C1.1 - ENZYMES & METABOLISM

Question 1

Outline the function and benefit of enzymes as a catalyst

Answer 1

1. Enzymes ARE catalysts
2. Speed up chemical reactions, and increase reaction rates
3. Are reusable/recycled
4. Specific enzymes bind to specific substrates
5. Typically proteins (some RNA too)

BENEFITS:
1. Products can be produced when needed (when substrate binds to the enzyme)
2 Reaction can occur at body temperature
3. Occur at low concentrations of the substrate or the enzyme

Question 2

Outline metabolism

Answer 2

METABOLISM: the sum of all enzyme-catalysed reactions within the cell/organism and the complete network of interdependent and interactive chemical reactions occurring in living organisms

1. Involves anabolism (synthesis of macromolecules from monomers) via condensation reactions, and catabolic reactions (digestion of macromolecules) via hydrolysis reactions
2. Involves a SERIES of enzyme-controlled reactions: product of one reaction is the substrate of the next, has chains/cycles
3. Enzyme-specific molecules bind to specific substrates

Question 3

Outline the role of enzymes in metabolism

Answer 3

1. Chemical reactions occurs in the presence of SPECIFIC ENZYMES
2. Enzymes can be reused/recycled
3. Living organisms require many different enzymes
4. Enzymes control the rate of metabolic reactions
5. Systems result in emergent properties at each level of biological organisation (cell - tissue-organ - system)

Question 4

Describe some example of catabolic and anabolic reactions

Answer 4

CATABOLIC REACTIONS:

DIGESTION:
1. Starch ( to glucose monomers amylase)
2. Lipids (glycerol + fatty acid via lipase)
3. Proteins (amino acid monomers via protease)
3. CELL RESPIRATION: Glucose broken down into Co2

ANABOLIC REACTIONS:
1. Photosynthesis: glucose monomers (sucrose) into starch
2. Protein synthesis: amino acid monomers join to form peptides/polypeptides
3. Glycogen: glucose monomers join to form glycogen

Question 5

Outline the structure and function of enzymes/active sites for catalysis

Answer 5

CATALYSIS: the process of adding a catalyst to facilitate a reaction.

1. Enzymes are globular proteins with an active site for catalysis
2. Substrates bind to the enzyme his active site, and it is complementary in shape – lock and key model (NOT THE SAMME SHAPE)
3. Eynzymes form enzyme-substrate complexes (ES)
4. Bonds in the substrate are weekend, or substrates are orientated to form bonds
5. Enzymes lower the activation energy

ACTIVE SITE:
1. location on the surface of the enzyme
2. Composed of amino acids

Question 6

Describe the interactions between the substrate and active site that allows for induced fit binding

Answer 6

1. Active site (and the substrate) can change shapes slightly
2. Allows active site/enzyme to bind to similarly shaped substrates
3. Catalyses a type or category of reaction
4. Polar regions attract the substrates, leading to a chemical reaction
5. When substrate binds to active site, it creates an enzyme-substrate complex (binding weaken/break bonds OR orient bonds/substrates to allow bonds to form)

Question 7

Outline the lock and key model

Answer 7

1. Specificity of active site
2. Complementary shapes
3. Substrate binds to active site

Question 8

Explain the role of molecular motion and collisions between substrates and active sites in enzyme catalysis

Answer 8

1. Molecules (substrates and enzymes) are dissolved in water (cytoplasm, blood, extra/intracellular fluid)
2. They have random movement and kinetic energy
3. Collision: substrate hits the active site at any angle, but ONLY CORRECT allows for binding to occur
4. This allows for enzyme-substrate complexes to form
5. Enzymes can be immobilised (stuck and attached to a surface) -> embedded in membranes like chloroplast/mitochondria, or in glass beads/entrapped in gel particles (lactose free milk)

Question 9

Outline the benefits of immobilised enzymes

Answer 9

Immobilized enzymes are enzymes that are attached to another surface or entraped in gels

1. Concentrations of the substrate or enzvme
2. Recycle the use of the enzyme
3. Separation of the enzvme from the product
   4.Stability of the enzyme sensitive to temperature / pH changes

Question 10

Explain the relationship between the structure of the active site, enzyme-substrate specificity, and denaturation

Answer 10

1. Active sites are 3D, on the surface of enzyme, consists of a few amino acids
2. Active sites are complementary in shape to substrate – binds to specific substrates
3. Substrates bind to active site and from the enzyme-substrat complex: chemical interaction as polar regions of AS are attracted to substrate
4. Denaturation is the change of shape of the active site ->changes h-bonding/ionic bonds/R-group interactions of active site -> enzyme and substrate can’t bind and from ES complexes
5. Denaturation is caused by a change (increase/decrease) in pH from optimal pH, or when temperatures are above the optimal

Question 11

Outline the effect of temperatures on enzymes

Answer 11

1) @ LOW TEMPERATURES
1. Low enzyme activity
2. Low molecular motion
3. Low kinetic energy
4. Low collisions between active site/substrate

2) As temperatures increase, enzyme activity, molecular motion, kinetic energy, and collisions increase

3) Each enzymes have an optimal temperature – where reaction rate is at the highest

4) Temperatures above/below optimal decreases rate of reaction

5) Denaturation occurs when temperature is too high:

1. R-group tertiary structure/ hydrogen/ionic bonds are broken
2. changes 3-d shape of protein and active site
3. substrate can’t bind
4. rate decreases
5. enzyme-substrate complex can’t form

!interpret graphs, reference collision theory and denaturation!

