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Chemistry Of Biological Interactions: > Enzymes and Kinetics of Biocatalysis: > Flashcards

Enzymes and Kinetics of Biocatalysis: Flashcards

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1
Q

What are enzymes?

A

Catalysts of biological reactions

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2
Q

How do enzymes lower the required activation energy for a reaction?

A
  • Provide a different route for reaction to take

- Make compounds/elements involved in reaction more stable

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3
Q

What are the advantages of enzymes in biological reactions?

A
  • They increase rate of desired reactions

- They are not used up in the reaction

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4
Q

Describe the structure of enzymes:

A
  • Enzymes are proteins made of polypeptide chains formed via the condensation of amino acid monomers to create the primary structure
  • Enzymes are globular shaped with an active site that is shaped to be specific and complementary to one molecule- this is due to it’s specific tertiary structure
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5
Q

What is the primary structure of a protein?

A

The sequence and type of amino acids in the polypeptide chain

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6
Q

What is the secondary structure of a protein?

A

The formation of hydrogen bonds between amino acids in a polypeptide to cause the chain to fold into either an alpha helix or beta-pleated sheets

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7
Q

What is the tertiary structure of a protein?

A

Further folding of the polypeptide chain due to formation of more hydrogen bonds, ionic bonds and sulphide bridges between amino acids. This can form the final shape of proteins consisting of one polypeptide chain

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8
Q

What is the quaternary structure of proteins?

A

The addition of more than one polypetide chain to each other and any prosthetic (side) groups attached

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9
Q

What enzyme isn’t a protein?

A

Ribozymes

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10
Q

What are ribozymes made out of?

A

RNA

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11
Q

How much faster can reactions involving enzymes be compared to the same reaction without enzymes?

A

5 to 17 orders of magnitude faster

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12
Q

What is activation energy?

A

The energy required for the reactants in a reaction to reach their transition states

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13
Q

Enzymes lower activation energy. How is this shown on an energy profile graph?

A

The energy barrier of the reaction with the enzyme is lower than without

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14
Q

What needs to be taken into account when deciding whether a reaction happens spontaneously or not?

A
  • Enthalpy

- Entropy

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15
Q

What is the definition of the change in Gibbs energy?

A

The energy that is freely available to be used to do work in a reaction

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16
Q

What does the change in Gibbs energy tell you?

A
  • Whether a reaction is spontaneous

- The position of thermodynamic equilibrium of a reaction

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17
Q

What is the equivalent to activation energy in a Gibbs energy diagram?

A

Gibbs activation energy

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18
Q

What is the equivalent to enthalpy change in a Gibbs energy diagram?

A

Change in Gibbs energy

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19
Q

What is the symbol for Gibbs activation energy?

A

ΔG‡

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20
Q

What is the symbol for change in Gibbs energy?

A

ΔG

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21
Q

How is it shown in a Gibbs energy diagram that enzymes don’t affect the energies of the reactants and products?

A

The pathway in which a reaction happens doesn’t affect the change in Gibbs energy between the reactants and products

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22
Q

Why are some reactions considered irreversible under normal conditions?

A
  • These reactions have a very large, negative change in Gibbs energy
  • Equilibrium position is is far to the right (favours products)
  • This makes it very difficult under the same conditions to make the reaction go back the other way
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23
Q

Explain the steps of how enzymes catalyse reactions:

A
  • Substrate(s) attache to enzyme’s active site
  • Intermediate is made called enzyme-substrate complex
  • Functional groups in the active site of enzyme react with that of the substrate to lower activation energy
  • This reduces the energy required to bond or hydrolyse the substrate(s)
  • The product(s) are released from the enzyme
  • Enzyme is available to bind another substrate
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24
Q

Why is it that usually one type of enzyme can only catalyse one type of reaction?

A
  • The tertiary structure of the polypeptide used to make the enzyme gives rise to a unique shape which is only complementary to a specific substrate
  • This means enzymes can carry out a very limited number of different reactions
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25
Q

How are enzymes named?

A

By adding the ‘ase’ to the end of the name of the substrate or name of reaction

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26
Q

In the past there were different ways of naming enzymes (after the person that discovered it etc), which makes it confusing to know which enzyme everyone is referring to. How was this counteracted?

