quiz 2 Flashcards
what does protein do
perform biochemical functions
catalyzed biochemical reactions
define protein
workhorse of life
made of amino acids by peptide bonds
how many amino acids are ionize
7
what groups make up an amino acid
amino group, carboxyl group, hydrogen, side chain
which amino acid is not chiral
glycine
which aminos are negative at pH 7
asp and glu
which aminos are positive at pH7
lys, arg, leu, asn, gln
which aminos are hydrophilic
ser, thr, cys
which aminos are hydrophobic
gly, ala, pro, val, leu, ile, met
which aminos are aromatic
phe, tyr, trp
name this amino
glycine
gly
g
name this amino
alanine
ala
a
name this amino
valine
val
v
name this amino
leucine
leu
L
name this amino
isoleucine
ile
I
name this amino
proline
pro
p
name this amino
methionine
met
m
name this amino
phenylalanine
phe
F
name this amino
tryptophan
trp
w
name this amino
tyrosine
tyr
Y
name this amino
serine
ser
s
name this amino
threonine
thr
T
name this amino
cysteine
cys
C
name this amino
aspartic acid
asp
D
name this amino
glutamic acid
glu
E
name this amino
asparagine
asn
n
name this amino
glutamine
gln
Q
name this amino
histadine
his
h
name this amino
histadine
his
h
name this amino
lysine
lys
k
name this amino
arginine
arg
R
describe primary structure
amino acid sequence
describe secondary structure
3D arrangements of polypeptide backbone
describe tertiary structure
folding and arrangement of secondary structures
describe quarternary structure
3D arrangement of separate polypeptide chains
what can primary structure be broken into
protease or peptidase
define residue
individual aminos in peptide chain
describe the 4 steps of enzyme catalysts
enzyme is available and empty
substrate binds to enzyme
substrate converts to product
products are released
define net charge
overall charge, depends on pH
define isoelectric point (pI)
average pH where molecule has no electric charge
define zwitterion
electroneutral molecule containing positive and negative charge
what is the equation of pI
(pKa1+pKa2)/2
what are the 7 ionizable groups
asp
glu
his
cys
tyr
lys
arg
describe proteins
flexible
noncovalent
always in motion
conformational changes
what are primary structures stabilized by
covalent bonds
what are the 3 secondary structures
a-helix
B-sheet
B-turn
describe a-helix
right-handed
3.6 residues per turn
contain n to n+4 H bonds
what are the side chain effects
interacts together
3-4 residues away
can be charged
bulkiness can cause steric hindrance
what is the helix breaker
proline
what makes a bad helix
glycine
helix has a…
overall dipole movement
what are amphiphatic helices used for
gating and fat hydrolysis
describe B-strand
extended polypeptide
side chain above and below backbone
an arrow pointing to C-term
describe B-sheet
side by side strands with H bonding
backbone is made of of N,H,O
can be parallel or antiparallel
describe B-turn
2 adjacent segments of antiparallel B-sheets
4 residues long
what allows for secondary structure to be possible
phi and psi rotation
what makes up phi
C’, N, Ca, C’
what makes up psi
N, Ca, C’, N
what are the factors of phi and psi
steric interference
H-bonding is maximized
with side chains, the phi angle of proline locks in
define rhamachandran plots
plots all phi and psi in a protein
what are the two main types of tertiary structures
globular
fibrous
describe globular proteins
spherical
soluble in H2O
hydrophobic core hydrophilic exterior
describe fibrous proteins
rod-shaped
insoluble in H2O
define domain
separate structural units of a protein
define desaturation
unfolding a protein
define renaturation
refolding a proteim
define disulfide
2 cysteine residues that interact after oxidation
a type of cross linking
what do enzymes do
catalyze rxns by lowering activation energy and increasing the rate of product formation
what do structural proteins do
maintains cell structure and allows it to change shape
forms polymers
what are examples of structural protein
actin
tubulin
collagen
what do cell signaling proteins do
transmit signals
describe nuclear receptors
regulate gene expression in response to ligand bonding
describe intracellular signaling proteins
molecular formation changes due to incoming signals
describe genomic caretaker proteins
maintain accessibility to genomic information
DNA repair, replication, recombination, and gene expression
describe transport protein
move molecules within and between cells
in plasma membrane
permit polar and charged molecules to pass
describe passive transport
energy independent
down the concentration gradient
describe active transport
requires energy (from ATP hydrolysis and ionic gradient)
up the concentration gradient
