BCH4024 EXAM 1 | LATEST
2024|2025 UPDATE | QUESTIONS
AND ANSWERS 100% CORRECT
Amino acids favor a-helix - Answer-KHMLACEQ (Katie Has Magic LACE Qtips)
Amino acids favor b-sheet - Answer-IVYFTW (IVY For The Win)
Amino acids favor reverse turn - Answer-SPDNG (SPeeDiNG)
A plot that shows the allowed values of phi and psi for all the amino acid residues in
pyruvate kinase (glycine removed) - Answer-Ramachandran Plot
A _____ is a-helix bundle with a recognizable folding pattern - Answer-motif
4 classes of motifs - Answer-1) all alpha
2) all beta
3) alpha / beta (segments interspersed)
4) alpha + beta (segments segregated)
The exact mech for _________ folding is not know but we know that folding begins at
the ________ - Answer-protein; ribosomes
proteins can unfold (_________) and refold (________). this is proof that amino acid
sequence determines the ____ structure but we cant predict how - Answer-denature;
renature; 3
Folding proteins achieves a more stable conformation which _______ energy cost -
Answer-decreases
Folding proteins gives a negative Detla S which is__________ - Answer-unfavorable
Intramolecular noncovalent interations gives a negative Delta H which is __________ -
Answer-favorable
Polar amino acids (h-bonding) - Answer-STNQ
Charged amino acids (ionic interactions) - Answer-RHKED
Nonpolar amino acids (hydrophobic interactions) - Answer-MILV FAW
,Burying hydrophobic residues in water gives a positive Delta S which is ___________ -
Answer-favorable
van der Waals interactions - Answer-lots have large effect
short distances overlapped dipoles
drives the dense packing of protein
hydrogen bonding - Answer-not a driving force in protein folding
hydrophobic interactions - Answer-major contributor to folding and stability
hydrophobic residues on inside
increase Delta S since water is less ordered in folding
2 cysteines form a ___________ bond to form cystine once a protein is folded - Answer-
disulfide
forming disulfide bonds = - Answer-oxidation
breaking disulfide bonds = - Answer-reduction
models for protein folding 2 types - Answer-1) folding in stages; some 2 structure ---> 3 -
---> final
2) folding in rapid collapse; gives compact state called molten globule then continues to
develop
Molecular __________ help to give the correct path of hydrophobic environment for
folding - Answer-chaperones
2 types of molecular chaperones - Answer-1) Hsp70
2) Chaperonins (dont like to fold)
- GroEL and GroES
- requires energy ATP
Consequence of protein misfolding in genetic disorders and disease - Answer-Prion
neurodegenerative disease (mad cow, Alzheimers, ect)
The function of normal prions (PrPc) is not know but aberrant prions (PrPsc) are _____
- Answer-misfolded which forms amyloid fibrils
Different properties to separate proteins by - Answer-1) solubility
2) size/shape
3) charge (pI)
4) binding properties
Basic process of protein separation - Answer-1) lyse cell to release proteins and
biomolecules into crude extract (2 ways)
, 2) centrifuge to separate (soluble and insoluble)
3) continue to separate (ammonium sulfate precip)
2 ways to lyse a cell - Answer-1) french press - pressure
2) sonicator - sound waves
centrifuged insoluble material forms .... - Answer-a pellet
soluble proteins from centrifuge are called .... - Answer-soluble lysate
(NH2)4SO4^-2 - Answer-ammonium sulfate
low salt concentration means ______ solubility (salting in) - Answer-high
high salt concentrations means ______ solubility (salting out) - Answer-low
Column chromatography basics - Answer-protein solution poured over the stationary
phase followed by a buffer solution
can separate by size/shape, pI, and binding props
effluent collected in fractions
Ion-exchange chromatography - Answer-separation based on charge
column matrix is resin with a charge
usually smaller charges will elute first and large will go last
Other factors for ion-exchange chromatography - Answer-1) net charge of molecule
2) solution pH
3) ionic strength
Cation exchangers (ion chrom) - Answer-resin has neg charge so it binds with cations
(+), which means anions (-) move faster
Anion exchanger (ion chrom) - Answer-resin has pos charge so its binds with anions (-),
which means cations (+) move faster
Size exclusion chromatography (gel filtration) - Answer-separation on size/shape
resin contains pores
a plot of Ve against log MW used to estimate MW unknown proteins
________ proteins get stuck in size exclusion pores - Answer-small
_____ proteins elute faster and at smaller volumes (Ve) - Answer-large
Given a list of proteins with MWs, which one comes first? - Answer-the largest ones
Affinity Chromatography - Answer-separation on binding properties
