Biochemistry: Peptide Bond Configuration

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Questions and Answers

What is the contribution of each amino acid residue to the polypeptide chain?

One alpha-carbon, two single bonds, and a peptide bond (correct)

One alpha-carbon and two peptide bonds

Two alpha-carbons and one peptide bond

One single bond and two alpha-carbons

Why are trans peptide bonds considered to be the most stable?

They have the lowest energy configuration.

They are always present in proline residues.

They avoid steric hindrance between side chains. (correct)

They form stronger ionic interactions.

Which configuration of peptide bonds is less favorable due to steric hindrance?

Neither configuration

Cis configuration (correct)

Trans configuration

Both cis and trans configurations

What does a pH value less than the pKa indicate about an amino acid?

It is positively charged. Signup and view all the answers

Which amino acids are classified as basic due to their high pKa values?

Arg and Lys Signup and view all the answers

In the Henderson-Hasselbalch equation, what does an increase in pH signify?

Decrease in the concentration of the conjugate acid Signup and view all the answers

At which pH does leucine exist in its zwitterion form?

pH 6.0 Signup and view all the answers

Which equation describes the relationship between pH and the ratio of conjugate base to conjugate acid?

Henderson-Hasselbalch equation Signup and view all the answers

What is the isoelectric pH (pI) for an amino acid?

The pH at which the amino acid is in its zwitterion form. Signup and view all the answers

At what pH would a protein have a negative charge?

pH > pI Signup and view all the answers

Which plasma proteins are predominantly negatively charged and migrate towards the anode at pH 8.6?

Albumin Signup and view all the answers

What happens to hydrophobic amino acids in a protein's tertiary structure?

They are usually buried away from the water solvent. Signup and view all the answers

Which condition is characterized by a selective loss of lower molecular weight proteins from plasma?

Nephrotic syndrome Signup and view all the answers

Which response causes an immediate increase in haptoglobins in the alpha2 mobility band?

Acute stress or inflammation Signup and view all the answers

What is a characteristic finding in hepatic cirrhosis regarding gamma-globulins?

Broad elevation of gamma-globulins. Signup and view all the answers

Monoclonal gammopathies result from which of the following?

Clonal synthesis of a unique immunoglobulin. Signup and view all the answers

What is the role of the second time delay rf pulse in NMR?

To differentiate between 1D and 2D NMR techniques. Signup and view all the answers

Which amino acid is primarily responsible for destabilizing the α-helix structure?

Proline Signup and view all the answers

What can increased bilirubin levels indicate in an individual?

Jaundice in the skin or eyes. Signup and view all the answers

How are the chains of antibodies (immunoglobulins) structured?

Antibodies are composed of two heavy chains and two light chains. Signup and view all the answers

What term describes a small molecule that alone cannot elicit an immune response but can do so when attached to a larger molecule?

Hapten Signup and view all the answers

What determines the antigen specificity of an antibody?

The complementarity-determining regions (CDRs) in the variable regions. Signup and view all the answers

Which class of immunoglobulin is known to be a pentamer?

IgM Signup and view all the answers

What effect do residues with large blocks of negative or positive charges have on α-helices?

They can destabilize the helix. Signup and view all the answers

What does the ratio k1/k2 represent in enzyme-catalyzed reactions?

Equilibrium constant, Keq Signup and view all the answers

What is the significance of Km in enzyme reactions?

It is the substrate concentration at half of Vm. Signup and view all the answers

Which statement describes the relationship between substrate concentration and reaction velocity when [S] is larger than Km?

The reaction velocity remains constant. Signup and view all the answers

In which condition is hexokinase favored over glucokinase for glucose phosphorylation?

When blood sugar is low Signup and view all the answers

What does a larger kcat value indicate for an enzyme's reaction rate?

Faster reaction with higher substrate saturation. Signup and view all the answers

Which enzyme is responsible for catalyzing glucose to glucose 6-phosphate in the liver?

Glucokinase Signup and view all the answers

What happens to the reaction velocity as substrate concentration [S] approaches Km?

Velocity increases proportionally with substrate concentration. Signup and view all the answers

The Michaelis-Menten equation describes which type of reaction?

