BIO 41 EXAM 3

Activated Carriers

Small molecules like ATP and NADH that store energy in a form the cell can easily use to perform work.

Stage 1 (Digestion)

The breakdown of macromolecules into smaller subunits (proteins to amino acids, polysaccharides to simple sugars, fats to fatty acids/glycerol) in the digestive system.

Stage 2 (Subunit Breakdown)

The conversion of subunits into Acetyl CoA, producing small amounts of ATP and NADH

includes Glycolysis.

Stage 3 (Complete Oxidation)

The final oxidation of the acetyl group in Acetyl CoA into CO2 and H2O in the mitochondria, yielding large amounts of ATP.

Glycolysis

The first step of glucose breakdown in the cytosol, it splits one glucose molecule into two pyruvates, yielding a net of 2 ATP and NADH.

Pyruvate

The 3-carbon molecule produced at the end of glycolysis.

Acetyl CoA

A molecule formed in the mitochondrial matrix from pyruvate or fatty acids that carries a 2-carbon acetyl group into the Citric Acid Cycle.

Citric Acid Cycle

A series of mitochondrial reactions that oxidize acetyl groups into CO2, producing 3 NADH, 1 FADH2 and 1 GTP per turn.

Oxaloacetate

The 4-carbon molecule that combines with an acetyl group to form Citrate at the start of the Citric Acid Cycle.

Citrate

The 6-carbon molecule created at the beginning of the Citric Acid Cycle.

GTP (Guanine Triphosphate)

An energy carrier similar to ATP used specifically in the Citric Acid Cycle.

Oxidative Phosphorylation

The membrane-based process where the ETC and ATP synthase produce ATP using oxygen as the final electron acceptor.

Electron Transport Chain (ETC)

A series of electron carriers in the inner mitochondrial membrane that uses high-energy electrons to pump protons (H+).

Fermentation

The incomplete oxidation of pyruvate occurring in the absence of oxygen which produces lactate in animal cells or ethanol in yeast.

Anabolic

Metabolic pathways that use energy to build larger molecules from smaller subunits.

Catabolic

Metabolic pathways that break down molecules to extract energy.

Glycogen

A branched polymer of glucose used by animal cells for long-term energy storage.

Mitochondrial Structure & Energetics
Matrix

The large internal space of the mitochondria containing enzymes for the Citric Acid Cycle.

Inner Mitochondrial Membrane

The highly folded membrane that houses the ETC and ATP synthase.

Outer Mitochondrial Membrane

The porous exterior membrane that allows molecules up to 5000 MW to pass through.

Intermembrane Space

The region between the inner and outer membranes where protons are concentrated.

Proton Gradient

A difference in H+ concentration across a membrane that stores potential energy.

Membrane Potential

The difference in electrical charge across a membrane.

Proton-Motive Force

The combined potential energy of the concentration gradient and the electrical charge used to drive protons through ATP synthase.

ATP Synthase

A membrane-bound enzyme that uses the flow of protons (H+) down their gradient to synthesize ATP from ADP.

Uncoupling

The process where the inner membrane becomes permeable to H+, allowing protons to bypass ATP synthase and releasing energy as heat.

Uncoupling Protein

A specialized protein in adipose tissue that generates body heat by allowing H+ permeability.

Redox Potential

A measure of electron affinity in millivolts (mV), electrons flow from molecules with low potential to those with higher potential.

Electron Affinity

The measure of how strongly a molecule attracts and holds onto electrons.

Photosynthesis & The Chloroplast
Photosynthesis

The process of using light energy to synthesize organic molecules (like glucose) from CO2.

Light-Dependent Reactions (Stage 1)

The phase capturing solar energy to produce ATP and NADPH.

Light-Independent Reactions (Stage 2)

The phase using ATP and NADPH to "fasten" CO2 together into glucose.

Chlorophyll

Light-absorbing pigment molecules that preferentially absorb red and blue light and reflect green light.

Antenna Complexes

Bundles of chlorophyll molecules that collect light energy and transfer it toward a reaction center.

Chlorophyll Special Pair

Specific chlorophyll molecules connected to an electron transport chain that receive energy from antenna complexes.

Photosystem II (PSII)

The complex that energizes electrons from water to produce ATP and oxygen as a waste product.

Photosystem I (PSI)

The complex that re-energizes electrons to produce NADPH.

NADPH

An activated carrier similar to NADH, containing an extra phosphate group, used exclusively in photosynthesis.

Thylakoid Membrane

The highly folded internal membrane of the chloroplast where light-dependent reactions occur.

Cell Signaling & Switch Mechanisms
Cell Signaling

The process of detecting, processing, and responding to environmental or chemical signals.

Endocrine Signaling

Long-range signaling using hormones distributed through the bloodstream.

Paracrine Signaling

Local signaling where chemicals are released into the extracellular fluid to act on nearby cells.

Neuronal Signaling

Fast signaling where electrical impulses travel down an axon to release neurotransmitters.

Contact-Dependent Signaling

Signaling that requires direct physical contact between a membrane-bound signal and a receptor.

Extracellular Signal

A chemical that binds to a specific receptor (surface or intracellular) to change cell behavior.

Acetylcholine

A signaling molecule that induces different responses in heart, salivary, and skeletal muscle cells.

Molecular Switches

Proteins that can be toggled between "on" and "off" states to control signaling pathways.

Kinase

An enzyme that adds a phosphate group to a protein (Phosphorylation) to change its activity.

Phosphatase

An enzyme that removes a phosphate group from a protein.

GTPase

A switch protein that is "on" when bound to GTP and "off" when it hydrolyzes GTP to GDP.

GAP (GTPase Activating Protein)

A protein that helps a GTPase hydrolyze GTP to GDP, turning it "off."

GEF (Guanine Exchange Factor)

A protein that helps a GTPase swap GDP for a new GTP, turning it "on."

Positive Feedback

A regulation mechanism where a downstream protein increases the activity of an earlier component to amplify a signal.

Negative Feedback

A regulation mechanism where a downstream protein inhibits an earlier component to decrease a signal.

Cell Surface & Intracellular Receptors
Ion-Channel-Coupled Receptor

Also called a ligand-gated ion channel

it opens in response to a signal, changing membrane voltage rapidly.

G-Protein Coupled Receptor (GPCR)

A 7-pass transmembrane receptor that activates a heterotrimeric G-protein.

Heterotrimeric G-protein

A membrane-associated protein with three subunits that activates signaling pathways when bound to GTP.

Second Messenger

Small, diffusible molecules like cAMP or Inositol Triphosphate that amplify a signal within the cell.

Adenylyl Cyclase

The enzyme that synthesizes cAMP from ATP.

Cyclic AMP Phosphodiesterase

The enzyme that degrades/breaks down cAMP.

Phospholipase C

An enzyme that cleaves membrane lipids to produce inositol triphosphate.

Enzyme-Coupled Receptor

A receptor that either acts as an enzyme or associates with one (e.g., RTK).

Receptor Tyrosine Kinase (RTK)

Receptors that dimerize and phosphorylate themselves to create docking sites for signaling proteins.

Ras

A monomeric GTPase often activated by RTKs to initiate a kinase cascade.

Kinase Cascade

A series of protein kinases that phosphorylate each other in sequence to amplify and regulate a signal.

Intracellular Receptor

Receptors inside the cell that bind to hydrophobic signals like steroid hormones (e.g., testosterone, cortisol).

Ethylene Signaling

A plant-specific pathway where the hormone inactivates its receptor to allow gene transcription.

Programmed Cell Death

A regulated process where a cell dismantles itself, often triggered by a lack of incoming survival signals.