Lecture Notes Flashcards: Intermolecular Forces, Solutions & pH, Protein Structure & Function

Vocabulary-style flashcards covering key concepts from the lecture notes.

Gibbs Free Energy (ΔG)

ΔG = ΔH − TΔS; a reaction is spontaneous when ΔG < 0; changes in free energy drive reactions.

Enthalpy (ΔH)

Internal heat content of the system; a negative ΔH favors a reaction.

Entropy (ΔS)

Disorder or randomness of the system; a positive ΔS favors a reaction.

Hydrophobic Effect

Nonpolar solutes disrupt water structure; water forms cages around them; aggregation releases ordered water and increases overall entropy.

Solvation

Interactions between a solute and water molecules; polar solutes dissolve via hydrogen bonding and ionic interactions.

Amphipathic Molecule

Molecule with both polar (hydrophilic) and nonpolar (hydrophobic) regions.

Micelle

Spherical assembly of amphipathic cells with the hydrophobic tails inward and hydrophilic heads outward, sequestering nonpolar regions from water.

Bilayer

Two-layer sheet of amphipathic molecules forming cell membranes. Hydrophilic heads form the outside of the bilayer while hydrophobic tails recede inside the layer to avoid water.

Hydrogen Bond

Electrostatic attraction between a hydrogen donor and an electronegative acceptor; directional and strongest when nearly linear.

Directionality of Hydrogen Bonds

Bond strength increases with linearity of bonds between atoms containing partial negative and partial positive charge (N, O, F, H); misalignment weakens the bond.

Noncovalent Interactions

Weak forces (hydrogen bonds, ionic interactions, hydrophobic effects, van der Waals) that help determine biomolecular structure.

Ionic (Charge-Charge) Interactions

Electrostatic attractions/repulsions between charged groups; important in solvation and molecular recognition.

van der Waals Interactions

Weak, short-range forces from transient dipoles; important for tight packing, especially in nonpolar regions.

Hydration Shell

Structured layer of water around a solute that mediates solvation.

Polar Biomolecule

Molecule with permanent dipole due to electronegative atoms; tends to be water-soluble.

Nonpolar Biomolecule

Molecule lacking significant charge/polarity; poorly soluble in water without special interactions.

pH

−log10[H+]; a measure of acidity/basicity of a solution; at 25°C, neutral pH is 7.

Ka

Acid dissociation constant; Ka = [H+][A-]/[HA].

pKa

−log10(Ka); pH at which an acid is 50% dissociated.

Conjugate Acid-Base Pair

Two species related by proton transfer; buffers rely on these pairs.

Buffer

A system containing a weak acid/base and its conjugate acid/base that resists pH changes.

Buffering Range

Optimal buffering within about ±1 pH unit of the pKa.

Henderson–Hasselbalch Equation

pH = pKa + log([A-]/[HA]); relates pH to pKa and the base/acid ratio.

Physiological pH

Blood pH ≈ 7.35–7.45; CO2/HCO3− buffer system maintains this range.

pCO2

Partial pressure of CO2 in blood; typically ~35–45 mmHg; influences pH via the Bohr effect.

HCO3− (Bicarbonate)

Blood buffer; normal range ≈ 21–28 mEq/L; regulated by kidneys.

Arterial Blood Gases (ABG)

Measurement of pH, pCO2, and HCO3− to assess acid–base status.

Respiratory Acidosis

pH < 7.35 with elevated pCO2; impaired ventilation or lung disease.

Metabolic Acidosis

pH < 7.35 with low HCO3−; metabolic origin; compensation by breathing.

Bohr Effect

Proton/CO2 changes decrease oxygen affinity of hemoglobin, promoting O2 release in tissues.

2,3-Phosphoglycerate (2,3-BPG)

Allosteric regulator that lowers hemoglobin’s O2 affinity; modulates oxygen delivery.

Allostery

Binding at one site affects binding at other sites, often via conformational changes.

Cooperativity

Ligand binding at one site increases affinity at other sites, seen in multimeric proteins like Hb.

Dissociation Constant (Kd)

Ligand concentration at which half the binding sites are occupied; lower Kd = higher affinity.

Hemoglobin (Hb)

Tetrameric protein with cooperative O2 binding; transitions between low-affinity T state and high-affinity R state.

Oxyhemoglobin vs Deoxyhemoglobin

Hb bound to O2 (oxy) has high affinity (R state); Hb without O2 (deoxy) has low affinity (T state).

Allosteric Modulators in Hb

Molecules like 2,3-BPG, CO2, and H+ alter Hb’s oxygen affinity by stabilizing T or R states.

Antibody (Immunoglobulin, Ig)

Multimeric protein that binds antigens with high specificity using variable regions.

Epitope

The specific part of an antigen recognized by an antibody.

Complementarity in Protein–Ligand Binding

Lock-and-key fit where shape and chemical interactions (charges, H-bonds) enable binding.

Active Site

Region of an enzyme where substrate binding and catalysis occur.

Inhibitor (Competitive)

Molecule that binds the active site, blocks substrate binding, often used in drug design.

Immunoglobulin Classes (IgG, IgM, IgA, IgE)

Different antibody isotypes with distinct roles in immunity and distribution.

Antigen–Antibody Binding Pocket

Binding pocket formed by variable domains of antibody chains that recognizes the antigen.

Disulfide Bond

Covalent linkage between cysteine thiols; stabilizes protein structure, often extracellularly.

Amino Acids

Building blocks of proteins; 20 standard L-form; chiral center at the α-carbon (glycine is achiral).

Amino Acid Classification

R-group-based categories: nonpolar, aromatic, polar uncharged, positively charged, negatively charged.

Amino Terminal and Carboxyl Terminal

Amino terminus (N-terminus) is the start of a polypeptide; carboxyl terminus (C-terminus) is the end.

Peptide Bond

Condensation between the carboxyl of one amino acid and the amino of the next; planar with partial double-bond character; typically trans.

Primary Structure

Linear sequence of amino acids from the amino terminus to the carboxyl terminus.

Secondary Structure

Local folding patterns: α-helix, β-sheet, and β-turn, stabilized by hydrogen bonding.

α-Helix

Right-handed coil stabilized by hydrogen bonds between carbonyl O and amide H of i+4; approximately 3.6 residues per turn.

β-Sheet

Sheets formed by hydrogen bonding between adjacent β-strands; can be parallel or antiparallel; R-groups alternate above and below.

β-Turn

180° turn in the polypeptide chain stabilized by H-bond between residues i and i+3; often Pro or Gly.

Tertiary Structure

Three-dimensional folding of a single polypeptide; motif and domain organization.

Motif

Recurring structural arrangement within a protein that has a specific function or fold.

Domain

Independent structural and functional unit within a protein; can fold independently.

Quaternary Structure

Assembly of two or more polypeptide chains into multimeric complexes with symmetry.

Hemoglobin Quaternary Structure

Two αβ dimers assemble to form a tetramer with cooperative O2 binding.

Protein Conformation

Three-dimensional arrangement of a protein’s atoms; can adopt multiple conformations (e.g., ON/OFF).