Biochem 5-7 Flashcards
1
Q
Enzyme
A
- Class of proteins that catalyze biochemical reactions
- in many cases extremely improved rates
- stereospecificity
2
Q
oxidoreductase
A
oxi-reduct reactions
- often called dehydrogenases
- usually need a coenzyme like NAD+ or NADP+
3
Q
Catalyst
A
increase the rate that equilibrium is reached by lowering Ea
4
Q
Transferases
A
- catalyze fxnal group transfers
- may require coenzymes
- includes kinases (they transfer phosphates)
5
Q
Hydrolase
A
- special kind of transferase that transfers to group to water
- Use water to break apart a compound
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
7
Q
Isomerase
A
- catalyze structural change within a single molecule
- ie. change L alanine to D alanine
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
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
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
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
12
Q
Catalytic Constant
A
when S»_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
13
Q
Michaelis-Menten Eqn
A
enzyme catalysis is 1st order
vo = Vmax[S] / Km + [S]
14
Q
Michaelis constant
A
Km = Vmax/2
enzyme is half saturated when Km = [S]
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
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
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
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
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
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
21
Q
Enzyme Inhib Example: Organophosphorous Inhibs
A
- Inactivate hydrolase enzymes through reaction with their serine residues in their active sites
- sarin gas
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
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
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
25
Two kinds of nucleophilic sub
1. tetrahedral intermediate (can be isolated)
| 2. pentavalent transition state (happens briefly)
26
Types of enzymatic mechanisms
Cleavage reactions
| Oxi-Red reactions
27
Reaction coordination
- how enzymes can increase the rate of reaction by decreasing Ea
- accomplished by stabilizing transition states
28
Enzymatic Catalysis
- 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
Polar residues in active sites
-usually there are polar residues in actvie sites
-reactive fxnal groups
pKa values differ from free AAs
30
Acid-Base Catalysis
- Proton transfer catalyzes reaction
| - often talked about in terms of general acids and bases
31
Covalent Catalysis
-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
pH dependence of enzymes
- many have an optimal pH range
| - ionizible AAs are the main players in an enzymes active site
33
Diffusion controlled reactions
-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
Diffusion controlled: Triose Phosphate Isomerase
Interconversion of DHAP and G3P
| using glutamate and histidine that shuttle protons
35
Diffusion controlled: Superoxide Dismutase
degradation of superoxide
-has a Cu atom wit catalytic activity
able to be reduced and then oxidized
36
Binding modes of enzymatic catalysis
1. Proximity effect
correct position decreases entropy, increase in reaction
2. Transition State Stabilization
37
Substrates bind weakly to enzymes
- not too tight, otherwise get a thermodynamic pit
- coenzymes are held a bit more tightly
- formation of ES is slightly unfavorable
38
Induced fit
- not rigid structures, flexible
- shift from inactive to active conformations
- activation by substrate induced change is called INDUCED FIT
- example: hexokinase
39
Transition State Stabilization
- process of distorting or straining a substrate towards the reaction's transition state conformation
- lock and key mechanism
40
Transition State Analogs
- stable compounds whose structures resemble presumed transition states
- sit in active site of enzyme
- often potent inhibs
41
Trans State Analogs: Adenosine Deaminase Inhibs
enzyme recognizes the -OH at the C6 position binding to adenosine deaminase
42
Lysozyme
- 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
Serine Proteases
- 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
Chymotrypsin
three catalytic residues-- His 57, Asp 102, Ser 195
catalytic triad!!
Turns Ser 195 into a strong nucleophile
45
Enzymatic Cofactors
- assist in the catalytic process but aren't enzymes
| - Apoenzyme (inactive) and Holoenzyme (Apoenzyme and cofactor (active))
46
Essential Ions
1. needed for metal activated enzymes
K, Ca, Mg
2. metalloenzymes
Zn, Fe, Cu, Co
47
Metalloenzymes
Zn can turn water into a good nucelophile
| Iron-Sulfur clusters can accept a single electron
48
Coenzymes
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
Vitamin
1. water soluble (B vitamins, vitamin C, folate)
2. fat soluble (vitamin A, D, E, K)
excessive intake is toxic!
50
Adenosine Triphosphate
ATP is one of the most abundant coenzymes.
**Cosubstrate
*water
versatile reactant that can donate Pi, PPi AMP or adenosyl group
51
Nucleotide Cosubstrates
- S-adenosylmethionine is biological methylating agent
| - Uridine diphosphate glucose (UDP) glycosyl donor
52
Nicotinamide coenzymes
```
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
Flavin adenine dinucleotide and flavin mononucleotide
```
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
Coenzyme A
involved in acyl group transfers
* **Vitamin B5
* *Active region is the free --SH group (CoA--SH)
* *Cosubstrate
* water
55
Thiamine Pyrophosphate
* **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
Pyridoxal Phosphate
* **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
Transminase Mechanism
- PLP mechanism
| - catalysis comes from transaminase but product comes from active site or near it
58
Tetrahydrofolate
* **folate, (vitamin B2 or folic acid)
* *two amine groups
* *Cosubstrate
* water
- needed by enzymes that perform one carbon transfers
59
Cobalamin
* **Cobalamin (vitamin B12)
* *Co atom
* *Prosthetic group
* water soluble
- corrin ring structure and a hexavalent Co atom ion
- coenzyme
60
Lipoamide
* **lipodic acid
* *Double SH groups
* *Prosthetic
* water
- swinging arm transfers acyl groups
- SH ester friends
61
Vitamin A
- Beta carotene
* **retinol
* *Prosthetic
* lipid
- retinal--prosthetic group for rhodopsin that makes neural impulses
- -retinoic acid which is a signaling molecule
62
Vitamin D
- calciferols
* **Vitamin D3 formed in the skin when exposed to sunlight
* lipid
63
Vitamin E
- helps to scavenge free radicals and oxygen
* *phenol group is active
* lipid vitamin
64
Vitamin K
- Helps in formation of proteins for blood coagulation
* *hydroquinone is active
* lipid vitamin
65
Ubiquinone
- coenzyme Q
- lipid membranes
- strong oxidizing agent can accept either one or two electrons
66
Protein Coenzymes
-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
