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BMB 401 > Exam 2 (Lectures 11-13) > Flashcards

Exam 2 (Lectures 11-13) Flashcards

1
Q

First Order Kinetics

A

there is only one reactant that is being worked on by the enzyme (unimolecular reaction)

v = k [A]

[=] s-1

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2
Q

Second Order Kinetics

A

deals with 2 substrates to combine into 1 product

v = k [A][B}

[=] mol-1s-1

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3
Q

Pseudo-First Order Kinetics

A

bimolecular reaction with one reactant far in excess

rate of reaction depends on the concentration of only one substrate (limiting reactant)

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4
Q

Zero Order Kinetics

A

steady state

the reaction is achieved at equilibrium

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5
Q

Carbonic Anhydrase

A

catalyzes hydration of CO2 to carbonic acid.

proceeds at moderate rate without the enzyme

can increase turnover rate to 106 mol/s

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6
Q

Zn+2 Metal Cofactor

A

4 coordination sites: 3 Histidine groups and water

destabilizes water and allows loss of proton and quickly converts to OH-

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7
Q

Protons diffuse too slowly to accomodate the turnover rate speed of 10-6s-1 so in order for catalysis to continue:

A

shuffling protons to a buffer of pH 7

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8
Q

Enzyme must be regulated to:

A

allow for optimal functioning to accomodate different metabollic needs

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9
Q

Ways to regulate Enzymes

A

Allosteric Control

Multiple Isozymes

Reversible Covalent Modification

Proteolytic Activation

Controlling Enzyme Levels

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10
Q

Allosteric Control

A

involves a regulatory sites other than the active site to which a small molecule can bind.

coopererativity beetween subunits within the same protein

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11
Q

Binding at a small molecule often results in a…

A

3-dimentional change in the conformation of the enzyme.

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12
Q

Cyclic AMP (cAMP)

A

a small molecule that is formed by cyclization of ATP

an important intracellular messenger and allosteric factor

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13
Q

Binding of regulatory small molecules

A
  1. Binding of cAMP to R (regulatory region)
  2. Confomational change in R
  3. Release of inhibiting R pseudosubstrate sequences
  4. 2 freed (active) protein kinase A molecules
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14
Q

Catalytic regions (Protein Kinase A)

A

phosphorylates target protein (enzymes) to either Activate or De-activate it

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15
Q

Reciprocal Regulation

A

two pathways (synthesis and degredation) of the same molecule are not working at the same time to the same extent

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16
Q

Protein Phosphatase

A

the enzyme that dephosphorylates a protein by hydrolyzing the phosphate from the target protein

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17
Q

Isozyme

A

different form of an enzyme, in the same individual, that catalyzes the same reaction but has slightly different amino acid sequence and usually different properties

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18
Q

Isozymes may be different in..

A

the mode of regulation

expression patterns

kinetic parameters

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19
Q

Lactate Dehydrogenase Enzyme

A

tetramer that is made up of H subunit and M subunit

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20
Q

H Subunit

A

higher afinity for the substrate that does M subunit

prevalent in heart because it can function very well in aerobic situation where plenty of oxygen is available

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21
Q

M Subunit

A

is negatively regulated by its product while H subunit is not

prevalent in muscle and liver because it can function very well in anaerobic situation

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22
Q

Native Gel Electrophrysis

A

Proteins are in their natural 3D conformation to preserve tertiary and quaternary structures

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23
Q

Thickness of the bands in gel electrophoresis

A

indicative of how much of a particular subunit is found in that particular sample

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24
Q

Reversible Covalent Modification

A

happens after the protein is translated

phosphorylation, acetylation, myristoylation, ADP ribosylation, Farnesylation, y-carboxylation, suflation, ubiquitination

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25
Q

Proteolytic Activation

A

cleavage of inactive zymogen to activate enzymes (happens to proteosys)

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26
Q

Zymogens

A

Pepsinogen (from stomach), Chymotrypsinogen (pancreas), Trypsinogen (pancreas), Procarboxypeptidase (pancreas), Proelastase (pancreas).

they are then transported to the duodenum where they are activated through proteolytic cleavage

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27
Q

Proteolytic Activation: Digestive enzymes

A

proteolytic cascade which begins with cleaving of trypsinogen by enteropeptidase, resulting in active trypsin which activates a digestive protease cascade

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28
Q

Proteolytic Activation: Clotting factors

A

proteolytic cascade resulting in cleaving fibrinogen to form fibrin to form blood clots

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29
Q

Proteolytic Activation: Peptide hormones

A

pro-insulin to insulin

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30
Q

Proteolytic Activation: Collagen

A

procollagen (solluble precursor) to extracellular matrix protein, collagen

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31
Q

Proteolytic Activation: Tissue remodeling enzymes

A

active enzymes that digest tissue, procollagenase to collagenase

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32
Q

Proteolytic Activation: Apoptotic enzymes

A

formation of proteases called caspases from procaspases. caspase activation results in a tightly regulated cell death called programmed cell death or apoptosis.

