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Bio II > Lecture 7: Enzymes and Metabolism (up to slide 37 for exam 1) > Flashcards

Lecture 7: Enzymes and Metabolism (up to slide 37 for exam 1) Flashcards

1
Q

What is metabolism

A

thousands of different chemical reactions in the body

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2
Q

How are chemical reactions in organisms linked?

A

through a network of metabolic pathways.

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3
Q

What are metabolic pathways?

A
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4
Q

What are the two types of metabolic pathways?

A

Anabolic and catabolic

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5
Q

What are anabolic pathways?

A

they result in the synthesis of larger molecules from smaller components that require inputs of energy. These pathways involve endergonic reactions.

ex photosynthesis

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6
Q

What are catabolic pathways?

A

they involve the breakdown of molecules and the release of energy. These pathways involve exergonic reactions.

ex digestion

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7
Q

What is primary metabolism?

Example of primary metabolite?

A

Primary metabolism is essential for cell survival and
reproduction in organisms.

ex amino acids

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8
Q

What is secondary metabolism?

Example?

A

Secondary metabolism is synthesis of secondary metabolites that are not essential for cell survival and reproduction but can help an organism survive and reproduce.

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9
Q

The metabolites to the right are not directly
required for survival or reproduction but
their production act as evolutionary
adaptations. How are they adaptations?

A

they can provide organisms with selective advantages in their environments

ex for sexual reproduction, hunting, pollinization, etc

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10
Q

Give the general formula for Oxidation Reduction Reactions.

A
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11
Q

Give the general formula for Condensation Reactions.

A
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12
Q

Give the general formula for Group Transfer Reactions.

A
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13
Q

Give the general formula for Hydrolysis Reactions.

A
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14
Q

Give the general formula for Cleavage Reactions.

A
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15
Q

Give the general formula for Isomerization Reactions.

A
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16
Q

What are the conditions for a reaction to happen?

A

A. Reactants collide in a precise orientation that brings electron involved in new bonds near each other and allows them to interact.
B. Reactants have enough kinetic energy to reach the transition state.

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17
Q

What is activation energy?

A

The activation energy (Ea) of a reaction is the amount of energy required for reactants to reach the transition state.

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18
Q

What is the transition state?

A
  • The transition state is an intermediate condition.
  • Transition state requires a reaction to overcome repulsive forces and involves molecules with a combination of old and new bonds.
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19
Q

The more _______ the transition state, the ______ the activation energy and the less likely an _____gonic reaction is to proceed quickly.

A

unstable, higher, exer-

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20
Q

How is the free energy during the transitional state?

A

The free energy of the transition state is high because the bonds that existed in the substrate are destabilized—it is a transition point between breaking old bonds and forming new ones.

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21
Q

What are the two characteristics of chemical reactions that can change.

A
  1. Direction
  2. Rate
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22
Q

What influences the direction of a reaction?

A

A. Change in potential energy
B. Change in disorder

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23
Q

Which change between these two will determine the change in free energy?

A

A. Change in potential energy
B. Change in disorder

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24
Q

What influences the change in potential energy and disorder (leading to change in free energy)?

A

temperature and concentration of reactants and products.

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25
Q

What influences the rate of a reaction?

A
  1. Temperature
  2. Concentrations of Reactants
  3. Catalysis
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26
Q

How do each variable affect the rate of a reaction? Which of the events do they help with?

  1. Temperature
  2. Concentrations of Reactants
  3. Catalysis
A
  1. Temperature: kinetic energy and number of collisions
  2. Concentrations of Reactants: collisions
  3. Catalysis: it lowers the activation energy necessary to reach by transitional state molecule
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27
Q

What does an increase in temperature do to a reaction?

A
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28
Q

What does an increase in concentration of reactants do to a reaction?

A
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29
Q

What is a catalyst?

A

a substance that provides an alternate reaction route (mechanism) with a lower activation energy and, therefore, increases the rate of the reaction since more reactants will have the kinetic/activation energy to reach the transition state.

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30
Q

How do catalysts lower the activation energy in the alternate mechanism?

A

by lowering the energy required to reach the transition state in some way.

*In many cases, the transition state molecule can be stabilized when they interact with the catalyst (lowering energy required to reach the transition state).

31
Q

Do spontaneous reactions necessarily happen quickly without a catalyst?

A

Even if a chemical reaction occurs spontaneously, it may not happen quickly without catalysis.

32
Q

What are the three characteristics of catalysts?

A
  1. Are required in small amounts.
  2. Are NOT consumed in the reaction and can repeat their activity.
  3. Do NOT influence the change in free energy and, therefore, the direction of a chemical reaction only the rate of a chemical reaction.
33
Q

How are biologic catalysts called? (more specifically proteins’)

A

Enzymes

34
Q

Catalysis is a vital function of what?

A

proteins and some RNAs.

35
Q

How are RNA catalysts called?

