobic
Hydrophobic interactions push hydrophobic R groups to the interior of a protein, which increases _____ of the surrounding water molecules and creates a negative Gibbs free energy.
entropy
Disulfide bonds occur when two cysteine molecules are ______ and create a covalent bond to form cystine.
oxidized
Quaternary structure is the interaction between _____ in proteins that contain multiple subunits.
peptides
