1/172
Name | Mastery | Learn | Test | Matching | Spaced |
---|
No study sessions yet.
with gel electrophoresis, which side has the anode, and which side has the cathode
anode is to the right, cathode is to the left
hydrophobic effects drives what level of protein structure formation?
tertiary structure
if pH>pI, does the protein gain (-) or lose (-) electrons?
loses protons, becomes deprotonated
if pH<pI, does the protein gain (-) or lose (-) electrons?
gains protons, becomes protonated
what is pI?
pH when protein’s charge is neutral
are integrated membrane proteins hydrophobic or hydrophilic?
hydrophobic
does phosphorylation cause a molecule to become more positive or negative?
more negative
does dephosphorylation cause a molecule to become more positive or negative?
more positive
are D- or L- amino acids more uncommon in nature?
D-amino acids
are D- or L- amino acids more recognized by proteases?
L-amino acids
do enantiomers have the same charge?
yes
amino acids with thiols (-SH) and hydroxyls (-OH) act as _____ in biological reactions
nucleophiles
when amino acids with thiols and hydroxyls are deprotonated, it _______ their nucleophilicity
betters
what is salt bridging?
when elements of H-bonding and ionic bonding are combined (occurs between oppositely charged molecules); leads to electrostatic interactions
between which amino acids does salt bridging occur?
aspartic acid or glutamic acid, and lysine or arginine
what are proteases?
enzyme that catalyzes hydrolysis of peptide bonds in polypeptide chains
why are proteases’ movement limited?
since the double bond can switch positions (between O and N)
what are G proteins?
signaling proteins in cells that are switched “on” a when they bind to GTP, and “off” after GTP is hydrolyzed (GTP—>GDP, where bonds are broken)
is glycine chiral or achiral?
achiral
is cysteine chiral or achiral?
chiral
does cysteine have (S)- or (R)- configuration?
(R)-configuration
is cysteine a D- or L- amino acid?
L-amino acid
when pH>pka, _____ form decreases, and _____ form increases
protonated, deprotonated
when pH<pka, _____ form decreases, and _____ form increases
deprotonated, protonated
why does tryptophan like fluorescence?
because of its conjugation
why is proline unique?
because it possesses a secondary amino (imine) group, which can help position neighboring atoms
which two amino acids are exclusively found at beta turns?
proline and glycine (other a.a’s are found at a-helices)
if it’s a hydrophilic molecule (i.e. peptide hormones), does it require a second messenger?
yes
if it’s a hydrophobic molecule (i.e. steroids), does it require a second messenger?
no
what does in vivo mean?
conducted in a living organism
what does in vitro mean?
conducted in a lab
what is a voltage-gated ion channel?
a channel that activates upon a change in membrane potential; usually caused by another ion channel
(forming) peptide bonds are thermodynamically _____ and kinetically _____
unstable (because it requires GTP hydrolysis/energy input), stable (because it has a high activation energy, meaning it’ a slow reaction)
which proteins migrate the fastest/slowest in SDS-PAGE?
smaller proteins migrate fastest, larger proteins migrate slowest
which proteins migrate the fastest/slowest in size exclusion chromatography?
larger proteins migrate fastest, smaller proteins migrate slowest
what do reducing agents do in SDS-PAGE/size exclusion chromatography?
break the bonds in between dimers, etc.
what is Western blot?
a protein separation and identification technique by using antibodies to detect specific proteins
what are the steps of Western blot?
protein electrophoresis: separates proteins based on size
protein transfer: transferred from gel —> membrane (blotting)
addition of blocking protein from milk/BSA: prevents non-specific binding of antibodies to membrane
addition of primary antibodies: specifically binds to protein of interest
addition of secondary antibodies: binds to primary antibody and is labeled with a marker for visualization
visualization: using fluorescence/chemiluminescence/autoradiography to visualize; shows up as a band on membrane
antibodies participate in _____ interactions
noncovalent protein-protein interactions
alpha helices are stabilized by _____
hydrogen bonds (like secondary structures)
what is affinity chromatography?
it allows protein to bind while other contaminants are wiped away; takes of advantages of specific protein-ligand interactions
how do you elite proteins gently in affinity chromatography?
use a structure found in the “tag” attached to the protein (basically one that is similar)
how do you gently elude proteins in an ion-exchange chromatography?
use a sodium chloride gradient
what does SDS do?