A

ribozymes

36
Q

How can most biological chemical reactions occur at meaningful rates?

A

with the presence of enzymes.

37
Q

By how much do enzymes increase the rate of reaction typically?

A

10^8 to 10^13 fold

38
Q

What reaction is this and what role does sucrase have?

A

Sucrose hydrolysis with the aid of the enzyme sucrase.

39
Q

What is the general effect of enzymes?

A
40
Q

Is catalyst or enzyme a more broad category

A

catalyst, an enzyme is a catalyst, a catalyst is not necessarily an enzyme

41
Q

How does a lower activation energy in a graph would look like? What would it allow?

A
42
Q

What are the 6 groups of enzymes? What type of reaction do each catalyzes?

A
43
Q

Are all enzymes as specific?

A
  • All have some degree of specificity. Range in specificity.
  • Can be specific for:
    A. One reaction
    B. Group of similar reactions
44
Q
A

Transfer of a phosphate group

45
Q

How specific is hexokinase?

A

Hexokinase can recognize glucose as a reactant but also other hexoses so is not specific for one reaction but one type of reaction. Glucokinase on the other hand only uses glucose as a substrate.

46
Q

What is it called when substrates (reactants) bind to the enzyme’s active site?

A

an enzyme-substrate complex.

47
Q

Whats is the green part called and what is it made of?

A

the active site made up of the side chains of amino acids that form a complementary pocket.

48
Q

Why the active site of an enzyme characterized as complementary?

A

because it is complementary in shape, charge, hydrophilic/hydrophobic characteristics.

49
Q

What is the enzyme’s active site responsible for?

A

specificity and catalysis.

50
Q

What is the model proposed before the Induced Fit model to explain enzyme activity?

A

Lock and Key

51
Q

What is the Induced fit model?

A

many enzymes undergo a conformational change when the substrates bind to increase the strength of binding and help in catalysis; this change is called an induced fit.

52
Q

What do enzymes do?

A
53
Q

What are the steps of enzyme catalysis?

A
54
Q

What are three ways an enzyme can facilitate transition state?

A
  1. Straining substrate bonds by induced fit.
  2. Functional groups on side chains can react with the substrate and change the substrate’s reactivity.
  3. Functional groups on side chains can interact with transition state and stabilize it.
55
Q

What is enzyme activity reference to?

A

rate of an enzyme-catalyzed reaction

56
Q

What does rate depend on?

A
  1. Cofactors
  2. EnzymeConcentration
  3. Substrate(Reactant)Concentration
  4. Affinity
  5. Temperature
  6. pH
  7. Regulation
57
Q

What are the three type of cofactors that some enzymes need to function normally?

A
  1. Metal ions: such as Fe2+, Mg2+, or Zn2+.
  2. Cosubstrates: organic molecules.
  3. Prosthetic groups: tightly bound organic molecules.
58
Q

To which part of an enzyme are cofactor on and what role do they play?

A

In many cases, the cofactor is part of the active site and is thought to play a role in stabilizing the transition state during the reaction.

59
Q

What is often required in a diet to produce cofactors?
Give an example.

A

Many vitamins in your diet are required for the production of cofactors for enzymes.

e.g. Thiamine (vitamin B1) -> thiamine pyrophosphate which is required by three different enzymes.

60
Q

What is the relation between the rate of a reaction and the enzyme concentration? Any condition applied?

A
61
Q

What is the relation between the rate of product formation and substrate concentration?

A
62
Q

What is Enzyme Saturation?

A
63
Q

What is Vmax?

A
64
Q

What is a protein’s affinity? How is it measured?

A
65
Q

What is

A
  • The Michaelis constant (KM): the substrate concentration where vo is 1⁄2 Vmax.
66
Q

With what is the Michaelis constant often associated with?

A

the affinity of the enzyme for substrate.

67
Q

A low KM = high or low affinity?

A

Low Km = High affinity between enzyme and substrate.

High Km = Low affinity between enzyme and substrate.

68
Q

Does temperature and pH affect enzyme function?

A
  • Enzymes function best at some particular temperature (optimum temperature) and pH (optimum pH).
69
Q

How can cells regulate enzyme activity?

A
  1. Increasing enzyme levels (slow)
  2. Enzyme activation (fast)
70
Q

What is competitive inhibition?

A

when a molecule similar in size and shape to the substrate competes with the substrate for access to the active site.

Competitive inhibition decreases the enzyme’s activity.

71
Q

What is allosteric regulation?

A

when a molecule causes a change in enzyme shape by binding to the enzyme at a regulatory site .

Allosteric regulation can activate or inactivate the enzyme and thereby increase or decrease the enzyme’s activity.

72
Q

What is an enzyme’s regulatory site?

A

location other than the active site that can be changed in shape on an enzyme to decrease or increase its activity

73
Q
A

Bio II (21 decks)

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