Biochem C785 Amino acids

Which of the following interaction can occur between two nonpolar amino acids?(0/1 Points) hydrogen bond hydrophobic interaction disulfide bond ionic bond none of these

hydrophobic interaction

Which of the following forces can lead to aggregation as a result of protein misfolding?(1/1 Points) disulfide bonds hydrogen bonds ionic bonds hydrophobic interactions

hydrophobic interactions

A mutation in the protein A gene results in a negatively charged amino acid, Glu, being replaced with the nonpolar amino acid Leu. This is an example of a _______ mutation that could potentially interrupt __________. (1/1 Points) nonsense, a hydrogen bond missense, a disulfide bond nonsense, a hydrophobic interaction missense, an ionic bond

missense, an ionic bond

Which of the following interaction can occur between two cysteine amino acids?(1/1 Points) hydrogen bond disulfide bond ionic bond none of these

disulfide bond

Which of the following interactions involve a covalent bond? (check all that apply)(0/1 Points) hydrogen bond disulfide bond ionic bond peptide bond hydrophobic interaction

disulfide bond peptide bond

Aggregation of proteins is the main reason behind many neurodegenerative diseases. Which one of the following mutations will likely cause a neurodegenerative disease? A. Replacing a polar amino acid with a nonpolar amino acid B.Replacing a negatively charged amino acid with a negatively charged amino acid C. Replacing a positively charged amino acid with a negatively charged amino acid D. Replacing a polar amino acid with another polar amino acid

A. 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.

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? A. An increase in glycogen formation in the brain cells B. Aggregation of the proteins in the brain C. Secretion of glucagon, leading to excessive ketogenesis D. An increase in anaerobic metabolism of glucose in the brain

B. Aggregation of the proteins in the brain This question is describing changes in protein structure. Aggregation occurs when proteins clump together inappropriately, causing plaques like amyloid deposits to accumulate.

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? A. Hydrogen Bond B. Hydrophobic Interactions C. Disulfide Bond D. Ionic Bonds

B. Hydrophobic interactions The correct answer is 'hydrophobic interactions'. The patient's temperature is much higher than normal. High temperatures disrupt hydrophobic interactions. Hydrogen bonds are stronger interactions than hydrophobic interactions and will not be easily disrupted by heat as hydrophobic interactions will. Hydrogen bonds are disrupted by changes in pH and by increasing the concentration of salts in the protein's environment.

Which change would most likely result in a permanent modification of an expressed protein's function? A. The mutation of a gene for an enzyme involved in protein synthesis following exposure to X-rays, causing the protein not to be synthesized B. A mutation of the gene for a protein that leads to the substitution of a hydrophobic amino acid with a nonpolar amino acid C. A mutation of the gene for a protein that leads to the substitution of a nonpolar amino acid with a charged amino acid D. An increase in the pH of a solution in which a protein is dissolved from 6.5 to 8.0, when it is known that the protein has an optimal activity of pH 7.8

C. A mutation of the gene for a protein that leads to the substitution of a nonpolar amino acid with a charged amino acid The mutation of nonpolar amino acid to a charged amino acid will disrupt the original hydrophobic interaction, permanently changing the function of the protein.

Primary structure consists of the order of ______ in a protein. These are held together with _______ bonds that are formed by a ________ reaction. A. Nucleotides, peptide, dehydration B. Nucleotides, phosphodiester, dehydration C. Amino acids, peptide, dehydration D. Amino acids, peptide, hydrolysis

C. Amino acids, peptide, dehydration The correct answer is 'amino acids, peptide, 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. While amino acids are held together by peptide bonds, these bonds are formed through a dehydration reaction, not a hydrolysis reaction.

Which of the following interactions involve a covalent bond? A. Hydrophobic Interactions and ionic bond B. Ionic bond and disulfide bond C. Disulfide bond and peptide bond D. Hydrogen Bond and peptide bond

C. Disulfide bond and peptide bond The correct answer is 'peptide bond and disulfide 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 type of bonding or interaction is correctly paired with a chemical or change in environment that will disrupt/break the interaction or bond? A. Peptide bonds: Change in pH B. Peptide bonds: Reducing agents C. Hydrogen bonds/ionic bonds: Change in pH D. Hydrophobic interactions: Change in pH

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

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 Glycine Cysteine Polymerase

Chaperone A chaperone functions to help proteins fold into the correct structure.

_____________________ amino acids are easy to recognize because they contain a charge. You will see a - or + sign. They are Ionic amino acids.

Charged amino acids

Which type of bonding or interaction is correctly paired with a chemical or change in environment that will disrupt/break the interaction or bond? A. Peptide bonds: Change in pH B. Peptide bonds: Reducing agents C. Hydrogen bonds/ionic bonds: Change in pH D. Hydrophobic interactions: Change in pH

D. Hydrogen bonds/ionic bonds: Change in pH

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? A. Disulfide bonds. Disulfide bonds are associated with the smell of cooking bacon. B. Hydrophobic interactions. Hydrophobic interactions are oily when the bacon grease cooks away from the bacon it takes away the hydrophobic interactions. C. Ionic bonds. As the bacon cooks, charged amino acids become neutral causing proteins to aggregate. This aggregation causes the characteristic look of crispy bacon. D. 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.

