Biology Unit 3 Aos2

Enzymes

proteins that act as biological catalysts that speed up biochemical reactions by reducing the activation energy required

activation energy

the amount of energy needed to break the bonds of reactant for the reaction to begin

what happens to enzymes during a reaction

enzymes are not consumed during a reaction so they can catalyse many reactions

enzymes can only catalyse reactions when in active form

catalysts

speed up reactions by influencing the stability of bonds in the reactants

Substrate

the compound on which an active enzyme acts as a reactant for an enzyme controlled reaction.

active site

a specific region on the enzyme where the substrate binds, usually a a cleft at the surface

• an enzyme may have more than one active site

active site shape

the substrate matches the shape of an active site, but complementary r groups are also important, such as opposite charges

substrate specific

enzymes are usually substrate specific meaning they will only act on one substrate. However some enzymes do have different active sites, so can act on more than one substrate

lock and key model

proposes that the substrate (s) and the active site fit perfectly

induced fit model

an alternative to the lock and key model that proposes that enzymes and substrates bind at non quite matching sites.

• this affects the stability of the bonds, enabling them to break so that new molecules can be formed

• weak bonds form and induce structural changes in the active site distorting the substrate (s) so that the active site is matched

• the shape of the active site changes slightly to allow a better fit

anabolic reactions

building larger macromolecules or polymers from smaller units called monomers

how anabolic reactions work

• enzyme aligns the substrate to lower the activation energy

• chemical bonds are formed as an input of energy is needed

• e.g. photosynthesis, protein synthesis, dna/rna synthesis in condensation reactions

Endergonic

chemical reaction that absorbs energy

Exergonic

chemical reaction releases energy

catabolic reaction

the breakdown of larger molecules into smaller subunits (polymers into monomers)

how catabolic reactions work

chemical bonds are broken, so energy is released

e.g. cellular respiration, fermentation

biochemical pathway

an ordered series of different reactions, each controlled by enzymes, with the outputs of one reaction being the inputs for the next. the steps can occur in different cells or locations within a cell

why are biochemical pathways needed

• they are essential for cellular functions, transforming initial reactants through multiple steps to produce end products that cells need for energy, growth and repair

• e.g. photosynthesis, cellular repsiration

2 types of pathways

linear

cyclic: starting molecule needs to be regenerated at the end of the pathways so that cycle can continue

enzyme affinity

a measure of the ease with which an enzyme will bind to a substrate. it can be affected by chemical inhibition

enzyme inhibitors

substances that prevent the normal action of an enzyme, slowing the rate of reactions

irreversible inhibition

the inhibition permanently covalently binds to the enzyme. there is no reaction (cyanide)

reversible inhibition

the inhibitor is temporarily bound to to the enzyme via a non-covalent bond, preventing its function. reversible inhibitors are used to control enzyme activity

(heavy metals, leads, mercury)

competitive inhibition

an inhibitor molecule, structurally similar to the substrate, competes with the substrate binding to the same active site, preventing it from binding at normal rates

build up of end product may deactivate the enzyme in this way

non-competitive inhibitors

bind to the enzyme, but not at the active site, but alter its shape. the substrate may still be able to bind, but the reaction rate is slowed because the enzyme is less able to perform its function

allosteric enzyme inhibitors

a type of non-competitive inhibitor that induce a shape change that alters (but doesn’t block) the active site, preventing the substrate from binding. the enzyme ceases to function

feedback inhibition

the end product of a metabolic pathway inhibits an earlier enzyme in the pathway, reducing or stopping further production of that product.

does this by inhibitor and activator molecules binding with enzymes to change their state

enzyme concentration is regulated by

• controlling gene expression

• controlling the rate of degradation of the enzyme

• regulatory molecules and cofactors that bind to enzymes

• feedback inhibition

Effect of Temperature

• little activity at low temperatures, as molecules don’t have much kinetic energy and therefore dont collide often

• enzyme gradually increases as temperatures increases, as more energy increases the collision rate of enzyme and substrate molecules

• when optimum temperature is reached, rate of reaction is highest

• After this temperature, activity sharply decreases, as enzyme denaturation occurs

denaturation

the bonds maintaining the sd shape of the active site are disrupted and the enzyme can no longer bind to the substrate.

Effect of pH

• enzymes are affected by pH

• extremes of pH away from the enzyme optimum range can result in denaturation

• enzymes are found in very diverse pH conditions, so they must be suited to perform in these environments

Substrate concentration

• rate of reaction increases with increasing substrate concentration, as there are more substrate molecules per unit volume to react with the available enzyme, creating more enzyme-substrate complexes

• (differs from total quantity of substrate, which determines the max amount of product that can be made)

• the rate of plateaus when all active sites are full when all the enzyme active sites are saturated. a fixed amount of enzyme is assumed

substrate concentration and inhibition

• increasing substrate concentration can displace competitive inhibitors, because the molecules are still in motion

• non-competitive inhibitors are not displaced by increasing substrate concentration

enzyme concentration

(given a fixed amount of substrate…)

• the reaction rate increases with an increase in enzyme concentration until the substrate runs out.

• there are more agents per unit volume to bind with substrate, to catalyse the reaction, leading to more frequent enzyme-substrate interactions

• the same amount of product is made

• usually another factor becomes limited, leading to plateau

cofactor

enzymes need cofactors or helper molecules to function. they work by altering the shape of enzymes to make active sites functional or by completing the active site

cofactors can be

• inorganic such as minerals

• organic such as coenzymes or prosthetic groups

coenzymes

an organic molecule that acts as a cofactor. they carry/transfer electrons or ions from one reaction to another in a biological reaction

• they bind loosley

• they are changed in reactions so must be replaced (thrown away) e.g. ATP

prosthetic groups

• bind rightly and permanently

• e.g. heme in haemoglobin

ADP

adenosine di phosphate

a coenzyme classed as a nucleotide

• it is composed of adenine and ribose, making the adenosine part and two phosphate groups

• ADP combines with a 3rd phosphate group and an input of energy to become ATP, which provides usable energy for cells

where is atp from

• ATP is produced during cellular repiration where energy released from glucose forms the bond that connects ADP with a phosphate, in the process of phosphorylation

• atp synthase catalyses reaction

ATP

ATP is a portable energy carrier that moves around the cell to supply energy where required. It releases energy when it is hydrolysed to form ADP and Pi, breaking a phosphate bond, which releases energy.

cycling atp and adp

• atp can release its energy quickly by hydrolysis of the terminal phosphate

• this reaction is catalysed by ATPase

• once ATP has released its energy, it becomes ADP again (low energy)

• ADP is then phosphorylated again with more energy from glucose and the cycle continues

ATP synthase

an enzyme found that catalyses the formation of ATP from ADP and inorganic phosphate (Pi) using energy.