DP Biology SL C1.1 Enzymes and Metabolism

DP Biology SL C1.1 Enzymes and Metabolism - Full notes

RevisionPrep

DP Biology SL | C1.1 Enzymes and Metabolism

DP BIOLOGY · THEME C: INTERACTION AND INTERDEPENDENCE

C1.1

Enzymes and Metabolism

Full notes for SL · IB-style

Contents

1	Metabolism: anabolism and catabolism
2	Enzymes as catalysts and the active site
3	Induced fit and enzyme-substrate specificity
4	Molecular motion and collisions
5	Factors affecting enzyme activity
6	Activation energy and measuring rates
7	Metabolism: anabolism and catabolism
8	Enzymes as biological catalysts
9	The active site and specificity
10	Induced fit model
11	Enzyme–substrate collisions
12	Effect of temperature
13	Effect of pH
14	Effect of substrate concentration
15	Measuring enzyme activity
16	Intracellular and extracellular enzymes
17	Heat generated by metabolism
18	Cyclical and linear pathways
19	Mixed review: worked problems
20	Additional exam-style practice
21	Enzymes in industry
22	Q10 and temperature coefficients
23	Common misconceptions and links
24	Exam-style question with markscheme
25	Check your understanding
26	Summary and topic map

These are full teaching notes. Read each section in order, try the Think about it question before you read on, and do every Quick check before moving to the next section.

Before you start

Rate yourself on each statement now, and again after you've worked through the notes. Shade R (not yet), A (getting there) or G (confident).

I can…	R	A	G
define metabolism, anabolism and catabolism with examples
explain how enzymes work, including the active site and induced fit
explain the role of molecular motion and collisions
explain the effects of temperature, pH and substrate concentration on enzyme activity
explain how enzymes lower activation energy
calculate rates of reaction from experimental data

This booklet covers the SL content of this subtopic. Additional Higher Level material is not included.

Guiding questions

How do enzymes speed up reactions in cells? How is metabolism controlled?

How this topic is examined

C1.1 is among the most heavily examined subtopics. Expect graphs of enzyme activity against temperature, pH or substrate concentration, and experimental design questions.

Always explain graph shapes in terms of collisions and active site shape: more collisions explain rising rates, denaturation explains sharp falls.

Command term	What the examiner wants
State / Identify	a brief answer with no explanation needed
Outline	a brief account or summary
Describe	a detailed account, including trends or features, without reasons
Explain	a detailed account including causes, reasons or mechanisms
Distinguish / Compare and contrast	give the differences (and similarities), point by point
Calculate	a numerical answer with working and units
Deduce / Suggest	reach a conclusion from data; propose a reasonable explanation
Evaluate / Discuss	weigh strengths and limitations and reach a judgement

How to use these notes

Each section teaches one part of the syllabus in full. You'll see these boxes throughout; each has one job:

Box	What it's for
Think about it	a question to get you thinking before a section; the answer comes in the section
Key point	the one idea you must not forget
Common mistake	an error examiners see every year, and how to avoid it
In the real world	where the biology shows up outside the classroom
Try this	something quick you can do yourself to test the idea
Worked example	full solutions with IB-style marks (M1 method, A1 answer, R1 reasoning)
Quick check	short questions to test yourself at the end of each section

1 Metabolism: anabolism and catabolism

Metabolism is the web of all chemical reactions in an organism.

Think about it

Your cells carry out thousands of chemical reactions every second at 37 °C. In a test tube, many of these reactions would take years. What makes the difference?

Metabolism is the complex network of interdependent and interacting chemical reactions that occur in living organisms. Most reactions are catalysed by enzymes, and many are linked in pathways, where the product of one reaction is the substrate of the next.

Anabolism is the building up of complex molecules from simpler ones, usually by condensation reactions. It requires energy (often from ATP). Examples: protein synthesis from amino acids, photosynthesis, glycogen formation, DNA replication.

Catabolism is the breaking down of complex molecules into simpler ones, usually by hydrolysis. It releases energy. Examples: digestion, cellular respiration, breakdown of glycogen to glucose.

