Amino Acids, Peptides, and Proteins Flashcards
Nonpolar, nonaromatic side chains
glycine, alanine, valine, leucine, and isoleucine
methionine (sulfur atom but considered relatively nonpolar)
Chirality of amino acids in eukaryotes ?
L-amino acids (S) absolute configuration;
exception: cysteine –> L amino acid (has R absolute configuration)
Only cyclic, nonpolar, nonaromatic
proline
Aromatic side chains?
tryptophan, phenylalanine, tyrosine
Polar side chains?
Serine, threonine (both have -OH groups), asparagine, glutamine (have amide side chains), cysteine (thiol, -SH)
negatively charged (acidic) side chain
aspartic acid (asparatate) and glutamic acid (glutamate)
positively charged (basic) side chains
lysine, arginine, histidine (has an aromatic ring with two nitrogen atoms/called a imidazole)
hydrophobic amino acids
alanine, isoleucine, leucine, valine, and phenylalanine
hydrophilic amino acids
charged side chains–> positively charged histidine, arginine, and lysine plus negatively charged glutamate and aspartate
alanine
ala, A
arginine
arg, R
asparagine
Asn, N
Aspartic acid
asp, D
Cysteine
cys, C
Glutamic acid
Glu, E
Glutamine
Gln, Q
Glycine
Gly, G
Histidine
His, H
Isoleucine
Ile, I
Leucine
Leu, L
Lysine
Lys, K
Methionine
Met, M
Phenylalanine
Phe, F
Proline
Pro, P
Serine
Ser, S
Threonine
Thr, T
Tryptophan
Trp, W
Tyrosine
Tyr, Y
Valine
Val, V
amphoteric species
can accept a proton or donate a proton
zwitterions
have a positive and negative charge
isoelectric point
where the net charge is 0, pH at which the molecule is electrically neutral
peptide bonds
when an amide bond is formed between the -COO- group of one amino acid and the NH3+ group of another amino acid
What type of reaction is the formation of a peptide bond?
A condensation/dehydration reaction…results in the removal of a water molecule; the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid
How are peptide bonds structured?
From N-terminus to C-terminus, free amino end on the left, carboxyl end on the right
primary structure
linear arrangement of amino acids coded in an organism’s DNA, can be determined by sequencing
secondary structure
local structure of neighboring amino acids, result of hydrogen bonding between nearby amino acids, most common secondary structures are alpha-helices and B-pleated sheets
What is an important component of keratin?
alpha helix, keratin is a fibrous structural protein found in human skin, hair, and fingernails
beta-pleated sheets
can be parallel or antiparallel, fibroin (a primary protein component of silk fibers) is composed of beta-pleated sheets, often see prolines, help turn between beta-pleated sheets
proline’s role in secondary structure
helps form turns in alpha helices or beta sheets, creates a kink
fibrous proteins
collagen, resembles long strands/sheets
globular proteins
globin, tends to be spherical, like a globe
tertiary structure
3-D shape of a protein, mostly determined by hydrophilic and hydrophobic interactions between the R groups of amino acids, have disulfide bonds
what forms disulfide bonds?
two cysteine molecules become oxidized to form cystine, disulfide bonds create loops in the protein chain
What is it called when a protein loses its tertiary structure?
Denaturation, it will lose its function, often irreversible
quaternary structure
not all proteins have quaternary structure, need multiple subunits to have it, hemoglobin and immunoglobulins are classic examples
prosthetic groups
covalently attached molecules
What is true at the pKa
[HA]=[A-]
What does the titration curve look like at the pKa values of the amino acid?
Nearly flat
What does the titration curve look like at the pI of the amino acid?
Nearly vertical
What type of reaction is the breaking of a peptide bond?
A hydrolysis reaction (water is used to break down the bonds of a particular substance)
Hydrophobic interactions
push hydrophobic R groups to the interior of a protein, which increases entropy of the surrounding water molecules to create negative Gibbs free energy
