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Med Chem > Biochem 5-7 > Flashcards

Biochem 5-7 Flashcards

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1
Q

Enzyme

A
  • Class of proteins that catalyze biochemical reactions
  • in many cases extremely improved rates
  • stereospecificity
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2
Q

oxidoreductase

A

oxi-reduct reactions

  • often called dehydrogenases
  • usually need a coenzyme like NAD+ or NADP+
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3
Q

Catalyst

A

increase the rate that equilibrium is reached by lowering Ea

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4
Q

Transferases

A
  • catalyze fxnal group transfers
  • may require coenzymes
  • includes kinases (they transfer phosphates)
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5
Q

Hydrolase

A
  • special kind of transferase that transfers to group to water
  • Use water to break apart a compound
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6
Q

Lyase

A
  • Catalyze lysis of the substrate, creating a double bond via elimination rxn
  • splits a molecule in two, creating a double bond
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7
Q

Isomerase

A
  • catalyze structural change within a single molecule

- ie. change L alanine to D alanine

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8
Q

Ligase

A
  • catalyze ligation, or joining of two molecules
  • also called SYNTHETASES (usually)
  • ie change glutamate to glutamine by adding a NH4 molecule
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9
Q

Enzyme Kinetics

A
  • unlike simple kinetics, enzyme kinetics is dependant on the formation of the enzyme-substrate complex. (ES)
  • happens in two steps with a distinct rate for each
  • depends on S and E
  • but if S»»>E than only E matters
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10
Q

initial velocity

A

E + S –k1 and k-1– ES –k2– E + P
k-2 is negligible
form of ES is rapid and E + P is slower
rate measured at beginning is called initial velocity

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11
Q

Steady State assumption

A
  • ES is formed at the same rate that is decomposes (no net change in ES)
  • can be used to derive Michaelis Menten
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12
Q

Catalytic Constant

A

when S&raquo_space;>E than the rate of the reaction is vmax and rate only depends on E
-vmax = kcat[E]tot
-kcat is the catalytic constant also called the turnover number
simple reactions = 2

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13
Q

Michaelis-Menten Eqn

A

enzyme catalysis is 1st order

vo = Vmax[S] / Km + [S]

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14
Q

Michaelis constant

A

Km = Vmax/2

enzyme is half saturated when Km = [S]

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15
Q

Line-weaver Burk

A

line form of Michaelis Menten
y int = 1/vmax
x int = -1/km
used to calculate Km and Vmax from experimental data

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16
Q

Inhibitor

A

compound that binds to an enzyme and interferes with its activity
-reversible ones bind via noncovalent forces
-irreversible ones bind covalently
THREE kinds of reversible:
competitive
uncompetitive
noncompetitive

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17
Q

Classical/Competitive Inhib

A
  • most common
  • only binds free enzyme (not ES)
  • competes with substrate but not always at the same active site
  • doesn’t affect Vmax
  • raises Km
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18
Q

Nonclassical/Uncompetitive Inhib

A
  • Only bind ES, not the free enzyme
  • only in multisubstrate reactions
  • both Vmax and Km are decreased.
  • parallel lineweaver burk
  • includes Allosteric
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19
Q

Noncompetitive Inhib

A
  • Bind to E or ES, effectively removing enzyme molecules from the reaction
  • typically not substrate analogs dont bind the same site as the substrate
  • decreases Vmax, no change to Km
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20
Q

Irreversible Enzyme Inhib

A
  • form stable covalent adducts with enzymes, effectively killing them.
  • often through acylation or alkylation of the active site residues
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21
Q

Enzyme Inhib Example: Organophosphorous Inhibs

A
  • Inactivate hydrolase enzymes through reaction with their serine residues in their active sites
  • sarin gas
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22
Q

Affinity Labels

A
  • Irreversible inhibs with affinity for an enzyme’s active site are called affinity labels
  • allow for site specific covalent mods
  • useful to know which residues are critical for activity
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23
Q

Allosteric enzymes

A
  • bind to another site away from the active site, but cause a change in the active site
  • causes conformational change and inhibition
  • Do not exhibit standard MM kinetics
  • useful for regulation–activators and inhibs
  • allosteric modulators noncovalent and arent chem modded by enzyme
  • multisubunit enzymes
  • sigmodial rate versus [S] for at least one substrate
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24
Q

