Video Notes: Water, Weak Interactions, Ionization, Buffers; Amino Acids, Peptides, and Proteins (Vocabulary Flashcards)

Vocabulary flashcards covering core terms from the lecture notes on water properties, weak interactions, ionization and buffering, amino acids, peptides, and protein structure and purification.

hydrogen bond

A relatively weak electrostatic attraction between a hydrogen atom bonded to an electronegative atom (usually O or N) and another electronegative atom nearby.

hydrogen bonding in water

Water’s ability to form hydrogen bonds with itself and with solutes, contributing to its unique solvent properties and to high boiling/melting points.

hydrophobic effect

The tendency of nonpolar regions to cluster in water to minimize their surface exposure, driven by entropy and solvent reorganization.

amphipathic

Molecules or regions having both polar (hydrophilic) and nonpolar (hydrophobic) parts.

micelle

An aggregate of amphipathic molecules in water, with hydrophobic tails inward and polar heads outward.

lipid bilayer

A two-layer membrane structure formed by amphipathic lipids in water, creating a barrier that is central to biological membranes.

dielectric constant (ε)

A solvent property that measures its ability to reduce electrostatic forces; water has a high dielectric constant (about 78.5 at 25 °C).

ion product of water (Kw)

The product [H+] [OH−] of water at a given temperature; at 25 °C Kw = 1.0 × 10−14 M^2.

pH

Negative logarithm of the hydrogen ion concentration; a measure of how acidic or basic an aqueous solution is.

pOH

Negative logarithm of the hydroxide ion concentration; pH + pOH = 14 at 25 °C.

Henderson–Hasselbalch equation

A relation that describes buffer pH: pH = pKa + log ([A−]/[HA]).

acid dissociation constant (Ka)

Equilibrium constant for the dissociation of an acid HA ⇌ H+ + A−.

pKa

The negative logarithm of Ka; a measure of an acid’s strength with lower values indicating stronger acids.

conjugate acid–base pair

Two species related by the gain or loss of a proton, e.g., HA and A−.

buffer

A solution that resists large pH changes when small amounts of acid or base are added, typically a weak acid and its conjugate base.

buffering capacity

The ability of a buffer to absorb added acid or base with minimal pH change.

buffering region

The pH range around the pKa where a conjugate acid–base pair effectively buffers.

isoelectric point (pI)

The pH at which a molecule (e.g., an amino acid) has no net electric charge.

zwitterion

A molecule with both positive and negative charges but overall neutral, common for amino acids at certain pH.

Amino acid

A small organic molecule with an amino group, a carboxyl group, a hydrogen, and an R group attached to an α-carbon; the building blocks of proteins.

α-amino acid

Amino acids with the amino group attached to the α-carbon; most are chiral except glycine.

chirality (chiral center)

A carbon atom bonded to four different groups, yielding non-superposable mirror-image (L/D) forms.

L- and D- stereoisomers

Two enantiomers of amino acids; most biological proteins use L-amino acids.

one-letter amino acid code

A shorthand single-letter symbol used to represent amino acids in sequences (e.g., A, R, N, D).

three-letter amino acid code

A shorthand abbreviation for amino acids (e.g., Ala, Arg, Asn, Asp).

peptide bond

A covalent bond formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of the next, producing a –CONH– linkage.

residue

The remaining part of an amino acid after it has joined to form a peptide bond.

oligopeptide

A short chain of amino acids linked by peptide bonds (a few to several residues).

polypeptide

A long chain of amino acids linked by peptide bonds; large polypeptides can comprise thousands of residues.

disulfide bond

A covalent bond between two cysteine thiol groups (–SH) that can stabilize protein structure when oxidized to form cystine.

cystine

Two cysteine residues linked by a disulfide bond.

primary structure

The linear sequence of amino acids in a polypeptide.

secondary structure

Regular local patterns in the polypeptide backbone, notably α-helix and β-pleated sheet.

α-helix

A right-handed helical structure stabilized by intrachain hydrogen bonds between the backbone amide and carbonyl groups.

β-sheet

Extended, zigzag backbone structure with hydrogen bonds between nearby strands; can be parallel or antiparallel.

β-turn

A tight turn in a polypeptide chain that reverses direction, often containing Gly or Pro.

Ramachandran plot

A plot of allowed φ (phi) and ψ (psi) dihedral angles for peptide backbones, illustrating permissible conformations.

motif (fold)

A recognizable folding pattern made of two or more secondary-structure elements.

domain

An independently folding, functional unit within a protein; often a discrete structural module.

coiled coil

A structural motif where two or more α-helices twist around each other, increasing stability and strength.

hydrophobic core

Interior of a folded protein rich in nonpolar residues, shielded from water.

intrinsically disordered protein

Proteins or regions lacking a stable 3D structure under physiological conditions.

proteostasis

Cellular networks that regulate protein synthesis, folding, refolding, and degradation to maintain protein homeostasis.

chaperone

Proteins that assist other proteins in folding properly or refolding after partial unfolding.

