What can you remember about enzymes? - Holyrood · PDF file · 2017-05-19“Effect of substrate concentration” Substrate Concentration Summary •The reaction rate...

What can you remember about enzymes?

Mr W

Human Cells (f) Enzymes and Metabolism

Learning Intentions

• Describe metabolism, synthetic (energy requiring) and breakdown (energy releasing) pathways

Cell Metabolism

• All the biochemical reactions that occur in a living cell are called cell metabolism

• Most of these reactions are catalysed by enzymes

Cell Metabolism

• Metabolic pathways involve biosynthetic processes (anabolism) and the breakdown of molecules (catabolism) to provide energy and building blocks.

Anabolic Reactions

• They make complex molecules from simpler ones

• They usually require energy

What reactions can you think of that are synthesis reactions?

Catabolic Reactions • Complex molecules are broken down into

simpler ones.

• These reactions release energy and provide building blocks for anabolic reactions.

What reactions can you think of that are break down reactions?

Learning Intentions

• State that metabolic pathways are controlled by the presence or absence of particular enzymes

• State that metabolic pathways rate of reaction are regulated by key enzymes within the pathway

Metabolic Pathways

• Metabolic pathways are regulated by enzymes that catalyse specific reactions

• A pathway often has reversible and irreversible steps that help with this control

Alternative Routes

• Metabolic pathways can also take alternative routes that allow steps to be bypassed.

• The example shown occurs when a cell has a plentiful supply of glucose.

Summary

• Metabolism is the integrated and controlled pathways of enzyme catalysed reactions within a cell.

• Metabolic pathways involve biosynthetic pathways (anabolic, require the input of energy) and pathways that break down molecules (catabolic, usually release energy).

• Metabolic pathways can have reversible and irreversible steps. they can also have alternative routes that can bypass steps in a pathway.

Group Task

Using the enzyme co – op cards, create a poster that includes information on the following:

• The effect of an enzyme on the activation energy of a reaction

• What is “induced fit” means

• The role of the enzyme active site including shape, substrate and product affinity

Learning Intentions

• Describe the effect of an enzyme on the activation energy of a reaction

Lesson starter

1. What is the difference between anabolism and catabolism?

2. What words did we use instead of these to describe these reactions, in enzymes?

3. Name one anabolic reaction and one catabolic reaction?

4. In what three ways can we prove enzymes are catalysts?

5. Come up with a way to remember q1

Activation Energy

• Every biochemical reaction is catalysed by an enzyme and enzymes speed up biochemical reactions.

• Biochemical reactions may involve joining molecules together or splitting complex molecules – in each case energy is needed to break chemical bonds and start the reaction.

• This is called the activation energy

Energy input needed to break chemical bonds and start a chemical reaction

(activation energy) is reduced when an enzyme

is used

Activation Energy

When the bonds break they become unstable and are now in the transition state - the reaction can start

Learning Intentions

• Describe what “induced fit” means

Induced Fit

• The shape of an active site is specific to the shape of a substrate

• However, the active site is flexible. The shape of the active site can change slightly when it comes into contact with a substrate molecule so that the active site fits it better.

Induced Fit

• It can be described as being like a slightly too small rubber glove forming a very tight fit round a hand

• Induced fit means that the active site comes into very close contact with the molecules of substrate and increases the chance of a reaction taking place.

• This lowers the activation energy required for the reaction to occur

Learning Intentions

• Explain the role of the enzyme active site including shape and substrate affinity

• At some point on the surface of an enzyme molecule, there is an active site. Only one substrate will fit into the enzymes active site.

• The enzyme is specific to its substrate and the substrates shape is complementary to the enzymes active site.

Specificity

Enzyme A

Substrate A

Perfect fit Active site

Enzyme B

Won’t fit..

Wrong shape!

Substrate A

• When there are two or more reactants, the shape of the active site determines the orientation of the reactants (how they line up)

• This ensures that they are held together in such a way that the reaction between them can take place. This lowers the activation energy required for the reaction to occur

Substrate Affinity

Product Affinity

• The active site holds the two reactants closely together in an induced fit.

• Once the reaction has taken place the, products have a low affinity for the active site and are released.

Active Site Summary • The substrate attaches to the active site on the

enzyme

• The active site orientates (lines up) the molecules.

• This causes an induced fit - the enzyme changes shape slightly so that the active site fits better

• This lowers the activation energy required for the reaction to occur

• Products are released as they have a low affinity for the active site

Quick questions

1. What is meant by metabolism?

2. What is meant by activation energy?

3. What is meant by induced fit?

Answers

1. Metabolism is the term for all the enzyme controlled biochemical reactions that occur in a living cell

2. Activation energy is the energy is needed to break chemical bonds and start the reaction

3. Induced fit is the changing of the shape of the active site so that it fits the substrate better

Extra Questions 1. What is meant by the affinity of substrate

molecules for an enzyme’s active site?

