Lectures 1-5: Bioenergetics and Metabolism

Bioenergetics and Metabolism

• Metabolism uses multienzyme systems for highly coordinated cellular activity via metabolic pathways
• Obtain chemical energy from solar radiation or nutrients
• Nutrient molecules convert to cellular molecules
• Macromolecules have precursors
• Monomeric precursors polymerize into macromolecules like proteins, nucleic acids, and polysaccharides
• Biomolecules for cellular function are synthesized and degraded including lipids and messengers

Autotrophs and 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 complex organic molecules like glucose
• Heterotrophs obtain nutrients from the degradation of organic nutrients produced by autotrophs
• Carbon, oxygen, and water cycle between heterotrophic and autotrophic worlds
• Solar energy drives the heterotrophic and autotrophic worlds

Nitrogen Requirements

• All living organisms need a source of nitrogen
• Nitrogen synthesizes amino acids and nucleotides
• Bacteria and plants use ammonia or nitrate as their sole source
• Vertebrates obtain nitrogen from amino acids and other organic compounds
• Carbon, oxygen, and nitrogen need to be balanced
• The transformations of energy begins with the sun, photosynthetic organisms and heterotrophic organisms
• Energy transformation causes a loss of useful free energy
• Energy transformation causes an increase in unusable energy (heat and entropy)

Metabolism, Pathways, and Metabolites

• Metabolism represents the sum of chemical transformations in a cell or organism
• Enzymes catalyze reactions, which constitute metabolic pathways
• Metabolic pathways are have consecutive steps, that create a chemical change which can be removal, transfer, or addition of an atom or functional group
• Metabolites convert precursors into products through a series of metabolic intermediates

Catabolism and Anabolism

• Catabolism degrades organic nutrient molecules like carbs, fats, and proteins into smaller ones
• Catabolic products include lactic acid, carbon dioxide, and ammonia
• Catabolism releases the production of ATP and reduced electron carriers
• Anabolism uses small precursors to produce larger, complex molecules
• Anabolic products include lipids, polysaccharides, proteins, and nucleic acids
• Anabolism involves ATP phosphoryl transfer and reducing power of electron carriers

Cellular Enzymes and Pathways

• Most cells utilize enzymes to both degrade and synthesize biomolecules such as fatty acids.
• Simultaneous degradation and synthesis would be wasteful
• Anabolic and catabolic pathways cannot be irreversible
• Anabolic and catabolic events occur at different locations within the cell.
• Metabolic regulation is tiered:
  • External factors influence internal cellular signals
• Intracellular enzyme substrate concentrations must be near Km
• The rate of reaction depends on substrate concentration
• Metabolic intermediaries or coenzymes regulate allosterically
• In multicellular organisms growth factors and hormones regulate metabolic activity

Bioenergetics and Thermodynamics

• Bioenergetics is the quantitative investigation of how energy is transduced
• Transformations from one form of energy to another plus the chemical processes underlying these changes
• Biological systems do not seem to follow the second law of thermodynamics
• Strangely it creates order from disorder.
• Living cells and organisms form open systems
• Open systems exchange energy and material within their surroundings
• Living systems achieve a disequilibrium with their surroundings

Gibbs Free Energy

• Gibbs free energy (G) describes the amount of energy capable of doing the work during reaction
• Measurements are made at constant temperature and pressure
• Gibbs free energy involves exergonic and endergonic reactions.
• Enthalpy (H) is the heat content of the reacting system, consisting of reacting molecules and the types of chemical bonds present within reactants and products.
• Exothermic reactions release heat
• Exothermic reactions occur when the heat content of products is less than reactants
• Endothermic reactions uptake heat from their environment having have a positive value.
• Entropy (S) is the extent of randomness or disorder in a system
• ΔG = ΔH - TΔS

Isothermal Systems

• Cells are isothermal systems, and heat flow does not provide energy
• Heterotopic cells secure energy via solar radiation or nutrient molecules
• A reacting system continues changing until a state of equilibrium is attained
• At equilibrium, forward and reverse reaction rates are exactly equal
• Reactant and product concentrations dictate the equilibrium constant
• Standard conditions require a temperature of 298K, concentrations of 1M, and partial pressures of 1 atm
• The driving force of a reacting system can be explained by “standard free energy.”