acts as a denaturing, disrupting protein interactions (like some organic solvents)
what is positive cooperativity?
when subsequent ligands bind with stronger affinity than the 1st; seen with sigmodial curves
what does ion-exchange chromatography do?
separates molecule by charge
what does a cation-exchange column do?
binds cations (+, pH<7)
what does an anion-exchange column do?
binds anions (-, pH>7)
what is an epitope?
a specific region within a protein where an antibody binds; can have amino acids that are close or far apart in primary structures
where are the most common phosphorylation sites?
serine, threonine, and tyrosine (usually at hydroxyls groups)
what is a common site for glycosylation?
asparagine
what is a common site for ubiquitination?
lysine
what type of structure only exist for multimetric proteins (where there are multiple polypeptide chains)?
quaternary structures
what amino acid groups are oxidized to form disulfide bonds and stabilize the protein?
cysteine thiol groups
protein bind hydrolysis is _____ and doesn’t need _____
spontaneous, GTP
quaternary structure proteins binds DNA at a _____ temperature, and blocks _____
lower, transcription
does tertiary structure proteins bind at a lower temperature or higher temperature?
also at a lower temperature, but transcription can still occur
how are tertiary structures stabilized?
by noncovalent interactions between side chains
ternary structures (3-part proteins) can form two ways:
a specific order or randomly
with native PAGE, protein structure is ______ and binding interactions _____ occur
preserved, can
with SDS-PAGE, protein structure is ______ and binding interactions _____ occur
denatured, can’t
what are cofactors?
non-amino acid groups used by proteins. they can be organic (coenzyme)/inorganic, and can bind tightly/loosely
what are prosthetic groups?
tightly bound cofactors
the function of a protein is determined by its _____
3D form
side chains interact through _____
electrostatic interactions; similar charges repel, different charges attract
disulfide bond formation is an _____ reaction
oxidation
the more disulfide bonds formed, the more _____ that occurs
dimerization
with high Gibbs free energy, a _____ is applied on the membrane
saturating agonist
with low Gibbs free energy, a _____ is applied on the membrane
spontaneous closing
what is a heterotetramer?
consists of 4 polypeptide subunits whose quaternary structure is mostly held together by noncovalent interactions; subunits are usually different sizes
what is a homotetramer?
same as a heterotetramer, but with subunits of the same sizes
_____, _____, and _____ usually act as nucleophiles
hydroxyls, thiols, amines
how do you find the number of possible combos for a peptide?
using a factorial (i.e. 3!)
what is precision?
same results multiple times
what is accuracy?
how close you are to a recorded/expected value
the right side of a NMR graph is _____
shielded
the left side of a NMR graph is _____
deshielded
Hill coefficient > 1 means…
positive cooperativity (sigmodial graph)
Hill coefficient < 1 means…
negative cooperativity (sigmodial graph)
Hill coefficient = 1 means…
noncooperativity (hyperbolic graph)
the urea cycle is powered by _____ and _____
deamination, deamidation
what is deamination?
where the nitrogen removed from amino acid backbone
what is deamidation?
where ammonia is released from amides, found in glutamine and asparagine
what is a haloprotein?
correctly folded protein that contains all cofactors
what is an apoprotein?
correctly folded protein that doesn’t contain all cofactors
describe a heme structure
a porphyrin ring with a central iron atom
hydrophobic interactions play a big role in _____
protein folding
when it’s a -deltaG, kd is _____ than 1
greater
when it’s a +deltaG, kd is _____ than 1
less than 1, but greater than 0
what is an allosteric effector?
they bind to proteins at one site and cause a conformation change at another
chiral amino acids rotate _____
plane-polarized light (every a.a. but glycine)
what are the amino acids with alkyl side chain groups?
alanine, proline, leucine, isoleucine, and valine
which amino acids have branched alkyl side chain groups?
leucine, isoleucine, and valine
nucleophiles are an electron _____ species and _____ an electron pair to form a chemical bond
rich, donates
electrophiles are an electron _____ species and _____ an electron pair to form a chemical bond
deficient, accepts
in the RHR, your thumb is the
magnetic force (F)
in the RHR, the index finger is
the moving charge (v)
in the RHR, your middle finger is
the magnetic field line (B)
if the magnetic field points into the page, z is
negative, and exerts an opposite force on the protons
if the magnetic field points out of the page, z is
positive, and exerts an opposite force on the protons