Cell Metabolism: Catabolism & Anabolism

Metabolism

• Metabolic activities in the cell include catabolism and anabolism.

Catabolism

• Catabolism is the metabolic process that harvests energy released during the breakdown of compounds like glucose.
• It uses this energy to synthesize ATP.
• Catabolism degrades compounds, releasing their energy.

Anabolism

• Anabolism is the metabolic process that synthesizes and assembles subunits of macromolecules.
• It uses the energy of ATP, also known as biosynthesis.
• Subunits of macromolecules, include amino acids, nucleotides, monosaccharides, and fatty acids.

Endergonic Reaction

• An endergonic reaction is a chemical reaction that requires a net input of energy as the products have more free energy than the starting compounds.
• Reactions that require an input of energy include those where the products have more free energy than the starting compounds.

Exergonic Reaction

• An exergonic reaction is a chemical reaction that releases energy as the starting compounds have more free energy than the products.
• Reactions that release energy include those where the starting compounds have more free energy than the products.

Coupled Reactions

• Anabolism cannot occur without catabolism.
• Coupled reactions must both be present to work.
• ATP made during catabolism is used during anabolism.

Enzymes

• Enzymes are biological catalysts that increase the rate at which substrates are converted into products.
• Chemical reactions can occur without enzymes, however, they would occur very slowly causing cells/bodies to die.
• Enzymes are neither consumed nor permanently changed during a reaction, allowing single enzyme molecules to be reused rapidly and repeatedly.

Activation Energy

• Activation energy is the initial energy required to break a chemical bond.
• It represents the energy needed to start a reaction.
• Enzymes catalyze chemical reactions by lowering the activation energy.

Enzyme Structure: Active Site

• The active site is the site on an enzyme where the substrate binds.
• It's also known as the catalytic site.
• When substrates bind to the active site, the shape of the flexible enzyme changes slightly.
• The "induced fit" model states that when a substrate binds, both the substrate and active site change shape to create an ideal fit for catalysis.

Enzyme Structure: Allosteric Site

• "Allosteric" refers to an enzyme or protein with a site where a small molecule can bind and alter the protein's activity.
• When a regulatory molecule binds to the allosteric site, the enzyme's shape changes.
• The distortion caused by the change alters the enzyme's affinity for its substrate.

Cofactor/Coenzyme

• A cofactor is a non-protein component required for the activity of some enzymes.
• Examples of cofactors include magnesium, zinc, copper, and other trace elements.
• A coenzyme is a non-protein organic compound that assists some enzymes acting as a loosely bound carrier of small molecules or electrons.
• Coenzymes are a subset of cofactors with the function of helping some enzymes in electron/molecule transfer.
• Examples include electron carriers like FAD, NAD+, and NADP+.

Binding Sites

Active Site

• Substrate molecules bind to the active site.
• Competitive inhibitors bind to the active site, blocking substrate access, an example being sulfa drugs which are used as antibacterial medications.

Allosteric Site

• The following can bind to the allosteric site:
• Allosteric inhibitors
• Allosteric activators
• Non-competitive inhibitors

Non-Competitive Inhibition

• A type of enzyme inhibition that results when a molecule binds to the enzyme at a site other than the active site.
• The binding changes the shape of the enzyme, preventing the substrate from binding to the active site.
• The binding can be permanent in the case of enzyme poisons.
• The binding can be reversible caused by regulatory molecules.

Factors Affecting Enzyme Activity: Temperature

• All bacteria have an optimal temperature at which they grow best.
• If the temperature is too high, proteins will denature and no longer function.

Factors Affecting Enzyme Activity: pH

• Most enzymes function best at a pH value slightly above 7 along with a low salt concentration.

Factors Affecting Enzyme Activity: Substrate Concentration

• Increased substrate concentration increases the reaction rate up to a certain point.
• Once all enzymes have bound to a substance, additional substrate additions will not affect the reaction rate.

Factors Affecting Enzyme Activity: Enzyme Concentration

• Increasing enzyme concentration will speed up the reaction rate as long as there is an available substrate to bind to.
• Once all substrate is bound, the reaction will no longer speed up, regardless of added enzymes.

Factors Affecting Enzyme Activity: Time

• As incubation time for an enzyme increases with its substrate, the product quantity increases.

Enzyme Inhibitors

• Non-competitive inhibitors bind to any site on the enzyme, not just the active site.
• The binding alters the enzyme's shape, preventing substrate binding.
• Can be either permanent or reversible.
• Competitive inhibitors bind directly to the active site preventing the substrate from binding.

Feedback Inhibition of a Metabolic Pathway

• A metabolic pathway is a series of sequential chemical reactions.
• Feedback inhibition is when a reaction product is used to regulate its own further production thus regulating enzyme activity.
• Some metabolic products inhibit the enzymes in the chemical pathway, while some reactants activate them.
• Allows cells to shut down specific pathways after product accumulation has reached a certain threshold.

