NPB 110A: Foundations - From Molecules to Individuals Review Flashcards

Comprehensive vocabulary flashcard set covering all 300 key terms, quantitative values, proper nouns, physiological pathways, and figures across NPB 110A Lectures 1 through 5.

Glycolysis

A sequence of enzyme-catalyzed reactions by which glucose is converted into pyruvate, capturing some oxidation free-energy in the synthesis of ATP and NADH + H+.

Preparatory Phase of Glycolysis

The initial phase of glycolysis in which glucose is phosphorylated and converted to glyceraldehyde 3-phosphate, consuming ATP in two priming reactions.

Payoff Phase of Glycolysis

The second phase of glycolysis involving the oxidative conversion of glyceraldehyde 3-phosphate to pyruvate, coupled with the formation of ATP and NADH.

Hexokinase

The glycolytic enzyme that catalyzes the first priming reaction, transferring a phosphate group from ATP to glucose to form glucose 6-phosphate.

Phosphohexose Isomerase

The glycolytic enzyme that catalyzes the reversible isomerization of glucose 6-phosphate into fructose 6-phosphate.

Phosphofructokinase-1 (PFK-1)

The key regulatory enzyme of glycolysis that catalyzes the second priming reaction, converting fructose 6-phosphate and ATP into fructose 1,6-bisphosphate and ADP.

Aldolase

The enzyme that catalyzes the cleavage of the 6-carbon sugar phosphate fructose 1,6-bisphosphate into two 3-carbon sugar phosphates: glyceraldehyde 3-phosphate and dihydroxyacetone phosphate.

Triose Phosphate Isomerase

The enzyme that catalyzes the reversible interconversion between dihydroxyacetone phosphate and glyceraldehyde 3-phosphate.

Glyceraldehyde 3-Phosphate Dehydrogenase

The enzyme that catalyzes the oxidation and phosphorylation of glyceraldehyde 3-phosphate to yield 1,3-bisphosphoglycerate and reduction of $\text{NAD}^+$ to NADH + H+.

Phosphoglycerate Kinase

The enzyme that catalyzes the first ATP-forming substrate-level phosphorylation reaction, transferring a phosphate group from 1,3-bisphosphoglycerate to ADP to yield 3-phosphoglycerate and ATP.

Phosphoglycerate Mutase

The enzyme that catalyzes the internal shift of the phosphate group from 3-phosphoglycerate to form 2-phosphoglycerate.

Enolase

The enzyme that catalyzes the dehydration of 2-phosphoglycerate to form the high-energy compound phosphoenolpyruvate (PEP).

Pyruvate Kinase

The enzyme that catalyzes the second ATP-forming substrate-level phosphorylation reaction, converting phosphoenolpyruvate and ADP into pyruvate and ATP.

Glucose 6-Phosphate

The phosphorylated sugar produced by hexokinase in step 1 of glycolysis that inhibits hexokinase when present in high concentrations.

Fructose 6-Phosphate

The product of the phosphohexose isomerase reaction in glycolysis, which serves as the substrate for phosphofructokinase-1.

Fructose 1,6-Bisphosphate

The 6-carbon sugar bisphosphate formed by PFK-1 that is cleaved by aldolase in step 4 of glycolysis.

Glyceraldehyde 3-Phosphate (G3P)

A 3-carbon sugar phosphate produced by aldolase cleavage and triose phosphate isomerase that directly enters the payoff phase of glycolysis.

Dihydroxyacetone Phosphate (DHAP)

A 3-carbon keto sugar phosphate generated by aldolase cleavage that is converted into glyceraldehyde 3-phosphate by triose phosphate isomerase.

1,3-Bisphosphoglycerate

An acyl phosphate intermediate in glycolysis containing a high-energy phosphate bond used to generate ATP via phosphoglycerate kinase.

3-Phosphoglycerate

The product generated along with ATP when phosphoglycerate kinase transfers a phosphate group from 1,3-bisphosphoglycerate to ADP.

