Study Notes on Enzymes and Energy
Chapter 4: Enzymes and Energy
Introduction to Enzymes
Enzymes: A class of proteins that function as biological catalysts.
Functions and Characteristics of Enzymes:
Increase Reaction Rate: Enzymes accelerate reactions by lowering the activation energy needed.
Do Not Change Reaction Nature: Reactions could occur without enzymes, but slower.
Unchanged Structure: Enzymes remain unchanged after a reaction and can be reused.
Activation Energy
Definition: The minimum energy needed for reactants to engage in a chemical reaction.
Molecule Behavior: Most molecules do not possess sufficient activation energy for reactions to occur.
Heat Addition: Increasing temperature raises the likelihood of reaction occurrence, thus speeding up reactions.
Cellular Effects: Heat can have damaging effects on cellular structures; hence, catalysts are critical for lowering reaction temperatures.
Activation Energy Diagram
Key Points:
The diagram compares reactions with and without a catalyst, illustrating differences in activation energy requirements:
Uncatalyzed Reaction Pathway has higher activation energy.
Catalyzed Reaction Pathway requires lower activation energy.
Naming Enzymes
Historical Naming: First enzymes were given arbitrary names, but an international committee standardized naming.
Suffix –ase: All enzyme names end with -ase.(protein is an enzyme)
They also decided to make the first part of the name apple to the function of the enzymes
Functional Naming:
Phosphatases: Remove phosphate groups.
Synthetases/Synthases: Catalyze dehydration synthesis.
Hydrolases: Facilitate hydrolysis.
Dehydrogenases: Remove hydrogen atoms.
Kinases: Add phosphate groups.
Isomerases: Rearrange atoms in a molecule.
Isoenzymes
Definition: Different forms of an enzyme that catalyze the same reaction but may vary slightly in structure (particularly outside the active site).
Because names are given to enzymes based on function an enzymes that does the same job in 2 difffrent organs has slight variations to their names
However the molecules may be slightly different in areas outside the active site and are called isoenzymes: useful for detecting and diagnosing certain diseases
Used to help diagnose certain conditions in the body
Clinical Relevance: Useful for disease detection/diagnosis.
Example: Creatinine phosphokinase (CK) has three forms: MM (skeletal muscle), BB (brain), and MB (cardiac muscle).
Diagnostic Value of Measuring Enzymes in Blood
Table 4.1: Examples of diagnostic values of common plasma enzymes and associated diseases:
Alkaline phosphatase: Obstructive jaundice, Paget's disease, bone carcinoma.
Acid phosphatase: Prostate cancer, benign hypertrophy of the prostate.
Amylase: Pancreatitis, perforated peptic ulcer.
Aldolase: Muscular dystrophy.
Creatine kinase (CK): Muscular dystrophy, myocardial infarction.
Lactate dehydrogenase (LDH): Myocardial infarction, liver disease, renal disease, pernicious anemia.
Transaminases (AST and ALT): Myocardial infarction, hepatitis, muscular dystrophy.
Mechanisms of Enzyme Activity
Structure-Function Relationship: The specific function of each enzyme is determined by its unique structure.
How the interacts with each other is on the active site either through a direct fit (lock and key model)
3D Conformation: Enzymes have a characteristic three-dimensional shape that includes active sites where substrates bind.
Substrate Interaction:
Lock-and-Key Model: Substrates fit exactly into the active site of the enzyme.
Induced-Fit Model: Initial fit may not be perfect; the enzyme adjusts to fit the substrate as it binds.
When a substrate binds to the active site of an enzyme it forms temporary bonds weakening the original bond of the substrate and allowing them to break easily
Enzyme-Substrate Binding
Complex Formation: When a substrate binds to an enzyme's active site, it forms temporary bonds that stress the substrate's bonds, aiding in the reaction.
Illustration:
Diagram showing:
A + B (Reactants)
→ C + D (Products)
Enzyme remains unchanged.
Measurement of Enzyme Activity
Determination: Enzyme activity is assessed by the rate of substrate conversion to product. Influencing factors include:
Temperature: if the temperature is too cold or hot they may not work sufficiently
pH: if it diverted from the pH range it will not work effectively
Concentration of coenzymes and cofactors: inorganic compounds to interact and help enzymes carry out functions
Concentration of enzymes and substrates:increase the amount of substraight you also increase the output
Inhibitory/stimulatory effects of products on enzyme function.
Effects of Temperature on Enzyme Activity
Temperature Increases: Reaction rate increases until a few degrees above body temperature (approx. 37°C).
