Unit 2 Quiz questions

Ionic Bonds and hydrogen bonds -Diabetic ketoacidosis leads to a lower pH than normal. Changes in pH can disrupt both hydrogen bonds and ionic bonds inside of a protein. -Hydrophobic interactions are not affected by changes in pH, but are disrupted by increases in temperature (heating).

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

missense, a disulfide bond -Changing the amino acid sequence is a missense mutation, whereas a nonsense mutation causes a stop codon to be introduced, thus shortening the protein. Additionally, Glutamate is a negatively charged amino acid, which participates in an ionic bond. Cysteine is the only amino acid that can participate in a disulfide bond.

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 ________.

Hydrophobic Interactions -The patient's temperature is much higher than normal. High temperatures disrupt hydrophobic interactions. -Ionic bonds are strong interactions that will not be easily disrupted by heat. Ionic bonds are disrupted by changes in pH and by increasing the concentration of salts in the protein's environment.

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?

Disulfide Bond -Reducing agents disrupt disulfide bonds. -Hydrogen bonds may be disrupted by changes in pH and increased salt concentrations.

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?

Replacing a polar amino acid with a nonpolar amino acid -Protein aggregation is caused by disruptions in hydrophobic interactions. Replacing a polar amino acid with a nonpolar amino acid can lead to aggregation due to the introduction of a nonpolar amino acid.

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

Aggregation of the proteins in the brain -

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?

Positive charged amino acids will be attracted to the negatively charged amino acids. -A negatively charged amino acid would not interact with another negatively charged amino acid.

Antibodies that enable our body to fight bacterial infections must bind to antigens on the surface of the bacterial cell. If the antigen on the surface of the bacterial cell has several negatively charged amino acids, which of the following amino acids would you expect to find on the portion of the antibody that binds to the antigen?

Hydrophobic interactions -Just as protein structure is stabilized primarily by the hydrophobic effect and hydrophobic interactions, disruption of hydrophobic interactions is the simplest way to denature a protein. This is generally done by applying heat. High temperatures cause the atoms in a protein to move so quickly that the structure loosens and causes the hydrophobic core to open up and expose the nonpolar residues to water. -Disulfide bonds are strong interactions that will not be easily disrupted by heat. Disulfide bonds are disrupted by reacting with reducing agents.

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?

A-variable group, B-amino group, C-carboxyl group -A is a variable group and can be any one of 20 different things, B is an amine group that contains one nitrogen and three hydrogens, C is a carbonyl group consisting of one carbon and two oxygens and, D is a hydrogen atom found attached to the central carbon (carbon alpha).

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

'A and B'. Interaction A is showing an ionic bond between a positive and negatively charged amino acid while interaction B is showing a hydrogen bond between two polar, uncharged amino acids. Both ionic and hydrogen bonds can be disrupted by a change in pH.

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?

Hydrophobic interaction -The amino acid pictured only has CH groups in its side chain, and therefore is non-polar. Non-polar amino acids make hydrophobic interactions. -Ionic bonds occur between polar, charged amino acids, specifically between a negatively charged side chain and a positively charged side chain.

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

No, not significant, Lysine and Arginine would have all the same interactions -The side chains of Lysine and Arginine are both long with a positive charge at the end. If Lysine is forming an ionic bond with another amino acid elsewhere in the protein, Arginine would be able to make that same ionic bond. The protein would, therefore, be stable, even with this mutation.

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?

The protein will not fold properly -Changing lysine (positively charged amino acid, forms ionic bonds, is hydrophilic) to leucine (a non-polar amino acid, does not form ionic bonds, is hydrophobic) eliminates one or more important interactions and will prevent the protein from properly folding.

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?

Chaperone -A chaperone functions to help proteins fold into the correct structure. A polymerase is associated with DNA replication or transcription, not protein folding.

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?

Dehydration -Protein primary structure is defined by the order of amino acids that make up the protein. The amino acids are linked together by peptide bonds, which are formed via dehydration reactions.

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

Placement of the protein in a solution with a low pH. -Changes in pH affect hydrogen bonds and ionic bonds. Hydrogen bonds in the backbone of amino acids occur in secondary structure, and both hydrogen bonds and ionic bonds occur in the side chains of amino acids in tertiary structure.

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

Primary structure -The original and substitute amino acid both have a negative charge and can both form an ionic bond with a positively charged amino acid. The amino acid sequence, however, has been altered, and so the primary structure has certainly been changed.

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?

