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