Biochemistry: Macromolecules and Amino Acids

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Questions and Answers

Which class of biologically important molecules does insulin belong to?

Carbohydrates

Nucleic acids

Proteins (correct)

Lipids

What does the first pKa in an amino acid titration curve represent?

Protonation/deprotonation of the amine (correct)

Deprotonation of the side chain

Protonation of the carboxyl group

Ionization of the zwitterion

Which amino acid is not optically active due to its side chain being a hydrogen atom?

Val

Ala

Pro

Gly (correct)

Which two amino acids among the standard 20 contain sulfur atoms?

Met and Cys Signup and view all the answers

What functional group do all amino acids contain, except for Pro?

Carboxyl group Signup and view all the answers

The chirality of an amino acid is due to its alpha carbon being bonded to what?

Four different chemical groups Signup and view all the answers

At pH = 7, what type of molecule is Glu primarily considered?

Zwitterion Signup and view all the answers

The titration reaction at pKa2 for valine is represented by which of the following equations?

--COOH + OH^-^ --COO^-^ + H<del>2</del>O Signup and view all the answers

For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:

A net positive charge Signup and view all the answers

Which of the following is true regarding Arg in protein chemistry?

Often found in β-turns due to the low steric constraints of the R group Signup and view all the answers

Amino acids are joined during a(n) _ reaction, forming a(n) _ bond/linkage.

Condensation; peptide Signup and view all the answers

What is the total number of proteinogenic amino acids (used to make proteins) in humans?

20 Signup and view all the answers

Which amino acid undergoes acetylation as a posttranslational modification?

Lys Signup and view all the answers

Which of the following forces stabilizes protein structure?

All of the above Signup and view all the answers

Which statement best describes parallel β-sheets?

Adjacent peptides are oriented so that N-terminus aligns with N-terminus Signup and view all the answers

Phosphorylation of a protein typically serves which purpose?

To change the protein's charge and thus its function Signup and view all the answers

Which statement regarding the binding of arsenic to protein is accurate?

Binding to one subunit does not affect others. Signup and view all the answers

Which of the following is true regarding the functions of heme?

It plays a role in group transfer reactions. Signup and view all the answers

During hemoglobin's transition from the T state to the R state, which event occurs?

The oxygen moves from one subunit to another. Signup and view all the answers

In the induced-fit model, which binding is essential for enzyme function?

Substrate must bind to the active site. Signup and view all the answers

What is incorrect regarding enzymes?

They do not show specificity in reactions. Signup and view all the answers

Which strategies are NOT used by RNase in its mechanism?

Covalent catalysis. Signup and view all the answers

What is NOT represented in the energy diagram for chymotrypsin?

The binding energy of substrate. Signup and view all the answers

Which cofactor specifically assists in acyl group transfer?

Coenzyme A. Signup and view all the answers

What role does Zn^2+^ likely play in enzyme catalysis?

Stabilize negative charges in the substrate to aid in binding Signup and view all the answers

Which type of inhibition is exemplified by the interaction of sarin with acetylcholinesterase?

Covalent irreversible Signup and view all the answers

What is the expected effect on reaction velocity when doubling substrate concentration [S] far above KM?

The v<del>i</del> will be approximately the same Signup and view all the answers

How does a competitive inhibitor affect apparent KM and Vmax?

Increases the apparent K<del>M</del> and decreases the apparent V<del>max</del> Signup and view all the answers

What effect does an inhibitor binding to the same active site region as the substrate have under saturating substrate levels?

The true V<del>max</del> can still be reached Signup and view all the answers

Which statement about noncompetitive inhibitors is true?

They decrease the apparent V<del>max</del> but do not affect K<del>M</del>. Signup and view all the answers

Which characteristic does NOT describe β-lactams?

They are effective against all bacterial types. Signup and view all the answers

What is a common effect of a noncompetitive inhibitor on enzyme kinetics?

It remains effective regardless of substrate concentration. Signup and view all the answers

Which statement accurately describes the effect of temperature and pH on protein structure?

Temperature and pH can cause proteins to unfold (denature). Signup and view all the answers

What characterization is NOT applicable to myoglobin?

It consists of multiple polypeptide chains. Signup and view all the answers

Which level of protein structure is predominantly formed by noncovalent bonds?

Secondary structure Signup and view all the answers

What is a characteristic of the quaternary structure of proteins?

It involves multiple polypeptide subunits. Signup and view all the answers

Which statement about the Asp to Met mutation in hemoglobin is true?

The mutation greatly affects oxygen binding compared to carbon monoxide. Signup and view all the answers

Which of the following statements does NOT accurately describe the properties of proteins?

