Collision Theory and Reaction Rates

Collision Theory

• Chemical reactions occur when chemical bonds are formed or broken, requiring atoms, ions, or molecules to collide.
• The collision theory elucidates how chemical reactions proceed and the factors influencing their rates
• The basis of this theory: atoms, ions, and molecules are in constant motion and collision.
• Energy transferred during collisions can disrupt electron structures, breaking or forming chemical bonds.

Factors Affecting Chemical Reactions

• Several factors affect the outcome of a collision in terms of causing a chemical reaction:
  • Velocities of colliding particles
  • Their energy
  • Specific chemical configurations are all influential
• Higher particle velocities correlate to a greater likelihood of reactions.
• Reactions require energy, even with the minimum energy, proper particle orientation is essential for the reaction to occur

Activation Energy & Reaction Rate

• Activation energy represents the collision energy for chemical reactions and it indicates the amount of energy needed to destabilize the electronic configuration of a molecule for electron rearrangement.
• Reaction rate is the frequency of adequate-energy collisions, relies on the quantity reactant above the activation energy threshold.
• Higher temperatures can accelerate reaction rates.
  • By boosting molecular speed, heat amplifies collision rates and the prevalence of molecules achieving activation energy.
• Similarly, collision frequency is amplified by increased pressure or reactant concentrations.

Enzymes in Biological Systems

• Enzymes increase reaction rates without increasing temperature within living systems
• Enzymes lower activation energy
• Consequently, more reactant molecules reach the necessary activation energy.
• Enzymes as catalysts speed up chemical reactions without being permanently altered
• Biological catalysts (enzymes) are highly specific, with each enzyme acting on a particular substrate and catalyzing only one reaction
  • Lipase is able to hydrolyze various lipids, like triglycerides and phospholipids, depending on their fatty acid makeup.
• Enzymes accelerate chemical reactions via an active site on the molecule, which interacts with a specific compound

Enzyme-Substrate Interactions

• Enzymes orient substrates which increases the likelihood of a reaction.
• Temporary binding between enzyme and reactants lowers activation energy.
• Enzymes accelerate reaction by boosting the number of molecules reaching activation energy.
• Enzymes accelerate reactions without high temperature to protect cellular proteins in living systems
• Crucially, enzymes expedite biochemical processes while maintaining conditions compatible with cell function.

Enzyme Specificity and Efficiency

• Enzyme specificity hinges on structure.
• Enzymes, globular proteins, vary widely in molecular weight, from 10,000 to millions.
• Each enzyme possesses a unique 3D structure stemming from its primary, secondary, and tertiary construction
• Unique configurations enable each enzyme to identify its specific structure.
• Enzymes are derived from amino acids, thus active sites get characteristics from those amino acids with varying side chains.
• Amino acid composition and configurations determine the active site's size, shape, and chemical properties, facilitating binding to specific substrates and aiding chemical reactions.

Efficiency

• Enzymes are very efficient and speed up reactions by 10^8 - 10^10 under optimum conditions.
• Turnover number: The maximum number of substrate molecules an enzyme can process into product per second; typically 1-10,000, but can reach up to 500,000.
  • DNA polymerase 1 has a turnover of 15.
  • Lactate dehydrogenase has a turnover of 1000.
• Enzymes can exist in both active and inactive states.

Naming Enzymes

• Enzymes can by classified based on the type of chemical reaction they catalyze:
  • Oxidoreductase aids oxidation-reduction reactions; such as cytochrome oxidase and lactate dehydrogenase
  • Transferase facilitates the movement of said groups; acetate kinase, alanine deaminase
  • Hydrolase catalyzes hydrolysis; lipase, sucrase
  • Lyase encourages the removal of groups; oxalate decarboxylase, isocitrate lyase
  • Isomerase catalyzes atomic rearrangement in a molecule; glucose-phosphate isomerase, alanine racemase
  • Ligase catalyze the joining of two molecules typically using energy from ATP breakdown; acetyl-CoA synthetase, DNA ligase

Enzyme Components

• Some enzymes consist of proteins exclusively, whereas protein and nonprotein components make up the majority of enzymes.
  • A protein portion(apoenzyme), must bind to a nonprotein portion(cofactor)
• Metal ions like iron, zinc, magnesium, or calcium serve as cofactors,while organic cofactors are coenzymes
• Apoenzymes need cofactors to be active.
• Together, the apoenzyme plus cofactor form a holoenzyme; the removal of the cofactor renders the apoenzyme useless.