Regulation by Covalent Mods

A
  • covalent mods to polypeptide chain
  • slower than allosteric
  • reversible processes, usually catalyzed by other enzymes
  • Phosphorylation of hydroxylated or basic AA residues
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25
Q

Two kinds of nucleophilic sub

A
  1. tetrahedral intermediate (can be isolated)

2. pentavalent transition state (happens briefly)

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26
Q

Types of enzymatic mechanisms

A

Cleavage reactions

Oxi-Red reactions

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27
Q

Reaction coordination

A
  • how enzymes can increase the rate of reaction by decreasing Ea
  • accomplished by stabilizing transition states
28
Q

Enzymatic Catalysis

A
  • reactants bound by enzyme brings them higher in free energy (lessens Ea)
  • reactants and transition state bound by enzyme lowers transition energy (brings Ea down even further)
29
Q

Polar residues in active sites

A

-usually there are polar residues in actvie sites
-reactive fxnal groups
pKa values differ from free AAs

30
Q

Acid-Base Catalysis

A
  • Proton transfer catalyzes reaction

- often talked about in terms of general acids and bases

31
Q

Covalent Catalysis

A

-substrates covalently bonded to enzyme forming a reactive intermediate
-20 % of enzymes use this
-nucleophilic catalysis more common
A net equation would look like this:
AX —> AB with an E intermediate in there thats not part of overall conversion

32
Q

pH dependence of enzymes

A
  • many have an optimal pH range

- ionizible AAs are the main players in an enzymes active site

33
Q

Diffusion controlled reactions

A

-If an enzyme is especially good, than its upper limit is controlled by rate of diffusion
10^8- 10^9 M-1 s-1

34
Q

Diffusion controlled: Triose Phosphate Isomerase

A

Interconversion of DHAP and G3P

using glutamate and histidine that shuttle protons

35
Q

Diffusion controlled: Superoxide Dismutase

A

degradation of superoxide
-has a Cu atom wit catalytic activity
able to be reduced and then oxidized

36
Q

Binding modes of enzymatic catalysis

A
  1. Proximity effect
    correct position decreases entropy, increase in reaction
  2. Transition State Stabilization
37
Q

Substrates bind weakly to enzymes

A
  • not too tight, otherwise get a thermodynamic pit
  • coenzymes are held a bit more tightly
  • formation of ES is slightly unfavorable
38
Q

Induced fit

A
  • not rigid structures, flexible
  • shift from inactive to active conformations
  • activation by substrate induced change is called INDUCED FIT
  • example: hexokinase
39
Q

Transition State Stabilization

A
  • process of distorting or straining a substrate towards the reaction’s transition state conformation
  • lock and key mechanism
40
Q

Transition State Analogs

A
  • stable compounds whose structures resemble presumed transition states
  • sit in active site of enzyme
  • often potent inhibs
41
Q

Trans State Analogs: Adenosine Deaminase Inhibs

A

enzyme recognizes the -OH at the C6 position binding to adenosine deaminase

42
Q

Lysozyme

A
  • Catalyzes the hydrolysis of polysaccharides that make up the cell wall.
  • MurNAc -beta (1–4) -GlcNAc glycosidic bond
  • substrate region can hold 6 saccharide units MurAc has to distort into a half chair to fit
43
Q

Serine Proteases

A
  • cleave the peptide bond of proteins
  • essential serine residue in their active sites
  • Tryspin for example cleaves at the COO- side of lys and arg residues
  • there are three interesting ones–trypsin, chymotrypsin, elastase
44
Q

Chymotrypsin

A

three catalytic residues– His 57, Asp 102, Ser 195
catalytic triad!!
Turns Ser 195 into a strong nucleophile

45
Q

Enzymatic Cofactors

A
  • assist in the catalytic process but aren’t enzymes

- Apoenzyme (inactive) and Holoenzyme (Apoenzyme and cofactor (active))

46
Q

Essential Ions

A
  1. needed for metal activated enzymes
    K, Ca, Mg
  2. metalloenzymes
    Zn, Fe, Cu, Co
47
Q