2. Rewrite the following sentences choosing he correct answer from each underlined choice:

The shape of the active site ensures that the reactants are correctly orientated/denatured so that the reaction can take place. This is made possible by the fact that the enzyme increases/decrease the activation energy needed by the reactants to reach the transitory/transition state

Extra Questions Answers 1. The chemical attraction between them

2. The shape of the active site ensures that the reactants are correctly orientated so that the reaction can take place. This is made possible by the fact that the enzyme decrease the activation energy needed by the reactants to reach the transition state

HW table

Word

Definition

Genomics

The study of human genome.

Involves determining the sequence of

nucleotide bases along DNA strands.

Bioinformatics

Use of computer technology to identify

DNA sequences.

Systematics

The study of a group of living things with

respect to their diversity, relatedness and

classification.

Pharmacogenetics

The study of and individual’s genetic

makeup and how this affects response to

certain drugs.

Lesson starter Explain the role of the active site in

enzyme-catalysed reactions (3 marks)

Answer 1. The substrate attaches to the active site (on the enzyme).

2. The active site orientates / lines up the molecules.

3. This causes an induced fit/the enzyme to change shape slightly so that the active site fits better.

4. This lowers the activation energy (required for the reaction to occur).

5. Products are released as they have a low affinity for /attraction to the active site.

Learning Intention

• State the effects of substrate concentration on the direction and rate of enzyme reactions

Factors Affecting Enzyme Action

• The direction and rate of enzyme reactions can be affected by temperature, pH and:

substrate concentration

end product concentration (feedback

inhibition – we’ll come back to this!)

Effect of Substrate Concentration on Enzyme Activity

• Into each boiling tube add 10 ml

of hydrogen peroxide – each should have a different concentration.

• Drop the piece of liver into the first boiling tube and time for time for 1 minute then measure the height of the oxygen foam.

• Repeat this for each concentration of hydrogen peroxide

• The reaction rate increases as substrate concentration increases.

• This will continue until a point where enzyme concentration becomes a limiting factor – all the active sites are used up.

Enzyme concentration a

limiting factor – all

active sites involved in

the reaction Substrate

concentration

a limiting

factor

Substrate Concentration

Change your graph on p9 and give it the title “Effect of substrate concentration”

Substrate Concentration Summary

• The reaction rate increases as substrate concentration increases. This will continue until a point where enzyme concentration becomes a limiting factor – all the active sites are used up.

Increasing the substrate concentration increases the rate of reaction until approximately 40mg/l when the rate of reaction then remains constant

Control

Reaction A

Reaction B

Describe the effect of increasing substrate concentration on the rate of reaction in the control.

Learning Intention

• Describe the control of enzymes in metabolic pathways by gene action and signal molecules

Metabolic Pathways

• A metabolic pathway is a sequence of enzyme controlled reactions that convert one metabolite to another

enzyme 1 enzyme 2 enzyme 3 enzyme 4

A B C D E

• Some examples of metabolic pathways include Glycolysis, Kreb cycle and photosynthesis.

Control of Metabolic Pathways

• Enzyme action in a metabolic pathway can be controlled at 2 levels. Either by:

gene expression (which genes are switched on and off)

or

enzyme action

If the pathway is interrupted by the lack of a particular enzyme, the pathway comes to a stop.

Intermediate metabolites will accumulate in the pathway.

enzyme 1 enzyme 2 enzyme 3 enzyme 4

A B C D E

Control of Metabolic Pathways

Complete

questions on

page 85

Control by Gene Action

• Some metabolic pathways are only required to operate under certain circumstances.

• To prevent resources being wasted, genes that code for the enzymes controlling each of their stages are “switched on” or “switched off” as required

Lactose

• Lactose is a sugar found in milk

• It is made up of a molecule of glucose attached to a molecule of galactose

• The enzyme b - galactocidase breaks down lactose to glucose and galactose

glucose Galactose

Lactose Galactose Glucose + B- galactocidase

Lactose Galactose Glucose + B- galactocidase

• Lactose is not present all of the time

• It would be very wasteful of energy and resources to produce b - galactocidase when there was no substrate for it to act on

• So organisms can switch the gene to make the enzyme off when it is not needed

Lesson starter

1. What is an enzyme?

2. What is meant by induced fit?

3. What is meant by specific?

4. Where do the enzyme and substrate meet?

5. What is meant by enzyme affinity?

6. What is another word for a degradation reaction?

7. Give an example

Jacob and Monod

• E.coli has a gene which codes for b-galactosidase – the enzyme is only found only when the substrate lactose is found in a cell.

• Jacob and Monod formulated a model of how the gene to make the enzyme b- galactocidase is switched off and on in the bacteria E. coli.

