The molecule shown below is primarily ______ because ___________

non-polar; it mostly contains atoms with similar electronegativity properties

Which molecule below is the most hydrophilic (water loving)? Hint: This molecule will be highly polar

Urea

This amino acid below is in the _____ category. It’s R-group has a _____ functional group, which means it will ______ when the pH is extremely low

Polar/amide/not change

hydroxyl

OH

Carboxylic acid

CO2H

Amine

NH2

Methyl

CH3

The primary structure of a protein is determined by the

the identity of the amino acids in the peptide sequence

Which is/are a true statement(s)? Use the figure and the table below for reference
and select all correct answers.
A) The primary amino acid sequence for myoglobin is identical to that of
hemoglobin.
B) hemoglobin is tetrameric and has quaternary structure.
C) myoglobin is monomeric and does not have quaternary structure.
D) The structure of hemoglobin and myoglobin mostly contain beta strands.
E) Hemoglobin binds to a small molecule cofactor, but myoglobin doesn’t.

hemoglobin is tetrameric and has quaternary structure.
myoglobin is monomeric and does not have quaternary structure.

Which of the following statements is TRUE (select all)?
A) Peptide bonds are the only covalent bonds that can link together two amino
acids in proteins.
B) The primary amino acid sequence is always read from carboxy to amino
terminus
C) The sequence of the atoms in the polypeptide backbone varies between
different proteins.
D) The primary amino acid sequence Proline-Alanine-Glycine-
Phenylalanine-Glycine is not likely to occur in an alpha helix

The primary amino acid sequence Proline-Alanine-Glycine-
Phenylalanine-Glycine is not likely to occur in an alpha helix

A peptide bond is stronger than a single covalent bond because it has a partial
double bond character. This means that not only is this bond stronger than a single
bond, but it can also limit the geometry of the molecule because (select one)

The rotation of the bond is limited due to resonance

Which statement correctly describes the bonds that form within a protein? (select all)
A) Primary structure depends on hydrogen bond formation between backbone
atoms.
B) Secondary structure depends on ionic or dipole-dipole interactions between
R-groups.
C) Tertiary structure only forms from non-covalent interactions between R-
groups.
D) Quaternary structure only involves interactions between multiple domains.
E) None of the above

None of the above

Glycine and proline are known as “helix breakers”. Explain why

Both amino acids disrupt the regular hydrogen bonding pattern essential for alpha
helical structure. Glycine’s R group is very small and rotation around the phi and psi
bonds are quite flexible. This flexibility makes it harder for the atoms to “settle” into
the position conducive for H-bond formation. Proline’s R-group is covalently bound
to the imide nitrogen, which means that rotation in the phi-psi bond space is severely
restricted. Consequently, proline is unable to complete the H-bonding chain of the
helix and it will cause a “kink” in the alpha helical structure

Which of the following statements are true about PrPC and/or Prp Sc ? (select one)
A. PrPC and Prp Sc have different primary structures AND tertiary structures.
B. PrPc can spontaneously undergo the conformational change to become PrPsc
C. Prions only infect humans
D. Prp Sc causes cellular damage because it forms aggregates through alpha helical
stacking

PrPc can spontaneously undergo the conformational change to become PrPsc

Protein folding is mostly driven by

hydrophobic effect

Molecular chaperones help the ∆F508 form of CFTR re-fold

False

Which of the following best describes the change in entropy that occurs during protein folding

A. Entropy of both the water and the protein increase.
B. Entropy of the water increases; entropy of the protein decreases.
C. Entropy of the water decreases; entropy of the protein increases.
D. Entropy of both the water and the protein decrease

Entropy of the water increases; entropy of the protein decreases

The K D of Protein A for Ligand B is 300 nM. The KD of Protein C for Ligand D is 10
μM. Which of the following statements are TRUE (select all)?
A. These two dissociation constants cannot be compared.
Week 3 Practice Problems | Biochem 285, FA24 Mearls
B. Protein A binds Ligand B with higher affinity than Protein C binds Ligand D
C. Protein C binds Ligand D with higher affinity than Protein A binds Ligand B
D. When the concentration of Ligand B is 300nM, half the binding sites on Protein A
will be filled.
E. When the concentration of Protein C is 10uM, half of Ligand D will be bound

Protein A binds Ligand B with higher affinity than Protein C binds Ligand D

When the concentration of Ligand B is 300nM, half the binding sites on Protein A will be filled

Explain what characteristics of the protein and its ligand provides specificity of binding (i.e. what dictates the Kd of a protein-protein or protein-ligand interaction?)

The architecture of the bonds, as well as the number of bonds, formed between the atoms on the ligand and the atoms on the amino acids in the binding pocket of the protein

Which types of chemical bonds typically hold the protein and ligand together?

Non-covalent bonds like hydrophobic interactions, van der Waals, hydrogen bonds and
electrostatic (ionic) bonds

A nuclear import peptide sequence can occur anywhere (inside or outside) on a folded
protein, and most often is made up of a string of charged amino acids such as -Lys-Lys-Lys-Arg-
Lys-.

FALSE; It is true that a nuclear import peptide typically has a string of basic amino acids, but
they must be present on the surface of a protein, not anywhere

GEF adds a phosphate to GDP to make GTP

FALSE; GEF triggers the release of GDP from a G-protein to allow GTP to bind in its place.

One of the ways that glycosylation is used in the ER is to mark proteins for sorting to other
cellular compartments

TRUE; the sugar groups that are added during glycosylation are continually modified as the
protein is made in the ER and passed through the endocytic/secretion pathways

Post-translational modifications refer to

The formation of covalent bonds between protein subunits
The addition of branched carbohydrates to a protein

A secreted protein, once translated, will follow which of the following pathways through
the cell?

ER, vesicle, Golgi, vesicle, PM

hydrophobic effect

tendency of nonpolar molecules to clump together in water, while being excluded by water molecules

how to know if amino acid is polar

Side chains contain amide or hydroxyl groups

How to know if amino acid is non polar

Side chains are mostly hydrocarbon

how to know if amino acid is basic

Side chains contain amine functional groups

how to know amino acid is acidic

Side chains contain carboxyl groups

nonpolar amino acids

glycine, alanine, valine, cysteine, proline, leucine, isoleucine, methionine, trypyophan, phenylalnine

polar amino acids

serine, threonine, tyrosine, asparagine, glutamine

basic amino acids

lysine, arginine, histidine

acidic amino acids

aspartic acid, glutamic acid