A polypeptide of unknown sequence was digested with staphylococcal protease in bicarbonate buffer (pH 10), and separately with chymotrypsin. Based on these results, what is the sequence of this polypeptide?

1. Staphylococcal protease digest (pH 10):

-GNFLIME

-TD

-DKAYE

2. Chymotrypsin digest:

-LIMETD

-DKAY

-EGNF

DKAYEGNFLIMETD

In which of the following techniques is the protein denatured?

2-D Gel Electrophoresis

What result would you expect, for the polypeptide, PRKLPR, treated with carboxypeptidase A?

A)PRK + LPR

B) PRKL + PR

C) P+ RKLPR

D) PRKLP + R

E) none

E) none

Which amino acid has a side chain that forms a covalent bond with its own α-amino group, creating a ring structure?

P, proline

Which of these following tripeptides is most positively charged at pH 4?

A)Tyr-Ser-Thr

B) Asn-His-Met

C)Tyr-Cys-Ala

D)Gly-Glu-Gln

E) Thr-Trp-Phe

B) Asn-His-Met

How does fetal hemoglobin (Hb-F) ensure the fetus gets oxygen from the adult's hemoglobin (Hb-A)?

Hb-F has a higher affinity for oxygen due to the replacement of β with γ subunits, resulting in reduced BPG binding.

What is the function of iodoacetate (IOAc)?

To prevent disulfide bonds from reforming

Which of the following forces best describes stabilization of a protein's quaternary structure?

Burial of non-polar sidechains between subunits

Which of the following best describes protein folding inside a cell?

A) Protein folding is driven by primary structure and may be assisted by molecular chaperones

B) Protein folding depends only on hydrogen bonding

C) Protein folding depends only on side-chain interactions

D) Proteins fold randomly until they reach their native structure

E) Proteins remain unfolded until they form quaternary structures

A) Protein folding is driven by primary structure and may be assisted by molecular chaperones

Which cleavage reagent could have produced the peptide INWARD as an internal fragment?

Note: "Internal" means the last amino acid shown is not the C-terminal amino acid of the full-length polypeptide.

Staphylococcal Protease at pH 7

What key product results from using Edman's reagent?

Amino acid-PTH derivative

All of the following describe the β-sheet, EXCEPT:

A) Amino acid side chains alternate above and below the sheet.

B) β sheets have a pleated, edge-on appearance.

C) Strands align either in parallel or anti-parallel, within a sheet.

D) No exceptions. All of these are true.

E) Parallel β sheets contain as few as two strands.

E) Parallel β sheets contain as few as two strands.

What best describes a protein's tertiary structure?

The overall three-dimensional shape of a single polypeptide chain

All of the following statements describe the amino acid glycine, EXCEPT:

A) Its hydrogen sidechain allows it to pack inside a collagen triple helix.

B) It is not found in alpha helices or beta sheets.

C) It is the only achiral amino acid.

D) It has a pI of 5.5.

E) Its permissive phi and si bond angles make it more flexible.

B) It is not found in alpha helices or beta sheets.

Which of the following correctly matches a scientist with their contribution?

A) Ramachandran: change in free energy accounts for the change in enthalpy and entropy, as a function of temperature.

B) Anfinsen: phi-psi dihedrals of structured proteins fall into clusters of secondary structure.

C) Bohr: a protein's tertiary structure is directed by its primary structure.

D) Levinthal: protein folding must follow a pathway.

E) Gibbs: metabolic CO₂ stabilizes hemoglobin in the T-state.

D) Levinthal: protein folding must follow a pathway.

If the red curve (3) is Hb-A, which of the following indicates cooperative oxygen binding by Hb-F, the fetal hemoglobin?

2

What structural consequence arises from the hydrophobic patch formed by the sickle-cell (Hb-S) mutation?

Hb-S molecules aggregate into insoluble fibers under low oxygen conditions.

How many amino acids make an α-helix 99 Å in length?

66

What was the key conclusion of Anfinsen’s experiment with ribonuclease A?

Protein structure is determined by its amino acid sequence

Which of the following statements is true about the Bohr effect?

A) Hemoglobin binding to oxygen is unaffected by pH

B) Hemoglobin binds oxygen more tightly at lower pH

C) Hemoglobin’s affinity for oxygen increases at higher [H⁺]

D) Myoglobin shows a Bohr effect similar to hemoglobin

E) Hemoglobin releases oxygen more efficiently at lower pH

E) Hemoglobin releases oxygen more efficiently at lower pH

What is the overall charge of histidine at pH 1?

+2

What explains cooperative binding in hemoglobin?

The binding of one oxygen molecule increases the affinity for additional oxygen molecules.