Hsp70

A family of heat shock proteins (~70 kDa) that bind unfolded polypeptides to prevent aggregation and assist folding.

GroEL/GroES

A bacterial chaperonin system that provides an isolated chamber for protein folding.

protein disulfide isomerase (PDI)

Enzyme that rearranges disulfide bonds during protein folding.

prolyl cis–trans isomerase (PPI)

Enzyme that speeds isomerization of peptide bonds at proline residues, aiding folding.

amyloid/amyloidoses

Aggregates of misfolded proteins with β-sheet-rich fibrils linked to diseases such as Alzheimer's.

prion

Infectious misfolded protein responsible for certain neurodegenerative diseases; PrP^Sc differs from PrP^C.

Protein Data Bank (PDB)

An international repository of 3D structures of biomolecules (proteins, nucleic acids, etc.).

mass spectrometry (MS)

Analytical technique to determine molecular mass and sequence by ionizing samples and analyzing mass-to-charge ratios.

MALDI MS

Matrix-assisted laser desorption/ionization mass spectrometry; ionization method for large biomolecules.

ESI MS

Electrospray ionization mass spectrometry; generates multiply charged ions from solution-phase samples.

MS/MS (tandem MS)

Mass spectrometry technique where selected ions are fragmented to provide sequence information.

electrophoresis

Technique to separate charged molecules in a gel under an electric field; used to estimate size and purity.

SDS–PAGE

Sodium dodecyl sulfate polyacrylamide gel electrophoresis; separates proteins by mass after denaturation.

isonlectric focusing

Electrophoretic method that separates proteins by their isoelectric point (pI) in a pH gradient.

two-dimensional electrophoresis

Combines isoelectric focusing and SDS–PAGE to separate proteins by pI and molecular weight.

ligand

A molecule bound by a protein (often in affinity chromatography).

column chromatography

Purification technique separating components based on interactions with a stationary phase.

ion-exchange chromatography

Chromatography that separates proteins by net charge using charged resins (cation vs anion exchangers).

size-exclusion chromatography

Also called gel filtration; separates proteins by size as they pass through pores in a gel matrix.

affinity chromatography

Chromatography that separates based on a specific interaction with a ligand attached to the matrix.

helicity/coil dipole

The net dipole along an α-helix caused by aligned peptide bonds, influencing stability and interactions.

buffer region (acid–base)**

The pH range around a weak acid/its conjugate base where buffering is most effective.

Henderson–Hasselbalch pH relation for buffers

pH = pKa + log ([base]/[acid]); shows how pH depends on the ratio of conjugate base to acid.

apparent pKa

A pKa value measured under specific buffered conditions, which can differ from the intrinsic pKa.

titration curve

Plot of pH versus added titrant (e.g., NaOH) used to determine pKa and buffering regions.

glycine pKa and pI

Glycine: pK1 ≈ 2.34 (COOH), pK2 ≈ 9.60 (NH3+); pI ≈ 5.97; becomes a zwitterion near neutral pH.

disulfide bond stability

Covalent link between cysteines; stabilized by redox environment and contributes to protein stability.

glycine’s role in buffers

Glycine can serve as a buffer around its pKa values due to its two ionizable groups.

histidine buffering near neutrality

His has a pKa near 6.0 for its imidazole side chain, enabling buffering close to physiological pH.

bicarbonate buffer system

Buffer in blood: carbonic acid (H2CO3) and bicarbonate (HCO3−), linked to CO2 levels in the lungs.

carbonic acid hydration constant (Kh)

Constant for CO2 hydration to H2CO3, used to express dissolved CO2 buffering calculations.

coiled coil

Two or more α-helices wound around each other to form a stable structural motif.

α-keratin

Fibrous protein with a right-handed α-helix that forms a left-handed coiled coil, providing strength.

collagen

Triple-helix fibrous protein with Gly–X–Y repeats (X often Pro, Y often 4-Hyp); left-handed triple helix in a right-handed supercoil.

PDB ID

Four-character identifier for a structure in the Protein Data Bank.

X-ray crystallography

Technique to determine atomic structure from diffraction patterns of x-rays through crystals.

NMR spectroscopy

Technique to determine molecular structure in solution by analyzing nuclear spin transitions.

cryo-EM

Cryo-electron microscopy; rapid freezing of samples for imaging large biomolecules without crystallization.

biochemical sequence conservation

Regions of protein sequences conserved across species indicate essential functional or structural roles.

proline cis–trans isomerization (PPI)

Catalyzed interconversion between cis and trans peptide bonds at Pro residues, influencing folding.