Metalloenzymes

A

Zn can turn water into a good nucelophile

Iron-Sulfur clusters can accept a single electron

48
Q

Coenzymes

A

Cosubstrates–substrates are chemically altered and dissociate with the enzyme
Prosthetic groups–remain bound to the enzyme throughout the reaction must be regenerated to retain enzymatic activity

49
Q

Vitamin

A
  1. water soluble (B vitamins, vitamin C, folate)
  2. fat soluble (vitamin A, D, E, K)
    excessive intake is toxic!
50
Q

Adenosine Triphosphate

A

ATP is one of the most abundant coenzymes.
**Cosubstrate
*water
versatile reactant that can donate Pi, PPi AMP or adenosyl group

51
Q

Nucleotide Cosubstrates

A
  • S-adenosylmethionine is biological methylating agent

- Uridine diphosphate glucose (UDP) glycosyl donor

52
Q

Nicotinamide coenzymes

A 
NAD+ and NADP+
****B3
**Cosubstrate 
**Active region is the nicotinamide 
*water
can accept pair of electrons/ a hydride
get reduced which makes them have an 'H' on the end
53
Q

Flavin adenine dinucleotide and flavin mononucleotide

A 
FAD and FMN
***both from riboflavin 
**Prosthetic group
**semiquinones
*water
prosthetic group for many oxidoreductases
-addition of proton and pair of electrons (usually hydride)
-get or lose ONE ELECTRON at a time
-semiquinones
54
Q

Coenzyme A

A

involved in acyl group transfers

  • **Vitamin B5
  • *Active region is the free –SH group (CoA–SH)
  • *Cosubstrate
  • water
55
Q

Thiamine Pyrophosphate

A
  • **derived from thiamine (vitamin B1)
  • *Active region is Thiazolium ring
  • *Prosthetic
  • water soluble
  • coenzyme form is TPP
  • several decarboxylase require TPP as a coenzyme (prosthetic group)
56
Q

Pyridoxal Phosphate

A
  • **Vitamin B6 is pyridoxal (or pyridoxamine)
  • *pyridoxal 5’-phosphate (PLP) is active ALDEHYDE
  • *Prosthetic
  • water soluble
  • PLP is a prosthetic group for enzymes that catalyze a variety of AA transformations including: isomerizations, decarby, eliminations, displacements
  • works as a Schiff base
57
Q

Transminase Mechanism

A
  • PLP mechanism

- catalysis comes from transaminase but product comes from active site or near it

58
Q

Tetrahydrofolate

A
  • **folate, (vitamin B2 or folic acid)
  • *two amine groups
  • *Cosubstrate
  • water
  • needed by enzymes that perform one carbon transfers
59
Q

Cobalamin

A
  • **Cobalamin (vitamin B12)
  • *Co atom
  • *Prosthetic group
  • water soluble
  • corrin ring structure and a hexavalent Co atom ion
  • coenzyme
60
Q

Lipoamide

A
  • **lipodic acid
  • *Double SH groups
  • *Prosthetic
  • water
  • swinging arm transfers acyl groups
  • SH ester friends
61
Q

Vitamin A

A
  • Beta carotene
  • **retinol
  • *Prosthetic
  • lipid
  • retinal–prosthetic group for rhodopsin that makes neural impulses
  • -retinoic acid which is a signaling molecule
62
Q

Vitamin D

A
  • calciferols
  • **Vitamin D3 formed in the skin when exposed to sunlight
  • lipid
63
Q

Vitamin E

A
  • helps to scavenge free radicals and oxygen
  • *phenol group is active
  • lipid vitamin
64
Q

Vitamin K

A
  • Helps in formation of proteins for blood coagulation
  • *hydroquinone is active
  • lipid vitamin
65
Q

Ubiquinone

A
  • coenzyme Q
  • lipid membranes
  • strong oxidizing agent can accept either one or two electrons
66
Q

Protein Coenzymes

A

-Thioredoxins
two cysteine residues separated by two aminos
disulfide bridge exposed = reducing enzyme
-Cytochromes
Heme containing Fe atoms undergo one electron reduction
different types based on heme group structure
a,b,c based on absorbance

Med Chem (3 decks)

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