uworld mistakes

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?

1. protein electrophoresis: separates proteins based on size

2. protein transfer: transferred from gel —> membrane (blotting)

3. addition of blocking protein from milk/BSA: prevents non-specific binding of antibodies to membrane

4. addition of primary antibodies: specifically binds to protein of interest

5. addition of secondary antibodies: binds to primary antibody and is labeled with a marker for visualization

6. 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