2-Phosphoglycerate

The product of the phosphoglycerate mutase reaction that is dehydrated by enolase to generate phosphoenolpyruvate.

Phosphoenolpyruvate (PEP)

The high-energy enol phosphate intermediate in step 9 of glycolysis that donates its phosphate group to ADP via pyruvate kinase.

Pyruvate

The 3-carbon end product of glycolysis under aerobic conditions, which can be oxidized further or fermented under anaerobic conditions.

First Priming Reaction

The phosphorylation of glucose to glucose 6-phosphate by hexokinase, consuming $1\text{ ATP}$.

Second Priming Reaction

The phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate by phosphofructokinase-1, consuming $1\text{ ATP}$.

Substrate-Level Phosphorylation

The direct synthesis of ATP (or GTP) from ADP by the transfer of a phosphate group from a high-energy phosphorylated metabolic intermediate.

Irreversible Steps in Glycolysis

The three non-equilibrium reactions in glycolysis catalyzed by hexokinase, phosphofructokinase-1, and pyruvate kinase.

Tumor Cell Glycolysis

The metabolic phenotype wherein cancer cells display dramatically elevated rates of glycolysis even in the presence of oxygen.

GLUT1 and GLUT3

Glucose transporters whose expression is upregulated in cancer cells to increase cellular glucose uptake.

HIF-1 (Hypoxia-Inducible Factor 1)

A transcription factor upregulated under hypoxic conditions that increases the synthesis of glycolytic enzymes in cells.

2-Deoxyglucose

An inhibitor molecule that targets hexokinase at the start of glycolysis.

Lonidamine

A drug compound that inhibits hexokinase in tumor cells.

3-Bromopyruvate

An investigational anticancer agent that acts as an inhibitor of hexokinase.

6-Amino Nicotinic Acid

An inhibitor molecule that targets glucose 6-phosphate dehydrogenase.

Oxythiamine

An enzyme inhibitor that targets transketolase in carbohydrate metabolism pathways.

Fates of Pyruvate

The three metabolic pathways available to pyruvate depending on oxygen availability: conversion to acetyl-CoA (aerobic), ethanol (yeast fermentation), or lactate (hypoxic/anaerobic muscle fermentation).

Lactate Fermentation

The reduction of pyruvate to L-lactate catalyzed by lactate dehydrogenase, which regenerates $\text{NAD}^+$ to allow glycolysis to continue under anaerobic conditions.

Lactate Dehydrogenase

The enzyme that reduces pyruvate to L-lactate while oxidizing NADH + H+ back to $\text{NAD}^+$.

L-Lactate

The final reduced end product of anaerobic fermentation in vigorously contracting muscle cells, erythrocytes, and certain microorganisms.

Anaerobic Respiration Output

Under anaerobic conditions, glycolysis yields a net of $2\text{ ATP}$ per glucose along with lactate or ethanol/$\text{CO}_2$, regenerating $\text{NAD}^+$ for continued glycolytic flux.

Citric Acid Cycle (CAC / Krebs Cycle)

A cyclic pathway of eight enzyme-catalyzed reactions in mitochondria that oxidizes acetyl-CoA to $\text{CO}_2$, generating NADH, $\text{FADH}_2$, and GTP/ATP.

Citrate Synthase

The enzyme that catalyzes the condensation of oxaloacetate and acetyl-CoA with water to form citrate and free CoA.

Aconitase

The enzyme that catalyzes the reversible isomerization of citrate to isocitrate via the intermediate cis-aconitate.

Isocitrate Dehydrogenase

The enzyme that oxidizes and decarboxylates isocitrate to $\alpha$-ketoglutarate, producing $\text{CO}_2$ and NADH + H+.

alpha-Ketoglutarate Dehydrogenase

The enzyme complex that oxidizes and decarboxylates $\alpha$-ketoglutarate in the presence of CoA, forming succinyl-CoA, $\text{CO}_2$, and NADH + H+.

