Amino Acids & Proteins Notes

Amino Acids & Proteins

Protein Structure

• Primary Structure:
  • The sequence of amino acids in a polypeptide chain.
  • Linear extended conformation is rare.
• Secondary Structure:
  • Conformation of the polypeptide backbone without considering the side chains.
• Tertiary Structure:
  • The overall 3D conformation of a protein.
  • Includes backbone atoms and side chains.
• Quaternary Structure:
  • Spatial arrangement of polypeptide chains in proteins with more than one polypeptide chain.

Levels of Protein Structure

• Primary Structure: The sequence of amino acid residues (e.g., -Lys-Val-Asn-Val-Asp-).
• Secondary Structure: The spatial arrangement of the polypeptide backbone.
• Tertiary Structure: The three-dimensional structure of an entire polypeptide, including all its side chains.
• Quaternary Structure: The spatial arrangement of polypeptide chains in a protein with multiple subunits, such as hemoglobin.

Peptide Bonds

• Peptide bonds have electrons that are somewhat delocalized.
• They exhibit two resonance forms.

Dipeptide

A dipeptide structure is formed through a peptide bond between two amino acids, involving the linkage of the carboxyl group of one amino acid to the amino group of another, with the elimination of water.

Characteristics of Peptide Bonds

• Partial Double-Bond Character: Peptide bonds exhibit approximately 40% double-bond character, which restricts rotation around the C-N bond.

Torsion Angles

• Torsion Angles: Describe the degree of rotation around bonds in the polypeptide backbone.
  • \phi (phi): torsion angle for the N-Cα bond.
  • \psi (psi): torsion angle for the Cα-C bond.

Secondary Structure

• Polypeptides fold to minimize steric strain under physiological conditions.
• They adopt conformations (secondary structures) that minimize steric strain.
• Side chains are positioned to minimize steric interference.
• The polypeptide backbone assumes a repeating conformation, resulting in regular secondary structures such as α helix or β sheet.

The Alpha Helix

• Identified by Linus Pauling.
• The polypeptide backbone twists into a right-handed helix.
• The carbonyl oxygen of each residue forms a hydrogen bond with the backbone NH group four residues ahead.
• Average α helix contains about 10 residues.

The Beta Sheet

• Aligned strands of polypeptide whose H-bonding requirements are met by bonding between neighboring strands.
  • Parallel: Strands run in the same direction.
  • Antiparallel: Strands run in opposite directions.

Parallel Beta Sheets

• Strands run in the same direction (e.g., both from N-terminus to C-terminus).
• H bonds are angled (not straight).
• Less stable compared to antiparallel sheets.

Antiparallel Beta Sheets

• Strands run in opposite directions (e.g., one from N-terminus to C-terminus, the other in the opposite direction).
• H bonds are straight and more aligned.
• More stable.

Beta Sheet Connections

• Parallel Beta Sheets: Often require longer loop regions to connect the strands.
• Antiparallel Beta Sheets: May be connected by shorter loops, sometimes just a hairpin turn.

Tertiary Structure

• Overall 3D shape of a single polypeptide chain.
• Includes regular and irregular secondary structures.
• Spatial arrangement of all side chains.
• Zinc Finger Motif: Small protein domains stabilized by coordination with Zn^{2+}, involved in DNA binding.

Zinc Fingers

• Zinc Finger with Two Cys and Two His Residues: Example from Xenopus transcription factor IIIA.
• Zinc Finger with Six Cys Residues: Example from yeast transcription factor GAL4.

Quaternary Structure

• Most proteins with masses greater than 100 kD contain multiple chains.
• Individual chains are called subunits.
• Quaternary structure: spatial arrangement of these polypeptides.

Subunits in Quaternary Structure

• Subunits may be identical (homodimer, homotrimer, homotetramer).
• If chains are not all identical, it is a hetero structure (e.g., Hemoglobin: Heterotetramer with 2 α and 2 β subunits).

