1.4 enzymes and biological reactions

metabolism

refers to all reactions of the body

metabolic pathways

the sequence which reactions occur in

what are the different metabolic pathways

-anabolic reactions

-catabolic reactions

anabolic reactions

building up molecules eg protein synthesis (forming or making bonds)

catabolic reactions

breaking molecules down eg digestion (breaking bonds)

what are metabolic reactions controlled by

enzymes

what do the products of one enzyme controlled reaction become

reactants --> pathway of overall reaction

what are enzymes

globular proteins that act as catalysts

what is a catalyst

molecule which speeds up a chemical reaction -> but remains unchanged by the end of the reaction

what are enzymes known as and why

called biological catalysts because they are made by living cells

what are the properties of enzymes and chemical reactions in the reaction they catalyse

-they speed up the reaction

-they are not used up

-they aren't changed

-they have a high turn over number

what do enzymes only catalyse

reactions that are energetically favourable and would happen anyway

what would happen without enzymes

reactions in the cells would be to slow to be compatible with life

what are enzymes? which structure do they have?

they are proteins with a tertiary structure

how are enzymes formed? (structure)

tertiary structure - the protein chain folds into a spherical or globular shape with the hydrophilic R groups on the outside of the molecule making enzymes soluble

what does each enzyme have

they have a particular sequence of amino acids

what do the elements in the r group determine

the bonds the amino acids make with each other

what do the hydrogen bonds, disulphide bridges and ionic bonds do

they hold the enzyme molecules in its tertiary form

active site

site on an enzyme with specific 3D structure that permits binding with a substrate

chemical bonds

vary in strength depending on the atoms that they join + on their chemical environment

hydrogen bonds

weak - but if there are many they have a significant binding effect

ionic and covalent bonds

eg disulphide bond, are stronger than hydrogen bonds

where are enzymes made

inside cells - extracellular, intracellular

extracellular

some enzymes are secreted from cells by exocytosis and catalyse extracellular reactions

intracellular in solution

in solution intracellular enzymes act in solution inside cells

eg. enzymes that catalyse glucose breakdown in glycolysis

intracellular membrane bound

membrane bound intracellular enzymes may be attached to membranes

eg. cristae of mitochondria and the grana of chloroplasts

How is an enzyme-substrate complex formed? (ESC)

an enzyme acts on its substrate, which it makes temporary bonds at the active site forming an ESC

what happens when the reaction is complete

products are released, leaving the enzyme unchanged and the active site ready to receive another substrate molecule

enzyme-substrate complex

an intermediate structure formed during an enzyme catalysed reaction in which the substrate + enzyme bind temporarily, such that the substrates are close enough to react

lock and key model

the substrate is imagined fitting into the active site as a key fits into a lock

how does the lock and key theory work

due to the unique shape of the active site means that an enzyme can only catalyse one type of reaction - other molecules with different shape won't fit (enzyme is specific for its substrate)

lysozyme and the induced fit model

observations that an enzyme shape was altered by binding its substrate - suggesting its flexible + not rigid as og thought

induced fit model

enzyme shape alters slightly to accommodate the substrate

if they are anabolic

they form

if they are catabolic

they break

what can cause the bonds to break

tensions from moulding around enzyme

activation energy

is the minimum energy that must be put into a chemical system for a reaction to occur.

what does lowering the activation energy mean

enzymes allow reactions to take place at lower temps found in cells

whats a way of making chemicals react

is it increase their kinetic energy, to make successful collisions between them more likely

what speeds up reactions

heat speeds up the reaction in all non living systems

what is the problem with heat in living organisms

temps above 40oc cause irreversible damage to proteins and they denature

how do enzymes work

by lowering the activation energy

what is the effect on the enzyme and activation energy when a substrate is added

when a substrate enters the active site of an enzyme the shape of the enzyme molecule alters - allowing reactions to occur at lower temp than in absence of ensume

when are most enzymes inactive

at 0oc - if temp raises they become active again

when do most enzymes in organisms denature

above 40oc + lowering the temp does not restore their activity

what do all reactions need to overcome

an energy barrier

what can the progress of an enzyme catalysed reaction for a given conc of substrate be followed by measuring....

formation of product or the disappearance of substrate

rate of production

increase in mass/time

% increase in mass

actual increase in mass/initial mass x100

where is the steepest part of the graph shown

at the start of the reaction

environmental factors affecting enzyme action

temperature and pH

what does the temp and pH affect

it changes the three-dimensional structure of enzyme molecules

what changes the rate of reaction in environmental factors

bonds are broken and the configuration of the active site is altered - changes the rate of reaction

concentrations of enzyme and substrate

also affect the rate of reaction by changing the number of enzyme - substrate complexes formed

4 factors which effect the rate of enzyme reactions

temp, ph, enzyme conc, substrate conc

what does increasing the temp do

increases the kinetic energy of enzyme and substrate molecules - they collide with enough energy more often - increasing rate of reaction

how does the temp in the rate of reaction double

the rate of reaction doubles for each 10oc rise in temp - up to a particular temp (40oc where they denature)

what occurs above a certain temp (40)

above this temp molecules have more kinetic energy but the reaction rates goes down because their increasing vibration breaks hydrogen bonds -changing the tertiary structure

what is the structure of enzymes

Tertiary globular structure.