Succinyl-CoA Synthetase

The enzyme that cleaves the high-energy thioester bond of succinyl-CoA to produce succinate, coupling it to substrate-level phosphorylation of GDP + Pi to GTP.

Succinate Dehydrogenase

The membrane-bound enzyme of the Krebs cycle (Complex II of ETC) that oxidizes succinate to fumarate while reducing FAD to $\text{FADH}_2$.

Fumarase

The enzyme that catalyzes the reversible hydration of fumarate to L-malate.

Malate Dehydrogenase

The enzyme that oxidizes malate to oxaloacetate, reducing $\text{NAD}^+$ to NADH + H+ to complete the Krebs cycle.

Oxaloacetate (OAA)

The 4-carbon dicarboxylic acid intermediate that accepts the acetyl group from acetyl-CoA to initiate the citric acid cycle.

Citric Acid Cycle Coupling

The tight functional coupling in mitochondria between the citric acid cycle, electron transport chain, and ADP phosphorylation.

Global Pathway of Respiration

The integrated flow of glucose from digestion through blood plasma into cell cytoplasm, undergoing glycolysis to pyruvic acid before aerobic entry into the mitochondrion for the Krebs cycle and electron transport.

Oxidative Phosphorylation

The process in which ATP is formed as a result of electron transfer from NADH or $\text{FADH}_2$ to $\text{O}_2$ by a series of electron carriers in the mitochondrial inner membrane.

Complex I (NADH Dehydrogenase)

The first protein complex of the mitochondrial inner membrane that accepts electrons from NADH and pumps $4\text{ H}^+$ from the matrix into the intermembrane space.

Complex II (Succinate Dehydrogenase)

The second complex of the inner mitochondrial membrane that accepts electrons from succinate/$\text{FADH}_2$ and transfers them to Coenzyme Q without pumping protons.

Complex III (Cytochrome bc1 Complex)

The third inner membrane complex that transfers electrons from reduced Coenzyme Q to cytochrome c, pumping $4\text{ H}^+$ across the inner membrane.

Complex IV (Cytochrome c Oxidase)

The terminal inner membrane complex that transfers electrons from cytochrome c to oxygen ($\frac{1}{2}\text{O}_2$), forming $\text{H}_2\text{O}$ and pumping $2\text{ H}^+$ into the intermembrane space.

Complex V (ATP Synthase)

The protein complex composed of $F_o$ and $F_1$ components that utilizes energy from returning matrix protons to couple ADP and Pi into ATP.

Fo Component

The membrane-embedded channel portion of ATP synthase through which protons flow from the intermembrane space back into the mitochondrial matrix.

F1 Component

The catalytic subunit of ATP synthase located on the matrix side that synthesizes ATP from ADP and inorganic phosphate.

Coenzyme Q (Ubiquinone / Q)

A lipid-soluble mobile electron carrier in the inner mitochondrial membrane that accepts electron pairs from Complexes I and II and delivers them to Complex III.

Cytochrome c (Cyt c)

A small water-soluble intermembrane protein carrier that shuttles single electrons from Complex III to Complex IV.

Uncoupling Proteins (UCP)

Mitochondrial inner membrane proteins that allow protons to flow back into the matrix without passing through ATP synthase, dissipating the electrochemical gradient as heat.

Cyanide Poisoning Effect

Inhibition of Complex IV by cyanide halts electron transport through the respiratory chain and causes the electrochemical proton gradient across the inner membrane to decrease and collapse.

Standard ATP Yield per Glucose

The standard empirical net yield of $30\text{ ATP}$ generated per molecule of glucose in aerobic respiration.

ATP Yield per NADH

Yields $2.5\text{ ATP}$ when processed via oxidative phosphorylation (or $3\text{ ATP}$ in theoretical maximum estimates).

ATP Yield per FADH2

Yields $1.5\text{ ATP}$ when processed via oxidative phosphorylation (or $2\text{ ATP}$ in theoretical maximum estimates).