	Anabolism	Catabolism
Process	builds larger molecules	breaks down molecules
Energy	requires energy	releases energy
Reaction type	often condensation	often hydrolysis
Examples	protein synthesis, photosynthesis	digestion, respiration

Quick check

1. Define metabolism.

2. Give one example each of anabolism and catabolism.

Answers: 1. all the chemical reactions in an organism 2. protein synthesis; respiration / digestion

2 Enzymes as catalysts and the active site

Globular proteins that speed up reactions without being used up.

Enzymes are biological catalysts: they speed up chemical reactions without being permanently changed, so a single enzyme molecule can catalyse the same reaction many thousands of times. Almost all enzymes are globular proteins (a few are RNA, the ribozymes of A2.1).

Each enzyme has an active site: a small region, usually a cleft or pocket, formed by a few amino acids brought together by the folding of the polypeptide. The active site has a specific shape and chemical properties that are complementary to the enzyme's substrate. The substrate binds to the active site, forming an enzyme-substrate complex; the reaction occurs, forming products, which are released. The enzyme is then free to bind another substrate molecule.

Enzymes can catalyse intracellular reactions (inside cells, such as the enzymes of glycolysis in the cytoplasm) or extracellular reactions (outside cells, such as digestive enzymes in the gut).

Figure 1. The enzyme cycle.

Quick check

1. What is the active site?

2. Why can a small amount of enzyme catalyse many reactions?

Answers: 1. the region of the enzyme where the substrate binds and the reaction occurs 2. it is not used up and can be reused

3 Induced fit and enzyme-substrate specificity

The active site moulds itself around the substrate.

Enzymes are specific: each enzyme catalyses one particular reaction or a small group of similar reactions, because only substrates with a complementary shape and charge pattern can bind to the active site.

The induced-fit model describes binding: the active site does not exactly match the substrate at first. When the substrate binds, both the active site and the substrate change shape slightly, so they fit more closely. This change in shape puts strain on bonds in the substrate, or brings reacting groups together, making the reaction easier. Once the products form, they no longer fit the active site and are released.

The induced-fit model replaced the earlier lock-and-key model, in which the active site was thought to be a rigid shape exactly complementary to the substrate. Induced fit better explains why enzymes lower activation energy and why some enzymes can act on a few similar substrates.

Quick check

1. Why are enzymes specific?

2. Describe the induced-fit model.

Answers: 1. only substrates complementary to the active site can bind 2. active site and substrate change shape on binding to fit closely, straining bonds

4 Molecular motion and collisions

Reactions happen when substrates collide with active sites.

Substrate and enzyme molecules are in constant random motion in solution. For a reaction to occur, a substrate molecule must collide with the active site with the correct orientation and with enough energy. Most enzyme-substrate collisions are successful because of the shape of the active site.

Often the substrate moves more than the enzyme, because enzymes are much larger. Some enzymes are fixed in membranes (immobilized), for example the enzymes of the electron transport chain; then only the substrate moves. Anything that increases the frequency of successful collisions (more substrate, higher temperature) increases the rate of reaction, up to a point.

5 Factors affecting enzyme activity

Temperature, pH and substrate concentration each produce a characteristic curve.

5.1 Temperature

As temperature increases, molecules move faster, so collisions between substrate and active site are more frequent and more energetic: the rate of reaction increases. Above the optimum temperature, the increased vibration of the enzyme breaks hydrogen and ionic bonds holding its tertiary structure. The active site changes shape, so the substrate no longer fits: the enzyme is denatured (B1.2) and the rate falls sharply. Most human enzymes have an optimum near 37 °C; enzymes of thermophilic bacteria may have optima above 70 °C.

5.2 pH

Each enzyme has an optimum pH. Changes in pH alter the charges on amino acid R groups in and around the active site, disrupting ionic and hydrogen bonds, changing the shape of the active site and reducing binding. Extreme pH denatures the enzyme. Pepsin, in the stomach, has an optimum of about pH 2; salivary amylase about pH 7; trypsin, in the small intestine, about pH 8.

5.3 Substrate concentration

At low substrate concentration, increasing the concentration increases the rate, because collisions with active sites become more frequent. As concentration rises further, more and more active sites are occupied at any moment. Eventually all active sites are saturated, and the rate reaches a maximum (Vmax). Further increases in substrate concentration have no effect; the enzyme concentration is now limiting.