Question 12

Outline the effect of pH on enzymes

Answer 12

1. Enzymes have an optimal pH (2 for stomach, and 7-8 for intestinal)
2. Above and below optimal pH lower enzyme activity, and can denature enzyme
3. Denatured enzymes change the shape of active site or tertiary structure
4. Hydrogen/ionic bonds are altered
5. Substrate can’t bind to active site, and substrate-enzyme complex can’t form, lowered reaction

H+ is acidic, low pH
OH- basic, high pH
Neutral is 7

Question 13

Outline the effect of substrate concentration of the rate

Answer 13

1. As you increase substrate concentration, increase collisions, increase the rate of substrate enzyme binding, formation of complexes, increase enzyme activity
2. At high substrate concentrations, enzyme activity plateaus. Further increase will not increase the enzyme activity any further

Question 14

Outline the effect of increasing substrate concentration of competitive/non-competitive inhibitors

Answer 14

INCREASE OF COMPETITIVE INHIBITORS: Increases enzyme activity, greater probability active site will collide with substrate

INCREASE OF NON-COMPETITIVE INHIBITORS: Does not increase enzyme activity, no more enzymes available

Question 15

Distinguish between intracellular and extracellular enzyme-catalysed reactions

Answer 15

INTRACELLULAR - within the cell:
1. Enzymes are in cytoplasm, embedded in membranes, inside organelles
2. Some enzymes (catalytic proteins) are produced for use within the cell/intracellular enzymes
3. Ex: Cell respiration, photosynthesis

EXTRACELLULAR - outside of the cell
1. Enzymes are transported out of the cell
2. They are exported via vesicles through exocytosis
3. Ex: chemical digestion in gut, mouth, and stomach

Question 16

Outline the creation of heat by the reactions of metabolism

Answer 16

1. Metabolism: Sum of all chemical reactions: anabolic (condensation/exothermic) and catabolic (hydrolysis/endothermic) reactions
2. Use/breakdown of organic molecules (carbs, fats, proteins) to produce ATP and release energy
3. Muscle contractions and movement, biosynthesis and chemical reactions, and active transport

Question 17

Explain cycles and chains in metabolic reactions

Answer 17

CYCLES: metabolic cycle of reactions, krebs cycle

CHAINS: series of enzymatically controlled reactions, glycolysis

Question 18

Compare competitive and non-competitive inhibitors

Answer 18

THEY BOTH DECREASE RATE OF REACTION.

COMPETITIVE:
1. Binds TO active site
2. Blocks the substrate from binding to the active site
3. Prevent enzyme-substrate complex from forming
4. Competitive inhibitors have a SIMILAR shape to active site
5. REVERSIBLE by increasing substrate concentration

NON-COMPETITIVE:
1. Binds AWAY from active site
2. Changes the chape of active site
3. Prevent enzyme-substrate complex from forming
4. Non-competitive inhibitors have a DIFFERENT shape
5 Allosteric are reversible, cyanide is irr inhibition eversible/permanent (binds to mitochondira)

Example: Statins: binds to the enzyme HMG CoA-reductase, which blocks the formation of cholesterol

Question 19

Outline mechanism-based inhibition

Answer 19

In COMPETITIVE inhibition:

Penicillin:
1. Binds to the enzyme transpeptidase in bacteria – the active site
2. Prevents cell wall synthesis in bacteria
3. Blocks the formation of peptide cross linkages between polysaccharide chains in peptidoglycan cell wall formation

Is irreversible due to chemical changes!!!!!!!

LINK: Bacteria become resistant to penicillin. Mutations in the bacterial genome lead to changes in the structure of the transpeptidase enzyme so that penicillin-binding is reduced.

Question 20

Describe allosteric enzymes/allostery

Answer 20

1. Allostery / allosteric enzymes is a reversible, noncompetitive inhibitor / activator.

2.Binding site away from the active site

3. The shape alternates between active and inactive forms
4. The non-competitive inhibitor binds to the allosteric site (away from the active site)
5. The non-competitive inhibitor doesn’t compete with the substrate for the active site

T6. he non-competitive inhibitor changes the shape of the active site

Question 21

Outline the examples of the regulation of metabolic pathways using allosteric enzymes

Answer 21

ISOLEUCINE production consists of a metabolic pathway / chain of 5 enzyme controlled reactions and is controlled by FEEDBACK INHIBITION

Isoleucine acts as a non-competitive inhibitor;
1. binds away from active site
2. changes the shape of the active site
3. is reversible — the metabolic pathway can be turned off, reducing the production of isoleucine
4. negative feedback occurs (level of product decreases formation of product)
5. Low concentrations of isoleucine removes the inhibition and the active conformation of the allosteric enzyme is stabilized
6. The enzymes recommences the conversion of threonine to isoleucine

Therenine + theorinen deaminsase (enzyme 1) -> intermediate A,B,C,D with enymes 2,3,4,5 -> Final product: isoleucine (essential amino acid)

GLUCOSE -> glycolysis -> link -> krebs -> Etz -> ATP

ATP -> ADP + Pi -> AMP + Pi
When ATP concentrations are high, AMP concentrations are low
When ATP concentrations are low, AMP concentrations are high

ATP binds to phosphofructokinase to turn off, AMP binds to phosphofructokinase to turn on

Question 22

Describe the regulation of metabolic pathways by feedback inhibition

Answer 22

1. Regulated based on the need for the end product
2. End product / final product can bind to / inhibit enzymes early in the metabolic pathway
3. Ex: High concentrations of Isoleucine bind to the the allosteric site of threonine deaminase