Oxygen-Binding Proteins

Myoglobin

• Monomer
• Lacks β structures entirely
• Composed of α helices and loops
• Fully functional myoglobin = polypeptide chain + iron-containing porphyrin derivative known as heme

Heme

• Prosthetic group
• An organic compound that allows a protein to carry out a function that the polypeptide alone cannot perform; in this case, binding oxygen.

Hemoglobin

• Heterotetramer
• Two α chains and two β chains
• Each subunit (globin) resembles myoglobin

Hemoglobin and Myoglobin Biochemistry

Myoglobin Oxygen Binding

• Equation: Mb + O2 \rightleftharpoons Mb "." O2
• K = \frac{[Mb][O2]}{[Mb "." O2]}
• Fractional Saturation: Y = \frac{[Mb "." O2]}{[Mb] + [Mb "." O2]}
• Simplified Equation: Y = \frac{[O2]}{K + [O2]} = \frac{pO2}{K + pO2}

Oxygen Dissociation Curve

• Relating fractional saturation to partial pressure of oxygen: Y = \frac{[Mb \cdot O2]}{[Mb] + [Mb \cdot O2]}
• Rewriting in terms of K: Y = \frac{\frac{[Mb][O2]}{K}}{[Mb] + \frac{[Mb][O2]}{K}} = \frac{\frac{[O2]}{K}}{1 + \frac{[O2]}{K}}
• Simplifying: Y = \frac{[O2]}{K + [O2]}
• Using partial pressure: Replacing [O2] with pO2 (partial pressure of oxygen, in torr).

Calculating Fractional Saturation

• Given: Y = \frac{pO2}{K + pO2}, K = 2.8 torr
• When pO_2 = 1 torr: Y = \frac{1}{2.8 + 1} = 0.26
• When pO_2 = 100 torr: Y = \frac{100}{2.8 + 100} = 0.97

Myoglobin Oxygen-Binding Curve

• The relationship between the fractional saturation of myoglobin (Y) and the oxygen concentration (pO_2) is hyperbolic.
• When pO_2 = K = 2.8 torr, myoglobin is half-saturated (Y = 0.5).

Hemoglobin Oxygen-Binding Curve

• Shows the relationship between fractional saturation (Y) and pO_2 in lungs and tissues.

Carbon Monoxide Poisoning

• Carbon monoxide (CO) can bind to the heme iron in hemoglobin.
• CO binds about 200–250 times more tightly than O_2.
• CO toxicity:
  • Carboxyhemoglobin rises > 25%: Neurological impairment (dizziness & confusion).
  • Carboxyhemoglobin > 50%: coma and death.

Myoglobin vs. Hemoglobin

Structural Proteins

• Give shape, strength, and support to cells and tissues.

Keratin

• Found in hair, nails, skin.
• Composed of 2 long α-helices twisted into coils.
• Strands form fibers via disulfide bonds between cysteines.

Collagen

• Found in connective tissues (tendons, skin, bone).
• Triple helix of three polypeptide chains.
• Glycine is every 3rd residue (small enough to fit in the center of the helix).
• Repeating amino acid sequence of Gly-X-Y, where X and Y are often proline and hydroxyproline.
• Requires hydroxyproline, made using vitamin C. Scurvy causes weak connective tissue.

Actin and Tubulin (Cytoskeleton)

• Actin: Forms thin microfilaments in cells; dynamic (grows and shrinks).
• Tubulin: Forms microtubules, hollow tubes used in cell division and transport.
• Both use ATP or GTP to power assembly.

Motor Proteins

Myosin

• Found in muscle cells.
• Has two heads that bind actin and hydrolyze ATP.
• The head “pulls” on actin, causing muscle contraction.
• Works through a lever arm mechanism: bind → pull → release → reset.

Antibodies

Immunoglobulins AKA Antibodies

• Synthesized mainly by plasma cells in response to antigens.
• Structure: 2 heavy chains and 2 light chains.
• Both chains are divided into constant and variable regions.

Antibody Regions

• Constant Region: Towards the Carboxyl end.
• Variable Region: Towards the Amino end.

Antibody Fragments

• Fab: Has both light + heavy chains; variable + constant regions; has antigen-binding site.
• Fc: Has heavy chains only; constant region only; has macrophage-binding site; determines Ig class.