2.1.4 Enzymes

what are enzymes?

biological protein catalysts that speed up reactions

what do enzymes do?

lower the activation energy (Eₐ) of a reaction - different reactions have different activation energies

they do this two ways:

1) to join two substrate molecules, it holds them together

2) to catalyse a break down, fitting into the active site puts strain on the bonds in the substrate and they break easier

what is metabolism?

all reactions that take place in the body

what is metabolic rate?

rate of all chemical reactions in the body

what two types of reactions do enzymes catalyse?

anabolic - making bonds and making the product, needs energy

catabolic - breaking bonds and breaking the substrate, releases energy

what is Vmax?

the maximum rate of enzyme controlled reactions

what are examples of reactions catalysed by enzymes?

protein synthesis

cellular reactions

photosynthesis

DNA replication

digestion

what is the structure of enzymes?

large 3D globular protein molecule

shape is determined by tertiary structure

soluble in water - due to position of the hydrophilic and hydrophobic R groups

have a groove called the active site

what is collision theory?

for a reaction to take place molecules need to collide in the right orientation

high temperature and high pH increase kinetic energy and speed - this increases the number of successful collisions and the rate of reaction

activation energy needs to be supplied for a reaction to start - enzymes help molecules collide successfully and therefore reduce the activation energy

how is the rate of chemical reactions increased?

increase concentration - more frequent collisions

increase temperature - more frequent and successful reactions

increase surface area - more frequent collisions

add a catalyst - reduces activation energy required

what are the two enzyme models?

lock and key theory (old model)

induced fit model (new model)

what is lock and key theory?

only one substrate (key) can fit into the enzyme’s active site (lock) - the shape of the active site is complementary to the substrate

when the substrate binds to the active site an enzyme-substrate complex is formed

the product is then released and the enzyme is unchanged

what is the induced fit model?

the active site and substrate are not complementary

instead the active site is flexible and changes shape which allows the substrate to fit

an enzyme-substrate complex is formed

the product moves away as it has become a different shape and the enzyme returns to its original shape

what are intracellular enzymes?

made and retained inside the cell

what are intracellular enzymes involved in?

lysosomal enzymes - intracellular digestion of cellular components and foreign matter

metabolic pathways - e.g. aerobic respiration, photosynthesis, protein synthesis

polymerases - DNA replication and transcription

ATPase - hydrolysis of ATP to ADP and Pᵢ to release energy for vital biochemical processes

phagocytosis

what are extracellular enzymes?

work outside of the cell

many polymers are too large to enter the cell and must be broken down before entering

what are extracellular enzymes involved in?

amylase - works outside of the cells in saliva, catalyses the breakdown of starch to maltose, is a single chain of amino acids with both alpha helix and beta pleated sheet sections

trypsin - type of protease, produced by pancreatic cells and released into the small intestine, catalyses the hydrolysis of peptide bonds of large polypeptides into smaller polypeptides which eventually get broken down into amino acids

what factors affect the rate of enzyme controlled reactions?

temperature

pH

enzyme concentration

substrate concentration

how does temperature affect the rate of enzyme controlled reactions?

enzymes have an optimum temperature at which they catalyse reactions at the maximum rate - 37°C (body temperature)

how do lower temperatures affect the rate of enzyme controlled reactions?

lower temperatures prevent reactions or slow them down

molecules have less kinetic energy and move slower

there is a lower frequency of successful collisions, and less formation of enzyme-substrate complexes

substrates and enzymes collide with less energy - it is less likely that bonds will form or break

how do higher temperatures affect the rate of enzyme controlled reactions?

high temperatures speed up reactions

molecules have more kinetic energy and move faster

there is a higher frequency of successful collisions, and more formation of enzyme-substrate complexes

substrates and enzymes collide with more energy - it is more likely that bonds will form or break

however, as temperature increases past the optimum temperature, the enzyme begins to denature and the rate of reaction drops sharply

the tertiary structure changes - bonds holding the enzyme together start to break

this permanently damages the active site, preventing substrates from bonding

what is a temperature coefficient?

Q₁₀

represents how much the rate of reaction changes when the temperature increases by 10°C

value is usually between 2 and 3

how are temperature coefficients calculated?

Q₁₀ = rate of reaction at temperature X + 10°C / rate of reaction at temperature X

how does pH affect the rate of enzyme controlled reactions?

all enzymes have an optimum pH

each enzyme’s optimum pH is different

what happens to enzymes at extreme pH?

enzymes are denatured at extreme pH

the H bonds and ionic bonds that hold the tertiary structure together break

this alters the shape of the active site and prevents substrates from binding

how does enzyme concentration affect the rate of enzyme controlled reactions?

increased enzyme concentration increases the number of active sites available for binding

increases the likelihood of enzyme-substrate complex formation

as long as there is sufficient substrate available, rate of reaction increases linearly

how does substrate concentration affect the rate of enzyme controlled reactions?

increased substrate concentration increases the likelihood of enzyme-substrate complex formation

what happens if the enzyme concentration is fixed and more substrate is added?

if enzyme concentration is fixed and more substrate is added - all active sites will become saturated

when all active sites are saturated, substrate molecules that are added will have nowhere to bind

what does the rate of reaction graph show?

1) rapid initial rate of reaction - lots of substrate molecules, frequent successful collisions

2) reaction slowing down - less substrate molecules, less chance of successful collisions

3) reaction has stopped - no substrate molecules left to collide with the active site

how is rate of reaction measured on a graph?

draw a tangent at the point which needs to be measured

draw a triangle

divide the height by the length - y/x

how is rate of reaction calculated?

rate of reaction = 1/time

time must be in seconds

what are the two types of enzyme inhibitors?

competitive inhibitors

non-competitive inhibitors

where do competitive inhibitors bind?

active site

how do competitive inhibitors reduce rate of reaction?

compete with substrates for the active site of the enzyme

whilst the competitive inhibitor is bound to active site substrates cannot collide with it and form enzyme-substrate complexes - reduces the rate of reaction

what is reversible competitive inhibition?

after a short time, the competitive inhibitor leaves the active site

can the effects of competitive inhibitors be overcome?

the effects of competitive inhibitors can be overcome by increasing the substrate concentration - creates a greater chance of a successful collision between the active site and a substrate

where do non-competitive inhibitors bind?

allosteric site

how do non-competitive inhibitors reduce the rate of reaction?

cause the tertiary structure to change - alters the shape of the active site so it is no longer complementary to the substrate

the substrate can no longer bind to the active site so rate of reaction is reduced

can the effects of non-competitive inhibitors be overcome?

the effects of competitive inhibitors cannot be overcome by increasing the substrate concentration - even if substrate concentration is increased, the substrate molecules still cannot bind with the active site

what are the three types of cofactors?

cofactors

coenzymes

prosthetic group

what all cofactors do?

enhance enzyme function

usually help to form the active site, but can bind to other parts of the enzyme

what is the difference between cofactors and coenzymes?

cofactors are inorganic - e.g. zinc, iron, copper ions

coenzymes are organic - e.g vitamins, NAD (a large complex molecule made from vitamin B3 involved in respiration)

what can happen if cofactors are damaged?

cofactors can be disabled or replaced by some substances - e.g. mercury

this can inhibit enzyme function

what is a prosthetic group?

cofactors that become a permanent part of the enzyme’s structure