Denaturation: Beyond this point, enzymes lose their tertiary structure and become nonfunctional.
Graph: Illustrates enzyme activity, peaking around body temperature before dropping as denaturation occurs. If
Effects of pH on Enzyme Activity
pH Optimum: Enzymes operate best at a specific pH that correlates with their functional environment.
Will work in a very narrow range
Changes in pH outside of the functional range will result in irreversible conformational a changes in structure of enzyme which render the enzyme which render the enzyme non functions
Irreversible Changes: pH levels outside this optimal range lead to structural modifications causing denaturation.
Example Enzymes: Trypsin, salivary amylase, and pepsin exhibit various optimal pH levels.
Coenzymes and Cofactors
General Role: Many enzymes require supplementary small molecules for optimal functioning.
Coenzymes: Organic molecules typically derived from water-soluble vitamins.
Examples:
Nicotinamide adenine dinucleotide (NAD+): Derived from vitamin B3 (niacin).
Flavin adenine dinucleotide (FAD): Derived from vitamin B2 (riboflavin).
Coenzyme A: Derived from vitamin B5 (pantothenic acid).
Cofactors: Inorganic molecules such as Ca²⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺ that assist enzyme activity
Function: Coenzymes and cofactors facilitate the formation of active sites on enzymes by inducing conformational changes for effective substrate binding.
Enzyme Activation
Zymogens: Many digestive enzymes are secreted as inactive precursors (zymogens), becoming active post-secretion.
Example: Pepsinogen → Pepsin.
Phosphorylation/Dephosphorylation: Activation often involves adding a phosphate group (phosphorylation) (turn on), while inactivation involves removing it (dephosphorylation).(turn off)
Enzyme Control: Enzyme activity may also be regulated through degradation via lysosomes.
Enzymatic Activities
Substrate Concentration: Increases in substrate concentration lead to increased reaction rates until enzyme saturation occurs. The products are
Saturation: When all active sites are occupied, adding more substrate will not further enhance the reaction rate.
Reversible Reactions
Definition: Some chemical reactions can progress in both forward and reverse directions, influenced by substrate/product concentration.
Law of Mass Action: Indicates that as the concentration of a product increases, the reaction will reverse to produce more reactants (example given: H₂O + CO₂ ↔ H₂CO₃ ↔ H⁺ + HCO₃⁻ facilitated by carbonic anhydrase).
When one side gets higher the reaction reverse this is called the law of mass action
Metabolic Pathways
Definition: Most biochemical reactions are interconnected, forming metabolic pathways from initial substrates to final products.
Most reactions are linked together in a chain (or web) called a metabolic pathway
These begin with an initial substrate and end with a final product
Every step of the reaction requires a specific enzyme
Enzyme Requirement: Each step within a pathway requires a specific enzyme.
Branched Metabolic Pathways
Nature of Pathways: Few pathways are linear; most have branches producing several end products from a common substrate.
Few metabolic pathways are linear
Most include branches where several products can be produced
End Product Inhibition
Mechanism: End-products can inhibit the pathway's branch point enzyme if they accumulate, exerting negative feedback to regulate metabolic pathways.
Branch points are often inhabiilited by a form of negative feedback in which one of the final products inhibits the branch point enzymes
Designed where the final step is the inhibitor
Methods of Inhibition:
Competitive Inhibition: The end product competes with substrates for binding at the active site.
Non-competitive or Allosteric Inhibition: The end product binds at a site away from the active site, inducing a conformational change that disables substrate binding.
Competitive inhibitor vs nonsompetive inhibitor (allosteric site)
Inborn Errors of Metabolism
Definition: Mutations in genes coding for enzymes result in enzymes that are either non-functional or with altered functions, leading to metabolic issues.
Occur when there is mutation in a single gene that codes for an enzyme in a metabolic pathway These begin
This results in an enzyme that has a new function or one that is nonfunctional
Products to be formed after this enzyme in the. Chain are not formed
Diseases occur due to loss of end products or accumulation of intermediate products those before the bad enzyme or alternative products
Consequences: May result in an accumulation of intermediate metabolites or a deficiency of end-products, causing diseases.
Examples of Inborn Errors of Metabolism
Table 4.4: Lists diseases related to amino acid, carbohydrate, and lipid metabolism, addressing clinical results.
Diseases:
Phenylketonuria (PKU): Accumulation of phenylpyruvic acid, causing mental retardation.
Albinism: Lack of melanin, increasing skin cancer risk.
