CHECKS

How many H-bond acceptors does this molecule have?
A- 5
B- 10
C- 4
D- 6

How many H-bond acceptors does this molecule have?
A- 5
B- 10
C- 4
D- 6

A

How many H-bond donors does this molecule have?
A: 3
B: 5
C: 10
D: 4

A

Why do we adjust the thermodynamic equation for reactions that occur in cells?
A: Because few, if any, reactions in biological systems occur under standard conditions
Choice 2 of 5: in standard conditions, all solutes must be present at 1M in concentration, which is not possible in the cellular environment
Choice 3 of 5: cells operate at standard pressure but not standard temperature
Choice 4 of 5: none of the above
Choice 5 of 5: just the top 2 are correct

E

Consider the H-H equation. In this equation, A- represents
A: Conjugate base
Choice 2 of 4: Acid
Choice 3 of 4: buffering region
Choice 4 of 4: ionization activity

A

Consider the H-H equation. In this equation, HA represents
Choice 1 of 4: Conjugate base
Choice 2 of 4: Acid
Choice 3 of 4: buffering region
Choice 4 of 4: ionization activity

B

Consider the H-H equation. Which component represents the proclivity of a substance to gain or lose a H+?
Choice 1 of 4: Conjugate base
Choice 2 of 4: Acid
Choice 3 of 4: buffering region
Choice 4 of 4: pKa

D

The reason the angle on water molecules is not 109.5, is because:
Choice 1 of 4: hydrogen bonds with other water molecules shift the angle to a lesser degree
Choice 2 of 4: lone pairs on the oxygen atoms repel one another and reduce the angle to 104.5 degrees
Choice 3 of 4: lone pairs on the oxygen atoms repel one another and increase the angel by several degrees
Choice 4 of 4: none of the above

B

The shorter the hydrogen bonding distance, the weaker the hydrogen bond
Choice 1 of 2: True
Choice 2 of 2: False

B

Which molecule will form the largest number of Hydrogen bonds with water molecules when resuspended in aqueous buffer?

A

Which 2 statements below represent Flickering water molecules or water molecules in the liquid state:
Choice 1 of 4: water molecules that are reorienting in space ever 10-7 s
Choice 2 of 4: water molecules whose hydrogen bonds break and reform continually over time
Choice 3 of 4: water molecules that are higher in energy because they are rigidly constrained
D: water molecules that are lower in energy because they are rigidly constrained

A, B

Which of the following statements are true of micelles and lipid bilayers:
A As non-polar tail groups become more ordered, entropy of the micelle or bilayer :
B. The overall solvation process is spontaneous because a large increase in entropy occurs when water molecules are less structured around tail groups
C. As non-polar tail groups become more ordered, the entropy of the micelle/bilayer increases
: D. The overall solvation process is spontaneous because a large decrease in entropy occurs when water molecules are less structured around tail groups
E: all of the above
F: only A and B
G: A, B and C

F

All amino acids share what features in common?
A: All possess a central alpha carbon
B: All possess a carboxylic acid attached to the alpha carbon
Choice 3 of 4: All possess an amino function attached to the alpha carbon
Choice 4 of 4: All of the above are common features of the 20 standard amino acids

D

Which group or classification of amino acids contains the largest number of amino acids?
The acidic amino acids
Choice 2 of 4: The basic amino acids
Choice 3 of 4: The aromatic amino acids
Choice 4 of 4: The hydrophobic/nonpolar amino acids

D

Which amino acids are characterized by there ability to absorb ultraviolet light at 280 nm?
Choice 1 of 4: Pro, Thr, and Phe
Choice 2 of 4: Tyr, Pro, and Trp
Choice 3 of 4: Trp, Tyr, Phe
Choice 4 of 4: His, Phe, Thr

C

All amino acids have pK1 values of approximately:
Choice 1 of 3: 2
Choice 2 of 3: 6
C-9

A

All amino acids have pK2 values of approximately:
A- 2
B-6
C-9

C

Which of the amino acids below would have 3 inflection points, corresponding to their 3 titratable groups, in their titration curve?
Choice 1 of 6: His
Choice 2 of 6: Lys
Choice 3 of 6: Glu
Choice 4 of 6: Asp
Choice 5 of 6: Arg
Choice 6 of 6: all of the above have3 titratable groups which would result in 3 inflection points in their titration curves.

