BIOL 1510 Exam III Vocabulary Review

Comprehensive vocabulary flashcards covering Chapters 7, 14, 15, and 16 of BIOL 1510, focusing on cellular respiration, DNA replication, gene expression, and gene regulation.

Cellular respiration

The catabolic process by which cells break down glucose to make usable $ATP$;

its aerobic equation is $C_6H_{12}O_6 + 6\,O_2 \rightarrow 6\,CO_2 + 6\,H_2O + \text{approximately } 30\,ATP$ in eukaryotes.

Substrate-level phosphorylation

A mode of $ATP$ synthesis where an enzyme directly transfers a phosphate group from an energy-rich substrate to $ADP$, occurring in glycolysis and the citric acid/Krebs cycle without the use of $ATP$ synthase.

Oxidative phosphorylation

The production of $ATP$ using an electron transport chain to pump $H^+$ across the inner mitochondrial membrane, driving $ATP$ synthase as $H^+$ flows down its gradient.

$NAD^+$ / $NADH$

$NAD^+$ is an oxidized electron-poor carrier that accepts electrons to become reduced to $NADH$; $NADH$ donates those electrons to the electron transport chain and is oxidized back to $NAD^+$.

Cristae

The folded inner membranes of a mitochondrion that increase surface area for the electron transport chain and $ATP$ synthase complexes.

Mitochondrial matrix

The internal fluid space enclosed by the inner mitochondrial membrane where pyruvate oxidation and the citric acid/Krebs cycle occur.

Glycolysis

An anaerobic metabolic pathway occurring in the cytosol that splits one six-carbon glucose into two three-carbon pyruvates, yielding a net of $2\,ATP$ by substrate-level phosphorylation and $2\,NADH$.

Pyruvate oxidation

An intermediate step in the mitochondrial matrix that converts each three-carbon pyruvate into a two-carbon acetyl-CoA, releasing one $CO_2$ and producing one $NADH$ per pyruvate ($0\,ATP$ made directly).

Citric acid cycle (Krebs cycle)

An eight-reaction cycle in the mitochondrial matrix that oxidizes acetyl-CoA, releasing $4\,CO_2$ and producing $2\,ATP$, $6\,NADH$, and $2\,FADH_2$ per glucose molecule.

Electron transport chain (ETC)

A series of protein complexes embedded in the inner mitochondrial membrane that transfer electrons from $NADH$ and $FADH_2$ to $O_2$, using the released energy to pump $H^+$ from the matrix to the intermembrane space.

Chemiosmosis

The passive facilitated movement of $H^+$ ions from the intermembrane space down their electrochemical gradient back into the matrix through $ATP$ synthase to power $ATP$ synthesis.

$ATP$ synthase

A membrane-bound enzyme complex that couples the passive flow of $H^+$ ions down their concentration gradient to the phosphorylation of $ADP$ into $ATP$.

Final electron acceptor

The terminal molecule accepting electrons at the end of the electron transport chain; it is $O_2$ in aerobic respiration (forming $H_2O$) and non-oxygen molecules like nitrate, sulfate, or carbon dioxide in anaerobic respiration.

Anaerobic respiration

A form of cellular respiration that utilizes an electron transport chain with an inorganic final electron acceptor other than oxygen (such as nitrate, sulfate, or carbon dioxide).

Fermentation

An anaerobic metabolic pathway without an electron transport chain that generates a net $2\,ATP$ per glucose via glycolysis while reducing pyruvate to regenerate $NAD^+$ from $NADH$.

Lactic acid fermentation

A fermentation process where electrons from $NADH$ reduce pyruvate to lactate (lactic acid), regenerating $NAD^+$ without producing extra $ATP$ beyond the $2\,\text{net } ATP$ from glycolysis.

Alcoholic fermentation

A fermentation pathway where pyruvate is converted into ethanol and $CO_2$, oxidizing $NADH$ to $NAD^+$ without producing extra $ATP$ beyond the $2\,\text{net } ATP$ from glycolysis.

Hershey–Chase experiment

A 1952 experiment utilizing bacteriophages labeled with radioactive sulfur-35 ($^{35}S$) in proteins and phosphorus-32 ($^{32}P$) in DNA, demonstrating that DNA enters host bacteria and constitutes the genetic material.

Complementary base pairing

The specific pairing in DNA where adenine (A) pairs with thymine (T) via two hydrogen bonds and guanine (G) pairs with cytosine (C) via three hydrogen bonds.

Antiparallel

The structural arrangement of DNA where the two strands run in opposite orientations, one in the $5'\rightarrow 3'$ direction and the other in the $3'\rightarrow 5'$ direction.

Semiconservative replication

The model of DNA copying where each newly formed double helix consists of one intact original parental strand and one newly synthesized daughter strand.

Origins of replication

Specific nucleotide sequences on a chromosome where DNA replication begins and replication forks open bidirectionally.

DNA gyrase

A topoisomerase enzyme that relieves torsional twisting strain and prevents excessive supercoiling ahead of the moving replication fork.