Figure 2. Effects of temperature, pH and substrate concentration on the rate of enzyme activity.

Common mistake

Saying enzymes are 'killed' at high temperatures. Enzymes are proteins, not living things; they are denatured.

Quick check

1. Why does rate increase with temperature below the optimum?

2. Why does rate level off at high substrate concentration?

3. What is the optimum pH of pepsin?

Answers: 1. more frequent, energetic collisions 2. all active sites occupied (saturated) 3. about 2

6 Activation energy and measuring rates

Enzymes lower the energy barrier.

For any reaction to occur, reactants need a minimum amount of energy, the activation energy, to break existing bonds. Enzymes lower the activation energy, so the reaction happens much faster at body temperature. They do this by binding the substrate in a way that stresses its bonds or brings reacting groups together. Enzymes do not change the overall energy released or absorbed by the reaction.

Measuring enzyme activity. The rate of an enzyme-catalysed reaction is measured as the amount of product formed or substrate used per unit time. For catalase, which breaks down hydrogen peroxide into water and oxygen, the volume of oxygen collected in a gas syringe can be measured over time. The initial rate is found from the gradient of a tangent to the curve at time zero.

Figure 3. Oxygen released by catalase over time.

WORKED EXAMPLE 1 Calculating rate

Using the graph, calculate the mean rate of oxygen production in the first 20 s, and explain why the rate decreases over time.

Solution

Mean rate = 21 ÷ 20 = 1.05 cm³ s⁻¹A1

Substrate (hydrogen peroxide) is used upR1

So fewer collisions with active sites; rate falls to zero when substrate is exhaustedR1

Quick check

1. Define activation energy.

2. How do enzymes affect activation energy?

Answers: 1. minimum energy needed for a reaction to occur 2. lower it

7 Metabolism: anabolism and catabolism

Building up and breaking down.

Metabolism is the complex network of interdependent, enzyme-catalysed reactions in a cell. Anabolism builds larger molecules from smaller ones (protein synthesis, photosynthesis, glycogen formation) and requires energy. Catabolism breaks larger molecules into smaller ones (digestion, respiration) and releases energy.

WORKED EXAMPLE 2 Classifying (standard)

Classify: (a) glycogen formation; (b) hydrolysis of starch; (c) DNA replication.

Solution

(a) and (c): anabolicA1

(b): catabolicA1

8 Enzymes as biological catalysts

Speeding up reactions.

Enzymes are globular proteins that speed up reactions by lowering the activation energy, without being used up. They are specific to their substrates and work under mild conditions (body temperature, near-neutral pH).

WORKED EXAMPLE 3 Activation energy (standard)

Explain how an enzyme speeds up a reaction.

Solution

Provides an alternative pathway with lower activation energyR1

More substrate molecules have enough energy to reactR1

9 The active site and specificity

Shape and chemistry.

The active site is a region with a specific shape and chemical properties (from particular R groups) that binds the substrate. Specificity arises because only substrates with complementary shape and charge can bind.

WORKED EXAMPLE 4 Specificity (standard)

Explain why amylase hydrolyses starch but not proteins.

Solution

Active site complementary to starch (α-glucose chains)R1

Proteins do not fit or interact with the active siteR1

10 Induced fit model

Flexible active sites.

In the induced fit model, the active site changes shape slightly as the substrate binds, giving a tighter fit and straining the substrate's bonds, which lowers the activation energy. This explains how some enzymes act on a range of similar substrates.

WORKED EXAMPLE 5 Induced fit (exam level)

Compare the lock-and-key and induced fit models.

Solution

Lock-and-key: rigid active site exactly complementaryR1

Induced fit: active site changes shape on binding; strains bondsR1

11 Enzyme–substrate collisions

Molecular motion matters.

Reactions require collisions between substrate molecules and active sites. Most collisions result from random movement of substrates; enzymes may also move. Immobilized enzymes (fixed in membranes or beads) rely on substrate movement.

Quick check

1. Why does increasing substrate concentration increase reaction rate at first?

Answers: 1. more frequent collisions with active sites

12 Effect of temperature

Kinetic energy and denaturation.

As temperature rises, molecules move faster: more collisions and more with sufficient energy, so rate increases. Above the optimum, bonds in the enzyme break, the active site changes shape and the enzyme denatures, so the rate falls sharply.