Coenzymes

• Coenzymes aid enzymes by taking and giving atoms when being removed from or donated to substrates.
• Electron carriers act as coenzymes, shuttling electrons between substrates and other molecules.
• Metabolism relies on nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+) as key coenzymes, both derived from vitamin B (niacin).
• Flavin coenzymes FMN and FAD feature derivatives of riboflavin plus act as electron carriers .
• Another coenzyme, coenzyme A (CoA), from pantothenic acid helps in the synthesis and breakdown offats and assists oxidizing reactions in the Krebs cycle.

Cofactors and Prosthetic Groups

• Some cofactors are ionic metals, like iron, copper, magnesium, manganese, zinc, calcium, and cobalt:
  • May initiate reactions by creating a link.
  • Magnesium acts as a cofactors for phosphorylating enzymes, helping to bind with ATP molecules.
• Certain organic molecules (coenzymes) or metal ions, which bond tightly/covalently with the enzyme protein are called prosthetic groups.

Enzyme Action

• The substrate makes contact with a specific region of the enzyme's surface, called the active site.
• A temporary intermediate, the enzyme-substrate complex, forms.
• The substrate is manipulated via rearranging or combining molecules.
• The products are released because they no longer fit in the space.
• The enzyme is then free to react with other substrate molecules.

Active Site Specifics

• Enzymes are large in size compared to substrates.
• An active site or center: region where the substrate binds and participates in the reaction.
• Conformation exists because of the tertiary protein structure.
• Amino acids make up the active site, including residues numbered 35, 52, 62, 63 and 101 in lysozyme.
• Active sites are pockets occupying a small section of the enzyme.
• The structure is flexible.
• The active site has both a binding site and a catalytic site.
• Active site contains cofactors that help enzymes.
• Weak bonds can bind the substrate to the active site.
• Enzymes are specific to to their active sites
• Active sites commonly consist of amino acids such as serine, aspartate, histidine, cysteine, lysine, arginine, glutamate, tyrosine

Enzyme-Substrate Complex Formation

• Prime requisite: substrate (S) must bind with the enzyme (E) at the active site. E+S --> ES --> E+P
• Catalysts boost the rate of a reaction but do not not affect reaction equilibria
• Ground state: the beginning of the state or reverse reaction, which contributes to system energy.
• Equilibrium: the balanced state.
• When free energy of P is lower than that of S, reaction is spontaneous.
• Conversion needs an impulse.
• In order for a reaction to take place, molecules must cross the energy threshold (Hill). This is called the transition state.

Transition State & Enzyme Catalysis

• S and P have an equilibrium that shows the free energies.
• In the transition state, substrate bonds are neither completely formed nor completely cleaved.
• Transition can react at detectable rate dependent on one parameter.
• To react, molecules must surpass energy barrier/hill. Catalysis lowers the energy needed to pass that, which leads to velocity up.

Reaction Rate and Energy

• Reaction rate reflects the activation energy: the greater the energy needed, the slower the rate will be.
• Reaction can be sped up through catalyst.
• The enzyme lowers barrier so reactions go faster.
• Catalyst/enzyme lowers energy (40C at body temperature)

Enzyme Binding Models

• Lock and key model: the substrate fits perfectly into the active site.
• Induced fit model: the enzyme changes to fit the substate. A stronger one.
• Substrate strain: enzyme binds to active site inducing strain.

