Knowledge Checks 1-9

A hydrogen bond forms when a partially positive hydrogen is attracted to a lone pair on another atom. The atom containing the lone pair is called the H-bond _____

acceptor

Which statement best explains why noncovalent interactions are useful in biological systems?

Option A

They are stronger than covalent bonds

Option B

They cannot be broken once formed

Option C

They can form and break as needed

Option D

They require metals to form

C

A carbon-carbon single bond and a carbon-carbon double bond have similar atoms involved, yet they behave differently.

Which statement best explains this difference?

Option A

Double bonds restrict rotation because of pi-bond overlap.

Option B

Single bonds are formed by complete electron transfer

Option C

Double bonds contain fewer electrons than single bonds.

Option D

Single bonds produce ionic interactions.

A

Which statement best describes why hydrophobic molecules tend to aggregate in water?

Option A

Water molecules donate electrons to nonpolar groups

Option B

Water becomes more ordered around isolated nonpolar surfaces

Option C

The nonpolar molecules form hydrogen bonds with water

Option D

The nonpolar molecules become charged in water

B

A bond between carbon and hydrogen is generally considered nonpolar because:

Option A

The bond contains a pi bond

Option B

Carbon and hydrogen completely transfer electrons

Option C

Carbon and hydrogen have similar electronegativities

Option D

Hydrogen is more electronegative than carbon

C

A molecule contains both a charged phosphate group and a long hydrocarbon chain.

How would this molecule be classified?

Option A

Hydrophilic

Option B

Amphipathic

Option C

Nonpolar

Option D

Hydrophobic

B

A water molecule can participate in up to four hydrogen bonds because it:

Option A

Contains four covalent bonds

Option B

Contains two ionic bonds

Option C

Contains four atoms

Option D

Contains a hydrogen-bond donor and acceptor

D

Because of its bent geometry, water possesses a net molecular _____

Dipole

Match the observations with the most likely explanation:

1. Ice Floats on Water

2. A nonpolar molecule dissolved poorly in water

3. Nonpolar groups cluster together in solution

A. Water cannot form favorable interactions with nonpolar surface

B. entropy increases

C. Water forms an open crystal lattice

1C

2A

3B

Water is a liquid at room temperature, whereas similar hydrides such as H₂S and NH₃ are gases.

What is the best explanation for this difference?

Option A

Water forms an extensive network of hydrogen bonds

Correct answer

Option B

Water contains more covalent bonds

Option C

Water contains heavier atoms than H₂S and NH₃

Option D

Water has a lower molecular weight

A

10.0 mL of 0.10 M HCl is diluted to a final volume of 100.0 mL.

What is the pH of the resulting solution?

2.0

A solution contains a weak acid with pKa = 4.8.

The acid concentration is 0.50 mM and the conjugate base concentration is 5.0 mM.

What is the pH?

5.8

A weak acid has a pKa of 6.2.

The concentrations of acid and conjugate base are equal.

What is the pH?

6.2

Which solution would have a pH exactly one unit above its pKa?

Option A

[Base] = 100[Acid]

Option B

[Base] = 10[Acid]

Correct answer

Option C

[Base] = [Acid]

Option D

[Base] = 2[Acid]

B

(Select any that apply)

Which form of an acid with a pKa= 4.7 would predominate at pH=8?

Option A

the ionized form would predominate.

Option B

the deprotonated form would predominate.

Option C

the unionized form would predominate.

Option D

the protonated form would predominate.

Option E

the cation would predominate.

Option F

the anion would predominate.

Option G

the ionized and unionized forms would be equal.

ABF

What is the form of this amino acid when it exists at ph=1?

ph at 1 is positive: look for answer with positive h3n and cooh

An amio acid has pKa values of 2.34 and 9.60.

What is its isoelectric point (pI)?

5.97

Select Any That Apply

Due to its side chain, this amino acid can be classified as ______________.

A. nonpolar

Option B

aliphatic

Option C

aromatic

Option D

polar

Option E

basic

Option F

acidic

AB

The one letter code for this amino acid is ______________.

P (for proline)

Match the amino acid to the MOST likely description.

1. Proline

2. Lysine

3. Tyrosine

4. Leucine

A. Frequently participates in interactions with the negative phosphate backbone of DNA

B. Often detected by absorbance near 280 nm

C. Commonly found in turns or kinks because of restricted backbone flexibility

D. Frequently buried in protein interiors due to hydrophobic side chain

1C

2A

3B

4D

Which area of the Ramachandran plot represents the allowed psi and phi angles for the most stable form of alpha helices?

