Enzymes Flashcards
1
Q
Oxidoreductases
A
- Transfer of electrons, changes oxidation state of atoms
- donor is oxidized
- acceptor is reduced
- systematic name: e- donor: e- acceptor oxidoreductase
2
Q
Transferases
A
- Transfer of functional group from one molecule to another
- kinases are a common type of this enzyme
- systematic name: original compound + functional group + transferase
3
Q
Hydrolases
A
- Breakdown of substrate into two products using water
- single bond cleavage using water (hydrolysis)
- systematic name: compound + hydrolase
4
Q
Lyases
A
- removal of a group to form a double bond
- doesn’t use water and there are no change in e-s
- systematic name: 2-phosphoglycerate lyase
5
Q
Ligases
A
- forms one product from two substrates
- systematic name: compound 1 + compound 2 + ligase
6
Q
Isomerases
A
- intramolecular rearrangement changes within a single molecule
- systematic name: compound + isomerase
7
Q
Proximity and orientation
A
- all enzymes use proximity and orientation to work efficiently
- proximity mechanic: refers to the crowding of two substrates into an active site - in an active site, the collision space decreases and enzyme helps thermodynamic stability
- orientation mechanic: enzymes have active sites that optimize the orientation of reacting molecules relative to one another
8
Q
Preferential binding to transition state
A
- an enzyme’s job is to stabilize the transition state, but also induces strain to substrate to ensure that the reaction continues progressing
9
Q
Acid catalysis
A
- active site have residues that can transfer hydrogen ions
- residue donates a proton which stabilizes good leaving groups
10
Q
Base catalysis
A
- residue grabs a proton which increases nucelophilicity (increasing the ability for the group to make an attack)
11
Q
Covalent catalysis
A
- residue in the active site can often form temporary covalent bonds with the substrate
- the intermediate is a new molecule
- and the temporary bond will be broken to regenerate enzyme
12
Q
Electrostatic catalysis
A
- active site can use charged residues to stabilize the transition state (any non-covalent interaction)
- most direct implications for the primary sequence
13
Q
Metal-ion catalysis
A
- cations in an enzyme called cofactors help hold onto the substrate or assist in catalysis
14
Q
Catalytic Triad
A
- ****Base - His or Lys******: deprotonates nucleophile to increase it’s strength
- **********Acid - Asp or Glu**********: stabilizes positive charge on base and aligns it
- ************Nucleophile - Ser, Cys, or Thr************: attacks electrophile
- Many species’ enzymes involve this triad even if they have no evolutionary relationship → convergent evolution
15
Q
What are the three assumptions needed for Michaelis-Menten Kinetics
A
- The formation of product is rate limiting
- [ES] is held at steady state
- P approximately equal to 0, so there is no P → ES reaction
- When analyzing enzymatic reactions with Michaelis-Menten equations we have to use initial equations since we need the initial velocity of product formation before any significant quantity being formed.
- **Initial velocities are the only accurate ones under the michaelis menten curves**
15
Q
What is Km, Vmax, Kcat, catalytic efficiency? How do they all relate?
A
- Km = [S] at 1/2 Vmax
- the degree of attraction of substrate to active site → **lower Km, higher attraction****
- Vmax= the rate of reaction at which the** enzyme is full saturated (enzyme → ES rate)**
- kcat (turnover number)= the maximal number of molecules of substrate that can be converted into product (ES → product rate)
- kcat = Vmax/[Etot]
- Vmax divided by total concentration of enzyme
- catalytic efficiency = how able the enzme is to take substrate and produce product quickly
- cat eff = kcat/km
16
Q
How do you read the lineweaver plot?
A
- Y-intercept: 1/Vmax
- X-intercept:1/Km
- X-axis:1/S
- Y-axis:1/V0
- slope = Km/Vmax
- Finding Vmax and Km from a lineweaver burke plot is fairly easy. The larger the vmax, the lower the y-intercept. The larger the km, the closer Km is to 0.
- given two points for the lines, convert [S] → 1/S and V0 → 1/V0. Then solve for the slope and find the x and y intercepts
17
Q
Competitive Inhibitor
A
- Binds only to free enzyme in active side
- Increases Km, leaves Vmax unaffected
- Examples: transition state analogs and substrate analogs - similar structurals features to substrate
18
Q
Noncompetitive Inhibitor
A
- Allosteric
- Binds equally to free enzyme and enzyme-substrate complex
- leaves Km unaffected, decreases Vmax
19
Q
Mixed Inhibitor
A
- Allosteric
- Binds to free enzyme and enzyme-substrate complex
- either decreases or increases Km, decreases Vmax
20
Q
Uncompetitive Inhibitor
A
- Allosteric
- Binds to enzyme-substrate complex only
- decreases Km and Vmax at a constant ratio
21
Q
Irreversible inhibitors
A
- binds to enzyme creating a permanent change so that enzyme can never regenerate
- binds covalently to important functional group on enzyme
- causes chemical change to functional group in enzyme
- form a strong non-covalent association
22
Q
Constitutive, inducible, repressible
A
- constitutive: always present at some level (glycolysis enzyme)
- inducible: absent until a specific environmental signal is triggered
- repressible: enzyme is consistently present until a specific environmental signal is triggered
23
Q
Two methods of control for enzyme availability
A
- control of gene expression in the enzyme (constitutive, inducible, repressible)
- Control of enzyme degradation (ubiquitin)
24
Q
Ubiquitin
A
- signal for degradation and help attach to target molecule
- extremely well conserved
25
Q
What are the three enzymes used with ubiquitin
A
- E1: activates ubiquitin by attaching itself onto ubiquitin and transfers it to E2
- E2: works with E3 to catalyze the addition of ubiquitin to target protein
- E3: recognizes degrons (protein motif) on target protein
26
Q
E3 and Degron Tag
A
- E3 substrate binding: binds to degron tag
- E2 binding site of E3: binds to E2 with ubiquitin
- Degron can be inherently embedded within the protein sequence or added post-translationally
27
Q
Proteosome
A
- large and highly conserved protein that attaches to polyubiquitin tail and degrades target protein
28
Q
Two methods of catalytic control
A
- covalent modification: reversible and irreversible
- non-covalent modification
29
Q
Zymogen
A
- inactive precursor of enzyme
- activated by proteolytic cleavage
- autocatalytic or induced by another enzyme
- only activated in specific environments as the cell doesn’t want to chew up other parts of the body
30
Q
Phosphorylation
A
- post-transcriptional modification
- kinases: attaches phosphoryl group
- phosphatases: removes phosphoryl group
- requires hydroyl group attaches to serine, theronine, and tyrosine
- charged bulky group causes significant electrostatic properties and conformational changes to increase or decrease catalytic efficiency
- having more than one phophorylation sites: allows for fine tuning of expression and different kinases can act on one protein
31
Q
Allosteric regulation
A
- ****homotropic:**** substrate regulates function
- ****heterotropic****: different molecule other than substrate regulates function
- ****positive****: increases activity
- ****negative:****** decreases activity