All of the following statements can describe SDS-PAGE, EXCEPT:

A) It uses an electrical current.

B) It does not involve protein denaturation.

C) It is following by Coomassie Brilliant Blue staining to visualize the protein bands.

D) It is an analytical technique.

E) It does not require DTT or β-ME.

B) It does not involve protein denaturation.

Which of the following defines the chirality of naturally occurring amino acids?

A) L configuration, based on glyceraldehyde

B) D configuration, based on glyceraldehyde

C) S configuration, based on glyceraldehyde

D) Naturally occurring amino acids are not chiral.

E) R configuration, based on glyceraldehyde

A) L configuration, based on glyceraldehyde

Which of the following amino acids can form a disulfide linkage?

A) C

B) S

C)Y

D) M

E) M and C

A) C

The oxygen-binding curve of myoglobin is

hyperbolic

What are the amino acid side chains that are always charged at physiological pH?

Glu, Asp, Lys, and Arg

What is the pI for the peptide, LATCH?

7.2

Which amino acid contains a sulfur atom in its side chain?

A) Lys

B) Try

C) Trp

D) Ser

E)Met

E) Met

Consider the schematic of the heterotrimeric protein below, where the dash, "-" indicates an intermolecular disulfide bond.

BO-X

What is/are the products of separation by SDS-PAGE, WITHOUT reducing agent?

B + O-X

Which of the following amino acids contains a non-polar, aromatic side chain?

A) N

B) R

C) S

D) E

E) F

F

Which of the proteins in this table can be purified BEST by anion-exchange chromatography at pH 7.4?

Insulin

Which statement about protein denaturation is true?

A) Denatured proteins lose their primary structure

B) Denatured proteins lose their native function

C) Denaturation breaks peptide bonds

D) Denaturation affects only tertiary and quaternary structures

E) Denaturation is another term for hydrolysis

B) Denatured proteins lose their native function

Can two different amino acids with the same side-chain pKa have different net charges, when the solution pH > side-chain pKa ?

Yes, because one side chain may be neutral when deprotonated, while the other has a negative charge when deprotonated.

What type of secondary structure is most prominent in myoglobin?

α-helices

What bond is primarily responsible for the primary structure of a protein?

peptide bonds

The______ sidechain of arginine is______when the solution pH is above its pKa of______.

guanidino, neutral, 12.5

What is the primary role of myoglobin in muscle tissue?

Binding and storage of oxygen in muscle cells

What mutation is responsible for sickle-cell anemia?

Valine instead of glutamate in the β subunit of hemoglobin

What type of secondary structure is characterized by hydrogen bonds forming between the carbonyl oxygen of one amino acid and the amide hydrogen of another amino acid four residues away?

α-helix

All of the following statements describe the peptide bond, EXCEPT:

A) The correct order for atoms in the peptide bond plane is C_α1, CO, NH, C_α2.

B) Peptide bonds are formed from a condensation reaction between two amino acids.

C) The partial charges of the amide NH and carbonyl O allow for hydrogen bonds within the polypeptide backbone.

D) The rigid peptide bond plane allows for no rotation of the side chains.

E) The peptide bond stays in a trans configuration due to its partial double-bond character.

D) The rigid peptide bond plane allows for no rotation of the side chains.

Which two amino acids act as helix breakers due to their ϕ and ψ angle flexibility?

Proline and Glycine

Which molecule stabilizes the T state of hemoglobin, reducing its affinity for oxygen?

2,3-bisphosphoglycerate

Which state of hemoglobin has a higher affinity for oxygen?

R (relaxed) state

Which of the following amino acids is most likely to be found in a protein’s interior, away from water?

A) K

B) R

C) V

D) E

E) S

C) V

What is the main characteristic of fibrous proteins?

Serve structural roles in cells and tissues

How does the coiled-coil structure in viral spike proteins facilitate fusion with host cells?

By undergoing a conformational change that brings viral and host membranes closer

Which of the following sequences could be found in α-keratin?

A) LMIWAFMVLFIIVILMFWAALIVALW

B) GPPGPPGPPGPPGPPGPPGPP

C) VSKINRSMKQFHEDVEELKNR

D) YSTDQRHDYSTDQRHDYSTDQRHD

E) GSGAGSGSGAGAGSGAGSGAGSGA

C) VSKINRSMKQFHEDVEELKNR

In affinity chromatography of a mixture of 3 proteins, the protein with no affinity for the ligand elutes ____, low K_d for the ligand elutes _____, and high K_d for the ligand elutes ____.

first; last; second

Which of the following functional groups is common to all standard amino acids?

A) Phosphate

B) Sulfhydryl

C) Amide

D) Carboxyl

E) Methyl

D) Carboxyl