BIO 2400 - Exam 2 Review Flashcards

Comprehensive vocabulary flashcards covering catabolism, anabolism, bacterial genetics, regulation, and recombinant DNA technology based on the BIO 2400 Exam 2 Review.

Chemo-auto/heterotroph

Classification of organisms based on their source of energy (chemical) and source of carbon (autotrophs use inorganic $CO_2$, heterotrophs use organic compounds).

Photo-auto/heterotroph

Classification of organisms based on their source of energy (light) and source of carbon (autotrophs use inorganic $CO_2$, heterotrophs use organic compounds).

Oxidation

The loss of electrons from a molecule, often paired with a reducing agent during metabolic reactions.

Reduction

The gain of electrons by a molecule, often paired with an oxidizing agent.

Catabolism

Metabolic pathways that break down complex molecules into simpler ones, releasing energy in the process.

Anabolism

Metabolic pathways that construct complex molecules from simpler ones, requiring an input of energy and reducing power.

Glycolysis and Entner-Doudoroff (ED) pathways

Pathways for the oxidation of glucose; they differ in the types of organisms that use them, their overall reactions, and their energy/reducing power yields.

TCA cycle

A series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetyl-CoA, producing precursor metabolites and reducing power.

Fermentation

A process where pyruvate is reduced to lactic acid (or other products) to oxidize NADH back to $NAD^+$ so glycolysis can continue in the absence of respiration.

Proton Motive Force (PMF)

An electrochemical gradient of protons generated across a membrane, used to produce ATP, drive motility, and facilitate active transport.

Electron Transport Chain (ETC)

A series of protein complexes that transfer electrons to a final electron acceptor, using the energy to generate a proton motive force for ATP synthesis.

Prototroph

An organism that can synthesize all the basic nutrients it needs for growth from simple inorganic compounds.

Auxotroph

A mutant organism that requires a specific additional nutrient that the normal (wild type) strain does not.

Calvin cycle

An anabolic pathway used by some organisms to fix $CO_2$ into organic compounds, requiring energy and reducing power.

Gluconeogenesis

The anabolic pathway that synthesizes glucose from non-carbohydrate precursors; it is functionally the reverse of glycolysis with different enzymes at certain steps.

Active transport

The process of moving substances across a membrane against a concentration gradient, which requires energy in the form of ATP.

Semi-conservative replication

The mechanism of DNA replication in which each original strand serves as a template for a new strand, resulting in two DNA molecules each with one old and one new strand.

DNA polymerase III

The primary enzyme that catalyzes the elongation of the DNA strand by adding nucleotides to the $3'$ end in the $5' \rightarrow 3'$ direction.

DNA primase

The enzyme responsible for synthesizing short RNA primers that provide the start point for DNA polymerase III during replication.

Okazaki fragments

Short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand.

Topoisomerase

An enzyme that helps relieve the torsional strain or supercoiling that builds up ahead of the replication fork.

Tus proteins

Proteins that bind to the termination sequences (ter) on DNA to stop the movement of the replication fork.

Sigma factor

A component of the RNA polymerase holoenzyme that is responsible for recognizing and binding to the promoter sequence to initiate transcription.

Rho-independent vs. Rho-dependent termination

Two mechanisms for ending transcription; one relies on specific RNA sequences to form a hairpin loop, while the other requires the Rho protein.

Wobble base pair

A pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules, contributing to the redundancy of the genetic code.

Shine-Dalgarno sequence

A ribosomal binding site in bacterial mRNA, generally located upstream of the start codon AUG, that is critical for the initiation of translation.

Transpeptidation reaction

The formation of a peptide bond between the amino acid in the A site and the growing polypeptide chain in the P site, catalyzed by the ribosome.

Sec pathway

A specific transport system used by bacterial cells to move hydrophilic proteins across or into the cell membrane.

Diauxic growth

A characteristic biphasic growth curve seen in bacteria like E. coli when two sugars are available, involving the regulation of the lac operon.

Silent, Missense, and Nonsense mutations

Types of base substitutions: silent (no amino acid change), missense (different amino acid), and nonsense (results in a premature stop codon).

Frameshift mutation

A mutation caused by the insertion or deletion of nucleotides not in a multiple of three, which shifts the reading frame of the genetic message.

Ames test

A biological assay used to assess the mutagenic potential of chemical compounds using a histidine auxotroph strain.

Natural competence

A physiological state in which a bacterial cell is able to take up exogenous DNA from its environment through transformation.

Bacteriophage and Transduction

A virus that infects bacteria and the process by which it transfers bacterial DNA from one cell to another.

Conjugation

The transfer of genetic material (usually a plasmid) between bacterial cells by direct cell-to-cell contact or a bridge-like connection.

Transposons (Tn)

DNA sequences, discovered by Barbara McClintock, that can move to different positions within a genome, often carrying antibiotic resistance genes.

PCR (Polymerase Chain Reaction)

A technique discovered by Kary Mullis used to amplify DNA regions through cycles of denaturation, annealing, and extension.