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33
Q

Matrix

A

innermost portion of the mitochondrion and is the site of many biosynthetic and catabolic reactions

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34
Q

Heme Synthesis

A

formation of protoporphyrin IX (asymmentric ring structure) and chelation of iron

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35
Q

Heme synthesis requires…

A

4 Mitochondrial and 4 Cytosolic enzymes

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36
Q

Heme Synthesis: Reaction 1

A

condensation between Succinyl CoA and Glycine to form d-Aminolevulinate (d-ALA)

also a rate limiting step (takes the longest time and dictates how fast or slow the whole pathway will go)

Enzyme: d-Aminolevulinate Synthase

Site: Mitochondrial Matrix

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37
Q

Heme Synthesis: Regulation

Reaction 1

A

Primarily by Negative feedback through heme

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38
Q

Heme Negative feedback effect on Regulation

A

inhibiting transport of d-ALA synthase into the mitochondrion by high heme concentration

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39
Q

Where is d-ALA synthase synthesized?

A

in the cytosol, however it is used in the mitochondrion

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40
Q

Heme negative feedback effect on:

A

transcription of d-ALA synthase, mRNA stability, and translation

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41
Q

Heme Synthesis: Reaction 2

A

Dehydration synthesis where d-ALA is transprted to cytosol and 2 d-ALA condeses to form each porphobilinogen molecule

42
Q

Heme Synthesis: Reaction 3

A

condensation reaction in which 4 molecules of porphobilinogen condense head to tail to form a linear tetrapyrrole molecule with release of one ammonium ion for each methylene bridge made

Enzyme: Porphobilinogen Deaminase

43
Q

Heme Synthesis: Reaction 4

A

Cyclization: synthesis of an asymmetric ring Uroporphyrinogen III (constructs one of the rings to have the substituents flipped compared to the rest)

Enzyme: Uroporphyrinogen III Synthase

44
Q

Ferrochelatase

A

the enzyme that chelates iron to form heme

45
Q

Heme Synthesis: Reaction 5

A

forms methyl and vinyl side chains and alters saturation of ring constituents ending with protoporphyrin IX.

Site: Mitochondrion

46
Q

Heme Synthesis: Final Reaction

A

Chelation of iron and positioned into the ring by the enzyme ferrochelatase

47
Q

Chelation

A

multiple bonds are made between a group and a central metal (in heme: between the pyrrol nitrogens and central iron)

48
Q

Porphyrias

A

problems with Heme Synthetic pathway

  1. Acute intermittent porphyria
  2. Congenital erythropoietic porphyria
49
Q

Acute Intermittent Porphyria

A

deficiency in the enzyme that catalysis reaction 3: Porphobilinogen Deaminase Deficiency

Excess porphobilinogen and d-ALA

50
Q

Symptoms of Acute Intermittent Porphyria

A

severe abdominal pain and neurologic involvement

51
Q

Congenital Erythropoietic Porphyria

A

Reaction 4: Uroporphyrinogen III Synthase Deficiency.

Causes uroporphyrinogen I to be formed in addition to III

52
Q

Symptoms of Congenital Erythropoietic Porphyria

A

photosensitivity and red fluorescent teeth

53
Q

What is the RBCs average life span?

A

120 days

54
Q

Primary site of RBC scavenging (filtering out of the bloodstream)

A

Spleen

55
Q

Hemoglobin Catabolism

A
  1. hemoglobin protein components, globin chains, are hydrolyzed to individual amino acids
  2. the iron is recycled
  3. heme is broken down in several steps to form 1-stercobilin (excreted in poop) and 1-urobilin (excreted in urine)
56
Q

Heme Oxygenase

A

breaking of alpha-methene bridge resulting in the release of Fe3+

Products are Biliverdin, CO, H2O, NADP+

57
Q

Biliverding Reductase

A

reduction of central methene bridge to form Bilirubin and NADP+

58
Q

Bilirubin is transported from…

A

the spleen to the bloodstream then the liver but it is poorly soluble (hydrophobic)

59
Q

Bilirubin is not very hydrophilic, what carrier is needed to transport it from the spleen to the bloodstream

A

Serum Albumin

60
Q

Glucuronyl transferase (liver enzyme)

A

the enzyme that catalyzes the transfer of glucuronide to bilirubin

61
Q

Bilirubin Diglucuronide

A

is made by transferring 2 activated glucuronide sugars to 2 propionate side chains of bilirubin

it is now hydrophilic enough to be transported in bile through bile duct to the small intestine for further processing

62
Q

Conjugated bilirubin

A

when glucuronyl transferase does its thing in the liver to form bilirubin diglucuronide

synthesized in and released by the liver

63
Q

once the conjugated bilirubin is in the intestine..

