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Biocheem > Lecture 19 > Flashcards

Lecture 19 Flashcards

1
Q

What is the speed of a favorable biochemical reaction determined by?

A

The size of the activation energy barrier

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2
Q

What is a transition state?

A

A high energy state that exists between the substrates and the products

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3
Q

What is the thermodynamic aspect of a reaction about?

A

The difference in energy between products and reactants

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4
Q

What does a negative 𝛥G indicate?

A

The reaction is spontaneous

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5
Q

What is the activation energy?

A

The difference in energy between the transition state and substrate state that determines the rate of a reaction

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6
Q

What happens to enzymes at the end of rxn?

A

They are returned to their original state

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7
Q

How is 𝛥G for a rxn affected by an enzyme?

A

𝛥G is the same

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8
Q

What leads to an increase in the rxn rate?

A

The decrease of the energy of the free energy state

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9
Q

How do enzymes affect the transition state?

A

The lower the free energy that is associated with the transition state

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10
Q

What are the four ways that enzymes use to reduce the free energy of the transition state?

A
  • Removing substrates from aqueous solutions (desolvation)
  • Proximity and orientation effects
  • Taking part in the rxn mechanism
  • Stabilizing the transition state
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11
Q

What is an Active Site?

A

A region of an enzyme where catalysis occurs

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12
Q

What do active sites determine?

A

Affinity, specificity and rate of a reaction

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13
Q

What are active sites with oxygen binding?

A

Oxygen binding sites

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14
Q

How much of a protein structure does an active site contain?

A

It is usually only a small part of the protein structure

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15
Q

How can an active site be complementary to the substrate/transition state?

A

By shape, hydrophobic interaction, H-bonds, and ion pairs

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16
Q

What does the design of an active site contribute to?

A
  • Affinity

* Specificity

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17
Q

What is Desolvation?

A

Exclusion of Water

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18
Q

What are the three advantages that exclusion of water provides?

A
  • Removal of water shell accelerates reactions
  • Enhances polar interactions (Hbonds, ion pairs)
  • Prevents side reaction
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19
Q

Which interactions become much stronger with Desolvation?

A

H-bond interactions and ion pair interaction

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20
Q

What is induced fit?

A

A change of shape of the enzyme active site as substrates bind into the active site

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21
Q

How does induced fit affect the active sight?

A

It closes off the acte site and excludes more water

22
Q

How does induced fit affect catalytic groups?

A

It brings catalytic groups together

23
Q

Where is the active side of Hexokinase?

A

In a cleft found between two separate domains within the protein

24
Q

What happens to Enterokinase when glucose and ATP bind?

A

It closes around the substrate to prevent a hydrolysis reaction occurring

25
Q

What is the induced Fit Model?

A

When the active site changes shape as substrates bind

26
Q

How does Proximity and Orientation affect a reaction?

A

Chemical reactions only occur if substrates come together in the right orientation to react

27
Q

How do active sites affect proximity and orientation?

A

Active sites bind substrates close to each other (proximity) and in the correct geometry (orientation)

28
Q

What is Covalent Catalysis?

A

When the enzyme provides a nucleophile and becomes covalently attached to an intermediate during a reaction mechanism

29
Q

When can metal ions be important in reactions?

A

When they act as redox centers

30
Q

How can some enzymes participate in reactions?

A

By positioning functional groups near the substrates in the active site

31
Q

What may the functional groups in some enzymes that participate in reactions function as?

A
  • Acid/base catalysis
  • Covalent catalysis
  • Metal ion catalysis
32
Q

What can enzyme participation in reaction be achieved by?

A

Amino acids, cofactors or both

33
Q

What property do all the amino acids that participate in acid base catalysis have?

A

They all have a pKa associated with it

34
Q

Which amino acids have pKa’s?

A
  • Asp
  • Glu
  • His
  • Lys
  • Cys
  • Tyr
  • Arg
35
Q

Which amino acids with pKa’s are frequently associated with acid base catalysis?

A
  • Asp
  • Glu
  • His
  • Lys
36
Q

Which amino acids can act as nucleophiles in Covalent Catalysis?

A
  • Ser
  • Tyr
  • Thr
  • Cys
  • Lys
37
Q

How can Ser, Tyr and Thr act in covalent catalysis?

A

With their OH group that can act as nucleophiles

38
Q

In what from can Cys act as a good nucleophile?

A

In the deprotonated form

39
Q

Which amino acids can act as good nucleophiles in the deprotonated form?

A

Cys, Lys, His

40
Q

What can a nucleophile in covalent catalysis form?

A

The formation of a covalent bond of the enzyme and the substrate

41
Q

Which amino acids can act as nucleophiles on Covalent catalysis and with what conditions of the R group?

A
  • Ser, Tyr, Thr (with their hydroxyl groups)
  • Cys, Lys, His (in their deprotonated form)
  • Asp, Glu (with their carboxylate groups)
42
Q

What are Cofactors?

A

Molecules that aren’t specifically polypeptide structures but end up being part of reaction mechanisms for enzyme catalyzed reactions

43
Q

What are the two subtypes of Cofactors?

A
  • Coenzymes

* Metal ions

44
Q

What are the two subtypes of metal ion cofactors?

A
  • Prosthetic groups

* Loosely bound

45
Q

What are the two subtypes of coenzyme cofactors?

A
  • Cosubstrates

* Prosthetic groups

46
Q

What is the difference between a cosubstrate and a prosthetic group?

A

Cosubstrates are converted within the active site and releases as products and prosthetic groups are a permanent part of protein tertiary structure and are permanent part of protein tertiary structure

47
Q

What is required of coenzymes after a reaction?

A

They need to be regenerated after reaction

48
Q

What is the difference between an apoprotein and a holoprotein?

A

Whether or not the prosthetic group is associated with the polypeptide chain

49
Q

What is a Holoenzyme?

A

When a polypeptide is combined with the prosthetic group to form the functional tertiary structure

50
Q

What is an Apoenzyme?

A

The name used to refer to an enzyme that contains a prosthetic group without the prosthetic group

Biocheem (38 decks)

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