BIO: Chapter 4 - Enzymes

CORE IDEA 1: BIOMOLECULES
CHAPTER 4 - ENZYMES

Defn of enzymes

Roles of enzymes in cells

General characteristics in enzymes

General characteristics
(1) Enzymes are mostly globular proteins

(2) Enzymes increase rate of rxn

(3) Enzymes operate at milder rxn conditions

(4) Enzymes exhibit specificity

Tutorial Qn 2(b) Explain why having the same sequence of amino acids in their active sites allows these two different enzymes to catalyse the same reaction. LO1p [2]
Type: Recall
Topic: Enzyme specificity Approach: 2 marks  = 2 points
How does the sequence of amino acids influence the active site? (Sequence  determines the way the polypeptide chain folds)
What are the important amino acids at the active site and what characteristic must they have to enable proper functioning of the enzyme?

QN (pg 6): What is the critical determinant in the biological function of a protein?

(p) Explain the mode of action of enzymes in terms of an active site, enzyme-substrate complex, lowering of Ea & enzyme specificity using lock-and-key hypothesis & Induced ft hypotheses.
(A) ACTIVE SITE
*defn of active site
- types of a.a in an enzyme

(A) ACTIVE SITE
- what do catalytic a.a & structural a.a do?
* defn of specificity btwn substrate & enzyme

(A) ACTIVE SITE
- 4 diff categories of aa residues

Tutorial Qn 2(a): Describe how amino acid residues at different positions in the protein may be brought together in the active site when such enzymes are synthesised. [4]
Type: Recall
Topic: Protein folding Approach: 4 marks = 4 points
- Primary structure (with amino acid residues at different positions) must fold to form the secondary structure
- What are the types of secondary structure? What are the bonds present? Where do the bonds occur?
- Further folding to form the tertiary structure. What are the bonds present? Where do the bonds occur?
- How does forming the tertiary structure affect the amino acid residues in question?

(C) ENERGY PROFILE OF RXN
How do enzymes enable rxn to take place faster?

(C) ENERGY PROFILE OF RXN
-Molecular basis of enzyme action: Molecular mechanisms which contribute to a lowering of Ea → enabling a rxn to occur at a lower temp
One or more of these mechanisms may work simultaneously in catalysis.

SUMMARY
***NOTE 3 KEY AREAS when answering qns :
- BINDING
-CATALYSIS
- RELEASE

Tutorial Exemplar Q(b) State why an enzyme-catalysed rxn is more likely to occur. [1]

Tutorial exemplar (c) Describe the ways in which an enzyme interacts w its substrate. [3]
- "describe" → give details
- "interacts" → how the substrate would bind w enzyme
Name the temp bonds btwn substrate & enzyme
Specificity of enzyme action must be mentioned

Tutorial Essay Qn 7(a): Describe the mode of action of enzymes. [7]

Tutorial Essay Qn 7(a): Describe the mode of action of enzymes. [7]
When stating factors that decrease Ea, state "proximity effects", then explain "temp binding of reactants..."

QN (pg 12): Explain what effect denaturation will have on the shape of the enzyme's active site?

Enzyme cofactors
*defn
-examples

(q) Investigate & explain effects of temp & pH, enzyme conc & substrate conc of an enzyme-catalysed rxn by measuring rates of formation of products or rate of disappearance of substrate
(A) FOLLOWING THE TIME COURSE OF ENZYME-CATALYSED RXN
2 methods to measuring rate of rxn

(AI) Measuring pdt formation over time
E.g Conversion of H2O2 to H2O & O2 by enzyme catalase
2H2O2 → 2H2O + O2
- independent variable?
-dependent?
-constant conditions?

Experimental set-up
For exp: Mention:
1) Rxn
2) Dependent variable
3) Independent variables
4) Constant variables / control set-up
5) Exp set-up & procedure
- be able to describe fully

Procedure of exp

Graph of exp
For graphs: Mention
(1) Describe trend (measured qty + rate of rxn)
(2) Explain trend

Explaining the trend of
(1) Vol of O2 increases w time
(2) Rate of O2 produced decreases with time

Graph of rate of rxn against time

(AII) Measuring disappearance of substrate over time
E.g. of conversion of starch (substrate) to reducing sugars by amylase
Starch → mostly maltose (use iodine test for starch)
1) Rxn
2) Dependent variable
3) Independent variables
4) Constant variables / control set-up
5) Exp set-up & procedure
- be able to describe fully

Set-up
Procedure

Q: Why need to aliquot at fixed time intervals instead of adding I2 directly to rxn mixture & monitoring colour change over time?

Investigating how the rate of enzyme rxn varies w one manipulated variable: [substrate]
- Carry out several experiments at diff [S]: [S1] [S2] [S3] [S4] [S5] etc.
* must hv at least 5 diff values for independent variable, w other variables kept constant

(q) Investigate & explain effects of temp & pH, enzyme conc & substrate conc of an enzyme-catalysed rxn by measuring rates of formation of products or rate of disappearance of substrate
(B) FACTORS AFFECTING RATE OF ENZYME -CATALYSED RXN
(i) Temp

Explanation
-when temp increased from low?

Exp
- temp coefficient?

- what happens at opt T?

- increase in T beyond opt T?

Tutorial Qn 2.(cii) Explain the effect of increasing temperature on the activity of this enzyme. [4]
“Explain” requires details in answer.
What is the effect of increasing temperature on the energy of the molecules in the reaction?
How does this lead to an increase in the rate of reaction? (think ES complexes)
Don’t forget to address the decrease in rate of reaction also as it can be clearly seen in the graph.
How does the molecular vibration affect the enzyme? Does this occur from the start or only after optimum temperature is reached?

TUTORIAL ESSAY 8(b) Explain how pH affects the rate of an enzyme catalysed reaction.

Michaelis constant (Km) *defn

(r) describe STRUCTURE of competitive & non-competitive inhibitors wrt to the binding sites of the inhibitor
s) explain EFFECTS of comp & non-comp inhibitors (including allosteric inhibitors) on rate of enzyme activity
ENZYME INHIBITION
types

(I) Competitive inhibition
*defn
STRUCTURE
EFFECTS

Tutorial 1(c) Explain effect of a competitive inhibitor on rate of enzyme catalysed reaction.[3]
- How does the competitive inhibitor bind to the enzyme?
- Important to qualify that the reaction is reversible (temporary binding)
- What does the degree of inhibition depend on?

Comparing graphs of comp & non-comp inhibition

Characteristics
****S-SHAPED GRAPH IN ENZYME QN → SHOWS ENZYME IS AN ALLOSTERIC ENZYME

Q(pg 24) How are enzymes regulated by non-competitive inhibition diff from enzymes regulated by allosteric regulation?

Key words defining:
(1) 3D conformation
(2) AT site
(3) Ea
(4) Complementary in shape & charge

(5) denaturation
(6) Effective collisions
(7) ES-complex

(8) Induced fit
(9) KE
(10) Lock & Key