Bioenergetics and Metabolism

Bioenergetics and Metabolism

• Metabolism is a coordinated cellular activity utilizing multienzyme systems.
• The steps in metabolic pathways obtain chemical energy from solar or nutrient sources.
• Metabolic pathways convert nutrient molecules into characteristic molecules.
  • The products act as precursors to macromolecules.
• Macromolecules are formed through the polymerization of monomeric precursors such as proteins, nucleic acids, and polysaccharides.
• Biomolecules are synthesized and degraded for cellular function involving lipids and messengers.

Autotrophs versus Heterotrophs

• Autotrophs include photosynthetic bacteria, green algae, and vascular plants.
  • Autotrophs use carbon dioxide from the atmosphere and are self-sustaining.
• Heterotrophs obtain carbon through environmental sources like complex organic molecules, including glucose.
  • Heterotrophs obtain nutrients through the degradation of organic matter produced by autotrophs.
• Carbon, oxygen, and water are cycled between the heterotrophic and autotrophic worlds.
• Solar energy serves as the driving force for both autotrophs and heterotrophs.

Nitrogen metabolism

• Organisms require nitrogen for amino acid and nucleotide synthesis.
• Bacteria and plants exclusively use ammonia or nitrate as a nitrogen source.
• Vertebrates obtain nitrogen from amino acids and other organic sources.
• The balance between carbon, oxygen, and nitrogen starts with the Sun, photosynthetic organisms, and heterotrophic organisms.
• Energy transformations lead to a loss of useful energy, known as free energy, and an increase in unusable energy in the form of heat and entropy.

Metabolic Pathways and Intermediates

• Metabolism constitutes the sum of all chemical transformations in a cell or organism in enzyme-catalyzed reactions and metabolic pathways.
• A metabolic pathway involves consecutive steps driving a small chemical change achieved by removing, transferring, or adding an atom or functional group.
• Metabolites is when a precursor is converted into a product by a series of metabolic intermediates through consecutive steps in a pathway driving a small chemical change.

Catabolism versus Anabolism

• Catabolism involves the degradation of organic nutrient molecules like carbs, fats, and proteins into smaller and simpler products, including lactic acid, CO2, and NH3, releasing energy to produce ATP and reduced electron carriers.
• Anabolism, or biosynthesis, uses small, simple precursors to create larger, more complex molecules like lipids, polysaccharides, proteins, and nucleic acids, requiring ATP phosphoryl transfer and reducing power of electron carriers.

Metabolic Enzyme Regulation

• Most cells possess enzymes for synthesizing and degrading biomolecules like fatty acids however fatty acid catabolism and synthesis cannot be irreversible.
• Simultaneous degradation and synthesis would be wasteful using the same enzymes in both directions thus anabolic and catabolic locations differ
• Enzyme levels and metabolic intermediates are regulated on many levels by outside external factors which influence internal cellular signals.
• Intracellular concentrations of an enzyme's substrate are near Km, which is the most common type.
  • The reaction rate is concentration dependent.
• Allosteric regulation occurs via a metabolic intermediate coenzyme.
• Metabolic activities in multicellular organisms are regulated by growth factors and hormones.

Bioenergetics and Thermodynamics

• Bioenergetics quantitatively studies energy transductions, detailing changes from one energy form to another.
• Bioenergetics also explores the relation to chemical processes.
• Living systems defy the second law of thermodynamics by creating order.
• Living cells are open systems, continuously exchanging energy and material and never reaching equilibrium.

Gibbs Free Energy (G)

• Gibbs free energy indicates the amount of energy available for work during a reaction which involves heat content of the reacting system.
  • Reactions that release heat are exothermic where heat content of product is less than reactants producing a negative value.
  • Reactions that uptake heat from surrounding are know to be endothermic producing a positive value.

Entropy and Gibbs Equation

• Entropy, (S), quantifies randomness/disorder.
  • Less complex, more disordered products gain entropy reflected in the equation ΔG = ΔH - TΔS.
• Cells are isothermal where heat isn't a source of energy.
• Heterotropic cells gain energy from nutrients while photosynthetic cells use solar methods.
• A reaction (chemical reactants and products) shifts until reaching equilibrium which ensures the forward and reverse rates are equal.
  • Concentrations of reactants and products define the equilibrium constant.
• Standard conditions are temperature @298K, concentration @1M, & partial pressure @ 1 atm
• Driving force under standard conditions is known to be standard free energy or ΔG’o

Standard Free-Energy Change ΔG'° & Equilibrium Constant

• The standard free-energy change reflects an alternative mathematical expression of the equilibrium constant = ΔG’o = -RTlnK’eq
• ΔG’o indicates the free-energy content difference between products and reactants under standard conditions leading to various reaction outcomes.
  • Negative ΔG’o indicates products possess less energy driving spontaneous processes.
  • Positive ΔG’o indicates products have more energy the process will go in reverse.

