Proteins Study Notes

Proteins

  • A protein is a naturally occurring, unbranched (linear) polymer in which the monomer units are amino acids.

  • MOST ABUNDANT BIOMOLECULE, next to water.

Amino Acids

  • An amino acid is an organic compound that contains both an amino (-NH₂) group and a carboxyl (-COOH) group.

  • Standard amino acids: 20 α-amino acids normally found in proteins.

  • Nomenclature: amino acids are abbreviated using three-letter codes; a newer one-letter code is popular in computer applications.

Four Categories of Standard Amino Acids

  • Non-polar amino acids - Hydrophobic; found in the Interior of Proteins

  • Polar neutral amino acids - NO CHARGE; serine is important here

  • Polar acidic amino acids - bares NEGATIVES CHARGE ; gives away proton ; Oxygen

  • Polar basic amino acids - bares POSITIVE CHARGE ; they Accept proton; Nitrogen

Essential Amino Acids

  • Essential amino acids are required for protein synthesis and must be obtained from dietary sources.

Chirality and Amino Acids

  • The α-carbon of all standard amino acids bears four different groups, giving them chirality.

  • EXCEPT LYSINE

  • Fischer projection demonstrates D- and L- isomers of amino acids (e.g., alanine and serine).

  • L - H2N (left)

  • D - NH2 (right)

Acid-Base Properties of Amino Acids

  • Each α-amino acid contains both an acidic carboxyl group (-COOH) and a basic amino group (-NH₂) on the same carbon.

  • In neutral solution, the -COOH can donate a proton to the -NH₂, forming a zwitterion (a molecule with both positive and negative charges).

  • Zwitterion : the molecule created by internal proton transfer; "double ion". NO NET CHARGE

  • For non-polar and polar neutral amino acids, the side chain does not carry a formal charge at all pH values; for polar acidic and polar basic amino acids, the side chain can also acquire a charge (additional protonation/deprotonation site).

  • Consequently, acidic and basic amino acids can have four charged forms in solution.

Isoelectric Point (pI) and Electrophoresis

  • Isoelectric Point (pI) is the pH at which an amino acid solution has no net charge (equal positive and negative charges).

  • Electrophoresis: separation of charged molecules by migration under an electric field.

  • For amino acids with two relevant pKa values (pKa1 for carboxyl, pKa2 for amino), pI is the average:
    PI = (pKa1 + pKa2) / 2

  • Example reference: Lysine (Lys), Phenylalanine (Phe), Glutamic acid (Glu) can be separated by electrophoresis at pH ~5.5

  • In amino acids with two ionizable groups, the pKa values define the pI as the halfway point between them.

Cysteine

  • Cysteine is the only standard amino acid with a sulfhydryl group (-SH) in its side chain.

Peptides: Amino Acid Chains

  • A peptide or polypeptide is an unbranched chain of amino acids joined by peptide bonds.

    • PLANAR - fixed; can’t rotate freely

  • A peptide bond is a covalent bond between the carboxyl group of one amino acid and the amino group of another.

  • By convention, the sequence is written with the N-terminal amino acid on the left.

  • Individual amino acids within a peptide chain are called Amino Acid Residues.

  • The repeating sequence of peptide bonds and α‑carbon -CH- groups constitutes the backbone of the peptide; the side chains (R groups) are substituents.

Peptide Nomenclature and Isomerism

  • Peptide nomenclature follows the order of amino acids in the chain.

  • Isomeric peptides: peptides that contain the same amino acids but in different orders are constitutional isomers with different biochemical properties and specificities.

Biochemically Important

  • Oxytocin: a natural hormone that stimulates uterine contractions and lactation

    • often called the LOVE HORMONE or Cuddle Hormone.

  • Vasopressin: regulates water excretion by the kidneys

    • Controls Osmotic Balance.

    • Blood regulation

    • Salt/ sodium Hemostasis and Kidney functioning

  • Enkephalins: pentapeptide neurotransmitters produced by the brain

    • PAIN-REDUCING

  • Glutathione: an ANTIOXIDANT protecting cellular contents from oxidizing agents.

    • Replenishes OLD CELLS in our body

    • Helps in Detoxification , Helps Liver

General Structural Features of Proteins

  • Protein forms can be monomeric or multimeric.

  • Types of proteins: simple proteins and complex/conjugated proteins; conjugated proteins may include a prosthetic group.

  • Examples: Albumin (a simple protein), Hemoglobin (a multimeric protein with a prosthetic group in some contexts).

Protein Structure: Four Levels

  • Primary structure

  • Secondary structure

  • Tertiary structure

  • Quaternary structure

1. Primary Structure

  • The sequence of amino acids linked by peptide bonds.

  • The primary structure is intrinsic to the protein and remains the same regardless of where the protein is found in an organism.

  • The overall three-dimensional shape is not yet determined by the primary sequence alone.

