Biochemistry Unit 2

Which portion of the amino acid below is likely to engage in a hydrogen bond with an oxygen in the carboxyl group of another amino acid as part of a beta pleated sheet?

A

Choose the answer that correctly labels the amino group, the carboxyl group, and the variable group on the amino acid from the image:

A - variable group B - amino group C - carboxyl group

Diabetic ketoacidosis can lower blood pH, which affects the structure of important proteins like hemoglobin. For the following interactions shown in the image, which pairs are most likely to be disrupted by a change in pH?

A and B

Which change would most likely result in a permanent modification of an expressed protein's function?

A mutation of a gene for a protein that leads to the substitution of a nonpolar amino acid with a charged amino acid

An increase in beta-pleated sheet structure in some brain proteins can lead to an increase in amyloid deposit formation, characteristic of some neurodegenerative diseases. What is the primary biochemical process that follows the increase in beta-pleated sheet structure that leads to the development of the amyloid deposits?

Aggregation of the proteins in the brain

Which portion of the amino acid is inside the box?

Alpha carbon

When Estrogen binds to the binding pocket of the Estrogen Receptor, it is stabilized by hydrogen bonds. Which amino acids listed could stabilize the interaction with Estrogen in the binding pocket of the Estrogen Receptor?

Amino acid 13

Which of the following best describes the nature of protein primary structure?

Amino acids linked together in a specific order by peptide bonds

Primary structure consists of the order of ______ in a protein. These are held together with _______ bonds that are formed by a ________ reaction.

Amino acids, peptide, dehydration

In order to fulfill their function, proteins must fold in proper, three-dimensional conformations. Which one of the following molecules, available in a cell, is likely to help a protein fold properly?

Chaperone

The amino acid at position 150 (not shown) helps to stabilize the protein by forming disulfide bonds. What amino acid is likely located at position 150? Could this amino acid form a disulfide bond with any of the amino acids in the provided sequence above?

Cysteine is at position 150. No, there are no amino acids shown that can form a disulfide bond.

Glutamine at position 16 forms an important interaction with Serine in a different location in the protein. How would the protein structure be affected if the Glutamine in position 16 were mutated to Leucine? Would this increase or decrease the stability of the protein?

Decrease. Glutamine and Serine formed a hydrogen bonding that stabilized the protein structure before the mutation. Serine and Leucine do not interact.

A toddler mistakenly swallows a bathroom cleaning solution, containing a strong reducing agent. Which interaction is most likely to be disrupted within a glycoprotein in the lining of the toddlerʼs esophagus?

Disulfide bond

Which bond or interaction can the R group of this amino acid form to stabilize tertiary structure?

Disulfide bond

True or False: This amino acid would prefer to interact with oil over water.

False

Which kind of interaction can the following pair of amino acids form between their side chains (R-groups)?

Hydrogen bond

Which force is most influential in determining the secondary structure of a protein?

Hydrogen bonding

Which type of bonding or interaction is correctly paired with a chemical or change in environment that will disrupt/break the interaction or bond?

Hydrogen bonds/ionic bonds: Change in pH

What type of reaction breaks peptide bonds apart?

Hydrolysis reaction

Alzheimer disease is caused by aggregation of the Amyloid beta peptide and tangle formation by the tau protein. What kinds of amino acids are likely to drive the formation of these protein aggregates?

Hydrophilic

Given the following amino acid structure, what is the strongest intermolecular force it would participate in to stabilize a protein structure?

Hydrophobic interaction

The two amino acids are part of the myosin protein. What interaction can these amino acids form, and where are they likely to be located in the protein?

Hydrophobic interaction, the core of the protein

A patient presents with a fever of 110°F. Which interaction(s) would be disrupted within a neuronal protein if the fever is not resolved quickly?

Hydrophobic interactions

As a piece of bacon is heated in a skillet on the stove, you observe that the appearance of the bacon changes. You may even notice that the bacon becomes crispy if left in the skillet. What types of bonds or interactions in proteins are susceptible to temperature changes?

Hydrophobic interactions

Which of the following forces can lead to aggregation as a result of protein misfolding?

Hydrophobic interactions

As a piece of bacon is heated in a skillet on the stove, you observe that the appearance of the bacon changes. You may even notice that the bacon becomes crispy if left in the skillet. What type of bonds or interactions in proteins are susceptible to temperature changes? Why?

Hydrophobic interactions. As the temperature increases, as it does in the skillet, the atoms in the proteins in bacon begin to move more rapidly. This causes the hydrophobic areas of the protein to become exposed.

A mutation in the beta-hemoglobin gene, which results in the replacement of the amino acid glutamate in position 6 with the amino acid valine, leads to the development of sickle cell anemia. The structures of glutamate and valine are shown below.

If the beta hemoglobin gene in a patient with sickle-cell anemia were to be edited so that the valine in position 6 was replaced with a different amino acid, which replacement for valine would be expected to have the best clinical outcome, in theory, for the patient? (Assume the valine can potentially be replaced with any amino acid other than glutamate.)

A diabetic patient is suffering from ketoacidosis. Which interaction(s) could be disrupted within the patientʼs hemoglobin due to this condition?

Ionic bonds and hydrogen bonds

Which of the following statements about protein structure and stability is true?

Ionic bonds between the side chains of the charged amino acids stabilize the protein structure

Which of the following statements describes the tertiary structure of a protein?

It involves hydrogen bonding between amino acid side chains

Which of the following does not occur when a protein is misfolded?

It loses its primary structure

If all of the Arginine amino acids (positions 2, 5, 8 and 12) in the sequence are mutated to Lysine, would there be a significant effect on the protein's stability?

Lysine: No, not significant. Lysine and Arginine would have all the same interactions.

A mutation in the protein A gene results in a negatively charged amino acid, Glutamate, being replaced with the nonpolar amino acid Leucine. This is an example of a _______mutation that could potentially interrupt ________.

Missense, an ionic bond

Which characteristic correctly describes the amino acid image?

Non-polar

Which of the following interactions can occur between two positively charged amino acids?

None of these

Which of the following interactions involve a covalent bond?

Peptide bond and disulfide bond

Secondary, tertiary, and quaternary levels of protein structure can all be impacted by exposing a protein to which treatment?

Placement of the protein in a solution with a low pH

What category does this amino acid belong to?

Polar, charged

Which level of protein structure is disrupted through the hydrolysis of peptide bonds?

Primary

The negatively charged amino acid, Glutamate, is replaced with the negatively charged amino acid Aspartate. Which level of protein structure is most significantly impacted by this change?

Primary structure

Which level of protein structure is determined by the sequence of amino acids?

Primary structure

Aggregation of proteins is the main reason behind many neurodegenerative diseases. Which one of the following mutations will likely cause a neurodegenerative disease?

Replacing a polar amino acid with a nonpolar amino acid

Which portion of the amino acid is inside the box?

Side chain

Which of the following statements about the different levels of protein structure is true?

The interactions between the side chains of the amino acids make up the teriary level structure of a protein

If lysine is required at position #150 in the peptide chain in order for a protein to properly fold and function, what happens if amino acid #150 is mutated from lysine to leucine?

The protein will not fold properly

True or False: This amino acid is polar.

True