Biochemical Reactions and Energetics

• Actual free energy (ΔG) differs from the standard conditions (ΔG’o) as it reflects reactant and product concentrations.
• The actual free energy fluctuates with temperature, especially at physiological temperatures like 37°C.
• Any spontaneous reaction heads toward equilibrium, releasing energy (-ΔG).
• The standard free-energy change (ΔG’o) indicates the likelihood of reactions where standard conditions are stable.
• Living systems are not closed but are isothermal making ATP very useful, and has standard conditions.
• They relate as follows:
  • ΔG = ΔG’o + RTlnQ
• Free energy is released in conditions that aren’t standard as reactions even with a positive charge are reversible due to measurable forces
• The main driver of reversible reactions is cAMP

Enzymes & Energetics

• Cells utilize enzymes as metabolic matches.
• Enzymes enhance reaction rate and provides alternative reaction pathways while enzyme properties exclude equilibrium fluctuation and can only be achieved via enzymes
• Enzymes catalyze these changes in a way substrate increases thermal energy and cannot change or change constant conditions
• Unfavorable reactions are coupled to exergonic processes to proceed.

BioRxn and Types

• There are five main types reactions that break carbon-carbon bonds and undergo internal rearrangements.
  • These type include Internal rearrangements (isomerization and eliminations), Free-radical reactions, Group transfers, and Oxidation-reductions
• Shared electrons are covalent and bond can undergo homolytic or heterolytic cleavage
  • The homolytic Cleavage atom leaves and the heterolytic retains.
• Nucleophilic functional groups are able to donate electrons while electrophiles seek electrons such as carbonyl and amino acids
• With this carbon can be either electrophiles or nucleophiles

More Carbone Rxn

• This bond requires nucleophilic carbanion & electrophilic carbocation
• Carbonyl are responsible since the bond is energetic
  • They facilitate carbanion with charged functions like an acid

More CarbonRxn

• Cabonyl are responsible with three major classes
  • Aldol condensations for carbon to carbon bond which occur with six carbon chains
  • Claisen reaction with stabilizing the thioester with in acid cycle.
  • Decarboxylation to produce Ketone bodies and cleave it
• The pathways are stabilized by phosphate and perform electron extractions to make the carbon bond high voltage
• Carbocations play a central role in making many things in the body like a cholesterol biosynthesis because it lowers the voltage/energy

RedoxRxn

• These structures undergo alteration due to the shifting on a electrical level due to bonding like the C double chain

GroupTxRxn

• A functional group can be moved and requires an enzyme so it can bind its components
  • Actives a good leaving Rxn with inorganic phosphates because they are unstable

Protein and lipids

• Integral proteins bind proteins as well
• Proteins perform interactions at 7x in membranes.

Gly and carb

• A glucose transfer is required and is not used on enzymes

Diabetic reactions

• High carbs allow glucose conc, increase to 5 MM which promotes uptakes in adipocytes
• Type 1 can be reversed at all and are related.

Electrochemical gradients.

• Move from a higher conc --> lower conc which is known as an electrochemical gradient.
• This is how ions form for function

Transport vs Rxn

• This step is required for rxn as they encode protein that affect ion transfer

Ion channel function

• It binds and transport it through by 5mm

Energy Transport

• Transporting proteins requires a lot of energy especially without counter ions
• It requires an imbalance of electrolytic which requires energy

ATAPases

• Active and transports and phosphoryolate reversibly
• It works towards gradient and is seen as signals in euk.
• It’s a series of transport proteins such as pumps due gradient atp regulation.
• These transports transport and has domains, it has sodium, potassium pumps that require 3 atp.

Eukaryotic Pump

• Requires an energy balance and are a couple of transfer pumps.

ABC transport

• It’s a way to ensure you’re good

Fibrosis

• They occur on Ctrf in cells that transfer electrons at a high frequency and require high energy to export

Nitrogen is Needed

• Ranked 4th it contributes to the mass
• They are incorporated in P and P. They are coded genetically based on the enzymes

Nitrogen Cycle

• Requires the action of Soil to convert ammonias it to water to produce other compounds by bacteria
• The goal is to maintain the nitrogen and atmospheric pressure for energy production which is known as .
• This process converts much nitrogen

Conversion requires atp

• To form and produce ammonium and its
• It is a major component and a costly event

More Nitrogen.

• Glutamine is responsible with a synthesis to convert it into a soluble liquid

Ribosomal action

• It codes and converts at all times for the cells

Trans action

• This function has a class and can perform chemical changes.

Glucoses energy

• They all required energy
• It can also create ribo and protein

Regulation of Amino

• It requires multiple enzymes to create it

Aromatic

• Tyrosine

Biosynthesis

• Carbon comes either from ept or Pep with a inhibited rate

Isomeration, transfer & Binding

• T needs binding

Membranes requires

• Binding

Inportant Points

• High energy can be obtained with C bond with high stability