Figure 4. Effect of temperature on enzyme activity: optimum near 40 °C.

WORKED EXAMPLE 6 Interpreting (exam level)

Explain the shape of the graph above 40 °C.

Solution

Bonds holding tertiary structure breakR1

Active site changes shape; substrate cannot bind; enzyme denaturedR1

Quick check

1. Why is the fall in rate above the optimum steeper than the rise below it?

Answers: 1. denaturation is rapid and irreversible

13 Effect of pH

Charges in the active site.

Each enzyme has an optimum pH. Changes in pH alter the charges on R groups in the active site and break ionic and hydrogen bonds, changing its shape. Pepsin (stomach) has an optimum near pH 2; trypsin (small intestine) near pH 8.

WORKED EXAMPLE 7 Pepsin (standard)

Explain why pepsin stops working in the small intestine.

Solution

pH about 8 is far from its optimum (about 2)R1

R group charges change; active site shape alteredR1

14 Effect of substrate concentration

Saturation.

As substrate concentration increases, rate increases until all active sites are occupied (saturation); then rate levels off at Vmax. Further increases have no effect unless more enzyme is added.

WORKED EXAMPLE 8 Saturation (standard)

Explain why the rate levels off at high substrate concentration.

Solution

All active sites occupiedR1

Enzyme concentration becomes limitingR1

15 Measuring enzyme activity

Rates from experiments.

Enzyme activity is measured by product formed or substrate used per unit time: e.g. volume of O2 from catalase and H2O2; disappearance of starch (iodine test) with amylase; colour change in a colorimeter. Initial rates are found from tangents at t = 0.

WORKED EXAMPLE 9 Rate (standard)

Catalase produces 36 cm3 of O2 in 2.0 minutes. Calculate the mean rate.

Solution

36/120M1

= 0.30 cm3 s−1A1

Try this

Drop filter-paper discs soaked in catalase (potato extract) into hydrogen peroxide at different concentrations and time how long they take to float.

16 Intracellular and extracellular enzymes

Inside or outside the cell.

Intracellular enzymes act inside cells (glycolysis enzymes in the cytoplasm, Krebs cycle enzymes in mitochondria). Extracellular enzymes are secreted and act outside cells (digestive enzymes in the gut, fungal enzymes in saprotrophic nutrition).

Quick check

1. Give an example of an extracellular enzyme.

Answers: 1. amylase in the mouth (or trypsin, or fungal cellulase)

17 Heat generated by metabolism

Metabolic heat.

Metabolic reactions are not 100% efficient; some energy is released as heat. Endotherms (birds and mammals) use this heat to maintain body temperature. Brown adipose tissue generates heat by uncoupling respiration from ATP synthesis.

Quick check

1. Why do mammals have a higher metabolic rate than reptiles of the same size?

Answers: 1. they use metabolic heat to maintain a constant body temperature

18 Cyclical and linear pathways

Metabolic pathways.

Metabolic pathways are chains (glycolysis) or cycles (Krebs cycle, Calvin cycle) of enzyme-catalysed steps. Each step is catalysed by a specific enzyme; intermediates link the steps.

Quick check

1. Name one cyclical metabolic pathway.

Answers: 1. Krebs cycle or Calvin cycle

19 Mixed review: worked problems

Bringing the ideas together.

WORKED EXAMPLE 10 Mixed problem (exam level)

Explain why enzymes in thermophilic bacteria from hot springs are used in PCR.

Solution

Their enzymes have high optimum temperatures and do not denature at about 95 °CR1

PCR requires repeated heating to separate DNA strandsR1

20 Additional exam-style practice

Paper 1 and Paper 2.

WORKED EXAMPLE 11 Paper 1 question (standard)

What happens when an enzyme is denatured? A. active site shape changes B. substrate concentration falls C. peptide bonds always break D. activation energy increases for all reactions

Solution

AA1

WORKED EXAMPLE 12 Paper 2 question (exam level)

Design an experiment to investigate the effect of pH on amylase activity.

Solution

Buffers at a range of pH values; same temperature, volumes, concentrationsR1

Sample at intervals into iodine; time until starch disappearsR1

Rate = 1/time; repeatR1

21 Enzymes in industry

Biotechnology applications.

