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2. biochemistry > Week 2 (enzymes) > Flashcards

Week 2 (enzymes) Flashcards

1
Q

What does a catalyst do?

A

Increase the rate of a reaction without being consumed by the reaction.
It does this by lowering the activation energy.

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2
Q

Give examples of enzymes in biology

A

There are lots of digestive enzymes that break down food and release nutrients needed for the body.
E.g., lipase, amylase, peptidase

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3
Q

Give examples of enzymes in industry

A

Rennet is a mix of enzymes used in cheesemaking. Pepsin breaks down the protein, chymosin curdles milk and lipases breaks down fats.
Invertase breaks down hard sugars into soft sugars and is used to make soft-centred chocolates.

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4
Q

Give an example of enzymes in agriculture

A

Phytases are added to animal feed to make minerals more bioavailable.

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5
Q

What are enzymes?

A

Usually proteins
Biological catalysts

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6
Q

Why are enzymes necessary?

A

Many biological reactions are chemically unfavourable so need enzymes.
Uncatalysed reactions in biology tend to be quite slow.
Enzymes are usually much better (specific and efficient) than catalysts in chemistry.
If human enzymes don’t work properly it can lead to disease.

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7
Q

Other than their amino acids what may enzymes also require to function?

A

Cofactors
Coenzymes

Some enzymes will only need either a cofactor or coenzyme whilst other enzymes will require both.

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8
Q

What are ribosozymes?

A

RNA enzymes
RNA molecules can have complex tertiary structure and so can be catalytically active.

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9
Q

Name two common cofactor metal ions

A

Iron
Zinc

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10
Q

What are cofactors?

A

An inorganic ion or a coenzyme required for enzyme activity.
They are often found in enzymes that catalyse redox reactions.
They also affect bonding, and can have a structural role.

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11
Q

What are coenzymes?

A

An organic cofactor require for the action of certain enzymes.
More complex organic cofactors.
They are often derived from vitamins and often act as transient carriers for functional groups.

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12
Q

What are prosthetic groups?

A

A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity.
They bind tightly or covalently to a protein, and act as structural elements.

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13
Q

What is an apoenzyme?

A

The protein portion of an enzyme that is inactive.
It is exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.

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14
Q

What is a holoenzyme?

A

A catalytically active enzyme, including all necessary subunits, prosthetic groups and cofactors.

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15
Q

Where does an enzyme-catalysed reaction take place?

A

Active site

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16
Q

What happens at the active site?

A

A substrate molecule binds in the active site and is acted upon by the enzyme.

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17
Q

Describe the active site

A

The surface of the active site is lined with amino acid residues that allow the substrate to bind and catalyse its chemical transformation.

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18
Q

What is chymotrypsin?

A

It is a protease that catalyses the hydrolysis of peptides bonds.
It is specific for peptide bonds next to aromatic amino acids.

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19
Q

What do and don’t enzymes affect?

A

Enzymes affect the rate of reaction but do not affect its equilibrium.

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20
Q

What leads to a change in Gibbs free energy of the system?

A

The progression of a reaction; conversion of substrates into products.

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21
Q

Describe what happens to bonds in reactions

A

In reactions old bonds are broken (uses energy) and new bonds are formed (gives out energy)

22
Q

What is the activation energy barrier?

A

The sum of the energy that must be expended to get the reaction going. There is an activation energy barrier to overcome before an enzyme reaction can occur.

23
Q

What is the ground state?

A

The energy level of ‘resting’ substrates or products.

24
Q

What is the transition state?

A

It is the activated form of the molecules at the top of the ‘energy hill’. At this precise point decay back to substrate or progress to reactants is less likely.

25
Q

What are introduced in enzymatic reactions?

A

Intermediates
- enzyme substrate complex
- enzyme product complex

26
Q

What will happen if an enzyme is outside its optimum pH range?

A

The amin acid side-chains will be incorrectly ionised leading to loss of function.

27
Q

What is pepsin and what does it do?

A

Pepsin is an endopeptidase and is found in the stomach.
It hydrolyses peptide bonds to break down proteins into smaller peptides.

28
Q

What is glucose 6-phosphatase and what does it do?

A

It is found in the liver and it hydrolyses glucose 6-phosphate to produce glucose and free phosphate.

29
Q

When would a reaction be more energetically favourable?

A

When a lot of substrate is converted into product.

30
Q

What is a rate-limiting step in enzymic reactions?

A

The stage of the reaction that requires the greatest activation energy or the transition state of highest free energy

31
Q

What are enzymes good at?

A

They are good at speeding up reactions and discriminating between very similar molecules.

32
Q

Where do chemical reactions take place between?

A

The substrate and some of the enzyme’s functional groups.

33
Q

What type of interactions increase reaction rate?

A

Covalent interactions between substrate and enzyme lower the activation energy and therefore increase the rate of reaction.

34
Q

What is binding energy?

A

The energy of weak interactions in the ES complex all added up.

35
Q

What can binding energy be used to do?

A

Lower the activation energy.

36
Q

What is the induced fit model?

A

When the enzyme undergoes a conformational change when it binds to the substrate.

37
Q

What is entropy reduction?

A

When enzymes restrict movement of substrates making it more likely that they will collide and react.

38
Q

Explain the removal of solvation shell

A

Dissolved substances are surrounded by water molecules that may block reactions sites. A substrate binding to an enzyme usually loses its associated water molecules.

39
Q

Explain the distortion of substrates

A

Binding energy can be used to ‘twist’ substrates into the right orientation.

40
Q

Explain the alignment of functional groups

A

The functional groups of the substrate and active site are positioned in way that aids the reaction.

41
Q

When are enzyme-substrate interactions optimised?

A

During the transition state

42
Q

What is initial velocity?

A

The rate at the beginning of the reaction, where the enzymes begin to actively transfer the reactants into products.

43
Q

What is maximum velocity?

A

The maximum amount of velocity the reaction can have. Maximum velocity is reached when increasing substrate concentration has no further impact on the rate of reaction.

44
Q

What is Michaelis constant?

A

The substrate concentration when the reaction is half of maximum velocity. It is an indicator of an enzyme’s substrate affinity. An enzyme with low Km has a high affinity for a substrate as it takes a lower concentration of substrate to reach 1/2 max velocity.

45
Q

What are Michaelis Menten plots useful to visualise?

A

The relationship between Michaelis constant and maximum velocity.

46
Q

What is the Lineweaver-Burk plot an example of?

A

A double reciprocal plot

47
Q

What do enzyme inhibitors do?

A

Reduce the rate of reaction or stop catalysis altogether.

48
Q

Name the two types of enzyme inhibitors

A

Reversible (competitive, uncompetitive, mixed)
Irreversible

49
Q

What is competitive inhibition?

A

When the inhibitor occupies the active site which prevents the substrate binding the enzyme.
It doesn’t inactive the enzyme; when the inhibitor dissociates the enzyme binds the substrate as normal.

50
Q

What is uncompetitive inhibition?

A

The inhibitor binds at a separate site from the active.
The enzyme has undergone a conformation change.

51
Q

What is mixed inhibition?

A

Inhibitors bind at a separate site to the active site, but may bind to either the enzyme or substrate.

52
Q

What are regulatory enzymes?

A

The product of one reaction may regulate another enzyme on the pathway in a positive way.

2. biochemistry (7 decks)

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