Decrease. Glutamine and Serine formed a hydrogen bonding that stabilized the protein structure before the mutation. Serine and Leucine do not interact -Glutamine and Serine formed a hydrogen bonding that stabilized the protein structure before the mutation. Serine and Leucine do not interact'. GIutamine and serine are both polar, uncharged amino acids that can interact by forming a hydrogen bond. Leucine is a nonpolar amino acid that would participate in hydrophobic interactions. With this mutation, a hydrogen bond would not form and protein stability would decrease.

The student explains how amino acids and proteins interact and affect the human body. 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?

True -The amino acid depicted in this problem is polar/hydrophilic because the end of the amino acid R group has an oxygen bound to a hydrogen. Other polar amino acids can have nitrogen bound to hydrogen, carbons bound to oxygens or carbons bound to nitrogens.

This amino acid is polar.

Polar, charged -The amino acid depicted is charged. There is a COO- group displayed as the R group of this amino acid with a visible charge.

What category does this amino acid belong to?

Hydrolysis Reaction -Peptide bonds are formed by dehydration reactions (named for the loss of water that occurs) and broken via hydrolysis (named for the addition of water). To break this down further, hydro- meaning water, and -lysis meaning cutting, the water cuts the peptide bond. -For an oxidation/reduction, this reaction transfers electrons from one molecule to another.

What type of reaction breaks peptide bonds apart?

Non-polar -Non-polar amino acids have R groups with C-H bonds.

Which characteristic correctly describes the amino acid image?

It involves hydrogen bonding between amino acid side- chains.

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

A -Secondary structures arise from hydrogen bonding between backbone atoms. The H attached to the more electronegative N can form a hydrogen bond to the carboxyl O. The R group is involved in side-chain interactions that determine tertiary structure and are not involved with secondary structure.

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?

*Glutamine is a polar amino acid and the amino acid asparagine is a polar amino acid, which contain C-N, C-O, O-H or N-H bonds on the outside surface of their R groups. The most likely replacement for a polar amino acid that would have less of an impact on protein structure would be another polar amino acid.

A missense mutation resulting in a change from asparagine to leucine at a specific position on an enzyme leads to a neurodegenerative disease. Is there an alternate amino acid substitution of a missense mutation listed below that would have less of an impact on the protein structure and consequently its function than the proposed leucine substitution would?

The original amino acid in a healthy patient is glutamate, which is negatively charged. The mutated amino acid is valine, which is non-polar. Valine is causing sickle cell anemia. The best amino acid to replace valine so that the patient is healthy again would be the one most like glutamate, so any negatively charged amino acid. Amino acid structure (2) is non-polar, not charged.

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.)

Hydrophobic -The Amyloid-beta plaque and tau protein become misfolded, exposing hydrophobic amino acids on their exterior. When hydrophobic amino acids are exposed to water, they actively seek out ways to avoid that water. One way to do this is to find other exposed hydrophobic amino acids, located on other misfolded proteins. When misfolded proteins begin to gather, they form aggregates, ultimately resulting in neuronal cell death.

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?

'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'. Heat disrupts hydrophobic interactions, due to increasing the movement of amino acids. Additionally, heat cannot cause a charge to become neutral.

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?

Cysteine is at position 150. No, there are no amino acids shown that can form a disulfide bond. -Cysteine only forms a disulfide bond with itself and it is the only amino acid with -SH and there are no cysteines in the sequence above. Position 9 is methionine that cannot form a disulfide bond, because it does not have the -SH needed to form a disulfide bond. Additionally, amino acid 150 must be cysteine, since it forms the disulfide bond.

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?

Hydrophobic interaction, the core of the protein -The two amino acids presented have side-chains comprised of only nonpolar C-C and C-H bonds. These amino acids belong to the nonpolar group and can form hydrophobic interactions. Because these amino acids cannot form hydrogen bonds they are hydrophobic in nature. This hydrophobic nature leads these amino acids to be in the interior/core of the protein, hidden away from the water surrounding the protein. While the two amino acids shown will tend to be in the core of the protein they have nonpolarized C-C and C-H bonds that cannot participate in hydrogen bonding.

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

False -The amino acid depicted in this problem is polar/hydrophilic because the end of the amino acid R group has a nitrogen bound to a hydrogen. Other polar amino acids can have oxygen bound to hydrogen, carbons bound to oxygens or carbons bound to nitrogens. Water is also polar and that is why this amino acid would like to interact with water and why the amino acid is categorized as hydrophilic (water loving). Oils are nonpolar and polar amino acids don't like nonpolar molecules.

This amino acid would prefer to interact with oil over water.

Amino acid 13 is a polar, uncharged amino acid that can participate in hydrogen bonds.

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?

Disulfide bond -Cysteine can also form a disulfide bond with its terminal S-H. van der Waals interactions form when atoms are close together, such as when hydrophobic interactions form in the core of the protein. Hydrophobic interactions are formed by non-polar amino acids that have R groups with C-H bonds.