Industrial enzymes: proteases and lipases in detergents, pectinase in fruit juice extraction, lactase for lactose-free milk, glucose isomerase for high-fructose syrup. Immobilizing enzymes allows reuse and easy separation from products.

In the real world

Lactose-free milk is made by adding lactase, which hydrolyses lactose into glucose and galactose; about 65% of adults worldwide have reduced lactase production.

Quick check

1. Give one advantage of immobilized enzymes.

Answers: 1. can be reused; product not contaminated by enzyme

22 Q10 and temperature coefficients

Quantifying temperature effects.

The temperature coefficient Q10 = rate at (T + 10 °C)/rate at T. For many enzyme-controlled reactions below the optimum, Q10 ≈ 2.

WORKED EXAMPLE 13 Q10 (standard)

Using the graph data, calculate Q10 between 20 °C and 30 °C.

Solution

34/18M1

= 1.9A1

23 Common misconceptions and links

Students often think…	Actually…
enzymes are killed by heat	they are denatured
enzymes are used up in reactions	they are reused
higher substrate always increases rate	rate levels off at saturation

How C1.1 connects to the rest of the course

Topic	Connection
B1.2 Proteins	structure and denaturation
C1.2 Respiration	metabolic pathways
C1.3 Photosynthesis	rubisco
D1.1 DNA replication	enzymes in replication
C3.2 Defence	antibiotics

24 Exam-style question with markscheme

Try this under exam conditions (about 15 minutes) before reading the markscheme.

Figure 5. Oxygen released by catalase.

(a) Calculate the mean rate of oxygen production in the first 20 s. [2]

(b) Explain why the curve levels off. [2]

(d) Explain why enzymes are specific. [2]

Markscheme

Part	Answer	Marks
(a)	21 ÷ 20	M1
	1.05 cm³ s⁻¹	A1
(b)	substrate used up	R1
	fewer collisions / no more product	R1
(c)	bonds in tertiary structure break	R1
	active site shape changes	R1
	substrate no longer binds: denaturation; rate falls	R1
(d)	active site has a specific shape and chemistry	R1
	only complementary substrates bind	R1

Examiner's comments. In (c), saying the enzyme is 'killed' lost marks. The best answers named the bonds broken.

25 Check your understanding

Section A: multiple choice

1. Anabolism involves

A. building complex molecules B. breaking down molecules C. releasing energy D. hydrolysis only

2. The induced-fit model states that

A. the active site is rigid B. enzymes are used up C. the active site changes shape when substrate binds D. all substrates fit

3. Above the optimum temperature, enzymes

A. work faster B. denature C. are killed D. are not affected

4. At high substrate concentration, rate levels off because

A. the enzyme is denatured B. products inhibit it C. temperature falls D. active sites are saturated

5. Enzymes speed up reactions by

A. raising temperature B. lowering activation energy C. increasing energy released D. adding energy

6. Pepsin works best at about pH

A. 2 B. 7 C. 9 D. 12

Section B: structured

7. Explain the effect of temperature on enzyme activity. [4]

8. Explain how enzymes lower activation energy. [3]

9. Describe how you would measure the effect of pH on catalase. [4]

Answers

1. A 2. C 3. B 4. D 5. B 6. A

7. Rate rises with collisions to an optimum; above it bonds break, active site changes, denaturation.

8. Substrate binding strains bonds / brings groups together; induced fit.

9. Buffers at different pH; same H₂O₂ and enzyme volume; constant temperature; collect O₂ in gas syringe; repeat.

26 Summary and topic map

Idea	Remember
Metabolism	anabolism and catabolism
Enzymes	globular proteins; active site; reused
Induced fit	active site changes shape on binding
Factors	temperature, pH, substrate concentration
Activation energy	lowered by enzymes

Before the exam, make sure you…

•explain curves using collisions and active site shape
•say denatured, not killed
•calculate rates with units
•describe controlled variables in experiments

Enzymes and Metabolism on one page

Cover this page with a sheet of paper and try to rebuild it from memory. Whatever you can't recall is what to revise next.

Figure 6. Topic map for Enzymes and Metabolism.

revisionprep.comIB-style notes · question bank · mock papers