D. 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.

Which of the following statements about protein structure and stability is true? A. Denaturation is the loss of primary, secondary, and tertiary structure B. Denatured proteins retain their tertiary structure C. Protein structure is not stabilized by the hydrophobic effect D. Ionic bonds between the side chains of the charged amino acids stabilize the protein structure

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

Secondary, tertiary, and quaternary levels of protein structure can all be impacted by exposing a protein to which treatment? A. Increase in the concentration of the protein in solution B. Change of a hydrophobic amino acid to a different hydrophobic amino acid C. Addition of a reducing agent D. Placement of the protein in a solution with a low pH

D. 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.

Which of the following statements about the different levels of protein structure is true? A. Peptide bonds between amino acids make up the secondary structure of a protein B. The interactions between the side chains of the amino acids make up the secondary level structure of a protein C. Two or more polypeptides each with their own secondary structures come together to form a single larger tertiary structure of a protein D. The interactions between the side chains of the amino acids make up the tertiary level structure of a protein

D. The interactions between the side chains of the amino acids make up the tertiary level structure of a protein The correct answer is '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.

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 ________. A. nonsense, a hydrophobic interaction B. missense, a disulfide bond C. nonsense, a hydrogen bond D. missense, an ionic bond

D. missense, an ionic 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.

Which of the following best describes the nature of protein primary structure? A. The overall three-dimensional shape of a chain of amino acids B. Two or more polypeptide chains coming together to form the final C. functional protein D. Structural elements such as alpha helices and beta-pleated sheets E. Amino acids linked together in a specific order by peptide bonds

E. Amino acids linked together in a specific order by peptide bonds The correct answer is '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. The overall three-dimensional shape of a chain of amino acids refers to a tertiary structure.

Which force is most influential in determining the secondary structure of a protein? Hydrophobic effect Hydrogen bonding Disulfide bonding Electrostatic interactions

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.

What type of reaction breaks peptide bonds apart? Oxidation/Reduction Reaction Hydrolysis Reaction Methylation Reaction Condensation Reaction

Hydrolysis reaction Correct! 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.

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 Hydrophobic Cysteine Polar

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.

Which of the following forces can lead to aggregation as a result of protein misfolding? Disulfide Bond Hydrogen Bond Hydrophobic Interactions Ionic Bonds

Hydrophobic Interactions Correct! 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.

________________ amino acids have C-H (carbon and hydrogen bonds) and C-C (Cardon and Carbon) in their R groups Are these polar or non-polar? _____________________ Where are they located within the protein? ___________________

Hydrophobic amino acids Non-polar They are hydrophobic and they cluster in the center of a protein.

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? Ionic Bonds Hydrophobic interactions Hydrogen Bonds Disulfide Bonds

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. Hydrogen bonds are stronger interactions than hydrophobic interactions and will not be easily disrupted by heat as hydrophobic interactions will. Hydrogen bonds are disrupted by changes in pH and by increasing the concentration of salts in the protein's environment.

A diabetic patient is suffering from ketoacidosis. Which interaction(s) could be disrupted within the patientʼs hemoglobin due to this condition? Disulfide Bonds Ionic Bonds and hydrogen bonds Hydrophobic interactions and ionic bonds Hydrophobic Interactions and hydrogen bonds

Ionic Bonds and hydrogen bonds Correct! Diabetic ketoacidosis leads to a lower pH than normal. Changes in pH can disrupt both hydrogen bonds and ionic bonds inside of a protein.

Which of the following statements about protein structure and stability is true? A. Denaturation is the loss of primary, secondary, and tertiary structure B. Denatured proteins retain their tertiary structure C. Protein structure is not stabilized by the hydrophobic effect D. Ionic bonds between the side chains of the charged amino acids stabilize the protein structure

Ionic bonds between the side chains of the charged amino acids stabilize the protein structure Correct! 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 describes the tertiary structure of a protein? *It includes beta pleated sheets as a common form. *It involves hydrogen bonding between amino acid side-chains. *It includes alpha helices as a common form. *It involves hydrogen bonding between the backbone atoms.

It involves hydrogen bonding between amino acid side- chains. Correct! Hydrogen bonding between side-chains contributes to protein tertiary structure, but not secondary structure.

Which of the following interactions can occur between two positively charged amino acids? ionic bond hydrophobic interaction hydrogen bond none of these disulfide bond

None of these Correct! Two positively charged amino acids would repel each other. Only opposite charges attract.

_________________ Protein structure is a sequence of a chain or amino acids

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? Tertiary structure Secondary structure Quaternary structure Primary structure

Primary structure Correct! 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.

_________________ Protein structure protein consisting of more than one amino acid chain. Hemoglobin is an example.

Quaternary

________________ Protein structure hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern

Secondary

____________________ Protein structure three-dimensional folding pattern of a protein due to side chain interactions

Tertiary

Which of the following interaction can occur between two positively charged amino acids?(1/1 Points) hydrogen bond hydrophobic interaction disulfide bond ionic bond none of these

none of these

The amino acid valine contains an 'R' group that consists of carbon and hydrogen atoms. Which of the following groups does valine belong to?(0/1 Points) charged polar nonpolar aromatic

nonpolar

_________________ amino acids have O-H, N-H, S-H in their R groups They are considered _____________ because oxygen and nitrogen are electronegative atoms

polar amino acids Polar

The negatively charged amino acid, Glu, is replaced with the negatively charged amino acid Asp. Which level of protein structure is likely to be impacted by this change?(1/1 Points) primary structure secondary structure tertiary structure quaternary structure

primary structure