Biochemistry: Structure, Energetics, and Binding Dynamics

Vocabulary flashcards generated from the biochemistry lecture notes covering nucleic acids, thermodynamics, acid-base chemistry, protein structure levels, hemoglobin allostery, and molecular immune recognition.

Deoxyribonucleic Acid (DNA)

A linear polymer composed of monomers consisting of deoxyribose sugar, a phosphate group, and one of four nitrogenous bases.

Hydrogen-Bond Donor

The group that includes both the electronegative atom to which a hydrogen atom is covalently bonded and the hydrogen atom itself.

Hydrogen-Bond Acceptor

The lone pair of electrons on an electronegative atom that is less tightly linked to the hydrogen atom.

First Law of Thermodynamics

The fundamental physical law stating that the total energy of a system and its surroundings is constant.

Second Law of Thermodynamics

The fundamental physical law stating that the total entropy of a system plus that of its surroundings always increases.

Gibbs Free Energy ($\Delta G$)

A thermodynamic quantity used to describe the energetics of biochemical reactions, defined by $\Delta G = \Delta H_{\text{system}} - T\Delta S_{\text{system}}$.

Ion Constant of Water ($K_w$)

The equilibrium ion product constant defined as $K_w = K[\text{H}_2\text{O}] = [\text{H}^+][\text{OH}^-] = 10^{-14}$.

$$\text{p}K_a$$

The negative logarithm of the acid dissociation constant ($-\log(K_a)$), indicating the susceptibility of a proton to removal by a base.

Henderson–Hasselbalch Equation

An equation relating pH, $\text{p}K_a$, and concentrations of conjugate base and acid: $\text{pH} = \text{p}K_a + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$.

$\alpha$-Amino Acid

A primary protein building block consisting of a central $\alpha$ carbon linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group.

Peptide Bond

An amide linkage formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another with the loss of a water molecule.

Residue

An individual amino acid unit incorporated within a polypeptide chain.

Cystine

A dimeric unit formed by the covalent oxidation and cross-linking of two cysteine residues via a disulfide bond.

Secondary Structure

The regular three-dimensional conformation formed by hydrogen bonds between peptide backbone $\text{N–H}$ and $\text{C=O}$ groups near each other in sequence.

$\alpha$ Helix

A tightly coiled, rodlike secondary structure where each backbone $\text{C=O}$ group hydrogen bonds with the $\text{N–H}$ group four residues ahead.

$\beta$ Pleated Sheet

A secondary structure motif formed by hydrogen bonding between adjacent, almost fully extended $\beta$ strands.

Motifs (Supersecondary Structures)

Specific combinations of secondary structural elements that recur in proteins and frequently exhibit similar biological functions.

Protein Domains

Independently folding compact regions within a single polypeptide chain that are often connected by flexible linker segments.

Quaternary Structure

The overall spatial arrangement and nature of interactions between multiple individual polypeptide subunits in a protein assembly.

Ribonuclease

A single polypeptide chain enzyme consisting of 124 amino acid residues cross-linked by four disulfide bonds.

Myoglobin

An abundant muscle protein that binds and stores oxygen using a prosthetic heme group.

Heme Group

A prosthetic complex consisting of a central iron atom bound to protoporphyrin IX, which is composed of four linked pyrrole rings.

Deoxymyoglobin

The oxygen-free form of myoglobin in which the central $\text{Fe}^{2+}$ ion is too large to fit inside the plane of the porphyrin ring.

Oxymyoglobin

The oxygen-bound form of myoglobin in which oxygen binding draws the central iron atom into the plane of the protoporphyrin ring.

Globin Fold

A characteristic structural motif consisting of a conserved arrangement of $\alpha$ helices found in myoglobin and hemoglobin subunits.

T (Tense) State

The constrained quaternary structure of deoxyhemoglobin that possesses lower affinity for oxygen.

R (Relaxed) State

The unconstrained quaternary structure of oxyhemoglobin in which oxygen-binding sites exhibit higher affinity.

Bohr Effect

The physiological phenomenon where carbon dioxide and lower pH promote oxygen release from hemoglobin by stabilizing the T state.

Innate Immune System

An ancient defense mechanism that uses pattern recognition receptors to identify and eliminate broad classes of foreign pathogens.

Pathogen-Associated Molecular Pattern (PAMP)

A conserved molecular structure unique to pathogens that is recognized by Toll-like receptors (TLRs).

Adaptive Immune System

A specialized defense system comprised of humoral and cellular responses that targets specific foreign antigens.

Antigens

Molecules that induce specific immune responses by binding to antibodies or T-cell receptors.

Immunoglobulin G (IgG)

The major serum antibody composed of two light chains and two heavy chains forming 12 total immunoglobulin fold domains.

Immunoglobulin Fold

A structural domain composed of a sandwich of two $\beta$ sheets cross-linked by a central disulfide bond.

Hypervariable Loops (CDRs)

Three highly variable loops situated at the end of an immunoglobulin fold domain that form the antigen-binding site.

T-Cell Receptor

A cell-surface receptor composed of two immunoglobulin-fold chains with hypervariable loops that recognizes peptide fragments presented on class I MHC proteins.

Association Equilibrium Constant ($K_a$)

The equilibrium constant for a binding association reaction $R + L \rightleftharpoons RL$, defined as $K_a = \frac{[RL]}{[R][L]}$ with units of $\text{M}^{-1}$.

Dissociation Equilibrium Constant ($K_d$)

The equilibrium constant for a dissociation reaction $RL \rightleftharpoons R + L$, defined as $K_d = \frac{[R][L]}{[RL]}$ with units of $\text{M}$.