Lecture 8 & 9 - Enzymes (intro)

Question 1

What are the three things mentioned that our biological systems are limited to?

Answer 1

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Question 2

What are enzymes?

What do they decrease?

Reactions speed up forward and reverse reactions equally - right?

Answer 2

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Question 3

Why are the reaction rates for catalysed reactions much faster and narrower in range?

Answer 3

Faster because we need products faster than uncatalysed in order to survive. Narrower because all the reactions in the pathway need to be about the same speed to effectively get from A to C faster. If A to B was 10 and A to C was 100 then range is 90. If A to B was 10 and A to C was 15 then range is 5. So they need be about the same speed.

Question 4

Does an enzyme change how thermodynamically favourable a reaction is?

Answer 4

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Question 5

So RNAse hasn’t completely changed how an inorganic catalyst would do their reaction - true or false?

Answer 5

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Question 6

Six classes of enzymes; what do they do?

1. Oxidoreductase
2. Transferases
3. Hydrolases
4. Lysases
5. Isomerases
6. Ligases

Answer 6

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Question 7

2.7.1.1.

What do each of the numbers mean?

Answer 7

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Question 8

Active site of the enzyme:

1. What is there projecting into the active site? How does this carry out the reaction?
2. How does the substrate bind to the active site? Give 3 examples
3. What determines specificity

Answer 8

1. Yeah, basically just state that side chains project into the active site and this interaction between side chains and substrates drive reactions e.g. hydrolysis

Question 9

Enzymes show geometric and _____specificity. What does this mean?

Answer 9

Specific because active site is particular space

The substrate needs to be in the right conformation

Question 10

Where does the change between reactant and product happen? So…..

Answer 10

Change happens in active site so product in active site for short period of time

Question 11

Induced fit model:

The interaction between enzyme and substrate causes what? What does this bring it closer to? So increases the probability of?

Answer 11

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Question 12

Difference between transition state and reaction intermediate

Answer 12

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Question 13

Catalytic mechanisms - describe what these are in general and then state the 6 of them

Answer 13

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Question 14

Acid-base catalysis:

1. If you solely rely on this, what would mild changes in pH in environment lead to?
2. Involves what? So the moment of what results in what?

Answer 14

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Question 15

Acid-base catalysis: Histidine

1. What is the pKa of it? Close to what?
2. Depending on environment, what can His do?
3. Talking about RNA cleavage (acid hydrolysis) - the same active site has two His and what do they do and what does this show?

Answer 15

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Question 16

Covalent catalysis:

1. Involves the formation of what?
2. What kind of interaction is this?
3. Describe the reaction and include the words: nucleophile, examples of nucleophiles, hydrolysis, covalent interactions.

Answer 16

This involves the formation of temporary covalent bond formed between enzyme and substrate - they’re usually stabilised by non-covalent but not in this case

The nucleophile attached to the enzyme will attack the bond between A and B and form a covalent bond via the nucleophile + side chain between E and A (releasing B in the process)

Then hydrolysis will cleave the bond and release A + E

Question 17

Metal ion catalysis

1. These metals provide what three things and how?

Answer 17

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Question 18

Metal ion catalysis: Hexokinase uses Mg2+ as a cofactor

How does it work?

Answer 18

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Question 19

Cofactors:

What may they be?

Are co-enzymes enzymes?

Answer 19

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Question 20

Go have a look at the inorganic elements for each enzyme on lecture slides

Answer 20

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Question 21

Coenzymes (a subset of cofactors)

1. What are they?
2. Co-_____?
3. Function as what?
4. Often derived from?

Answer 21

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Question 22

What do these coenzymes transfer and what is their dietary precursor:

1. Thiamine pyrophosphate
2. FAD
3. NAD

How does NAD help?
Alcohol dehydrogenase oxidises to aldehyde, how does NAD help?

Answer 22

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