Structure and regulations of biochemical pathways

Question 1

Enzymes

What are the two models of enzyme/substrate interactions

Answer 1

• Lock and key; fit together

- Induced fit; active site being more flexible and changing shape.

Question 2

Enzyme are a type of…

Answer 2

Catalyst (increase the reaction rate by lower the activation energy)

Question 3

Enzymes

Characteristics of enzymes..
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Answer 3

• Are biological catalysts in that they are proteins
• Only catalyses one specific metabolic (reactions in body) reaction.
• Enzymes act by binding to the reactants (substrates) to form an enzyme- substrate complex
• substrates can only bind when they have the complementary shape to their active site.
• Can only work at specific temp and pH

Question 4

Enzymes

Define transition state

Answer 4

Substrate is strained when bonded to the enzyme, resulting in it breaking into two

Question 5

Enzymes

Factors that affect enzyme function
Temperature
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Answer 5

• lower; move slower -less kinetic energy - less collisions therefore slower reaction
• high; break H bonds - change tertiary structure -cant bind - denatured!

Question 6

Enzymes

Factors that affect enzyme function
pH
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Answer 6

• altering pH changes the location and strength of ionic interactions between side groups.
• Changes tertiary structure ….denatured

Question 7

Enzymes

Factors that affect enzyme function
Concentration of enzyme

Answer 7

-higher concentration of enzyme, the more frequency enzyme-substrate complexes would form, resulting in higher reaction rate

Question 8

Enzymes

Factors that affect enzyme function
Concentration of substrate
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Answer 8

• As the concentration increasing, so does the rate of formation of enzyme-substrate complex and hence reaction rate.
• Saturation point

Question 9

Enzymes

Factors that affect enzyme function
Reversible and irreversible inhibition of enzyme
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Answer 9

• A reversible inhibitor bind non-covalently to an enzyme and can dissociate from it relatively quickly/easily.
• A irrversible inhibitor will generally bind to an enzyme covalently and therefore has a more permanent effect on the enzyme.

Question 10

Enzymes

Factors that affect enzyme function
Competitive inhibitor 
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Answer 10

• Are chemicals that have a similar shape to the substrate and can also bind to the active site of the enzyme.
• They block the substrate from binding to the enzyme, which slows the reaction rate.
• Can be removed by added more substrate.

Question 11

Enzymes

Factors that affect enzyme function
Noncompetitive inhibitor 
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Answer 11

• Bind to the enzyme at a site other than the active site.
• Causing the enzyme to change shape (active site)
• Therefore the enzyme wont be able to bind to the substrate

Question 12

Define coenzyme

Answer 12

Some enzyme need additional components to enable them to catalyses a reaction. They may themselves be additional reactant molecules. (small organic)

Question 13

Coenzyme

Define Adenosine triphosphate (ATP)

Answer 13

Is a modified RNA nucleotiude with adenine as the base, except there are three phosphate groups present instead of one.

Question 14

Coenzyme

Adenosine triphosphate (ATP) use

Answer 14

The breakdown of ATP to ADP and Pi releases chemical energy- this chemical energy is used to fund the conversion of the substrate into the product.

Question 15

Coenzyme

Adenosine triphosphate (ATP)
In some chemical reactions...

Answer 15

such as the synthesis of a protein from amino acids, the chemical energy of the product is higher than the chemical energy of the substrate. There fore we need a supply of chemical energy. This kind of reaction is called an endergonic reaction

Question 16

Coenzyme

Define Nicotinamide adenine dinucleotide (NAD+)

Answer 16

Is a coenzyme that is used to remove electrons from substrates.

Question 17

Coenzyme

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Answer 17

-NAD+ removes electrons from the substrate to be converted until NADH (oxidation reaction)
NAD+ + H+ + 2e- —-> NADH

-NADH donates electrons to the substrate, when being converted back to NAD+ (reduction reaction)
NADH —-> NAD+ + H+ + 2e-

Question 18

Coenzyme

Define Nicotinamide adenine dinucleotide phosphate (NADP)

Answer 18

(Same function as NAD) alternate coenzyme that allows for donation or acceptance of electrons from substrates.

Question 19

Coenzyme

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Answer 19

-NADP+ removes electron from the substrate to be converted into NADPH
NADP+ + H+ + 2e- —-> NADPH

-NADPH donates electrons to the substrate, when being converted back to NADP+
NADPH —-> NADP+ + H+ + 2e-