Enzyme Catalysis

• The enzyme-substrate complex forming is crucial to production.
• It's estimated that reaction processes 10^6-10^12 faster when an activated enzyme is involved.
  • Acid-base catalysis;
  • Substrate strain;
  • Covalent catalysis;
  • Entropy effects.

Acid-Base Catalysis

• Enzyme function depends on acid, such as histadine, tyrosine, cysteine, lysine, and carboxyl ions.
• Ribonuclease is a common acid base example.
• Reactions that don't use enzymes, just water donors/acceptors result in catalyzation.

General Acid-Base Catalysis

• General acid-base catalysis: unstable reactions break faster when molecules are transferred. Where water is lacking.
• Organic acids=donor; organic bases= acceptor.

Covalent Catalysis

• In covalent catalysis, a charged group interacts with the substrate, binding it to the enzyme.
• Serine proteases undergo covalent catalysis coupled with acid-base catalysis.
• Enzymes transfer an electron.
• Catalyst is only successful when it has low energy, with a substrate. Must be faster though.

Proximity and Enzymes

• Effective Catalysis increases with an increased number of reactants.
• More than one enzyme catalyzes when at the active site.
• At least 1000 fold increase. Enzymes act simultaneously which improves production. Subst rates have transition points.

Enzyme Kinetics

• Enzyme kinetics measure changes in reaction in relation.
• Study of enzymes/ catalysts.

Substrates and Speed

• Key to catalysts is concentration. [symbol?].
• [symbol?] changes as sub state becomes product.
• Simplified initial rate (VO; much of VO over [symbol?]).
• Low catalyst, VO goes up. Increased catalyst. More limited. Maximum velocity= plateau,. VO or VMax.

Victor Henri

• The mixing of enzymes with sub state creates enzymes which is necessary for enzymatic catalytic.

Steady State

• Rate depends on [ES].
  • At a constant point in reaction. Enzymes creates 2 forms. - Free combined/ bound ES
  • Equilibrium is high when at a low state. Enzymes can't touch substrate without enzyme. This is only 2 parts of enzymes. -[symbol?] can't be measured in equation number (II). -Need to make expression.
  • Free enzyme can be determined in equation. Number (1).

Reaction Rate

• Reaction rate and breakdown of ES depends on how ES created.

Michaelis constant

• Km = (k2+k-1)/k1 (breakdown of ES/formation of ES).
• V.
• In steady state VO is determined by k-[ES].
• Max = (2 [E] S /Km + [S]
• Constant is defined as (symbol?] equal sKm in enzyme reaction.

Enzymes and Reaction Numbers

• 50% bound enzyme= Km/ Km number is for ES strength

Effect of pH on Enzymes

• Enzymes work best at an optimal PH and decrease when at either PH.
• Enzymes and side chains serve as acids with critical function that depend on maintaining interaction with protein structure.
• Removing a proton eliminates the stabilizing active transformation.
• H concentration changes due to pH.
• Extreme changes to pH can cause enzyme denaturation because hydrogen bonds and ionic bonds are competing in the reactions.

pH Levels

• Optimal enzyme function is within pH 6-8
• Except:
  • Pepsin 1-2 -Acid posphatase 4-5
  • Alkaline phosphatase 10-11.
• Fungie and plants are very active with 4-6 pH.
• Effectiveness relies on pKa values.

Temperature and Reaction Rates

• Reaction rages increase with temperature, but elevation beyond optimal temperature can reverse the reaction process.
• Reactions decrease beyond a certain temperature due to loss of structure.
• Denaturing: breaking atoms and breaking weak hydrogen levels.

Denaturation Effects

• Changing the structure makes it have lesser catalytic ability.
• Can be reversible and irreversible.
• Q10 increases enzyme velo when the reaction is increase 10c in degrees.
• Temp increase activates molecules
• Enzymes range from 35-40 C exvept Taq Dna Plolymerase active @ 100c / plant are @ 60.