Standard Free-Energy Change

• The standard free-energy change describes a any chemical reaction
• Alternate mathematical way of expressing its equilibrium constant.
• ΔG’o = -RTlnKeq
• ΔG’o is difference between free-energy content of initial reactants and final products, or standard conditions
• During a negative, the products have less free energy that renders the transformation spontaneous
• Positive values denote that the products contain more free energy causing the reverse reaction

Biochemical Energy

• Reactions move toward negative free energy with greater product to reactant ratios
• Actual free energy is affected by temperature during the reaction
• As living things exist higher than 37 degrees C, the body operates with heat
• Spontaneously reactions move toward equilibrium
• Relation with aA + bB cC + dD (a,b,c,d designate the number of moles present)

Enzymes and Rxn Rates

• Enzymes are matches that provide alternative reaction pathways
• Enzymes are catalysts with lower activation energy
• Thermal substrate molecules gain thermic energy
• Enzymes do not affect final product concentration numbers
• Energy values of sequential reactions additivity
• The coupling of highly exogenic reactions can drive unfavorable reactions

Chemical Reaction Types

• Chemical reactions can be categorized five ways
  • Reactions that break carbon-carbon bonds
  • Internal rearrangements with isomerizations and eliminations
  • Free Rad reactions
  • Group transfers
  • Oxidation reactions
• Covalent bonds share electron pairs
• Homolytic cleavage features single electron with atoms
• Heterolytic cleavage causes one atom to collect both electrons

Donating Electrons

• Nucleophiles have groups that donate electrons
• Electrophiles seek electrons in function
• Carbon performs both as nucleophile and electrophile

Carbon Bonds

• The formation of a carbon bond results in an energetically impossible reaction or unstable form
• Carbonyl groups exist to assist metabolic functions
• Facilitation of carbanion formation with delocalization of negative bond
• Imines have group function and is enhanced by catalysts

Carbonyl Reactions

• Carbonyl groups are a necessary component in C-C reactions
• Aldol condensation can create a 6-carbon group in reactions with 2 three-carbon compounds to assist glycolytic function
• Claisen ester condensation provides stability in citrate formation and citric acid cycle function
• Fatty acids decarboxylate due to fatty acid process.

Isomerization

• Intramolecular redistributions of oxidation states to be same on both side
• Molecules undergo RedOx without changing oxidation states
• Cis groups can enter Trans changes
• Double bonds undergo transposition

Free Rads

• Homolytic cleavage requires free rads
• Isomerization involves use of adenosyl-cobalamin like vitB12
• Certain decarboxylations can occur
• Oxireductases are catalysts of reductase rxns
• Catalyzing ribonucleotide process
• Catalysis of photolyase enzymes to rearranges

Group Transfers

• Acyls, glycosyls, phosphoryl groups transfer around or to nucleophiles
• Acyl transfers need certain reactions
• Glycosyl need nucleophilic substitutions by lysosomes

Metabolic Rxns

• High phosphoryl transfers of ATP are useful in substrate transfers
• Pi form creates the active intermediate
• PPi inorganic phosphates have to have anhydrase properties

Energy and Oxidation

• Hydrophillic and lipophillic transfers
• Biological molecules and lipid environments must interact
• Use H2O and lipid properties
• Oxidation reduction occurs with two transfer electrons

Adenosine Triphosphate

• ATP is made of of sugar rings with 3 Phosphoryls with different roles
• Negative charges exist on both sides of molecule
• Requires Mg assist
• Reactions are better if broken by Pi
• Group additions are favored by hydrolysis of ATP

Glucose Regulation

• Passive transport allows equal flow via gradient
• Active transport uses force for the product
• Both use different transporters

Bacterial Porins

• Porins form the wall and allow access through outer portions
• Beta barrels have different binding properties/characteristics for different substrates or molecules

Membrane Properties

• Amphoteric parts of lipid and molecules allow for biological regulation
• GPI are able to attach and regulate
• Protein glycans can be made or broken

Lipids and Environments

• Noncovalent bonds exist between them driving water out
• Temperature dictates structural states where lipids are restricted to vary degree with varying motion through lipid layers
  • Hydrophilic and Hydrophobic interactions must balance as bacteria make do
• Dynamic actions and functions occur throughout environment
• Lipids can go transbilayer leaflet transfer between head groups

Bilayer Processes

• Lipids are able to undergo rapid leaflet change (a-b type) with polar headgroups.
• ER parts perform leaflet surface modification to maintain levels
• Active changes provide more energy with diffusion and relocation for curvature to occur
• Bilayer budding and active transportation need ATP
• Lipid concentrations can shift

###Lipid Flow

• Membranes have random flows
• Lipids travel well within membrane by moving bilayers
• Short spaces must be localized for movement

Membrane Domains

• Transmembrane protein flow can be influenced with interactions to other membrane components
• This allows specific domains to allow interaction of different functions

Proteins

• Lipid anchors stabilize but dont anchor
• Domains are often found between lipids and proteins with lipid anchors which contain high interactions

Membrane Rafts

• They also contain long chain saturations and lipid portions
• Often present at the outer leaflet and thicker

Lipid Modifications

• Modification occur during exodermal stimulus during traffic with endo or exodermal stimulus during response