Video Notes Vocabulary: Amino Acids and Spectroscopy

A set of vocabulary flashcards covering key terms from the lecture notes on Beer's Law, spectrometry, and amino acid chemistry.

Beer's Law (Beer-Lambert Law)

A = εlc; absorbance is proportional to concentration for a single absorbing species within a linear range.

Linearity (Beer's Law linear range)

The concentration range over which absorbance and concentration are directly proportional; deviations occur outside this range.

Calibration curve

Plot of instrument response vs. known concentrations used to establish linear range and quantify unknown samples.

Dilution step

Reducing sample concentration by adding solvent to stay within the linear range of an assay.

Stray light

Unwanted light reaching the detector, causing artifacts such as apparent changes in absorbance.

Cuvette misalignment

Improper alignment or covers allowing room light to reach the detector, altering readings.

Wideband pass

A broad light-band transmitted through the system, allowing unwanted wavelengths to reach the detector.

Photodetector loss

Decrease or failure in detector sensitivity, degrading measurement accuracy.

Electronic nonlinearity

Nonlinear response of electronic components that distorts absorbance readings at certain signals.

Stray-to-detector coupling

Unintended light paths that bypass the intended sample path, affecting the signal.

Limited reactive ingredient

Reagent concentration is insufficient to drive the reaction to the expected extent, causing deviations.

Product inhibition

High product concentration shifts the reaction equilibrium, reducing product formation (Le Chatelier’s principle).

Byproduct effects

Other reaction products accelerate or inhibit the desired reaction, skewing results.

Absorbing product in equilibrium

A product that absorbs light at the measurement wavelength and is in equilibrium with another species having different molar absorptivity.

Bright stain

A carcinogenic dye used in slides; safety considerations drive limits on reactive ingredient levels.

PPE (gloves, lab coat)

Personal protective equipment used to minimize exposure to hazardous reagents.

Carcinogen exposure risk

Higher concentrations of certain reagents increase the risk of toxic or cancer-causing effects.

Cysteine

Amino acid with a thiol (-SH) group that can form disulfide bonds with another cysteine.

Disulfide bond

S–S linkage between two cysteine residues (cystine when formed between two molecules).

Cystine

Dimer formed by two cysteines linked through a disulfide bond.

Guanidine group

Arginine side chain feature; highly basic nitrogen-containing group).

Imidazole ring

Five-membered ring in histidine side chain important for basicity and catalysis.

Amino acid alpha carbon

Central carbon in an amino acid to which the amino group, carboxyl group, hydrogen, and side chain (R) attach.

Carboxyl group

Weak acid (-COOH) in amino acids; tends to lose a proton to form -COO⁻.

Amino group

Weak base (-NH₂) in amino acids; can gain a proton to form -NH₃⁺.

pKa

Negative log of the acid dissociation constant (pKa = -log10 Ka); indicates acidity strength.

pH

Negative log of hydrogen ion concentration; measures how acidic or basic a solution is.

Conjugate acid/base

The species formed when an acid donates a proton (conjugate base) or a base accepts a proton (conjugate acid).

Henderson-Hasselbalch equation

pH = pKa + log([base]/[acid]); used to predict the ratio of base to acid at a given pH.

Isoelectric point (pI)

pH at which a molecule has net zero charge (no overall positive or negative charge).

Zwitterion

Molecule with both positive and negative charges but overall neutral (common for amino acids at physiological pH).

Amphoteric

Molecule that can act as both an acid and a base.

Acidic amino acids

Aspartic acid (ASP) and Glutamic acid (GLU); side chains behave like acids (pKa around ~4).

Basic amino acids

Lysine (LYS), Arginine (ARG), Histidine (HIS); side chains behave like bases (pKa ranges ~6–12).

Nonpolar (hydrophobic) amino acids

ALA, VAL, LEU, ILE, PRO (and others); side chains are hydrophobic and lack charge at physiological pH.

Polar, uncharged amino acids

SER, THR, ASN, GLN, CYS, TYR; have polar side chains but are not charged at physiological pH.

Acidic vs. basic side chains behavior

Acidic side chains (Asp, Glu) are deprotonated at physiological pH; basic side chains (Lys, Arg, His) are protonated.

Alanine (ALA) pI consideration

A simple nonpolar amino acid; isoelectric point lies between its carboxyl and amino pKa values.

Cysteine vs. cystine

Cysteine has a thiol group; two cysteines can form a disulfide bond to create cystine.

Amino acid abbreviations

Three-letter and one-letter codes (e.g., ASP = aspartic acid, D; GLU = glutamic acid, E; LYS = lysine, K; ARG = arginine, R; HIS = histidine, H).