S

Operator gene (controls the structural gene)

O

S

Regulator gene (makes the repressor protein )

O R

S

Structural gene (makes the enzyme)

DNA

S O R

Repressor protein molecule

Repressor binds with the operator and blocks it

No enzyme ( b galactocidase) made

Structural Gene is OFF

NO LACTOSE PRESENT

S O R

Repressor molecule

enzyme ( b galactocidase made)

Structural Gene is ON

Lactose blocks repressor

Structural gene makes enzyme

Operator switches structural gene on LACTOSE PRESENT

** enzyme digests

lactose until supply

runs out then

repressor combines

with operator to

switch it back off.

Lesson Starter

1. What is lactose?

2. What enzyme breaks lactose down?

3. What are the products?

4. What is the function of the structural gene?

5. What is the function of the operator gene?

6. What is the function of the repressor?

7. A)What blocks the operator?

B) When does this occur?

C) Is the enzyme produced?

D) Is the gen switch on/off?

8. Describe what happens when lactose is present.

Lesson starter

1. Describe the catabolic reaction that can occur at the lac operon

2. State the difference in molecules during a catabolic and anabolic reaction

3. Describe what is meant by affinity and induced fit in the one sentence

4. If the pathway is interrupted by the lack of a particular enzyme, the

pathway comes to a stop. What result does this have with regards to

metabolites?

5. State 4 factors that can affect enzyme activity

6. State what is meant by specific

7. What is the substrate for : a) catalase b) amylase c) phosphorylase

Control by Signal Molecules

• In the lac operon sytem, a gene is switched off in response to a signal molecule in the cell’s environment – lactose.

•This signal molecule was produced outside the cell so is called an extracellular signal •A signal molecule produced within the cell is said to be an intracellular signal

Summary of Gene Control

• Some metabolic pathways are only required on certain occasions.

• To prevent resources being wasted, the genes that code for their enzymes are switched on or off in response to signals from either within the cell (intracellular) or outwith the cell (extracellular).

Enzymes in Metabolic Pathways

As metabolite A becomes available enzyme 1 becomes active

Enzyme 1 converts metabolite ___ into metabolite ___

As metabolite B becomes available enzyme ___ becomes active

Enzyme 2 converts metabolite ___ into metabolite ____

As metabolite C becomes available enzyme ____ becomes active

Enzyme 3 converts metabolite ____ into metabolite ____

A continuous supply of metabolite A drives the direction of the pathway from A to D

A B

2

B C

3

C D

Learning Intention

• Describe the control of enzymes in metabolic pathways by enzyme action through competitive and non-competitive inhibition

Control by Enzyme Action

• Genes for some enzymes are continuously expressed.

• These enzymes are always present in the cell and their control involves regulation of their rate of reaction.

Non Competitive Inhibition

• Non competitive inhibition involves the binding of molecules that change the shape of the active site.

Competitive Inhibition

• Competitive inhibition involves molecules that resemble the substrate binding to the active site so it can’t bind with the correct substrate

Lesson starter

1. Draw the 3 genes present in the lac operon and state their functions

2. State what happens when lactose is absent

3. State what happens when lactose is present

4. Name two enzymes and state their substrates and products, also state whether anabolic or catabolic

5. Draw a diagram to describe a catabolic reaction

6. What is the difference between bioinformatics and systematics?

Show me boards

Show me boards

Show me boards

Show me boards

Show me boards

What name is given to process X? A. Gene expression C. Post transitional modification B. RNA splicing D. Polymerase chain reaction

Competitive Inhibition

• Competitive inhibition can be reversed by increasing substrate concentration

Competitive Inhibition Example

• As well as lactose, the chemical ONPG also acts as substrate for the enzyme -galactosidase.

• Galactose acts as a competitive inhibitor of the enzyme, competing with ONPG for the active site.

Competitive Inhibition Example

• At high concentrations galactose will inhibit the reaction by preventing ONPG forming a complex with the active site.

• This inhibition can be overcome if the ONPG concentration is sufficiently increased.

Competitive and Non Competitive Inhibition Summary

• Genes for some enzymes are continuously expressed. These enzymes are always present in the cell and their control involves regulation of their rate of reaction.

• Non competitive inhibition involves the binding of molecules that change the shape of the active site.

• Competitive inhibition involves the binding of molecules to the active site that resemble the substrate. This can be reversed by increasing substrate concentration.

Learning Intention

• Describe the control of enzymes in metabolic pathways by enzyme action through feedback inhibition

Feedback Inhibition • In a metabolic pathway, an enzyme early in

the pathway can be inhibited by high levels of the final product of the whole pathway.

• A high level of end product means it is not being used and it is wasteful to make.

Feedback Inhibition • To overcome

this, the end product binds to an early enzyme and reduces it’s activity - this is known as end product inhibition

Feedback Inhibition Summary • Feedback inhibition occurs when an end

product binds to an enzyme that catalyses a reaction early in the pathway.

• This binding causes the enzyme activity to reduce and reduces the amount of product being formed.