A

the glucuronides are removed and further breakdown carried out by gut bacteria

Product: urobilininogen

64
Q

Urobilininogen (orange yellow color)

A

some is reabsorbed and transported into the kidneys and then excreted in the urine.

the remaining is further broken down into 1-stercobilin and excreted in feces

65
Q

Unconjugated bilirubin

A

bilirubin that came straight from the spleen

formed in the spleen

66
Q

Tests for Serum Bilirubin Levels

A
  1. Indirect (unconjugated) bilirubin
  2. Direct (conjugated bilirubin)
67
Q
  1. Indirect Test for bilirubin
A

increased unconj. bilirubin results in:

Anemia

neonatal jaundice

resolution of large hematoma

68
Q

Increased of the levels of Unconj. bilirubin is caused by…

A

the body trying to get rid of a lot of heme all at once overwhelming the system, generally caused by an increased in red blood cell lysis

69
Q

Anemia

A

can result in the rupturing of RBCs and a lot of heme must be prossesed

70
Q

Neonatal Jaundice

A

a lot of bilirubin must also be processed at once and can build up in the tissues

UV light can make bilirubin go in a conformational change making it easier to extract out of the body

71
Q

Why do bruises change color from red to green to yellow?

A

because it is the process of going from heme to biliverdin to biliruben

72
Q
  1. Direct Test for bilirubin
A

increased conj. bilirubin liver disease:

bile duct obstruction

cirrhosis: scarring of the liver
hepatitis: infection of the liver

73
Q

Increased of the levels of Conj. biliruben is caused by…

A

the liver itself due to the liver being unable to dispose of it normally through the bile

74
Q

Total Serum Biliruben

A

measures both indirect and direct serum bilirubin

75
Q

Enzymes

A

are catalysts that specifically recognize their binding partners through complementarity of 3-D structure

76
Q

Most enzymes are:

A

proteins and there are some that are RNA that functions as a catalyst

77
Q

What do enzymes do to the transition state?

A

they stabilize the transition state by decreasing the activation energy required to form it

78
Q

ΔG‡

A

is the activation energy, the amount of energy needed to initiate the reaction

79
Q

Enzyme function:

A
  1. Bring reactants and cofactors close enough and in the correct orientation long enough for reaction to occur
  2. Provide an optimal environment for catalysis:
    a. Supply residues that participate in the reaction:
    i. act as proton donor/acceptor in acid/base catalysis
    ii. acidify functional groups in a reactant
    iii. stabilize a developing charge in a reactant
    b. Provide torsional energy that allows catalysis:
    i. conformational change upon reactant or cofactor binding
80
Q

Cofactors can be divided into 2 groups:

A

Metals - tightly bound, inorganic

Coenzymes - small, organic molecules

81
Q

Prosthetic Cofactor Groups

A

tightly bound cofactors

82
Q

Apoenzyme

A

an enzyme without its required cofactor

83
Q

Holoenzyme

A

enzyme with its required cofactor

84
Q

Active Sites

A

the place a place on the enzyme where the substrate binds

85
Q

Characteristics of the Active Site

A
  1. 3-D cleft or crevice that involves residues from different parts of the protein primary structure
  2. Takes up only a small portion of the total enzyme
  3. Provides a favorable microenvironment for the reaction
  4. Binds substrates through many weak interactions
  5. Binding specificity depends on cleft architecture and the presence of amino acids in specific positions
86
Q

Michaelis-Menten Kinetics

A

enzymes that have a hyperbolic regression that describes its reaction velocity as a function of substrate concentration

87
Q

Vmax/2

A

the velocity at which half of the enzyme binding sites said to be filled with substrate

88
Q

KM (Michaelis-Menten Constant)

A

the concentration of substrate at which half of all the possible enzyme binding sites are full

[=] micromolar/millimolar

89
Q

The lower the KM the more…

A

efficient the binding of the enzyme is for that substrate

90
Q

the higher the Vmax, the more…

A

efficient the enzyme and substrate are at producing the product

91
Q

Vo =

A

( [S] Vmax ) / ( [S] + KM )

[S] - substrate concentration

92
Q

Lineweaver-Burk Plot

A

a double reciprocal plot of the original regression function where the y and x axes are 1/Vo and 1/[S] respectively.

93
Q

In a Lineweaver-Burk Plot, where in the plot are KM and Vmax

A

the x-intercept is equal to -1/KM while the y-intercept is equal to 1/Vmax

94
Q

Reversible Inhibitors

A

inhibitors that dont covalently change or modify the enzyme

95
Q

Reversible inhibition has 4 types:

A

Competitive

Uncompetitive

Non-competitive

Mixed

96
Q

Ki

A

measure of inhibitor potency;

the low this calue is, the more potent the inhibitor

97
Q

Kmapp

A

Km in the presence of inhibitor

98
Q

Vmaxapp

A

Vmax in the presence of inhibitor

99
Q

Competitive Inhibitor

A

competes with substrate for the active site.

addition of more substrate can overcome the effect of the inhibitor

Vmax stays the same

KM is increasing

100
Q

Non-competitive Inhibitor

A

binds to another site other than the active site that prevents the enzyme from doing its job well

Vmax > Vmaxapp

KM = KMapp

101
Q

Uncompetitive Inhibitor

A

binds to an enzyme already bound to a substrate that decreases the efficiency of the enzyme

Vmax > Vmaxapp

KM > KMapp

BMB 401 (6 decks)

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