Maple-syrup disease: Increased leucine, isoleucine, and valine; can lead to severe brain degeneration.
Homocystinuria: Accumulation of homocystine, leading to mental retardation.
Lactose intolerance: Inability to utilize lactose contributing to diarrhea.
Gierke's disease: Glycogen accumulation in the liver, causing hypoglycemia.
Tay-Sachs disease: Glycolipid accumulation, leading to brain degeneration.
Hypercholesterolemia: Increased blood cholesterol leading to atherosclerosis.
Bioenergetics
Definition: The study of energy flow in biological systems.
Laws of Thermodynamics
First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed; this energy transformation is not 100% efficient.
Example: Photosynthesis converts light energy into glucose
Second Law of Thermodynamics: Energy transformations result in a loss of usable energy as heat, reducing available free energy (energy capable of doing work), increasing entropy (disorder).
Entropy: Degree of disorder increases with each energy transformation. (In the form oh heat)
Relation to Reactions: Connects to definitions of endergonic (requiring energy input) and exergonic (releasing energy) reactions.
Endergonic and Exergonic Reactions
Endergonic Reactions:
Require energy input, resulting in products with more free energy than reactants.
Characterized by increased order (lower entropy in products).
Example: Photosynthesis where energy from light converts CO₂ and H₂O into glucose.
Exergonic Reactions: more explosive and produces heat as a byproduct
Release energy, leading to products with less free energy than reactants.
Example: The breakdown of glucose into CO₂ and H₂O provides energy for ATP production.
Energy Obtained from Glucose
Total Energy Calculation and Representation: Breakdown of glucose releases energy, represented in biochemical equations.
Calories
Definition: A measurement of energy which quantifies the heat required to raise the temperature of 1 cubic centimeter of water by 1°C.
Nutrition: Mention of kilocalories (1,000 calories) termed as Calories (capital C) in food.
Coupled Reactions
Principle: Energy from food (exergonic reactions) drives endergonic reactions in the body by forming ATP as an energy carrier.
Used to drive another process
Exergonic reaction to drive th endergonic reactions in our body
ATP Formation: ATP production is an endergonic process typically coupled with an exergonic reaction, emphasizing its role as a universal energy carrier.
The ATP molecule stores energy in its bonds to be used elsewhere ATP is called the universal energy carrier
Mechanism of Coupled Reactions: Diagram illustrated how coupling occurs between endergonic and exergonic reactions, showcasing fluid energy transfer.
Exergonic reaction drives endergonic reactions
Everything requires energy
Coupled Reactions in ATP Formation
Diagram Explanation: Provides a straightforward depiction of ATP synthesis from ADP and inorganic phosphate (Pi).
Coupled Reactions: Oxidation-Reduction
Reduction: Process in which an atom or compound gains electrons, reducing its charge.
Reduction reaction: when an atom or compound gains or accepts electrons (it becomes reduced)
Oxidation: Process of losing electrons from an atom or compound, increasing its charge.
When an atoms compound loses or donates an electrons
These reactions are always coupled for one molecule to lose an electrons These it has to give it to another molecule
The molecule that donates the electrons acts as the reducing agent
The molecule that accepts the electrons acts as a n oxidizing agent
Coupling of Reactions: Reducing agents donate electrons to oxidizing agents, perpetuating a continuous cycle.
Electron (Hydrogen) Carriers
Key Examples:
NAD+: Derived from vitamin B3, assists hydrogen transfer, reduces to NADH + H⁺. Oxidized state NAD+, and NADH+ is reduced
FAD: From vitamin B2, reduces to FADH₂ after accepting electrons and hydrogen FAD oxidized state FADH reduced state
MWCO is the same thing as this is the permeability of that method
If the MWCO is too small
When you place sodium chloride into a solution sodium chloride is able to defuse across the membrane
Bc the sodium chloride is one of the primary ionic compounds
Anytime we put an ionic compound it will dissociate th never go back together
To change the rate of diffusion you simply change the permutioaton of that solute
If you put one type of solute with passive transport we have simple diffusion, osmosis the enzymatic
Snare protien
Conclusion
Summary: The chapter on enzymes and energy emphasizes their crucial roles in facilitating biochemical reactions, understanding metabolic pathways, and the significance of energy transformations governed by thermodynamic principles.
Implications: Comprehension of these biological principles is vital for fields ranging from biochemistry to medical diagnostics, as illustrated through enzyme functionality, metabolic diseases, and energy dynamics in cells.