C

Which statement correctly describes the primary structure represented by W-H-P-Y?

Trp-His-Pro-Tyr

Which one letter code corresponds to the amino acid at the C- terminal end of this tetrapeptide?

Q

If a peptide has the sequence: Leu-Gly-Tyr-Val

How many peptide bonds are present?

3

The primary sequence of this tetrapeptide is?

Cys-Leu-His-Thr

A researcher replaces a glycine residue in a β-turn with proline.

Why might this substitution be tolerated better in a β-turn than in an α-helix?

Option A

Proline readily donates hydrogen bonds in helices.

Option B

Proline often occurs in turns and can introduce changes in chain direction.

Option C

Proline forms disulfide bonds that stabilize turns.

Option D

Proline stabilizes β-sheets through aromatic interactions.

B

Which secondary structural element is shown by arrow #4?

beta strand

Which interaction is responsible for maintaining the level of protein structure shown here?

Option A

Backbone hydrogen bonds that stabilize α-helices and β-sheets

Option B

Covalent bonds between amino acids and water

Option C

Peptide bonds within a single amino acid sequence

Option D

Interactions between folded polypeptide chains

D

A folded protein is exposed to high concentrations of urea and loses its native three-dimensional structure.

This process is called:

denaturation

The Ramachandran plot below shows four regions labeled A-D. Match each region with the structural feature most commonly associated with that region.

Region A

Region B

Region C

Region D

1. Beta strand/sheet

2. Right-handed alpha helix

3. Left-handed alpha helix

4. Allowed but uncommon conformations often occupied by glycine

A1

B4

C2

D3

A formulation scientist discovers that a protein-based cosmetic ingredient gradually develops visible particles and loses activity during storage, even though no peptide bond cleavage is detected.

What is the most likely explanation?

Option A

Glycation of lysine side chains

Option B

 Oxidation of aromatic amino acids

Option C

Protein aggregation

Option D

Deamidation of asparagine residues

C

A drug discovery team is evaluating the shelf-life of a protein therapeutic. After several months of storage, the biologic exhibits reduced activity and altered structural properties. Further analysis shows that multiple asparagine side chains have been chemically modified.

Option A

Phosphorylation

Option B

Acetylation

Option C

Ubiquitination

Option D

Deamidation

D

A patient with poorly controlled diabetes develops progressive neuropathy and retinopathy. Researchers suspect that long-term protein damage is contributing to these complications.

Which process is most directly linked to the protein damage?

Option A

Proteolytic degradation of proteins

Option B

Reaction of glucose with amino groups on proteins

Option C

Ubiquitin-mediated protein turnover

Option D

Addition of phosphate groups to proteins

B

A structural biologist needs to determine the structure of a 500-kDa protein complex containing multiple membrane proteins.

Which technique would be the most appropriate starting point?

Option A

Mass spectrometry

Option B

X-ray crystallography

Option C

NMR

Option D

Cryo-electron microscopy

D

A researcher wants to study how a small protein moves and changes shape while dissolved in solution.

Which technique would be most appropriate?

Option A

X-ray crystallography

Option B

NMR

Option C

Cryo-electron microscopy

Option D

Mass spectrometry

B

Match each with correct option

1. ATP binds myosin

2. ATP Hydrolysis

3. Pi releases

4. ADP releases

A. Myosin head becomes cocked

B. Strong actin binding occurs and force generation begins

C. Actin released from myosin

D. Occurs after completion of power stroke

1C

2A

3B

4D

A drug discovery teams wants to inhibit force generation by preventing the conformational change that occurs after ATP Hydrolysis. Which step of the contraction cycle would be most directly affected?

a. exposure of the actin-binding site

b. cocking of the myosin head

c. assembly of actin filaments

d. binding of calcium to troponin c

B

Calcium initiates contraction by binding to ____

Troponin C

A patient accidently ingests a toxin that prevents release of intracellular calcium in skeletal muscle. Which is mostly likely to occur?

a. enhanced power strong generation

b. reduced muscle contraction

c. increased ATPase activity

d. continuous muscle contraction

B

Match each with its description

1. Sarcomere

2. Myofibril

3. Thick filaments

4. Thin filaments

A. composed of actin

B. composed of myosin

C. Thread like structure that runs length of muscle fiber

D. Repeating contractile unite extending from z-line to z-line

1D

2C

3B

4A