amino acids and proteins Flashcards
basic structure of amino acids
nh3 group
central carbon
cooh group
hydrogen
all amino acids are
L- amino acids
what kind of organisms have d amino acids
bacteria
which orientation are most amino acids? R/s?
most are S with the exception of cystine
what is the R/S configuration of cysteine
R
aliphatic amino acids
G, A, V, L, I, P
is methionine polar or nonpolar
nonpolar
what is unique about proline?
it disrupts secondary protein stucture and causes proline kinks
which amino acids can be phosphorylated
serine, threonine, tyrosine on their -OH residues
what is unique about histidine?
pka of 6.0 so it acts as a buffer at physiological pH
amide amino acids
glutamine (Q) asparagine (N)
sulfur containing amino acids
cysteine and methionine
which amino acids are achiral
glycine only
peptide bond
hydrolysis reaction that takes the OH group from a COOH and the next H from an NH3 group
proteases
hydration reaction that breaks up primary structure/ breaks the peptide bonds
average protein size
50 kDa
how are proteins assembled in the ribosome
from the N to C terminus
terciary structure
interactions are typically non-covalent and charge driven.
- salt bridges
- disulfide bridges
2- mercatoethanol
a reducing agent that breaks up disulfide bonds
what kind of bond are disulfide bridges
COVALENT
- very strong compared to most tericiary interactions
where does hydrogen bonding occur in secondary structure of proteins
between the COOH anf NH3 residues of the protein backbone
what structure do proteases cleave
primary
what structure do denaturing agents cleave?
2, 3, 4
- not permenent
taq polymerase
a protein that is challenging to denature at high temp and is used in PCR technique
entropy relationship with protein folding
proteins will fold in a way that encourages entropy, so it is considered favorable
- example: why hydrophobic tail is on side of lipid bilayer
zwitterion
ion where one group of amino acid is negative (coo-) and 1 is positive (nh3+)
- so for normal amino acid at physiological ph charge is 0
henderson - hasselbach eqn
pH = pKa + log [A-/HA]
pKa
pH= -log[H+]
pka
point where half of a functional group is positive and half is 0
when pka> pH
not abundant amounts of h+ in solution so functional group is deprotinated
when pka<pH
plentiful h+ in solution and species is protinated
pka1
cooh, around 2.3
pka2
nh3 around 9.5
isoelectric point pI
pH where average charge is 0
isoelectric point for diprotic amino acids
average pka1 and pka2
isolelectric point for triprotic amino acids that are acidic
pka1 + pkar / 2 (two acidic)
isolelectric point for triprotic basic amino acids
pka2 + pkar / 2 (2 basic
flat region of a titration curve
pka and half of species is prot/ deprot
-buffer zone
vertical region of a titration curve
isoelectric point
ph = pka
half equivalence point
equivalence point
isoelectric point = pH
- the middle of the vertical region
where charge is 0
what stabilizes a peptide bond
resonance between c=o bond and makes the bond unable to rotate bc of planar
stecker synthesis
making amino acids from aldehydes via
1. imine
2. add cyanide (form nitrile)
3. hydrolysis to form cooh
imine group
C=N where n has 1 or 2 R groups
nitrile group
c triple bond N
precursor to gabriel synthesis
N-pththalidicmalonic ester “THAD”
- use nitrogen for amine group
- central c and cooh