  • In the accompanying figure for human myoglobin, the primary sequence comprises 153 amino acids.

2. Secondary Structure

  • The spatial arrangement of the backbone; held together by hydrogen bonds.

  • Two main types:

    • Alpha-helix: a single polypeptide chain coiled into a helix stabilized by hydrogen bonds.

    • Beta-pleated sheets: extended chain segments linked by hydrogen bonds, can be in the same or different molecules.

3. Tertiary Structure

  • The overall three-dimensional shape of a protein arising from interactions among side chains that are distant in the primary sequence.

  • The folded protein is also known as the native state.

  • Correct three-dimensional structure is essential for function.

4 .Quaternary Structure

  • Organization among multiple peptide chains in a multimeric protein.

  • Multimeric proteins are composed of two or more polypeptide chains (identical or different) held together by intermolecular forces.

  • Hemoglobin is a classic example (a tetramer).

Protein Hydrolysis

  • Complete hydrolysis: all peptide bonds are broken, yielding constituent amino acids.

  • Partial hydrolysis: some peptide bonds are broken, producing a mixture of free amino acids and small peptides.

Protein Denaturation

  • Partial or complete disorganization of a protein’s characteristic three-dimensional shape due to disruption of secondary, tertiary, and quaternary interactions.

Protein Classification Based on Shape

  • Proteins folded into their tertiary and quaternary structures can be classified as:

    • Fibrous

    • Globular

    • Membrane

  • Keratin: protective coatings in nature.

  • Collagen: most abundant protein in humans; major structural material in tendons, ligaments, blood vessels, and skin.

Proteins in the Bodies

  • Hemoglobin and Myoglobin are notable examples.

  • Biomedical applications include:

    • 2,3-BPG (2,3-bisphosphoglycerate) level affects hemoglobin’s oxygen affinity; higher 2,3-BPG lowers affinity, promoting oxygen release to tissues.

    • High altitude adaptation: prolonged exposure can decrease 2,3-BPG, contributing to hypoxia and conditions like high altitude pulmonary edema.

    • Chronic anemia: RBCs increase 2,3-DPG (often several-fold) to boost oxygen delivery.

Methemoglobinemia

  • Fe²⁺ in blood oxidized to Fe³⁺; blood appears chocolate colored.

  • Congenital Methemoglobinemia: due to Cyb5R deficiency.

  • Acquired Methemoglobinemia: induced by certain drugs (dapsone, chloroquine, nitrates, topical anesthetics).

  • Investigated using CBC (Hb status) and ABG (methemoglobin levels; PaO₂ may be normal or reduced).

Sickle-Cell Anemia

  • Mutation: substitution of Val for Glu in the beta chain of hemoglobin (HbS).

  • Causes abnormal red blood cell shape that can clog capillaries.

Thalassemia

  • Absence of one or more globin chains in hemoglobin.

  • Inherited blood disorder; reduced Hb quantity.

  • Bone marrow produces fewer healthy RBCs.

  • Diagnosis often includes CBC to evaluate RBC size, shape, and color.

Myoglobinuria

  • Indicates muscle injury (rhabdomyolysis); myoglobin released into circulation.

  • Urine may appear dark brown.

Glycoproteins

  • Immunoglobulins are glycoproteins involved in the immune response.

Lipoproteins

  • Chylomicrons: transport dietary triacylglycerols from intestine to liver and adipose tissue.

  • Very-low-density lipoproteins (VLDL): transport TAGs synthesized in the liver to adipose tissue.

  • Low-density lipoproteins (LDL): transport cholesterol from liver to cells throughout the body.

  • High-density lipoproteins (HDL): collect excess cholesterol from tissues and return it to the liver for degradation to bile acids.

Additional Notes (references from slides)

  • Insulin is cited as an example of a multimeric protein.

  • Hemoglobin and myoglobin are repeatedly highlighted for biomedical relevance.

  • Albumin is given as an example of a simple protein; prosthetic groups are mentioned for conjugated proteins.

  • The importance of primary sequence, secondary structures (α-helix and β-pleated sheets), and higher-order structures in determining function is emphasized throughout.

Summary: Key Concepts to Remember

  • Proteins are amino-acid polymers with a defined sequence that determines structure and function.

  • Amino acids have an amino group, a carboxyl group, an α-carbon with four substituents (chirality), and a side chain (Rgroup) that defines properties.

  • The four generic classes of amino acids reflect polarity and charge, influencing protein folding and function.

  • Peptide bonds link amino acids; the backbone vs side chains concept helps explain protein architecture.

  • Proteins have four hierarchical levels of structure, each critical to function.

  • Protein hydrolysis and denaturation alter function by changing bonds and structure.

  • Various protein types (glycoproteins, lipoproteins) extend function into signaling, immunity, and metabolism.

  • Understanding abnormalities in protein structure (e.g., HbS in sickle-cell) links biochemistry to disease.