A
  • Enzyme commission made an international system for classifying enzymes
  • This involves 6 classes each with sub-categories
  • Enzymes are organised into these classes according to the reaction they catalyse using four numbers
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27
Q

What are the six classes in the classification of enzymes?

A
  1. Oxireductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
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28
Q

What do Oxidoreductases do?

A

Catalyse reactions involving electron transfer

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29
Q

What do Transferases do?

A

Catalyse reactions involving transferring chemical groups

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30
Q

What do Hydrolases do?

A

Catalyse the break down of polymers (using water)

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31
Q

What do isomerases do?

A

Catalyse the making of different isomers of the substrate by moving groups within the molecule

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32
Q

What do lyases do?

A

The splitting of the following bonds by elimination:

  • Carbon- Carbon bonds
  • Carbon-oxygen bonds
  • Carbon- Nitrogen bonds
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33
Q

What don’t lyases affect?

A
  • Double bonds
  • Rings
  • Groups added to double bonded atoms are unaffected
34
Q

What do ligases do?

A

Catalyse the production the following bonds via condendation reaction:

  • Carbon- Carbon bonds
  • Carbon-oxygen bonds
  • Carbon-sulphur bonds
  • Carbon- Nitrogen bonds
35
Q

What are the reactions that ligases carry out coupled with?

A

ATP hydrolysis (or other co-factor)

36
Q

What are the subclasses of Oxidoreductases?

A
  • Dehydrogenases
  • Oxidases
  • Peroxidases
  • Reductases
37
Q

What are the subclasses of transferases?

A
  • Glycosyltransferases
  • Aminotransferases
  • Phosphotransferases
38
Q

What are the subclasses of Hydrolases?

A
  • Peptidases
  • Amylases
  • Phosphatases
39
Q

What are the sub-classes of lyases?

A
  • C-C lyases
  • C-O lyases
  • C-N lyases
40
Q

What are the sub-classes of ligases?

A
  • C-C ligases
  • C-O ligases
  • C-N ligases
41
Q

What enzyme catalyses glucose phosphorylation?

A

Hexokinase

42
Q

Hexokinase has the numbers EC.2.7.1.1. What does this mean?

A
  • EC is enzyme commission number
  • 2 is the class number hexokinase is in (transferase)
  • 7 is the 7th sub-class (phosphotransferases)
  • 1 is for the enzyme with a hydroxyl acceptor
  • 1 standards for D-hexose as the acceptor of the phosphate group
43
Q

What is the name given to studying the rate at which chemical reactions happen?

A

Chemical kinetics

44
Q

What are enzyme kinematics?

A

Studying the rate of reactions that are catalysed by enzymes

45
Q

Why is enzyme kinematics vital in development of drugs?

A
  • Inhibiting the function of an enzyme is often what many drugs do
  • Data is used to find out how well a possible enzyme inhibitor will work and understand how it will act
46
Q

What is represented by the symbol V?

A

Initial speed of the reaction

47
Q

What is represented by the symbol S?

A

Starting concentrations of substrate

48
Q

How would a graph drawn of reaction speed against starting substrate concentration look for first order kinetics?

A
  • At small concentration of substrate, the reaction rate is directly proportional to the substrate concentration
  • Graph starts at zero and is a straight, diagonal line
49
Q

What is required for a graph of reaction velocity against substrate concentration to be directly proportional?

A
  • A fixed amount of enzyme
  • A low concentration of substrate
  • No inhibitor present
50
Q

When does the reaction speed against substrate concentration graph look like a straight, horizontal line?

A
  • When the reaction is at zero order kinetics
  • When high amounts of substrate are present
  • No inhibitor involved
  • Fixed enzyme amount
51
Q

What does it mean if a reaction has zero-order kinetics?

A

Any increase in substrate concentration doesn’t affect how fast the reaction is

52
Q

What does the symbol Vmax represent?

A

The maximum rate at which an enzymes can work at

53
Q

When is the maximum speed at which an enzyme can work achieved?

A
  • At optimal temperature
  • At high substrate concentration
  • At optimal pH
  • No inhibitor
54
Q

How does substrate concentration affect the rate at which enzymes can work?

A

This enables all the available active sites to be occupied

55
Q

Why does the graph for reaction rate against substrate concentration plateau with no inhibitor, a large substrate concentration and a fixed amount of enzymes?

