Energy, Enzymes and Metabolism

Key Concepts

• Explored concepts are: Energy and Chemical Reactions, Enzymes and Ribozymes, Overview of Metabolism, and Recycling of Organic Molecules

Chemical Reactions

• One or more substances transform into other substances through a chemical reaction
• Metabolism comprises all chemical reactions within an organism

Energy and Chemical Reactions

• Energy facilitates doing work or promoting change
• Kinetic energy is associated with movement
• Potential energy is due to structure or location
• Chemical potential energy, stored in molecular bonds, is a form of potential energy

Types of Energy

• Light is a form of electromagnetic radiation, visible to the eye, packaged in photons, and captured by pigments in chloroplasts during photosynthesis to produce organic molecules
• Heat transfers kinetic energy and helps organisms maintain body temperature through chemical reactions
• Mechanical energy is possessed by an object due to its motion or position, enabling movement like muscle contraction
• Chemical potential energy is stored in molecular electrons, like glucose and ATP, and released when bonds are broken to drive cellular processes
• Electrical or ion gradients from charge separation provide energy, with ion concentration differences across membranes constituting a source of potential energy

Thermodynamics

• Thermodynamics studies energy interconversions
• The First Law of Thermodynamics states energy cannot be created or destroyed, only transformed, it is also known as the "Law of conservation of energy"
• The Second Law of Thermodynamics states energy transfer increases entropy (disorder) within a system, reducing available energy for organisms

Free Energy

• Energy transformations lead to increase in entropy
• Free energy (G) is the energy amount available for work and is also known as Gibbs free energy

Calculating Free Energy

• The formula is: H = G + TS
• H is enthalpy or total energy
• G is free energy, the amount available for work
• S is entropy, the unusable energy
• T is absolute temperature measured in Kelvin (K)

Spontaneous Reactions

• Spontaneous reactions occur without additional energy input, but can be slow, such as the breakdown of sucrose
• A key factor is free energy change, where a negative ΔG indicates an exergonic and spontaneous process

Exergonic vs Endergonic Reactions

• In exergonic reactions, ΔG is less than 0, energy is released, and the reaction is spontaneous
• In endergonic reactions, ΔG is greater than 0, it requires energy, and the reaction is not spontaneous

ATP Hydrolysis

• The change in free energy is -7.3kcal/mole
• It favors product formation
• The released energy supports diverse cellular processes

ATP Usage in Cells

• Linking an endergonic reaction to an exergonic reaction makes it coupled
• Reactions become spontaneous when the net free energy change is negative
• In coupled reactions, phosphate are directly transfered from ATP to glucose, phosphorylating it
• Typical cells consume millions of ATP molecules per second for endergonic processes
• Food breakdown releases energy enabling ATP production from ADP

Proteins that use ATP

• Metabolic enzymes use ATP to catalyze endergonic reactions
• Hexokinase uses ATP to attach phosphate to glucose, producing glucose-6-phosphate
• Ion pumps, like Na+/K+-ATPase, utilize ATP to pump ions against a gradient
• Motor proteins use ATP to enable cellular movement, like myosin in muscle contraction
• Chaperones use ATP in protein folding and unfolding
• DNA-modifying enzymes use ATP to change DNA conformation
• Aminoacyl-tRNA synthetases use ATP to attach amino acids to tRNAs
• Protein kinases, regulatory proteins, use ATP to phosphorylate proteins, impacting their function

ATP and Proteins

• Each ATP undergoes 10,000 hydrolysis and re-synthesis cycles daily
• Particular amino acid sequences in proteins function as ATP-binding sites
• It is predictable if a newly discovered protein uses ATP or not
• On average, 20% of all proteins bind ATP, possibly an underestimate
• This indicates ATP is an important energy source

Enzymes and Ribozymes

• A spontaneous reaction does not necessarily mean it is a fast reaction
• Catalysts accelerate chemical reaction rates without being consumed
• Enzymes are protein catalysts in living cells
• Ribozymes are catalytic RNA molecules

Activation Energy

• Activation energy is the initial energy input needed to start a reaction
• Overcoming the energy threshold allows molecules to be close enough to cause bond rearrangement
• A transition state where bonds are stretched can now be achieved
• Activation energy can be overcome by large amounts of heat, or enzymes can be used which lower activation energy

Enzyme Terminology

• Active site - Location where reaction takes place
• Substrates - Reactants that bind to active site
• Enzyme-substrate complex - Formed when enzyme and substrate bind

