Metabolism and Bioenergetics

Metabolism

• Sum of all chemical transformations in cells.

Bioenergetics

• Study of energy transformations in biological systems.

Autotrophs

• Organisms that produce their own food from CO2.

Heterotrophs

• Organisms that obtain nutrients from organic sources.

Macromolecules

• Large molecules like proteins and nucleic acids.

Catabolism

• Degradative phase converting nutrients into simpler products.

Anabolism

• Biosynthesis phase forming complex molecules from precursors.

Metabolic Pathway

• Series of enzyme-catalyzed reactions for specific changes.

Metabolites

• Products formed from precursors via metabolic pathways.

Energy Transformation

• Conversion of energy from one form to another.

Nitrogen Source

• Essential for amino acids and nucleotides synthesis.

Photosynthetic Organisms

• Use sunlight to convert CO2 into organic compounds.

Free Energy Loss

• Energy not available for work, often as heat.

Entropy Increase

• Measure of disorder in a system, increases over time.

Substrate Availability

• Immediate factor affecting enzyme activity and reaction rate.

Allosteric Regulation

• Enzyme activity modulated by metabolic intermediates or coenzymes.

Km

• Substrate concentration at which reaction rate is half-max.

Fatty Acid Synthesis

• Anabolic process converting acetyl-CoA into fatty acids.

Fatty Acid Catabolism

• Degradative process breaking down fatty acids for energy.

Enzyme Regulation

• Control of enzyme levels and activity in metabolism.

Growth Factors

• Substances that regulate metabolic activities in multicellular organisms.

Solar Energy

• Primary driving force for autotrophic and heterotrophic cycles.

Chemical Energy

• Energy stored in chemical bonds, released during metabolism.

Open systems

• Living cells exchange energy and materials with surroundings.

Equilibrium

• State where forward and reverse reaction rates equal.

Gibbs free energy (G)

• Energy available for work in a reaction.

Exergonic reaction

• Releases energy, ΔG is negative.

Endergonic reaction

• Absorbs energy, ΔG is positive.

Enthalpy (H)

• Heat content of a reacting system.

Exothermic reaction

• Releases heat, products have lower heat content.

Endothermic reaction

• Absorbs heat, products have higher heat content.

Entropy (S)

• Measure of disorder or randomness in a system.

ΔG equation

• ΔG = ΔH - TΔS relates energy changes.

Isothermal systems

• Cells maintain constant temperature during reactions.

Heterotrophic cells

• Obtain energy from nutrient molecules.

Photosynthetic cells

• Acquire energy from solar radiation.

Equilibrium constant

• Defined by concentrations of reactants and products.

Standard conditions

• 298K temperature, 1M concentrations, 1 atm pressure.

Standard free energy change (ΔG'o)

• Difference in free energy under standard conditions.

Spontaneous reaction

• Occurs when ΔG is negative.

Non-spontaneous reaction

• Occurs when ΔG is positive.

Actual free energy (ΔG)

• Free energy based on current concentrations.

Enzymes

• Catalysts that lower activation energy of reactions.

Covalent bonds

• Chemical bonds formed by shared electrons.

Nucleophiles

• Functional groups that donate electrons.

Electrophiles

• Functional groups that accept electrons.

Reaction types

• Includes carbon bond breaking, rearrangements, and redox.

Carbanion

• Nucleophilic species with a negatively charged carbon.

Carbocation

• Electrophilic species with a positively charged carbon.

Reaction Intermediates

• Unstable species formed during chemical reactions.

Carbonyl Groups

• Functional groups crucial for metabolic pathways.

Delocalization

• Spreading out of charge over multiple atoms.

Acid Catalyst

• Substance that increases reaction rate via proton donation.

Aldol Condensation

• Reaction forming C-C bonds, producing six-carbon compounds.

Claisen Ester Condensation

• Reaction involving thioester stabilization in citric acid cycle.

Decarboxylation

• Process forming ketone bodies during fatty acid metabolism.

Prenyltransferase

• Enzyme catalyzing condensation in cholesterol biosynthesis.

Isomerization

• Intramolecular rearrangement without changing oxidation state.

Cis-Trans Rearrangement

• Rearrangement altering spatial configuration of double bonds.

Homolytic Cleavage

• Breaking covalent bonds to form free radicals.

Adenosylcobalamin

• Vitamin B12 involved in isomerization reactions.

Ribonucleotide Reductase

• Enzyme catalyzing free radical reactions.

Group Transfer Reactions

• Transfer of functional groups between nucleophiles.

Acyl Transfer

• Transfer of acyl groups, e.g., in chymotrypsin reaction.

Glycosyl Transfer

• Transfer of sugar groups during nucleophilic substitution.

Phosphoryl Group Transfer

• Key in metabolic pathways, activating intermediates.

Good Leaving Group

• Group that easily departs during chemical reactions.

Oxidation States

• Carbon can exist in five distinct oxidation states.

Dehydrogenases

• Enzymes catalyzing biological oxidation reactions.

ATP Hydrolysis

• Reaction releasing energy through phosphate bond cleavage.

Standard Free Energy of Hydrolysis

• Energy change during ATP hydrolysis, -30.5 kJ/mol.

Phosphorylated Compounds

• Compounds with high or low phosphoryl group transfer.

Standard Free Energy

• Energy change during hydrolysis of compounds.

Catabolism

• Metabolic process focused on breaking down molecules.

High-Energy Phosphate Compounds

• Compounds that activate transformations in metabolism.

Thermodynamically Unstable ATP

• ATP readily breaks down to release energy.

Activation Energy

• Energy required to initiate a chemical reaction.

SN2 Nucleophilic Displacement

• Type of reaction ATP undergoes during transfers.

Nucleophilic Attack

• Reaction where nucleophiles attack electrophilic centers.

Adenylylation

• Transfer of adenylyl groups from ATP.

Fatty Acid Activation

• Process requiring ATP for fatty acid metabolism.

Nucleoside Triphosphates

• Building blocks for DNA and RNA synthesis.

Phosphoanhydride Linkage

• Bond between alpha and beta phosphates in ATP.

PPi Release

• Byproduct of polymerization reactions involving nucleotides.

Bioluminescence

• Light production via biochemical reactions, requires ATP.

Luciferin

• Biochemical compound activated to produce light.

Luciferase

• Enzyme catalyzing the reaction to produce light.

Biological Membranes

• Structures defining cell boundaries and controlling transport.

Selective Permeability

• Membranes allow specific substances to pass through.

Fluid Mosaic Model

• Describes the dynamic structure of biological membranes.

Glycoproteins

• Proteins with oligosaccharides affecting stability and function.

Membrane Thickness

• Biological membranes are 50-80 Å thick.

Asymmetric Protein Orientation

• Proteins in membranes have specific functional arrangements.

Lateral Diffusion

• Movement of proteins and lipids within the membrane.

Lipids

• Insoluble in water, form aggregates in membranes.

Hydrophobic interactions

• Driving force for bilayer formation and stability.

Micelles

• Spherical lipid structures with head > tail area.

Bilayers

• Two monolayer leaflets create a membrane sheet.

Vesicles

• Closed lipid structures with no exposed hydrophobic ends.

Integral membrane proteins

• Firmly attached proteins requiring detergents for removal.