Helicase

An enzyme that untwists and separates the two complementary parental strands of DNA by disrupting base-pair hydrogen bonds to establish replication forks.

RNA primase

An enzyme that synthesizes a short complementary RNA primer on single-stranded DNA to provide a free $3'$ hydroxyl end required for DNA polymerase activity.

DNA polymerase III

The primary enzyme responsible for synthesizing new DNA strands, reading the template $3'\rightarrow 5'$ and adding complementary nucleotides in the $5'\rightarrow 3'$ direction.

Leading strand

The continuous DNA strand synthesized by DNA polymerase III moving in the $5'\rightarrow 3'$ direction toward the opening replication fork.

Lagging strand

The discontinuous DNA strand synthesized away from the replication fork in short segments called Okazaki fragments, requiring multiple RNA primers.

DNA polymerase I

An enzyme that removes RNA primer sequences, replaces them with complementary DNA nucleotides, and provides proofreading capabilities.

DNA ligase

An enzyme that catalyzes phosphodiester bonds to seal breaks or nicks in the sugar-phosphate backbone, joining Okazaki fragments into a continuous strand.

Promoter

A specific DNA sequence upstream of a gene where RNA polymerase or general transcription factors bind to initiate transcription.

TATA box

A core eukaryotic promoter sequence located approximately $25\text{ to }35$ base pairs upstream of the transcription start site that binds general transcription factors.

Prokaryotic terminator

A DNA termination sequence that produces an RNA hairpin rich in C–G pairs followed by four or more uracil ($U$) nucleotides, stalling RNA polymerase and releasing the transcript.

$5'$ cap and poly-A tail

Modifications added to eukaryotic pre-mRNA comprising a GTP-derived cap at the $5'$ end and a sequence of $100\text{ to }200$ adenines at the $3'$ end, both functioning to stabilize the transcript and protect it from degradation.

Spliceosome

An RNA-protein complex composed of small nuclear RNAs and proteins (snRNPs) that excises noncoding introns and ligates coding exons together in eukaryotic pre-mRNA.

Alternative splicing

The selective inclusion or exclusion of different exons from a single pre-mRNA transcript, allowing a single gene to encode multiple distinct protein variants.

Codon

A sequence of three consecutive nucleotides on an mRNA molecule that specifies a particular amino acid or signals translation termination.

Anticodon

A triplet sequence of nucleotides on a transfer RNA (tRNA) molecule complementary to an mRNA codon.

Ribosomal A, P, and E sites

Three tRNA-binding sites on the ribosome: the A site binds incoming aminoacyl-tRNAs, the P site holds the tRNA carrying the growing polypeptide, and the E site is where uncharged tRNAs exit.

Silent mutation

A nucleotide substitution that changes a codon without changing the encoded amino acid due to redundancy in the genetic code.

Missense mutation

A nucleotide substitution that alters a codon so that it codes for a different amino acid.

Nonsense mutation

A nucleotide substitution that converts an amino acid-specifying codon into a premature stop codon, resulting in a truncated, incomplete polypeptide.

Frameshift mutation

The insertion or deletion of nucleotides in numbers not divisible by three, shifting the reading frame and changing all downstream amino acid codons.

Gene expression

The overall process of utilizing information encoded in DNA (genotype) through transcription and translation to produce functional RNA and proteins that determine cell phenotype.

Operon

A functional unit of bacterial genomic DNA containing a cluster of genes transcribed under the control of a single promoter and shared operator.

Operator

A regulatory DNA sequence within a bacterial operon to which a repressor protein can bind to physically block RNA polymerase transcription.

Repressor

A regulatory protein that mediates negative control by binding to specific DNA sequences (such as operators) to prevent or reduce transcription.

Activator

A regulatory protein that mediates positive control by binding to regulatory DNA (such as enhancers) to stimulate transcription by recruiting RNA polymerase.

Lac operon

An inducible bacterial operon encoding lactose-metabolizing enzymes; it is switched OFF when a repressor binds the operator in lactose's absence, and turned ON when lactose binds and inactivates the repressor.

Trp operon

A repressible bacterial operon containing genes for tryptophan synthesis; it is switched ON when tryptophan is absent, and turned OFF when tryptophan binds the repressor, enabling it to block the operator.

Enhancers

Eukaryotic regulatory DNA sequences that bind specific transcription factors (activators), stimulating transcription when DNA loops to allow activators to contact the RNA polymerase II initiation complex.

Translation-repressor proteins

Proteins that regulate gene expression post-transcriptionally by binding mRNA sequences to block ribosome translation, such as the iron-regulatory protein (IRP) binding ferritin mRNA at low iron concentrations.

Ubiquitin

A small, conserved eukaryotic regulatory protein that covalently tags misfolded, damaged, or unneeded proteins, marking them for destruction.

Proteasome

A large, cylindrical protein complex that recognizes ubiquitin-tagged proteins and degrades them into small peptides and amino acids.