Physiology Ch.3 Part 1 Metabolic Reaction and Enzymes

Ligand

• A molecule or ion that is bound to a protein with one of the weak physical forces

- H-bond

- Ionic bond

- van der Waals forces

- hydrophobic forces between non-polar regions

Binding site

• Region of the protein where a ligand can bond

- Binding typically changes protein function by activating or inhibiting

Affinity

• Strength of interaction between ligand and protein

• High affinity = less ligand needed to bind

• Based on shape and chemical specificity

Chemical specificity

• How exclusive a protein is with ligands to accepts

- Determined based off amino acids in binding site and shape of binding site

• High chemical specificity = few kinds ligands can fit into the binding site on the protein

• Low chemical specificity = many kinds of ligands can fit into the binding site on the protein

Saturation

• How many binding sites are occupied at one time

- Measured in % with 100% being the max

• Determined by amount of unbound ligand and affinity of binding towards available ligand

Competition

• Different ligands compete with one another for the same binding sites

• Some ligands are inhibiters that stop a reaction from happening at all

Metabolism

• The sum of all chemical interaction in the body

• Subdivided into anabolism and catabolism

Anabolism

• Synthesis of organic molecules

• Does not happen spontaneously

- Products have more energy than reactants

• Memory hack: An = add

Catabolism

• Destruction of organic molecules

• Happens spontaneously

- Reactants have more energy than products

• Memory hack: Cat = catastrophe

Exergonic

• A chemical reaction that gives off energy in the body

Endergonic

• A chemical reaction that takes in energy in the body

Relation between exergonic and endergonic reactions

• Energy from exergonic reactions can be transferred to endergonic reactions to power them

- Energy transported through high energy electrons, if not trapped it is given off as heat

Catabolic / decomposition

• Type of chemical reaction

• Molecules break down into smaller molecules

• AB turns into A and B

Anabolism / synthesis

• Type of chemical reaction

• Molecules add together into bigger molecules

• A and B turn into AB

Exchange

• Type of chemical reaction

• Parts of large molecules exchange themselves with parts of other large molecules to make different large molecules

• AB and CD turn into AD and BC

Dehydration Synthesis

• Combine molecules by taking an OH off of one and an H off of the other

• Gets its name from the fact that it pulls water out of the molecule

- A–B + H2O → A–OH + H–B

Hydrolysis

• Breaks up a molecule using water

• Gets its name from the fact that water “hydro” is lysing “cutting apart” a molecule

- A–OH + H–B → A–B + H2O

Reactions using water

• Hydrolysis

• Dehydration synthesis

Reactions using phosphorus (P)

• Phosphorylation

• Dephosphorylation

Phosphorylation

• Change the same of a protein or transport energy in the phosphate bond

• ADP + Pi → ATP + H2O

Dephosphorylation

• Change the same of a protein or transport energy in the phosphate bond

• ATP + H2O → ADP + Pi

Oxidation-reduction reactions

• Made up of oxidation and reduction, both will always happen together

Oxidation

• Part of a Redox-reaction

• An electron is transferred to another molecule

• A• + B ⇌ A + B•

Reduction

• Part of a Redox-reaction

• An electron is gained from molecule

• HA-BH ⇌ A=B + 2H

Equilibrium

• Products are turning into reactants and reactants are turning into products at an equal rate

• There is no noticeable change in matter

• Possible when the reactants and products are at equal energy levels

Reversible Reaction

• A chemical reaction that can be performed in both directions

- The energy requirements to reverse the reaction fall in practical range

Irreversible Reaction

• A chemical reaction that can’t be performed in both directions

- The energy requirements to reverse it fall out of the practical range

Reaction rate

• How fast a reaction is happening

- Based on concentration of reactants and products

- Based on activation energy

- Based on temperature

- Based on the presence of a catalysis

Law of Mass Action

• Reaction rate based on the concentration of both reactants and products

• More will be made of the least concentrated half of the reaction

- If product are less concentrated than reactants more products will be made

- If reactants are less concentrated than products more reactants will be made

Activation energy

• Amount of energy needed to destabilize the reactants

• Reaction can’t happen unless reactants are testable destabilized

• Lower activation energy = more reactions

- Enzymes lower activation energy

Enzymes

• Reduce the activation energy required

• Able to be re used in many different reaction

• Have no chemical effect on the reaction

Substrate Specificity

• Based on how the shape of an enzyme and site it’s binding to

• Shown in two different models

- Lock-in-key model

- Induced-fit model

Lock-in key model

• The shape of the protein is ridges

Induced-fit model

• The shape of the enzyme changes in order to fit enzymes

Cofactor

• Substances that bind to an enzyme and are needed for the enzyme to function

- Trace metals are these

Coenzymes

• Organic vitamins-derived cofactors that directly participate in a reaction by transferring chemical groups during reaction

Substrate Concentration

• Factor in enzyme-catalyzed reactions

• Rate of reaction increases until enzymes are at maximum saturation

Regulating factors of enzyme-catylized reactions

• Catalytic rate of enzyme

• Substrate concentration

• Enzyme concentration

• Affinity

• Temperature

• pH

Enzyme concentration

• Higher enzymes concentration mean higher reaction rate

- Enzyme concentration regulated by changing the amount of proteins that are available

Affinity

• Higher affinity means between enzymes and reactants means the reaction rate will increase faster

- Less enzyme concentration required for same result

Allosteric regulation

• Protein must contain more than 1 binding site

• When a ligand binds to a regulatory / allosteric site can alter the shape of the active site

• Can increase or decrease activity

Covalent regulation

• When a protein bonds to an amino acid side chain it alter the protein shape and therefore the enzyme activity

• Phosphorylation: Phosphate group transferred from one molecule to another

- Can both increase or decrease activity

Protein kinase

• Enzymes that catalyze the transfer of phosphate from ATP to a protein side chain

Protein phosphatase

• Enzymes that remove phosphate groups

Metabolic Pathways

• A sequence of enzyme-mediated reactions that lead to a formation of a specific product

• The rate-limiting reaction has the slowest reaction rate of all reactions in the pathway and limits the reaction

Feedback Regulation

• An intermediate or end enzyme regulates a previous enzyme in the metabolic pathway

• Holds reactions at a steady rate, maintaining body’s needs

• Regulation is done to the first enzyme at a branch point

Inborn errors of metabolism

• A mutation in a single gene that codes for an enzyme pathway causing it to fail

• Causes disorders from not having needed end product or an unhealthy accumulation of intermediate products

Intermediate products

• Products in an enzyme chain that aren’t starting or ending products

End products

• The final result product of a metabolic pathway