Biochemistry: Peptide Bond Configuration

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.

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.