2024|2025 UPDATE | QUESTIONS
AND ANSWERS 100% CORRECT
Amino acids favor a-helix - Answer-KHMLACEQ (Katie Has Magic LACE Qtips)
Amino acids favor b-sheet - Answer-IVYFTW (IVY For The Win)
Amino acids favor reverse turn - Answer-SPDNG (SPeeDiNG)
A plot that shows the allowed values of phi and psi for all the amino acid residues in
pyruvate kinase (glycine removed) - Answer-Ramachandran Plot
A _____ is a-helix bundle with a recognizable folding pattern - Answer-motif
4 classes of motifs - Answer-1) all alpha
2) all beta
3) alpha / beta (segments interspersed)
4) alpha + beta (segments segregated)
The exact mech for _________ folding is not know but we know that folding begins at
the ________ - Answer-protein; ribosomes
proteins can unfold (_________) and refold (________). this is proof that amino acid
sequence determines the ____ structure but we cant predict how - Answer-denature;
renature; 3
Folding proteins achieves a more stable conformation which _______ energy cost -
Answer-decreases
Folding proteins gives a negative Detla S which is__________ - Answer-unfavorable
Intramolecular noncovalent interations gives a negative Delta H which is __________ -
Answer-favorable
Polar amino acids (h-bonding) - Answer-STNQ
Charged amino acids (ionic interactions) - Answer-RHKED
Nonpolar amino acids (hydrophobic interactions) - Answer-MILV FAW
,Burying hydrophobic residues in water gives a positive Delta S which is ___________ -
Answer-favorable
van der Waals interactions - Answer-lots have large effect
short distances overlapped dipoles
drives the dense packing of protein
hydrogen bonding - Answer-not a driving force in protein folding
hydrophobic interactions - Answer-major contributor to folding and stability
hydrophobic residues on inside
increase Delta S since water is less ordered in folding
2 cysteines form a ___________ bond to form cystine once a protein is folded - Answer-
disulfide
forming disulfide bonds = - Answer-oxidation
breaking disulfide bonds = - Answer-reduction
models for protein folding 2 types - Answer-1) folding in stages; some 2 structure ---> 3 -
---> final
2) folding in rapid collapse; gives compact state called molten globule then continues to
develop
Molecular __________ help to give the correct path of hydrophobic environment for
folding - Answer-chaperones
2 types of molecular chaperones - Answer-1) Hsp70
2) Chaperonins (dont like to fold)
- GroEL and GroES
- requires energy ATP
Consequence of protein misfolding in genetic disorders and disease - Answer-Prion
neurodegenerative disease (mad cow, Alzheimers, ect)
The function of normal prions (PrPc) is not know but aberrant prions (PrPsc) are _____
- Answer-misfolded which forms amyloid fibrils
Different properties to separate proteins by - Answer-1) solubility
2) size/shape
3) charge (pI)
4) binding properties
Basic process of protein separation - Answer-1) lyse cell to release proteins and
biomolecules into crude extract (2 ways)
, 2) centrifuge to separate (soluble and insoluble)
3) continue to separate (ammonium sulfate precip)
2 ways to lyse a cell - Answer-1) french press - pressure
2) sonicator - sound waves
centrifuged insoluble material forms .... - Answer-a pellet
soluble proteins from centrifuge are called .... - Answer-soluble lysate
(NH2)4SO4^-2 - Answer-ammonium sulfate
low salt concentration means ______ solubility (salting in) - Answer-high
high salt concentrations means ______ solubility (salting out) - Answer-low
Column chromatography basics - Answer-protein solution poured over the stationary
phase followed by a buffer solution
can separate by size/shape, pI, and binding props
effluent collected in fractions
Ion-exchange chromatography - Answer-separation based on charge
column matrix is resin with a charge
usually smaller charges will elute first and large will go last
Other factors for ion-exchange chromatography - Answer-1) net charge of molecule
2) solution pH
3) ionic strength
Cation exchangers (ion chrom) - Answer-resin has neg charge so it binds with cations
(+), which means anions (-) move faster
Anion exchanger (ion chrom) - Answer-resin has pos charge so its binds with anions (-),
which means cations (+) move faster
Size exclusion chromatography (gel filtration) - Answer-separation on size/shape
resin contains pores
a plot of Ve against log MW used to estimate MW unknown proteins
________ proteins get stuck in size exclusion pores - Answer-small
_____ proteins elute faster and at smaller volumes (Ve) - Answer-large
Given a list of proteins with MWs, which one comes first? - Answer-the largest ones
Affinity Chromatography - Answer-separation on binding properties
