Metabolism, Molecular Genetics & Gene Transfer Review

Vocabulary flashcards covering metabolism, DNA replication, transcription, translation, and bacterial gene transfer concepts from the lecture notes.

Catabolism

Metabolic pathway that breaks down complex molecules into simpler ones, releasing energy (ATP, NADH).

Anabolism

Energy-requiring synthesis of complex molecules from simpler precursors; builds macromolecules.

Enzyme

Protein catalyst that lowers activation energy and speeds up specific biochemical reactions without being consumed.

Substrate

The specific reactant molecule upon which an enzyme acts.

Product

Molecule(s) formed as the result of an enzyme-catalyzed reaction.

Active Site

Region of an enzyme where the substrate binds and the reaction occurs.

Dehydration Synthesis (Condensation)

Reaction that joins two molecules by removing water; important in building macromolecules.

Hydrolysis

Reaction that breaks bonds by adding water; central to macromolecule degradation.

Endoenzyme

Enzyme that functions inside the cell; e.g., DNA polymerase.

Exoenzyme

Enzyme secreted outside the cell to digest environmental substrates; e.g., amylase.

Induction (enzyme regulation)

Activation of enzyme synthesis in response to substrate presence.

Repression (enzyme regulation)

Inhibition of enzyme synthesis when product accumulates or is unnecessary.

Constitutive Enzyme

Enzyme synthesized continuously at a constant level regardless of substrate.

Competitive Inhibition

Regulation in which an inhibitor resembling the substrate competes for the enzyme’s active site.

Noncompetitive (Allosteric) Inhibition

Inhibitor binds a regulatory site, altering enzyme shape and reducing activity without occupying active site.

Feedback Inhibition

End product of a pathway allosterically inhibits an early enzyme, preventing overproduction.

Oxidation

Loss of electrons (often H atoms) by a molecule in a redox reaction.

Reduction

Gain of electrons (often H atoms) by a molecule in a redox reaction.

NAD (Nicotinamide Adenine Dinucleotide)

Electron carrier reduced to NADH during metabolism; donates electrons to the ETC for ATP generation.

FAD (Flavin Adenine Dinucleotide)

Electron carrier reduced to FADH₂; delivers electrons to the ETC.

Substrate-Level Phosphorylation

Direct transfer of a phosphate from a substrate to ADP, forming ATP (glycolysis, Krebs).

Oxidative Phosphorylation

ATP synthesis driven by electron transport and chemiosmosis via ATP synthase.

Aerobic Respiration

Catabolism using O₂ as terminal electron acceptor; yields up to ~38 ATP per glucose.

Anaerobic Respiration

Respiratory catabolism using inorganic acceptors other than O₂ (e.g., NO₃⁻); yields less ATP.

Fermentation

Anaerobic process using organic molecules as electron acceptors; yields 2 ATP per glucose.

Glycolysis

Pathway converting glucose to 2 pyruvate, producing 2 ATP (net) and 2 NADH.

Krebs Cycle (Citric Acid Cycle)

Cyclic pathway oxidizing acetyl-CoA to CO₂ and generating NADH, FADH₂, and ATP.

Electron Transport Chain (ETC)

Series of membrane carriers transferring electrons to O₂ (or other acceptor) while pumping protons for ATP synthesis.

Central Metabolism

Core pathways (glycolysis & Krebs) that integrate catabolism and anabolism by providing energy and precursors.

Antiparallel

Orientation of DNA strands running in opposite 5'→3' directions.

5' End

DNA/RNA terminus with a free phosphate on the 5' carbon of the sugar.

3' End

DNA/RNA terminus with a free hydroxyl group on the 3' carbon of the sugar.

Semiconservative Replication

Each daughter DNA molecule contains one parental and one newly synthesized strand.

Leading Strand

DNA strand synthesized continuously toward the replication fork.

Lagging Strand

DNA strand synthesized discontinuously as Okazaki fragments away from the fork.

Okazaki Fragment

Short DNA segment produced on the lagging strand during replication.

Helicase

Enzyme that unwinds the DNA double helix at the replication fork.

Primase

RNA polymerase that synthesizes short RNA primers for DNA polymerase.

DNA Polymerase III

Main bacterial polymerase that elongates new DNA and proofreads during replication.

DNA Polymerase I

Enzyme that removes RNA primers and fills gaps with DNA; also repairs DNA.

Ligase

Enzyme that seals nicks by forming phosphodiester bonds between DNA fragments.

DNA Gyrase (Topoisomerase II)

Relieves supercoiling ahead of the replication fork by cutting and rejoining DNA.

Replication Fork

Y-shaped region where parental DNA is unwound and new strands are synthesized.

Central Dogma

Flow of genetic information: DNA → RNA → Protein (replication, transcription, translation).

mRNA (Messenger RNA)

RNA copy of a gene that carries coding information to the ribosome.

tRNA (Transfer RNA)

Adapter molecule that delivers specific amino acids to the ribosome via anticodon-codon pairing.

rRNA (Ribosomal RNA)

Structural and catalytic RNA component of ribosomes.

RNA Polymerase

Enzyme that synthesizes RNA from a DNA template during transcription.

Ribosome Binding Site

mRNA sequence where the ribosome assembles to begin translation (Shine-Dalgarno in bacteria).

Start Codon

AUG codon signaling initiation of translation and coding for methionine.

Stop Codon

UAA, UAG, or UGA codon that signals termination of translation.

A Site

Ribosomal site where incoming aminoacyl-tRNA binds during elongation.

P Site

Ribosomal site holding the tRNA with the growing polypeptide chain.

E Site

Ribosomal exit site for discharged tRNAs.

Transpeptidation

Peptide-bond-forming reaction between amino acids at P and A sites inside the ribosome.

Reading Frame

Grouping of mRNA nucleotides into sequential, non-overlapping codons set by the start codon.

Conjugation

Direct plasmid DNA transfer between bacteria via a pilus.

Transformation

Uptake of free DNA by a competent bacterial cell from the environment.

Transduction

Transfer of bacterial DNA via bacteriophage infection.

F Factor

Plasmid encoding genes for pilus formation and conjugative DNA transfer (F⁺ cells).

Hfr Conjugation

Conjugation from a donor with F factor integrated into its chromosome, transferring chromosomal genes.

Generalized Transduction

Random bacterial DNA fragments packaged into phage particles and transferred to another cell.

Specialized Transduction

Transfer of specific bacterial genes adjacent to a prophage insertion site due to improper excision.

Mutation

Permanent change in DNA nucleotide sequence.

Missense Mutation

Base substitution altering a codon and resulting in a different amino acid.

Silent Mutation

Base substitution that does not change the encoded amino acid.

Frameshift Mutation

Insertion or deletion that shifts the reading frame, often yielding nonfunctional proteins.