Substrate Binding

• Enzymes exhibit high specificity for substrates
• The lock and key metaphor shows that substrates will only interact with enzymes if they "fit together"
• Induced fit phenomenon involves conformational changes during the interaction to increase binding

Enzyme Reactions

• Affinity - Degree of attraction between an enzyme and its substrate
• Saturation - Plateau where most active sites are occupied by substrate
• Michaelis constant is the substrate concentration where velocity is at half its max value
• High KM leads to the need for higher substrate concentrations (inversely related to affinity)
• Vmax is the velocity of reaction near maximal rate

Inhibition

• Competitive inhibition - Molecule binds to active site, inhibits substrate binding, increases its apparent value, and requires more substrate
• Noncompetitive inhibition - Lowers without affecting lowers Inhibitor binds to allosteric site
• Irreversible Inhibition - Usually involves enzymes that bind covalently to inhibit their functions, it is not typically used for regulation for for cells to control enzymes

Requirements for Enzymes

• Prosthetic groups are small molecules permanently attached to the enzyme
• Cofactors are usually inorganic ions that temporarily bind to the enzyme
• Coenzymes are organic molecules that participate in the reaction, unaltered afterward

Environment

• Enzymes function best within a narrow temperature and pH ranges

Discovery of Ribozymes

• It was believed all biological catalysts from the 1980s onwards were proteins
• Ribonuclease P (RNase P) exists in all organisms and is involved in cleaving tRNA molecules
• RNase P is a Ribonucleoprotein, with the catalyst being a RNA subunit
• The RNA subunit can cleave substrate on its own.
• An RNA molecule is a true catalyst, accelerating reaction rates without being altered
• Thomas Cech determined a different RNA molecule also had catalytic activity, located in Tetrahymena thermophila
• Altman and Cech won the Chemistry Nobel Prize in 1989 for discovering ribozymes, which are RNA molecules catalyzing chemical reactions

Types of Ribozymes

• RNase P cleaves precursor tRNA molecules forming mature tRNAs
• Spliceosomal RNA removes introns from eukaryotic pre-mRNAs within spliceosomes
• Ribosomes have an RNA component catalyzing covalent bond formation between amino acids during polypeptide synthesis

Overview of Metabolism

• Metabolic pathways are where chemical reactions occur
• Specific enzymes coordinate each reaction
• In catabolic pathways, cellular components break down and are exergonic
• In anabolic pathways, cellular components synthesize, are endergonic, and must be coupled to exergonic reactions

ATP Synthesis

• Substrate-level phosphorylation - Enzyme directly transfers phosphate from one molecule to another
• Chemiosmosis - Involves energy stored in an electrical gradient that is used to make ATP from ADP and Pi

Redox Reactions

• An electron transferred from one molecule to another
• Oxidation is the removal of electrons
• Reduction is the addition of electrons

NADH

• Electrons from organic molecule oxidation create energy intermediates like NADH
• NAD+ is Nicotinamide adenine dinucleotide
• NADH releases energy upon oxidization that can be used to make ATP
• NADH can donate electrons to energize synethsis reactions

Anabolic Reactions

• Reactions that make large macromolecules or smaller unavailable molecules from food
• Require energy inputs from intermediates (NADH or ATP) to drive reactions

Regulation of Metabolic Pathways

• Regulation can be done via gene regulation, turning genes on or off
• Hormones regulate through cellular pathways
• Biochemical regulation occurs with the product of a pathway inhibiting early stages
• Rate limiting steps have great influence
• Feedback inhibition prevents an abundance of a product

Recycling Organic Molecules

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• Half-life is the time it takes for 50% of molecules to be broken down
• All living organisms use and recycle molecules

Recycling of Organic Material

• Gene expression enables cell response to environment
• RNA and protein production occurs when needed
• RNA and proteins are broken down when no longer needed

Proteasomes for recycling

• A large protein complex breaking down proteins via protease enzymes
• Proteases cleave bonds between amino acids
• Ubiquitin tags target proteins for proteasomal breakdown
• Ubiquitin tagging allows cells to degrade unfolded proteins, degrade proteins to respond to change, and recycle amino acids for new proteins

Lysosomes

• Organelles that contain hydrolases to break down proteins, carbohydrates, lipids, and nucleic acids
• They can digest endocytosed substances
• A process called autophagy takes place, recycling worn out organelles via autophagosomes