F

Which amino acid below can be characterized as "hydrophilic" and "polar uncharged"
Choice 1 of 5: Gly
Choice 2 of 5: Glu
Choice 3 of 5: Thr
Choice 4 of 5: Cys
Choice 5 of 5: Both Thr and Cys can be characterized as "hydrophilic" and "polar uncharged"

E

Peptide bond FORMATION is what type of reaction?
Choice 1 of 3: elimination reaction
Choice 2 of 3: condensation reaction
Choice 3 of 3: electrophilic aromatic substitution reaction

B

Which of the following would have the greatest influence on a peptides net charge?
Choice 1 of 3: pH
Choice 2 of 3: temperature
Choice 3 of 3: H-bonding potential

A

All peptides and single subunit proteins possess:
Choice 1 of 3: 2 distinct N and C termini
Choice 2 of 3: a single N terminus and C terminus
Choice 3 of 3: a variable number of N and C termini depending on the total number of amino acids

B

Free rotation around a peptide bond is described by the torsion or dihedral angles:
Choice 1 of 4: phi and theta
Choice 2 of 4: theta and psi
Choice 3 of 4: phi and psi
Choice 4 of 4: alpha and beta

C

Which characteristic of the peptide bond is primarily responsible for its partial double bond character
Choice 1 of 3: H-bonding capacity
Choice 2 of 3: resonance
Choice 3 of 3: ionization state

B

The lowest free energy state of adjacent alpha carbons connected by a peptide bond is:
Choice 1 of 2: Cis
Choice 2 of 2: Trans

B

Consider the following polypeptide: Ala-Val-Phe-Glu-Tyr How many peptide bonds does it contain?
Choice 1 of 3: 5
Choice 2 of 3: 4
Choice 3 of 3: 6

B

Which of the following forces stabilize protein 3-dimensional structure?
Choice 1 of 6: ionic interactions
Choice 2 of 6: H-bonding
Choice 3 of 6: Van der Waals forces
Choice 4 of 6: metal ions
Choice 5 of 6: disulfide bonds
Choice 6 of 6: all of the above

F

The linear sequence of amino acids in a protein is called:
Choice 1 of 4: primary structure
Choice 2 of 4: secondary structure
Choice 3 of 4: tertiary structure
Choice 4 of 4: quaternary structure

A

alpha helices and beta strands correspond to what level of protein 3-dimensional structure:
Choice 1 of 4: primary structure
Choice 2 of 4: secondary structure
Choice 3 of 4: tertiary structure
Choice 4 of 4: quaternary structure

B

Which of the following would show you the sterically and energetically allowed combinations of torsion/dihedral angles in a protein?
Choice 1 of 3: theta plot
Choice 2 of 3: titration curve
Choice 3 of 3: Ramachandran plot

C

The primary stabilizing force in beta sheets is:
Choice 1 of 3: n and n+4 Hydrogen bonding
Choice 2 of 3: Hydrogen bonding between adjacent R-groups
Choice 3 of 3: H-bonding utilizing component atoms of the polypeptide backbone

C

The two main types of beta strands are:
Choice 1 of 3: antiparallel and parallel
Choice 2 of 3: alpha sheets and beta sheets
Choice 3 of 3: left and right handed helices

A

Beta strands (or beta sheets) and alpha helices possess the same combinations of phi and psi
Choice 1 of 2: Ture
Choice 2 of 2: False

B

Which level of protein structure takes into account the molecular contributions of amino acid R-groups?
Choice 1 of 3: primary
Choice 2 of 3: secondary
Choice 3 of 3: tertiary