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

Mutation of the gene for a protein that leads to the substitution of a nonpolar amino acid with a charged amino acid. -A "hydrophobic amino acid" is the same thing as a "non-polar amino acid". Therefore, the protein's function will not be disrupted.

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

Hydrogen bonding -The secondary structure of a protein is built by hydrogen bonds between the carboxyl groups and amino groups on the backbones of the amino acids. Disulfide bonding occurs due to bonding between polar, uncharged side chains with SH groups, and only occur in tertiary and quaternary structure.

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

Hydrogen bond -Hydrogen bonds are made between R groups that have polar bonds within them N-H, O-H, C-O or C-N but do not display a visible charge (+/-) on their R group.

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

Primary structure -The primary structure of a protein is simply the sequence of amino acids held together by peptide bonds. The secondary structure of a protein contains alpha-helices and beta-pleated sheets made by hydrogen bonding between the carboxyl groups and amino groups on the backbones of the amino acids.

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

Primary -The primary structure of a protein is the sequence of amino acids held together by peptide bonds. Peptide bonds are formed by dehydration reactions and disrupted by hydrolysis. The quaternary structure of a protein is when two or more polypeptide chains ("subunits") work together to perform the function of the protein. The two or more polypeptide chains are held together by side chain interactions, including the hydrophobic effect, ionic bonds, disulfide bonds, and hydrogen bonds.

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

Nonpolar amino acid, with a side-chain comprised of only nonpolar C-C and C-H bonds that is hydrophobic. This hydrophobic nature leads this amino acid to be in the interior of the protein, hidden away from the water surrounding the protein. -The side-chain of the amino acid in Option 3 contains an O- which allows it to form ionic bonds. This amino acid side-chain can interact favorably with water and is hydrophilic, so it can be on the surface of the protein next to water without issue.

Which of the following amino acids would you expect to find in the interior of a protein rather than on its exterior?

Amino acids linked together in a specific order by peptide bonds -The sequence of amino acids connected by peptide bonds in a specific order defines the protein primary structure.

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

It loses its primary structure. -The primary structure is determined by the peptide bonds between amino acids in the protein, which are strong covalent bonds that are not broken by the protein changing shape or from conditions which cause the protein to misfold and denature.

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

Hydrophobic Interactions -Misfolded proteins can have sections of hydrophobic amino acid residues exposed to water. This can lead to misfolded proteins to aggregate in order to form favorable hydrophobic interactions between nonpolar amino acids in adjacent protein chains and to keep these hydrophobic residues away from water. -Hydrogen bonds can form between polar amino acid side-chains and water, so there is no driving force for polar amino acids to form hydrogen bonds specifically with other polar amino acids on other proteins.

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

none of these -Two positively charged amino acids would repel each other. Only opposite charges attract. -Ionic bonds occur between two oppositely charged amino acids.

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

Disulfide bond and peptide bond -A covalent bond is a bond between two atoms involving the electrons being shared between them. In proteins, these include peptide bonds and disulfide bonds. -In an ionic bond, there is no sharing of electrons. Instead, they are attracted to each other by opposite charges on the two sidechains.

Which of the following interactions involve a covalent bond?

Because the side-chains of aspartate and glutamate are both negatively charged, they will repel each other. Opposite charges attract and like charges repel.

Which of the following pairs of amino acids are NOT likely to interact with one another to stabilize tertiary structure?

Ionic bonds between the side chains of the charged amino acids stabilize the protein structure -Ionic bonds help stabilize both the tertiary structure of a protein chain and the quaternary structure of a protein with multiple subunits.

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

'The interactions between the side chains of the amino acids make up the tertiary level structure of a protein'. The hydrogen bonding between backbone atoms in a protein makes up its secondary structure, whereas the interactions between the side chains of the amino acids make up the tertiary level structure of a protein.

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 tertiary level structure of a protein. The hydrogen bonding between backbone atoms in a protein makes up its secondary structure, whereas the interactions between the side chains of the amino acids make up the tertiary level structure of a protein.

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

Alpha carbon -The alpha carbon is the central carbon on an amino acid that holds together the other groups of the amino acid. It is always attached to the amino group, the carboxyl group, the side chain, and a single hydrogen. It is part of the backbone of the amino acid and is found in every amino acid.

Which portion of the amino acid is inside the box?

Side chain -The side chain is the variable group of the amino acid, also called the R group. Every amino acid has the same amino group, carboxylic acid group, and an alpha carbon, but the side chain is different.

Which portion of the amino acid is inside the box?

Hydrogen bonds/ionic bonds: Change in pH -Changes in pH instead disrupt hydrogen bonds and ionic bonds.

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