A

All the active sites of the enzymes have become occupied so enzyme concentration is the limiting factor, and the rate of reaction has reached saturation point

56
Q

What is the Michaelis-Menten equation? Explain what each parameter is:

A

K1 K2
E + S <=> ES —-> E + P
K-1

  • K1 is the rate at which enzyme-substrate complexes are made
  • K-1 is rate constant for the release of the substrate from the enzyme
  • K2 is the rate constant for the product being made from the enzyme-substrate complex
  • E is the enzyme
  • S is the substrate
  • P is the product
57
Q

What is K2 also known as?

A

Kcat

58
Q

Explain the Michaelis-Menten equation:

A
  • The enzyme and substrate combine
  • From here there are two options: produce enzyme and the product or dissociate to produce the enzyme and unaltered substrate again
  • Each of the three routes have a rate constant
59
Q

What does Km stand for?

A

The Michaelis constant

60
Q

What is the Michaelis Constant?

A

The concentration of substrate that which the reaction rate is half that of when at maximum saturation of enzymes, which is specific to every enzyme

61
Q

What is the equation for Michaelis Constant?

A

Vmax[S]
V= —————–
Km + [S]

                     K-1 + K2 where    Km = ---------------
                           K1
62
Q

What does not affect the value of Km?

A

Enzyme concentration

63
Q

What makes Km and Vmax difficult to calculate?

A

The fact that the maximum rate of reaction can never be reached (though the reaction rate gets closer and closer to the value)

64
Q

How do we calculate Vmax and Km if the maximum reaction rate is never reached?

A
  • Plot 1/V against 1/S
  • This produces a straight line graph
  • 1/Vmax is the y-intercept
  • 1/Km is the x-intercept
  • Km/Vmax is the slope gradient
  • This is called the Lineweaver-Burk plot
65
Q

What is the Lineweaver-Burk plot also called?

A

Double reciprocal plot

66
Q

What is Kcat?

A

The highest number of times substrates are converted to products per second in a catalytic site given a specific concentration of enzymes

67
Q

What is the catalytic efficiency of enzymes?

A

The integrated effects of the catalytic potential and the enzyme’s capability to bind to the substrate even when substrate is at low concentration

68
Q

What values measure catalytic efficiency?

A
  • Km

- Kcat

69
Q

What are the measures of Km and Kcat when an enzyme is very efficient?

A
  • Km is small

- Kcat is large

70
Q

What are inhibitors?

A

Substances that slow down the rate of enzyme controlled reactions by reducing catalytic efficiency

71
Q

What is the function of naturally existing inhibitors?

A

Control the rate of biochemical reactions catalysed by enzymes in the body

72
Q

How can the study of inhibitors be used in developing treatments?

A
  • Inhibitors can be used to slow down or stop reactions that cause damage to the cell and are catalysed by enzymes
  • Inhibitors can be used to stop/slow down reactions that are vital in order to kill abnormal cells
73
Q

What are the two types of inhibitors?

A
  • Reversible

- Irreversible

74
Q

What makes some inhibitors reversible?

A

When they collide with the enzyme, the non-covalent bonds formed is not permanent

75
Q

What are the three types of reversible inhibitor?

A
  • Competitive
  • Uncompetitive
  • Non-competitive
76
Q

Describe how competitive inhibitors affect the rate of enzyme controlled reactions:

A
  • Inhibitor has a similar shape to that of the substrate so can bind to active site
  • Therefore it is fighting to get into the active site of the enzymes alongside the substrate
77
Q

Which type of reversible inhibitor’s effects can be overcome?

A

Competive inhibitors

78
Q

How do you overcome the effects of a competitive inhibitor?

A

By increasing the substrate concentration so that there is a higher chance that the substrate will reach the active site first

79
Q

How do uncompetitive inhibitors affect the rate of enzyme controlled reactions?

A
  • Binds to the enzyme’s allosteric site only when enzyme-substrate complex has formed
  • This stops the enzyme from being able to release the product of the reaction
80
Q

How do non-competitive inhibitors effect the rate of enzyme-controlled reactions?

A
  • Binds at the allosteric site of an enzyme, causing the active site’s shape to change
  • This prevents substrates binding to the enzyme and forming an enzyme-substrate complex
81
Q

What affect do competitive inhibitors have on the value of Km and Vmax?

A
  • Km increases

- There is no change in Vmax

Chemistry Of Biological Interactions: (4 decks)

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