denatured

An enzyme's active site is permanently distorted by the irreversible breaking of hydrogen bonds, preventing substrate binding and reducing the rate of reaction

what happens when an enzyme is denatured

its primary structure, the order of amino acids, is unaffected but loses higher levels of structure

what happens to the enzymes at lower temps

the enzyme is inactivated as the molecule have very low kinetic energy - shape is unchanged + enzymes will work again when temp is raised

what is inactivation

reversible reduction of enzyme activity at low temps as molecules have insufficient kinetic energy to form enzyme substrate complexes

what do most enzymes have

an optimum pH - at which rate of reaction is highest

what do small ph changes around the optimum cause

cause small reversible changes in enzyme structure and reduce its activity, but extremes of pH denature enzymes

what occurs if the enzyme concentration is constant

the rate of reaction increases as the substrate concentration increases

at low substrate concentrations

enzyme molecules only have few substrate molecules to collide with - active sites aren't working at full capacity

what does the conc of substrate control

controls the rate of reaction - so limiting factor

what happens when a high concentration of substrate is added

reaches critical concentration so all active sites become occupied - rate of reaction is at maximum

what happens when too much substrate has been added

the reaction cannot be catalysed any fast so line plateaus

when does a factor become limiting

when an increase in its value causes an increase in rate of reaction

what happens when the product leaves the active site

the enzyme molecule can be re used - so only a low enzyme conc is needed to catalyse a large number of reactions

what is the turn over number

number of substrate molecules that one enzyme can turn into products in given time

what is the fasting acting enzyme

catalase - it breaks down highly toxic waste, hydrogen peroxide

what happens as enzyme concentration increases

there are more active sites available - rate of reaction increases

what happens if temp + pH are optimal + an excess of substrate

the rate of reaction is directly proportional to enzyme conc

enzyme inhibition

the decrease in rate of an enzyme controlled reaction by another molecule (an inhibitor)

how does the formation of an enzyme substrate complex prevented

an inhibitor combines with an enzyme

inhibitor

a molecule or ion that reduces the rate of an enzyme controlled reaction

competitive inhibitor

have a molecular shape complementary to active site similar to that of a substrate, so they compete for the active site + prevent the substrate from binding

equation for enzyme succinic dehydrogenase

succinic acid ----->(^succinic acid dehydrogenase) fumaric acid + 2H

who competes for the active site of succinic dehydrogenase

malonic acid has similar shape to succinic acid - so compete for the active site

what happens when you increase the concentration of succinic acid

reduces the effect of the inhibitor - because more substrate molecules present the greater their chance of binding to active sites which leaves fewer available for the inhibitor

what happens in inhibitor concentration increases

it binds to more active sites so reaction rate is slower

When does end product inhibition occur?

when a product of a series of reactions inhibits an enzyme that acts earlier in the series so it slows down the whole sequence of reactions

why is inhibition reversible

because the mass of product formed ends up the same because the inhibitor can bind to the active site and unbind

what happens when you increase inhibitor concentration

the ratio of substrate:inhibitor decreases

non-competitive inhibitor

reduction of the rate of an enzyme controlled reaction by a molecule or ion that binds to the enzyme somewhere other than the active site, altering the shape of the active site so substrate can't bind

example of cyanide ion inhibitor

cyanide ion - but unusual as it combines to the active site

allosteric site

site other than the active site - so they do not compete with the substrate

when are the enzymes immobilised

when they are fixed, bound or trapped on an inert matrix like sodium alginate beads or cellulose microfibrils

What are immobilised enzymes?

an enzyme molecule bound to an inert material, over which the substrate molecules move

how is the immobilised enzyme reaction set up

these can be packed into glass columns, substrate is added to the top of column, when it flows down, the molecules bind to enzyme molecules active sites, both on bead surface + inside the beads as substrate molecules diffuse in

what happens when the column has been set up

the column can be used repeatedly - the enzyme is fixed so doesn't contaminate products

different processes which immobilised enzymes are used for

industrial processes, like fermentation - they can readily be recovered for reuse

what are the advantages of using enzymes rather than inorganic catalysts

-they have a higher turn over number

-they are very specific

-they are more economical because they work at lower temperatures

why are smaller beads better than larger beads

as there is a large surface area - the substrate molecules will have easier access to enzyme molecules so they will produce a higher rate of reaction

how can you make enzymes more stable

immobilising the enzymes with a polymer matrix making them more stable because it creates a microenvironment allowing the reaction to occur at higher temps and more extreme pHs

what is the only problem with using enzymes

enzyme instability - as the organic solvents, higher temps and extreme pHs can denature the, with consequent loss of activity

what do enzyme immobilised beads have

a lower rate of reaction than those immobilised on a membrane, if all other factors are constant