Pentose Phosphate Pathway

• The pentose phosphate cycle generates NADPH+H+ (amount varies) and two different precursor metabolites.
• It's used to break down glucose.
• No energy in the form of ATP is produced or used in this pathway

Classification of Organisms: Energy

• Energy is the capacity to do work, existing as:
• Potential energy (stored energy).
• Kinetic energy (energy of motion).
• Energy can never be created nor destroyed which can only be changed from one form to another.

Phototrophs

• Organisms that use light as a source of energy.
• Includes plants, algae, and photosynthetic bacteria.

Photoautotrophs

• Organisms that use light as an energy source and CO2 as a major carbon source.

Photoheterotrophs

• Organisms that use light as energy source and organic compounds as carbon source.

Chemotrophs

• Organisms that obtain energy by oxidizing chemical compounds.
• Mammalian cells, fungi, and many prokaryotes use organic chemicals, such as sugars, amino acids, and fatty acids as energy sources.

Chemolithotrophs

• Organisms that obtain energy by oxidizing reduced inorganic compounds such as hydrogen gas, and use CO2 as a carbon source

Chemoorganotrophs

• Organisms that harvest energy by oxidizing organic chemicals.
• Obtain energy by degrading organic compounds.
• Organism that obtain both energy and carbon from organic compounds.

Cell Respiration Equation

• C6H12O6 + 6O2 + 38 ADP + 38 P = 6CO2 + 6H2O + 38 ATP + Heat

Cell Respiration Purposes

• The two major purposes of cell respiration are to make ATP for cell activities and precursor metabolites

Glycolysis

• Glycolysis produces 2 ATP (via S.L.P), 2 NADH + 2H+, and six different precursor metabolites.
• Glycolysis converts glucose to pyruvate, two pyruvate molecules are created per glucose molecule.
• Occurs in the cytoplasm for both eukaryotic and prokaryotic cells.

Transition Step

• The transition step produces 2 NADH + 2H+ and one precursor metabolite, which is repeated.
• Links glycolysis/pentose-phosphate pathway with the TCA cycle.
• Occurs in the cytoplasm for both eukaryotic and prokaryotic cells.
• CO2 is first removed from pyruvate, a step called decarboxylation.

Krebs Cycle/TCA Cycle

• The TCA cycle generates 2 ATP (by S.L.P), 6 NADH + 6H+, 2 FADH2 and two different precursor metabolites, this repeated with acetyl CoA.
• Completes the oxidation of glucose.
• Contains acetyl groups from transition step, ultimately releasing two molecules of CO2.
• Takes place in the matrix of the mitochondria for eukaryotic cells.
• Takes place in the cytoplasm for prokaryotic cells.

Electron Transport Chain

• Cellular respiration uses the reducing power generated in glycolysis, the transition step, and the TCA cycle to synthesize ATP.
• Oxidative phosphorylation is the synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy.

ETC Functions

• Uses the reducing power of NADH and FADH2 to generate a proton motive force.
• ATP synthase uses the energy of the proton motive force to drive the synthesis of ATP.
• The ETC is a cluster of membrane-embedded electron carriers that transfer electrons, creating a proton motive force.
• In prokaryotic cells, the ETC is in the cytoplasmic membrane, while in eukaryotic cells, it is in the inner membrane of mitochondria.

Substrate-Level Phosphorylation

• Produces 2 ATP from glycolysis (net gain)
• Produces 2 ATP from the TCA cycle
• 4 ATP total

Oxidative Phosphorylation

• Produces 6 ATP from the reducing power (glycolysis).
• Produces 6 ATP from reducing power (transition step).
• Produces 22 ATP from reducing power (TCA cycle).
• 34 ATP total

Total ATP Gain

• Total ATP gain (theoretical maximum) through cell respiration is 38.
• 2 NADH = 6 ATP in glycolysis.
• 2 NADH = 6 ATP in transition step.
• 6 NADH = 18 ATP in the TCA cycle.
• 2 FADH2 = 4 ATP in the TCA cycle.

Roles of NADH and FADH2

• NADH and FADH2 generate reducing power by donating electrons to the ETC.
• Reducing power is carried by reduced electron carriers like NADH, NADPH, and FADH2 with energy-filled bonds to be potentially tapped into by a cell.
• 2 NADH = 6 ATP in glycolysis.
• 2 NADH = 6 ATP in the transition step.
• 6 NADH & 18 ATP = TCA cycle.
• 2 FADH = 4 ATP in the TCA cycle.
• Assumes both 3 ATP per NADH and 2 ATP per FADH.

Stages Producing NADH and FADH2

• NADH production:
• Glycolysis - Transition Step - TCA Cycle
• FADH2 Production:
• TCA cycle
• How are these molecules used to make ATP?
• They are used to donate electrons to the ETC.