Theoretical Maximum ATP Yield

Calculated as $36\text{ ATP}$ to $38\text{ ATP}$ per glucose molecule depending on whether cytoplasmic NADH enters as $\text{FADH}_2$ or NADH.

Direct ATP Gain in Glycolysis

A net gain of $2\text{ ATP}$ directly generated per glucose molecule by substrate-level phosphorylation in the cytoplasm.

Direct ATP/GTP Gain in Krebs Cycle

A direct production of $1\text{ ATP}$ (or GTP) per turn of the Krebs cycle, equaling $2\text{ ATP}$ per original glucose molecule.

Atom

The most fundamental chemical level of structure listed in the biological levels of organization.

Molecule

A chemical structure consisting of two or more atoms held together by chemical bonds, such as membrane phospholipids.

Organelle

A specialized subunit within a cell that has a specific function, such as mitochondria or lysosomes.

Cell

The fundamental structural and functional unit of living organisms.

Tissue

An aggregate of specialized cells and extracellular material organized to perform a common function.

Organ

A body structure composed of two or more primary tissues integrated together to perform specific functions.

Body System

A collection of organs that perform related functions and interact to accomplish a common physiological purpose.

Organism

A complete individual living entity composed of integrated body systems working together.

Levels of Organization Hierarchy

The structural ordering of complex biological life from atom to molecule, organelle, cell, tissue, organ, body system, and organism.

Muscle Tissue

One of the four primary tissue types specialized for contraction and force generation, categorized into skeletal, cardiac, and smooth muscle.

Skeletal Muscle Tissue

Striated muscle tissue attached to bones responsible for voluntary body movements.

Cardiac Muscle Tissue

Involuntary striated muscle tissue found exclusively in the wall of the heart.

Smooth Muscle Tissue

Involuntary unstriated muscle tissue found in the walls of hollow organs and tubes such as the stomach and blood vessels.

Nervous Tissue

A primary tissue type specialized for initiating and transmitting electrical signals, divided into central and peripheral nervous systems.

Central Nervous System Tissue

Nervous tissue comprising the brain and spinal cord responsible for integrating and processing physiological signals.

Peripheral Nervous System Tissue

Nerves extending throughout the body that communicate signals between the central nervous system and distant target tissues.

Epithelial Tissue

A primary tissue type specialized for exchange of materials, forming boundary sheets and secretory glands.

Epithelial Sheets

Layers of tightly joined epithelial cells that line outer and inner body surfaces to form protective boundaries.

Exocrine Glands

Glands derived from epithelial tissue that secrete products through ducts into external environments or hollow body cavities.

Endocrine Glands

Ductless glands derived from epithelial tissue that secrete regulatory hormones directly into the blood.

Connective Tissue

A primary tissue type that provides structural support and connects body parts, characterized by sparse cells in an extracellular matrix.

Tendons

Cords of dense connective tissue that anchor skeletal muscle to bone.

Bone Tissue

Rigid calcified connective tissue that forms the skeletal frame of the body.

Blood

A fluid connective tissue consisting of cells suspended in a liquid plasma matrix.

Four Primary Tissue Types

The four fundamental tissue classifications: muscle (contraction), nervous (signals), epithelial (exchange), and connective (structural support).

Stomach Tissue Integration

An organ example integrating epithelial tissue (protective barrier and digestive secretion), smooth muscle (wall contraction), nervous tissue (contraction regulation), and connective tissue (structural support).

Circulatory System

The body system comprising the heart, blood vessels, and blood responsible for transporting materials throughout the body.

Digestive System

The body system including the mouth, esophagus, stomach, and intestines that breaks down food and absorbs nutrients.

Respiratory System

The body system consisting of lungs and major airways involved in gas exchange ($\text{O}_2$ uptake and $\text{CO}_2$ elimination).

Urinary System

The body system comprising kidneys and associated structures responsible for filtering blood plasma and removing metabolic wastes.