C

A heterodimeric protein possesses how many total N and C-termini?
Choice 1 of 3: 1 N-terminus and 1 C-terminus
Choice 2 of 3: 2 N-termini and 2 C-termini
Choice 3 of 3: 3 N-termini and 3 C-termini

B

Which of sequence of amino acids (1-letter code given) would you most likely find on the exterior of a water soluble protein?
Choice 1 of 3: FPWA
Choice 2 of 3: TLGP
Choice 3 of 3: RNED

C

True or False. A fully folded protein in a cell is at a higher energetic level than the unfolded state.
Choice 1 of 3: Unable to tell
Choice 2 of 3: False
Choice 3 of 3: True

B

Anifinsen's experiment demonstrated that:
Choice 1 of 3: protein folding is random
Choice 2 of 3: primary sequence determines higher order protein structures such as alpha helices and tertiary structure
Choice 3 of 3: the order in which you remove BME and Urea has no effect on final protein structue

B

True or False. If a protein possesses 2 or more Cys residues, it must also possess disulfide bonds.
Choice 1 of 2: True
Choice 2 of 2: False

B

Which of the following tends to be an irreversible method of unfolding proteins?
Choice 1 of 3: heat
Choice 2 of 3: pH
Choice 3 of 3: chaeotropic salts such as ammonium sulfate

A

Christian Anfinsen unfolded RNase A by adding Urea and BME. The order in which he removed them was of critical importance. If Anfinsen unfolded RNase A with Urea and BME, then removed BME first and Urea second, what would be the result?
Choice 1 of 3: the protein would refold correctly
Choice 2 of 3: the protein would refold incorrectly due to random disulfide formation
Choice 3 of 3: the protein would refold correctly, but disulfide bond formation would be random

B

A protein with a pI values of 8.9 would be classified as a(n):
Choice 1 of 3: acidic protein
Choice 2 of 3: basic protein
Choice 3 of 3: hydrophobic protein

B

When you are interested in purifying your favorite soluble protein (YFSP) from living cells, after you lyse the cells it is important to:
Choice 1 of 5: A. avoid changes in pH during the purification process
Choice 2 of 5: B. keep the protein containing solution cool/cold to prevent protein degradation or unfolding
Choice 3 of 5: C. match the pH of your lysis and purification buffer to that of the pI of your favorite soluble protein (YFSP)
Choice 4 of 5: answer choices A., B., and C.
Choice 5 of 5: Only choices A. and B.

?

If you wanted to purify a water soluble protein using ion exchange chromatography, what intrinsic property of the protein would be most useful to know when selecting either a cation or anion exchange resin?
Choice 1 of 4: the primary sequence of the protein
Choice 2 of 4: the pI of the protein
Choice 3 of 4: the molecular weight of the protein
Choice 4 of 4: the subunit composition of the protein

B

In gel filtration (size exclusion) chromatography, proteins with high molecular weight would elute from the column ____ proteins with low molecular weight

Choice 1 of 3: before

Choice 2 of 3: after

Choice 3 of 3: could be either before or after depending on the pI of the proteins themselves

A

SDS confers which of the following on all protein molecules
Choice 1 of 4: same charge to mass ration
Choice 2 of 4: a net negative charge independent of the protein's intrinsic pI
Choice 3 of 4: the same overall morphology (roughly linear) independent of what their 3-dimensional structure looks like under cellular conditions
Choice 4 of 4: all of the above

D

In SDS-PAGE, proteins with the lowest molecular weight will have the (fastest or slowest) electrophoretic migration and be found towards the ( top or bottom) of the gel?
Choice 1 of 4: fastest and top
Choice 2 of 4: fastest and bottom
Choice 3 of 4: slowest and top
Choice 4 of 4: slowest and bottom

B

Assume you wanted to purify your favorite protein using cation exchange chromatography at pH 7, which of the resins below would most likely employ? You may want to look up the structures of these resins
Choice 1 of 3: CM (carboxymethyl) resin
Choice 2 of 3: DEAE (diethyl amino ethane) resin
Choice 3 of 3: Sephadex G50 resin

A