Reactants in Each Stage

• Glucose in Glycolysis
• Oxygen in Glycolysis

Products Made in Each Stage

• Carbon dioxide:
• Transition step
• TCA cycle
• Water:
• TCA cycle
• Glycolysis
• ATP (38):
• Glycolysis
• 2 with S.L.P.
• 6 with O.P.
• Transitions step
• 6 with O.P.
• TCA/ETC
• 2 with S.L.P.
• 22 with O.P
• Fermentation

Cellular Respiration Oxidation

• Glucose is oxidized during cell respiration
• Why is energy released when a molecule is oxidized?
• Bonds are broken during oxidation releasing energy, and an electron is lost.

Cellular Respiration Reduction

• Oxygen is reduced during CR

Substrate-Level Phosphorylation

• Uses energy from exergonic chemical reactions during breakdown of energy source.
• During glucose oxidation, a relatively small amount of ATP is made by SLP.
• In aerobic respiration, 2 ATP in glycolysis and 2 ATP in the TCA cycle (4 total).
• Fermentation creates 2 ATP in glycolysis.

Oxidative Phosphorylation

• Synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy.
• The reducing power accumulated during oxidation steps can be used in CR to generate ATP by oxidative phosphorylation.
• In aerobic respiration, 34 ATP are created by OP. SLP is when ADP is converted to ATP, the phosphate group is donated/transferred from a phosphorylated intermediate; chemiosmotic gradients are used to power the phosphorylation process.
• SLP is a direct process with no middle man with OP having middle men made up of NADH and the electron transport enzymes.
• In OP, the phosphate comes from a pool of inorganic phosphates instead of directly from another molecule.
• Energy to phosphorylate the ADP comes from proton gradient, not from linked processes.
• OP is a process by which energy is released by chemical oxidation of nutrients which is used for ATP synthesis; SLP is a process where the phosphate group of a chemical compound is removed and added to ADP directly.
• OP energy:
• Energy generated from the reaction of ETC; SLP energy from coupled reactions.
• OP is common in aerobic SLP anaerobic and fermentative metabolism.
• OP electron donors are completely oxidized; SLP is partially oxidized.

Hydrogen Ion Gradient to Create ATP

• Spatial arrangement of the two carrier types in the membrane allows protons to move from one side of membrane to the other.
• The hydrogen carrier then receives electrons from the electron carrier which results in intake of protons (come from inside the cell). When a hydrogen carrier passes electrons to a carrier that accepts electrons, but not protons, the protons are released to the outside of the cell.
• The electron transport chain pumps protons from one side of the membrane to the other, generating the concentration gradient across the membrane

Cell respiration vs. fermentation vs anaerobic cell respiration

• Stages/locations
• ATP production
• Oxygen requirements
• Final electron acceptors
• End products
• Presence of ETC

Aerobic Respiration

• Uses molecular oxygen as final hydrogen/electron acceptor with oxidative and substrate phosphorylation by Oxidative and subtrate-level.
• Molecular oxygen creates H2O with 38 ATP molecules produced in bacteria, 36 ATP molecules of eukaryotes

Anaerobic Respiration

• Uses inorganic substance H2S or NO3 where substrate is a variable of less than 38 and more than 2 ATP

Fermentation

• Substrates used ethanol, lactic acid with 2 ATP yield

Purpose of Fermentation

• Fermentation is used by organisms that cannot respire if a suitable acceptor is unavailable or because they lack an ETC.
• When an organism is fermenting glucose, ATP reactions are usually the SLP of glycolysis while fermentation oxidizes NADH to generate NAD What determines the end products of a fermentation reaction?
• Fermentation reactions produce NAD+ and an organic product, mainly ethanol/lactic acid/carbon dioxide/ hydrogen gas.
• The terminal carbon acceptor determines the end products Why are fermentation reactions so useful for bacterial identification?
• End products help identify bacterial isolates since each species uses a fermentation pathway

Lactic Acid

Used when pyruvate serves as terminal electron acceptor; contributes food texture and flavor as well as tooth decay

Ethanol

Is produced in the pathway that first removed CO2 from pyruvate, making acetyldehyde, which yields products of of ethanol/ CO2

Can other molecules (proteins, lipids, carbohydrates other than glucose, etc) enter the CR pathway? What needs to happen before other molecules can enter? Do they result in the production of equal amounts of ATP? Why/why not? Macromolecules in the medium use the cell's secretion enzymes to to break the compound into to their subunits

• Precursor metabolics can be oxidized in one of central metabolic pathways
• Don't equal ATP due to different macromolecules amounts release more or less energy

Used of CRI

Can molecules in the cell respiration pathway be used for purposes other than energy production? (i.e: synthesis of molecules needed by the cell) Molecules can be pooled at some stages to build building material ex proteins Prokaryotes synthesize subunits by anabolic pathways the equal cell the various macromolecules

Prokayotes v Eukaryotes

Why do prokaryotic cells net more ATP than eukaryotic cells from aerobic CR? cytoplasm= prokaryotes only need ATP to start glycolysis eukaryotic cells the TCA cycle and the ETC are in the mitochondria and to get the needed molecules into the mitochondria ATP is needed