Biology Final Fall 2025

Chloroplast

Organelle where photosynthesis occurs; contains thylakoids, grana, and stroma.

Thylakoid

Membrane sacs inside chloroplasts where light reactions occur.

Stroma

The fluid of the chloroplast where the Calvin Cycle occurs.

Pigments

Molecules (like chlorophyll) that absorb light energy for photosynthesis.

Water Splitting (Photolysis)

Occurs in Photosystem II; provides electrons and releases oxygen.

Light Reactions

Chloroplast processes that use light to produce ATP, NADPH, and O₂.

Proton Gradient (Photosynthesis)

Gradient created inside the thylakoid lumen that powers ATP synthase.

Calvin Cycle

Series of reactions in the stroma that fix carbon into sugars.

RuBP / Rubisco

RuBP is the CO₂ acceptor; Rubisco is the enzyme that fixes carbon.

Carbon Fixation

Incorporation of CO₂ into organic molecules.

C₄ Plants

Plants that separate carbon fixation spatially to reduce photorespiration.

CAM Plants

Plants that open stomata at night and fix carbon temporally.

Redox Reaction

Reaction involving transfer of electrons; oxidation = loss, reduction = gain.

Substrate-Level Phosphorylation

Direct ATP formation by transferring a phosphate to ADP.

Chemiosmosis

Using a proton gradient to power ATP synthase.

Glycolysis

Cytoplasmic pathway that breaks glucose into pyruvate, ATP, and NADH.

Krebs Cycle

Mitochondrial matrix pathway producing CO₂, ATP, NADH, and FADH₂.

Electron Transport Chain

Inner mitochondrial membrane proteins that create the proton gradient.

ATP Synthase

Enzyme that uses proton flow to form ATP.

Polymer

Large molecule made of repeating monomers.

Dehydration Synthesis

Forms polymers by removing water.

Hydrolysis

Breaks polymers by adding water.

Carbohydrates

Sugars and starches; monomer = monosaccharides.

Proteins

Polymers of amino acids; have primary, secondary, tertiary, and quaternary structure.

Lipids

Hydrophobic molecules such as fats and phospholipids.

Nucleic Acids

DNA/RNA; monomer = nucleotide.

Cell Membrane Structure

Phospholipid bilayer with embedded proteins controlling transport.

Chromosome

A DNA molecule tightly wrapped around proteins.

Mitosis

Division of somatic cells to produce identical daughter cells.

Meiosis

Division to form gametes with half the chromosome number.

Crossing Over

Exchange of DNA between homologous chromosomes during meiosis I.

Linked Genes

Genes close together on a chromosome that are inherited together.

Gene

A DNA sequence that encodes a trait.

Allele

Variant form of a gene.

Dominant Allele

Expressed even when only one copy is present.

Recessive Allele

Expressed only when two copies are present.

Segregation

Alleles separate into different gametes during meiosis.

Pleiotropy

One gene influences multiple traits.

Pedigree

Diagram showing inheritance of traits through generations.

DNA Replication

Semi-conservative copying of DNA using enzymes like helicase and DNA polymerase.

Leading Strand

Continuously synthesized DNA strand.

Lagging Strand

Discontinuously synthesized strand made of Okazaki fragments.

Central Dogma

Flow of information: DNA → RNA → Protein.

Mutation

A change in DNA that may alter protein sequence.

Transcription

Process of making RNA from a DNA template in eukaryotic nuclei.

Coding Strand

DNA strand with the same sequence as RNA (except T/U).

Template Strand

DNA strand used by RNA polymerase to build RNA.

Gene Expression (Bacteria)

Control of transcription, translation, or post-translation to regulate proteins.

Negative Control

Repressor prevents transcription.

Positive Control

Activator increases transcription.

Chromatin Remodeling

Chemical modification of DNA/histones allowing or blocking transcription.

DNA Methylation

Addition of methyl groups that reduce gene expression.

Histone Acetylation

Loosens chromatin to increase transcription.

General Transcription Factors

Proteins required for basic transcription initiation.

Regulatory Transcription Factors

Proteins that enhance or repress transcription of specific genes.

Alternative Splicing

Process allowing one gene to produce multiple proteins.

Ubiquitin

Tag that marks proteins for degradation.

Proteasome

Enzyme complex that degrades ubiquitin-tagged proteins.