Enzyme structure and functioning Flashcards
What are enzymes?
Biological catalyst that lowers the activation energy
What kind of proteins are most enzymes?
Globular
What are all metabolic processes catalysed by?
Enzymes
Are enzymes specific catalysts?
Yes
What is the substrate?
The molecule or atom that an enzyme acts on
What is substrate transformed into?
Product
Why are biocatalysts better than inorganic catalysts?
More effective
Greater specificity (avoids side products)
Milder reaction conditions
Higher reaction rate
Capacity for regulation
Can active sites of enzymes recognise stereoisomers?
Yes
What do proteolytic enzymes do?
Catalyse the hydrolysis of peptides and also the hydrolysis of an ester bond
Do different enzymes have different degrees of specificity?
Yes they do
What are cofactors?
Small molecules that some enzymes require for activity
Two main classes of cofactors
Coenzymes (organic molecule derived from vitamin)
Metals
What are tightly bound coenzymes called?
Prosthetic group
What are holoenzymes?
Enzymes with its cofactor
What are apoenzymes?
Enzymes without its cofactor
Are there any disorders and deceases that are caused by deficiency of one enzyme or excessive activity of an enzyme?
Yes both
Can enzymes be used therapeutically?
Yes
Do many drugs act through interactions with enzymes
Yes
What are isoenzymes?
Same catalytic action and same name (like exokinese) but there are more variants (like I II III …) which are produced by different organs
6 major classes of enzymes
Oxidoreductases
Transferases
Hydrolases
Lyases (synthases)
Isomerases
Ligases (synthetases)
What do transferases do?
Transfer groups
What do hydrolyses do?
Use water to break proteins
What do lyases?
Fuse two molecules to form one molecule
What do isomerases do?
Transfer isomers, move groups
What are ligases?
Uses energy to fuse two molecules together
5 types of enzyme regulations
Allosteric regulation
Reversible covalent modifications
Proteolytic cleavage
Feedback regulation
Regulation by isoenzymes
What is the allosteric site?
Site that is different from the binding site
Can feedback regulation be positive or negative?
Both
Can allosteric regulation be positive or negative?
Both
What is the rate of enhancement?
How much the enzymes enhances the reaction compared to without the enzymes
Is the tertiary structure of a protein destabilised by the hydrophobic effect?
No
Where does the strength of alpha kreatin protein come from?
Cross-linking alpha helices by disulfide bonds
The motif in the glycolysis enzyme hexokinase could contain what?
Beta turn
Beta sheet
Alpha helix
Disulfide bonds
What feature is not associated with globular proteins?
Alpha and beta classification
What characteristics of protein is associated with proteostasis?
Synthesis
Refolding
Degradation
What does denaturing followed ny renaturing of a protein demonstrate?
That primary structure dictates tertiary structure
Are chaperones always required?
No
What does gibbs free energy provide information about?
Spontaneity and not the rate of reaction
What does the Gibbs free energy have to be for a reaction to occur?
Negative
What is a reaction called when the gibbs free energy is negative?
Exergonic reaction
What is Gibbs free energy when the reaction is at equilibrium?
0
What is a reaction called if Gibbs free energy is positive?
Endergonic reaction
Do enzymes affect the equilibrium?
No
Can enzymes effect the Gibbs free energy of a reaction?
No
What is the velocity of a reaction?
Product/time
Which has the highest activation state:
Product to substrate
or
Substrate to product
Product to substrate
What does enzymes do to lower the activation energy?
Organise the reactive groups into close proximity and proper orientation
What do enzyme bind best?
Transition states
Does speed matter when it comes to enzymes?
Yes speed matters a lot
What is binding energy?
Major source of free energy used by enzymes to lower the activation energies of reactions
Common features of active sites of enzymes
3d cleft or crevice created by AA from different parts of the primary structure
Active site constitutes a small portion of the enzyme volume
Unique microenvironment
Multiple weak interactions take place between enzyme and substrate
specificity depends on the molecular architecture at the active site
Does the specificity of an enzyme effect the rate of reaction?
Not necessarily
Is the ligand binding site and active site the same?
Yes, both connect with substrate and change into a product
The ligand binding site is a part of the active site
4 factors contributing to the barrier to reaction
Entropy of molecules in solution
Salvation shell of hydrogen bonded water
The distortion of substrates that must occur in many reaction
The need for proper alignment of catalytic functional group
What kind of energy can be used to overcome all the barriers contributing to the reaction barrier?
Binding energy
What is the desolvation of the substrate?
Removing of molecules surrounding substrate
What is acid-base catalysis?
Give and take protons
What is covalent catalysis?
Change reaction paths
What is metal ion catalysis?
Use redox cofactor, pKa, shifters
3 kinds of catalysis
Acid-base
Metal ion
Covalent
Are enzymes specific for a particular substrate?
Generally yes
Difference between number of products produced by an enzyme and a nonbiological catalyst
An enzymes yields a specific product where nonbiological catalyst may produce more than one product because of side reactions
Effects of enzymes on reaction
Activation energy lowered
Formation of transition state is promoted
Rate constant for reverse reaction increases
2 ways enzymes increase the rate of reaction
Lower the activation energy of the reaction
Promote the formation of a transition state
Difference between lock and key and induced fit model
In induced fit the conformation changes when the substrate binds where in lock and key the structure is rigid
2 things both the induced fit and lock and key model have in common
The substrate binds at the active site, forming an enzyme-substrate complex
The substrate binds to the enzyme through non covalent interactions
What inorganic ion does not serve as a cofactor?
Ca2+
What is an apoenzyme?
An enzyme that requires a cofactor for its activity
What is the inorganic ion called when it is very tightly or covalently bound by the enzyme?
A prosthetic group
Is polymerases one of the 7 EC classes of enzymes?
No
What is the free energy starting point for a reverse reaction designated as?
Ground state
Why is the conversion of sucrose to CO2 not spontaneous?
Because it has a very large activation energy barrier
What does an enzyme change relative to an uncatalyzed reaction?
The rate of the reaction
Can small changes in free energy lead to large changes in the equilibria?
Yes
What a reaction where the rate depends on the concentration of two molecules called?
Second-order reaction
Binding energy is defined as
The energy derived from non covalent enzyme-substrate interaction
What is the primary source of the energy enzymes used to reduce activation energies?
Noncovalent enzyme-substrate intercation
How does the induced fit mechanism of enzyme catalysis work?
The enzyme undergoes a conformational change to maximise weak interactions to the substrate
Which amino acid has the least effect on the function of an enzyme if it replaces a Glu residue in the enzyme?
Asp
True or false: does covalent catalysis by enzymes never involve coenzymes?
False
What does it mean that enzymes can be stereoselective?
They can be so elective they distinguish L-amino acids and D-amino acids
What do proteolytic enzymes catalyse?
The hydrolysis of peptide bonds
2 bonds proteases bread
Peptide bonds
Ester bonds
2 proteolytic enzymes
Trypsin
Thrombin
Do trypsin and thrombin have the same specificity?
No
During which state does the enzymes bind most tightly?
Transition state
Which amino acid residue is especially agressive in acid-base catalysis?
Serine
What does covalent catalysis require on the enzyme?
A nucleophile
Examples of nucleophiles used in covalent catalysis
Serine
Thiolate
Amine
Carboxylate
What is chymotrypsin?
A peptidase
Can one enzyme use multiple enzymatic mechanisms?
Yes