Each polypeptide of the same type has a unique tertiary structure. Signup and view all the answers

Which statement is true regarding the binding characteristics of the recently discovered protein that binds arsenic?

It binds arsenic with a low affinity of K<del>D</del> = 3 mM. Signup and view all the answers

What role does calcium play in the context of proteins?

It regulates protein function and aids in blood clotting. Signup and view all the answers

Study Notes

Macromolecules

Insulin is a protein
Proteins are one of the four major classes of biological molecules

Amino Acids

The titration curve of an amino acid shows two pKa values
The first pKa represents the protonation or deprotonation of the carboxyl group
Glycine is the only amino acid that is not optically active, because its side chain is only a hydrogen atom
Cysteine and Methionine are the only two amino acids containing sulfur
Aside from proline, all other amino acids contain a primary amino group, a carboxyl group, and a hydrogen atom bonded to the alpha carbon
The chirality of an amino acid derives from the alpha carbon, which is bonded to four different chemical groups
Glutamate (Glu) has a side chain that can act as an acid or base and participate in acid-base catalysis.

Protein Structure

Amino acids are joined by peptide bonds through condensation reactions, forming a polypeptide chain
There are 20 proteinogenic amino acids incorporated into proteins
Proteins can be modified after translation, including acetylation of lysine
Protein structure is stabilized by hydrogen bonds, hydrophobic effects, electrostatic interactions, and disulfide bonds.
The peptide bond can rotate around the Cα – C and the Cα – N bonds, which creates a pivot point at the peptide bond
Parallel beta-sheets occur when adjacent polypeptide chains are oriented with the N-terminus of one aligned with the C-terminus of the other
Phosphorylation of a protein is a posttranslational modification that often regulates the function of the protein
Quaternary structure describes the arrangement of multiple polypeptide chains (subunits) into a functional oligomer
Primary, secondary, and tertiary protein structures are formed and maintained predominantly by noncovalent bonds
Protein tertiary structure folds into a specific conformation due to the amino acid sequence and sometimes with the help of chaperones
Proteins can unfold (denature) due to changes in temperature or pH.

Protein-Ligand Binding

Myoglobin is a single polypeptide chain that lacks quaternary structure.
Mutations, like changing an Asp to Met in hemoglobin, can alter the binding affinity for oxygen, changing the binding constants of the protein
sigmoidal binding curves indicate positive cooperativity. Positive cooperativity means that the binding of one ligand molecule to a protein increases the affinity of the protein for subsequent ligand molecules.
Heme binds to the protein by noncovalent interactions with the pyrrole groups of the porphyrin ring.
The porphyrin ring binds ferrous iron (Fe^2+^).
Heme functions as an oxidation-reduction cofactor during oxygen transport.
When hemoglobin transitions from the T to the R state, the oxygen ligand is not transferred from one subunit to another. Instead, iron moves into the heme plane, causing a movement of the α-helix containing the proximal His.

Enzyme Structure/Function

In the induced-fit model, the substrate must bind to the enzyme's active site to induce a conformational change that facilitates the catalytic reaction.
Enzymes are catalysts that increase the rate of a chemical reaction without being consumed themselves.
Enzymes are highly specific for their substrates.
Enzymes lower the activation energy of a reaction.
The catalytic mechanism of RNase does not involve metal ion catalysis.
The mechanistic step for chymotrypsin involves covalent catalysis and acid-base catalysis.
Coenzyme A participates in acyl group transfer reactions
Zinc ions can stabilize negative charges in the substrate to aid in binding and help stabilize negative charge developed during the transition state.

Inhibitors and Enzyme Kinetics

Organophosphorus compounds such as sarin are examples of covalent irreversible inhibitors, because they form a stable covalent bond with the enzyme.
At very high substrate concentrations, the reaction rate approaches the maximum velocity (Vmax) for the enzyme.
Competitive inhibitors increase the apparent K_M, because the substrate is competing with the inhibitor for binding to the active site.
Noncompetitive inhibitors decrease the apparent V_max, because they bind to the enzyme at a site other than the active site, altering its activity.
Allosteric inhibitors bind to the enzyme at a site other than the active site, changing the conformation of the enzyme and reducing its activity.
β-lactams are a class of antibiotics that inhibit bacterial cell wall synthesis. They do not directly bind to the active site but inhibit the enzyme by blocking the formation of the peptide cross-links in peptidoglycan.

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Description

Explore the fascinating world of macromolecules and amino acids in this quiz. Learn about the structure and function of proteins, the importance of different amino acids, and their unique properties. Test your knowledge on titration curves, chirality, and protein structure.