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Biochem > Lecture 18 Enzymes I > Flashcards

Lecture 18 Enzymes I Flashcards

1
Q

Enzyme

A

A protein (or protein-based molecule) that speeds up a chemical reaction in a living organism.

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2
Q

Enzyme acts as

A

A catalyst for specific chemical reactions, converting a specific set of reactions (substrates) into specific products

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3
Q

Catalysis

A

Increasing the speed of chemical reactions
Ex. O2 + iron = rust (takes centuries)
Add H2O and takes days

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4
Q

Enzymes and the energy of activation

A

Enzymes lower the energy of activation by forming an enzyme-substrate complex by allowing products of the enzyme reaction to be formed and released much faster

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5
Q

ES

A

Enzyme-substrate complex

Intermediate

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6
Q

Sir Archibald Edward Garrod

A

-inborn errors of metabolism
alkaptonuria - relation between disease and fundamental errors in biochemical reactions
-enzymes must be a link

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7
Q

Enzyme Specificity

A

3D structure of enzyme protein contributes to specificity of reaction
-lock and key

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8
Q

Active Site

A

Substrate binds, undergoes chemical alteration

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9
Q

Enzyme substrate complex

A

Lock and key VS. Induced fit

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10
Q

Evidence of an enzyme substrate complex

A

With a constant concentration of enzyme and increasing concentration of substrate, reaction rates increased to maximum
-Indirect evidence of ES complex

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11
Q

The limit in reaction rate is due to

A

Substrate occupying all the available catalytic sites

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12
Q

Maximal Velocity

A

Substrate is saturated all the enzymes

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13
Q

Evidence of an enzyme substrate complex

A

-X-ray crystallography

Ex. cytochrome P450 bound to its substrate camphor

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14
Q

Active Site

A

3D cleft or crevice formed from the residues of various protein regions and occupies small total volume
–shape dictates specificity
Specificity of binding depends on the precisely defined arrangement of atoms in the active site

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15
Q

Active site microenvironment

A

Active site contains a unique microenvironment, usually void of water and controls the proper shape, pH and polarity for substrate binding and chemical reactivity

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16
Q

Trypsin cleaves after

A

Arginine

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17
Q

1st Law of Thermodynamics

A

Conservation of energy

-in biochemical reactions - E is transferred from one form to another

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18
Q

Transition State

A

Intermediate structure that is not the substrate and not yet the product

  • unstable and highest free energy
  • double cross denotes the transition state
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19
Q

Gibbs Free Energy of Activation

A

The difference in free energy of the transition state and the substrate
Enzymes function to lower the activation energy

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20
Q

Delta G =

A

Free energy of substrate-free energy of product

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21
Q

Enzymes and reactions

A

Enzymes accelerate reactions by facilitating the formation of the transition state/lower activation energy

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22
Q

Cofactors

A

Small molecules that contribute to the chemical reaction of the enzyme

  • many different roles in catalysis
  • enzymes that use the same cofactor share similar mechanisms of catalysis
  • Apoenzyme
  • Haloenzyme
23
Q

Apoenzyme

A

Enzyme without its cofactor

24
Q

Haloenzyme

A

Cofactor bound and catalytically active

25
Q

Metal Cofactors

A

Positively charged
Stable coordination of active site groups
Contribute to chemical reactivity
Ex. Zinc activates H2O to form OH- nucleophile

26
Q

Coenzymes

A

Small organic molecules often derived from vitamins (bigger than ions)
When bound tightly called a prosthetic group

27
Q

Prosthetic Group

A

When coenzymes are bound tightly

28
Q

2 Types of Cofactors

A

1 Metals

2 Coenzymes

29
Q

Scurvy

A

Cofactor deficiency

Vitamin C

30
Q

Ariboflavinosis

A

Cofactor deficiency

Riboblavin (B2) required for FAD synthesis

31
Q

NAD+ binding site of dehydrogenases

A

Binds the active site in a well-defined arrangement for substrate activation

32
Q

6 Major Classes of Enzymes

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases
33
Q

Oxidoreductases

A

Enzyme class
Oxidation - reduction
Ex. Lactate dehydrogenase

34
Q

Transferases

A

Enzyme class
Group transfer
Ex. Nucleoside monophosphate kinase (NMP kinase)

35
Q

Hydrolases

A 
Enzyme class
Hydrolysis reactions (transfer of functional groups to water)
Ex. Chymotrypsin
36
Q

Lyases

A 
Enzyme class
Addition or removal of groups to form double bonds
Ex. Fumarase
37
Q

Isomerases

A 
Enzyme class
Isomerization (intramolecular group transfer)
Ex. Triose phosphate isomerase
38
Q

Ligases

A

Enzyme class
Ligation of two substrates at the expense of ATP hydrolysis
Ex. Aminoacyl-tRNA synthetase

39
Q

Oxidoreductases

A

Enzyme that catalyzes the transfer of electrons from one molecule to another

  • Reductant
  • Oxidant
40
Q

Reductant

A

Hydrogen or electron donor

41
Q

Oxidant

A

Hydrogen or electron acceptor

42
Q

ADH

A

Alcohol dehydrogenases

43
Q

Alcohol dehydrogenases

A

Converts alcohols to aldyhydes or ketones with the reduction of NAD+ (cofactor) to NADH

  • Alcohol = oxidized
  • NAD+ = reduced
44
Q

Opposite of alcohol dehydrogenase

A

Fermentation

45
Q

Transferases

A

Enzyme that catalyzes the transfer of a functional group from one molecule to another

  • donor molecules required
  • –Source of methyl groups or phosphates (ATP) as examples
46
Q

Kinase Receptors

A

Phosphorylate proteins and themselves

-usually at tyrosine (TKRs), serine and threonine residues

47
Q

Hyrolases

A

Enzyme that catalyzes the hydrolysis of covalent bonds

  • cleave covalent bonds using water in the process
  • transfer function groups to water
48
Q

Disaccharidases

A

Hydrolases

  • Cleave double sugars to single sugars
  • Defects in lactase = lactose intolerance
49
Q

Lyases

A

Enzyme that catalyzes the addition or removal of groups to form double bonds

50
Q

Aldolase

A

Lyases

-catalyzes second step of glycolysis

51
Q

Isomerases

A

Enzyme that catalyzes isomerization

  • intramolecular group transfer
  • product is an isomer of the substrate
  • *bonds are just moved around
52
Q

Triose phosphate isomerase

A

Isomerases example

-Intramolecular oxidation-reduction reaction

53
Q

Ligases

A

Enzyme that catalyzes the covalent linkage of two substrates

  • usually at the expense of ATP hydrolysis
  • *glue things together, uses ATP
54
Q

DNA Ligase

A

Forms two covalent phophodiester bonds between 3’ hydroxy ends of one nucleotide with the 5’ phosphate end of another
*uses ATP

Biochem (12 decks)

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