BCH5024 Lecture 1.1.2

Vocabulary flashcards covering key concepts from Module 1 topics including physical foundations, energy and thermodynamics, genetic foundations, evolution, and protein structure.

Biochemistry and Molecular Biology

The scientific discipline studying the physical, genetic, and evolutionary foundations of biomolecules and living systems.

Photoautotrophs

Organisms that obtain energy from light to synthesize organic molecules from CO2.

Chemotrophs

Organisms that obtain energy from chemical reactions of inorganic or organic compounds.

Dynamic steady state

A stable condition in living cells maintained by continual energy input, far from equilibrium with the environment.

First law of thermodynamics

Energy in the universe is conserved; it can change form but is neither created nor destroyed.

Second law of thermodynamics

Entropy (disorder) tends to increase in isolated systems; energy transformations increase overall disorder.

Entropy (S)

A measure of the randomness or disorder of a system.

Free energy (G)

The energy available to do work in a system; G = H − TS.

Enthalpy (H)

Heat content of a system; reflects the bonds present and their energies.

Temperature (T)

Absolute temperature used in thermodynamic equations (e.g., G = H − TS).

ΔG (Gibbs free-energy change)

The actual free-energy change of a reaction; ΔG = ΔH − TΔS.

ΔG° (Standard free-energy change)

Free-energy change of a reaction under standard conditions (298 K, 1 atm, 1 M).

Equilibrium constant (Keq)

The ratio of product to reactant concentrations at equilibrium for a given reaction.

Mass-action ratio (Q)

The ratio of product concentrations to reactant concentrations at a given moment; indicates distance from equilibrium.

ATP hydrolysis

Hydrolysis of ATP to ADP + Pi (or HPO4^2−), releasing energy to drive cellular processes.

Energy coupling

Driving a nonspontaneous reaction by coupling it to a favorable one, such as ATP hydrolysis.

Central Dogma

Genetic information flows from DNA to functional RNAs and proteins via transcription and translation; includes codons and anticodons.

DNA

Deoxyribonucleic acid; polymer of deoxyribonucleotides that encodes genetic information.

Deoxyribonucleotide

Monomeric subunit of DNA.

Replication

Process by which DNA is copied to produce identical DNA molecules.

Codon

A three-base sequence that codes for an amino acid (as described in the notes, in DNA bases).

Anticodon

A three-base RNA sequence complementary to a codon; part of tRNA enabling amino acid incorporation.

Mutation

A change in the nucleotide sequence of DNA.

Wild type

The typical, non-mutated form of a gene or organism.

Hemoglobin / Sickle cell anemia

A mutation in hemoglobin altering protein shape/function, used as an example of a genotype–phenotype change.

Homologs

Proteins encoded by genes that share detectable sequence similarities.

Orthologs

Homologous genes separated by speciation (in different species).

Paralogs

Homologous genes that diverged by gene duplication within the same genome.

Analogs

Proteins with similar function but no detectable sequence similarity.

Primary structure

The linear sequence of amino acids in a protein.

Secondary structure

Local folded structures (e.g., alpha helices, beta sheets) stabilized by hydrogen bonds.

Tertiary structure

The overall three-dimensional shape of a single polypeptide.

Quaternary structure

The arrangement of multiple polypeptide chains into a protein complex.

Amino acid

The building blocks of proteins, containing amino and carboxyl groups.

Peptide

A short chain of amino acids linked by peptide bonds.

Ionization of amino acids

Ionizable groups in amino acids can gain or lose protons depending on pH.

pH

A measure of hydrogen ion concentration that influences acid-base balance.

Buffers

Substances that resist changes in pH by neutralizing added acids or bases.