Simple enzyme-catalyzed reactions Signup and view all the answers

What effect does insulin have on cAMP levels?

Decreases cAMP levels Signup and view all the answers

How does epinephrine affect glycolysis in the heart?

Stimulates glycolysis Signup and view all the answers

Which enzyme's activity is primarily increased by the action of fructose 2,6-bisphosphate in cancer cells?

6-phosphofructo-1-kinase Signup and view all the answers

What is the primary role of 6-phosphofructo-2-kinase/fructose 2,6-bisphosphate in the heart?

Increases fructose 2,6-bisphosphate levels Signup and view all the answers

What effect does fructose 1,6-bisphosphate have on pyruvate kinase in the liver?

Activates pyruvate kinase activity Signup and view all the answers

What distinguishes the isoenzymes of 6-phosphofructo-2-kinase/fructose 2,6-bisphosphate in the heart from those in the liver?

Phosphorylation activates the kinase in the heart Signup and view all the answers

What is the primary signaling pathway through which epinephrine promotes glycolysis in the heart?

Activation of protein kinase A Signup and view all the answers

How does ATP regulate pyruvate kinase activity?

ATP inhibits pyruvate kinase Signup and view all the answers

Study Notes

Peptide Bond Configuration

The polypeptide chain is formed by amino acid residues contributing one alpha-carbon, two single bonds, and a peptide bond.
Trans configuration is the most stable because the two side chain groups are on opposite sides of the C=N bond.
Cis configuration is unfavorable because of steric hindrance between the side chains, with two side chain groups on the same side of the C=N bond.
Most peptide bonds in proteins are in the trans configuration except when a proline residue is present.
The proline side chain includes the alpha-imino group, and both cis and trans configurations have unfavorable interactions.

Amino Acids and Charge

Basic amino acids have R groups containing nitrogen atoms (Lys and Arg) with high pKa values and positive charges.
Acidic amino acids have side chains containing a carboxylic acid group with low pKa values and negative charges.
pH is expressed using the acid dissociation constant (Ka): pKa = log(1/ Ka).
Henderson-Hasselbalch equation: pH = pKa + log [conjugate base]/[conjugate acid]
The equation shows how the ionization state and charge of a molecule change with pH.

The Isoelectric Point (pI)

The pI of an amino acid is the pH at which it exists in its zwitterion form (no net charge).
The pI value is constant for a compound.
For simple amino acids, like leucine, pI is calculated as the average of the two pKa values that regulate the boundaries of the zwitterion form.
A protein's charge is negative when pH > pI and positive when pH < pI.
The degree of charge depends on the magnitude of the difference between pH and pI.
Examples of protein charge:
- When pH is 1.0, leucine has a +1 charge.
- When pH is 6.0, leucine has a zero charge.
- When pH is greater than 11, leucine has a negative charge.

Plasma Proteins

Plasma proteins are separated at pH 8.6, allowing negatively charged proteins to migrate towards the anode.
The major fractions are albumin, alpha1-globulins, alpha2-globulins, beta-globulins, and gamma-globulins.

Polarity of Amino Acids

The hydrophobicity of amino acid side chains is crucial for protein folding.
Hydrophobic amino acids are buried away from the water solvent.
Nonpolar side chains may be found dispersed among polar side chains on protein surfaces.
Clustering of nonpolar side chains on the surface usually indicates a specific function, like binding hydrophobic interactions.
Transmembrane proteins exhibit reversed side-chain polarity compared to water-soluble globular proteins.
They position hydrophobic side chains on the outside and ionic groups on the inside for binding and ion channel formation.

Plasma Protein Variations

Haptoglobins are elevated in the alpha2 mobility band during stress, inflammation, infection, injury, or surgery.
Increased gamma-globulin peaks indicate a delayed response to infection, often due to elevated immunoglobulins.
Hypo-gamma-globulinemia associated with immunosuppressive diseases results in lower gamma-globulin levels.
Hepatic cirrhosis involves a broad elevation of gamma-globulins with reduced albumin levels.
Monoclonal gammopathies are characterized by sharp gamma-globulin bands caused by clonal synthesis of a unique immunoglobulin.
Nephrotic syndrome leads to a loss of lower molecular weight proteins from plasma, resulting in decreased albumin but increased alpha2-macroglobulin and beta-lipoproteins in the alpha2 band.
Protein-losing enteropathy involves plasma loss through exudation in the intestinal tract.

