General Biology/Cells/Energy and Metabolism

Energy

 * The capacity to do work.
 * Kinetic energy: energy of motion (ex. jogging).
 * Potential energy: stored energy (ex. a lion that is about to leap on its prey).
 * Many forms of energy: e.g.,
 * Heat
 * Sound
 * Electric current
 * Light
 * All convertible to heat
 * Most energy for biological world is from sun
 * Heat (energy of random molecular motion, thermal energy)
 * Convenient in biology
 * All other energy forms can be converted to heat
 * Thermodynamics: study of thermal energy
 * Heat typically measured in kilocalories
 * Kcal: 1000 calories
 * 1 calorie: amount of heat required to raise the temperature of one gram of water one degree Celsius (°C)
 * Heat plays major role in biological systems
 * Ecological importance
 * Biochemical reactions

Oxidation–Reduction

 * Energy flows into biological world from sun
 * Light energy is captured by photosynthesis
 * Light energy raises electrons to higher energy levels
 * Stored as potential energy in covalent C-H bonds of sugars
 * Strength of covalent bond is measured by amount of energy required to break it
 * 98.8 kcal/mole of C-H bonds
 * In chemical reaction, energy stored in covalent bonds may transfer to new bonds. When this involves transfer of electrons, it is oxidation–reduction reaction
 * Always take place together
 * Electron lost by atom or molecule through oxidation is gained by another atom or molecule through reduction
 * Potential energy is transferred from one molecule to another (but never 100%)
 * Often called redox reactions
 * Photosynthesis
 * Cellular Respiration
 * Chemiosynthesis
 * Autotrophs
 * Heterotrophs

NAD+

 * Common electron acceptor/donor in redox reactions
 * Energetic electrons often paired with H+

Free energy

 * Energy required to break and subsequently form other chemical bonds
 * Chemical bonds: sharing of electrons, tend to hold atoms of molecule together
 * Heat, by increasing atomic motion, makes it easier to break bonds (entropy)
 * Energy available to do work in a system
 * In cells, G = H - TS
 * G = Gibbs’ free energy
 * H = H (enthalpy) energy in molecule’s chemical bonds
 * TS (T, temperature in °K; S, entropy)
 * Chemical reactions break and make bonds, producing changes in energy
 * Under constant conditions of temperature, pressure and volume, ΔG = ΔH - TΔS
 * ΔG, change in free energy
 * If positive (+), H is higher, S is lower, so there is more free energy; endergonic reaction, does not proceed spontaneously; require input of energy (e.g., heat)
 * If negative (–), H is lower, S is higher. Product has less free energy; exergonic; spontaneous

Activation energy

 * Reactions with –ΔG often require activation energy
 * e.g., burning of glucose
 * Must break existing bonds to get reaction started
 * Catalysts lower activation energy

Enzymes

 * Biological catalysts
 * Protein
 * RNA (ribozyme)
 * Stabilizes temporary association between reactants (substrates) to facilitate reaction
 * Correct orientation
 * Stressing bonds of substrate
 * Lower activation energy
 * Not consumed (destroyed) in reaction

Carbonic anhydrase

 * Important enzyme of red blood cells
 * CO2 + H2O → H2CO3 -> HCO3 + H+
 * Carbonic anhydrase catalyzes 1st reaction
 * Converts water to hydroxyl
 * Orients the hydroxyl and CO2

Enzyme mechanism

 * One or more active sites which bind substrates (reactants)
 * Highly specific
 * Binding may alter enzyme conformation, inducing better fit

Factors affecting enzyme activity

 * Substrate concentration
 * Product concentration
 * Cofactor concentration
 * Temperature
 * pH
 * Inhibitors
 * Competitive: bind to active site
 * Noncompetitive: bind to 2nd site, called allosteric site; changes enzyme conformation
 * Activators
 * Bind to allosteric sites, increase enzyme activity

Cofactors

 * Required by some enzymes
 * Positively charged metal ions
 * e.g., ions of Zn, Mo, Mg, Mn
 * Draw electrons away from substrate (stress chemical bonds)
 * Non-protein organic molecules (coenzymes)
 * E.g., NAD+, NADP+, etc.
 * Major role in oxidation/reduction reactions by donating or accepting electrons

ATP

 * Adenosine triphosphate
 * Major energy currency of cells, power endergonic reactions
 * Stores energy in phosphate bonds
 * Highly negative charges, repel each other
 * Makes these covalent bonds unstable
 * Low activation energy
 * When bonds break, energy is transferred
 * ATP → ADP + Pi + 7.3 kcal/mole

Biochemical pathways
Evolution of biochemical pathways
 * Metabolism: sum of chemical reactions in cell/organism
 * Many anabolic and catabolic reactions occur in sequences (biochemical pathways)
 * Often highly regulated
 * Protobionts or 1st cells likely used energy rich substrates from environment
 * Upon depletion of a substrate, selection would favor catalyst which converts another molecule into the depleted molecule
 * By iteration, pathway evolved backward