NMR Spectroscopy

Two-dimensional (2D) NMR differs from one-dimensional (1D) NMR by the addition of a second time delay radio frequency (rf) pulse.

Alpha-Helices

A stable alpha-helix requires hydrogen bonding between peptide bonds at four amino acid intervals.
Proline is infrequent in alpha-helices as it introduces a kink, destabilizes the helix, and cannot hydrogen bond with other residues.
Large blocks of glutamate, aspartate, lysine, or arginine will destabilize the helix due to their charges.
Ankyrin mutations causing spherocytosis disrupt alpha-helical domains and interfere with ankyrin stacking, affecting red blood cell shape.
This alteration reduces red blood cell survival, increases hemolysis, and leads to increased heme conversion to bilirubin.
Elevated bilirubin levels can cause jaundice (yellowing of skin and whites of the eyes).
Increased bilirubin storage in the gallbladder may form gallstones and cause cholecystitis (inflammation), leading to abdominal pain and possible cholecystectomy (gallbladder removal).

Immunoglobulins

Immunoglobulins (antibodies) are produced by lymphocytes in response to foreign particles called antigens.
A hapten is a small molecule that cannot induce antibody production alone but does when attached to a larger molecule.
Antibodies are glycoproteins composed of two light chains and two heavy chains [(LH)2].
The four chains are linked by disulfide bonds.
The variable (V) regions at the NH2-terminal of the light and heavy chains contain hypervariable regions known as complementarity-determining regions (CDRs).
CDR's form the 3D antigen-binding site, complementary to the antigen.
The constant (C) regions at the COOH-terminal of the light and heavy chains provide for binding of proteins and contain the site for placental membrane crossing.
The V regions determine the antigen specificity of the antibody.
Different immunoglobulin classes include:
- IgA: dimers
- IgM: pentamers
Heavy chains are designated gamma, alpha, delta, mu, and epsilon in IgG, IgA, IgM, IgE, and IgD classes, respectively.
There are two types of light chains, lambda and kappa.
IgG is the primary immunoglobulin in plasma.

Enzyme Kinetics

Enzyme-catalyzed reactions are akin to second-order reactions, slowing down as substrate concentration depletes or product accumulates.
The rate of product formation is proportional to the concentration of the enzyme-substrate complex.
Michaelis-Menten equation: d[P]/dt = k3[ES]
Km: the substrate concentration where velocity is half the maximum velocity (Vm).
Vmax: maximum velocity achieved when all available enzyme is bound to substrate.
Turnover number (kcat): molecules of substrate converted to product per unit time per enzyme molecule.
The larger the kcat value, the faster the enzyme reaction.
When [S] is >> Km: velocity is independent of [S].
When [S] is << Km: the plot of velocity versus [S] is linear.

Glycolysis Regulation

Fructose 2,6-bisphosphate is a key regulator of glycolysis.
It activates phosphofructokinase-1 (PFK-1), the rate-limiting enzyme of glycolysis.
6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase is a bifunctional enzyme.
Insulin opposes glucagon and epinephrine by activating its receptor's tyrosine kinase activity, lowering cAMP levels, inhibiting protein kinase A, and activating phosphoprotein phosphatase to stimulate glycolysis.
Epinephrine stimulates glycolysis in the heart by activating protein kinase A, which phosphorylates the heart isoenzyme of 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase.
Phosphorylation increases fructose 2,6-bisphosphate levels, leading to increased glycolysis.
Cancer cells often express a special isoform of 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase, resulting in a high fructose 2,6-bisphosphate concentration, and enhanced glycolytic flux.
Pyruvate kinase, the final enzyme of glycolysis, is inhibited by ATP.
The liver isoenzyme is activated by fructose 1,6-bisphosphate (FBP), providing a feed-forward mechanism for regulation.

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Description

Explore the fascinating world of peptide bonds and amino acids in this quiz. Learn about trans and cis configurations, their stability, and how they affect protein structure. Additionally, discover the charge properties of basic and acidic amino acids and their significance in biochemistry.