Enzymes Flashcards
What are enzymes for?
- Most reactions in biological systems don’t occur at observable rates unless enzymes are present
- Vital for cellular and body functions
- Most enzymes are proteins except for ribozymes (RNA)
- 25% of all genes code for enzymes
Describe enzyme nomenclature
- Suffix -ases to root name of substrate it acts upon
- Some enzymes discovered early also have common or tribial names
- Latest system is international enzyme commission (EC) system based on type of reaction catalysed
How do enzymes work?
- Increase reaction rates by factors of at least a million
- They do this by lowering the activation energy for a reaction
- Bring substrates/domains in favourable orientations into an enzyme substrate complex
- Anabolic: building of molecules
- Catabolic: breaking down substrate
What is the active site?
- Determines substrate binding- residues that participate in making/breaking bonds
- Substrates are bound by multiple weak attractions
- Specificity depends on precise arrangement of atoms in the site- non-polar residues
Describe the lock-and-key model of enzyme action
- Substrate fits enzyme
- Forms ES complex
- Highly specific
Describe the induced fit model of enzyme action
- Enzyme folds around substrate
- Breaks it down
- Enzyme returns to original shape
What evidence is there for the active site?
- At a constant conc. of enzyme, reaction rate increases with increasing substrate conc. until maximal velocity reached
- Occurs due to all catalytic sites being filled (Leanor Michaelis, 1913)- Vmax
What is the Vmax?
- The maximum velocity of enzyme reaction
- When the substrate concentration increases, there are no enzymes left
Describe the Michaelis-Menten plot
- Sub conc (x) against Reaction rate (y)
- Curve that is steep at first, then plateaus
V = Vmax[S]/ (Km+[S])
What is Km?
- A constant that is equal to [s] at half the Vmax
- Represents the most efficient substrate concentration at a specific enzyme concentration
What is the Lineweaver-Burke plot?
- Reciprocal of the Michaelis-Menten plot
- Kinetic
What types of catalysis are there?
- Metal ion catalysis
- Electrostatic catalysis
- Covalent catalysis
- Acid-base catalysis
Describe metal ion catalysis
Metal ion serves as an electrophilic catalyst (copper, zinc, iron)
Describe electrostatic catalysis
Active site residues or cofactor form ionic bonds with intermediate
Describe covalent catalysis
Active site residues or cofactor from transient covalent bond with the substrate to stabilise the intermediate
Describe acid-base catalysis
Active site contains chemicals which proton donors or acceptors
Describe mechanisms of enzyme regulation
- Feedback inhibition
- Gene expression controlling enzyme protein synthesis
- Proteolytic regulation through zymogen activation
- Cofactor binding
- Post-translational modification
- Substrate availability
- Control protein binding
Describe feedback regulation
- Downstream reaction products inhibit initial enzymic reaction
- Essential process or regulatory enzymes at the beginning of reaction series, TCA cycle enzymes such as pyruvate dehydrogenase are inhibited by NADH
- Enzyme pathway leads to final product that eventually inhibits original enzyme
Describe allosteric regulation
- ‘Other site’- i.e. binding at remote site affects normal substrate binding
- Saturation curve does not follow Michaelis-Menten characteristics, e.g. sigmoidal
- E.g. feedback regulation
- ATP allosteric inhibitor of pyruvate kinase during glycolysis
- Can be activating- allows substrate to bind
- Or inhibiting- prevents substrate binding
Describe enzyme regulation through synthesis
- Transcription/translation, e.g. methlyation
- Changes in total amount of enzyme
- Post-translational modifications
- Glycosylation, hydroxylation, sulphation
Describe proteolytic regulation
- Examples include pepsinogen conversion to pepsin in acidified gastric juice
- Protein cleavage
- Positive feedback
What are co-factors?
Many enzymes require co-factors ‘helper molecules’- non protein chemical compounds/metal ions
What are co-enzymes?
Soluble and may diffuse between different enzymes, i.e. ATP, NADH
What metal ions?
Often bound by dipole interactions with histidine and other amino acids with lone pairs, e.g. iron 2 in catalase
What are prosthetic groups?
Strongly bound to enzyme, either covalently or by other means, i.e. haem
Describe pharmacological interventions
- Many diseases result from enzyme mutations
- Leading to loss of enzyme activity- causing potential harmful effects
- Many drugs that alter enzyme activity improve health conditions
Give examples of diseases caused by enzyme mutations
- Niemann-Pick disease- sphingomyelinase deficiency- accumulation of unmetabolised sphingomyelin and cholesterol- lipid build up in organs- increased CVD risk
- Krabbe disease- galactosylceramidase deficiency- affect myelin- degeneration of motor skills
Describe non-specific inhibitors of enzyme activity
- Denaturing
- Extreme pH
- Heavy metals
- Heat
- Reducing agents
- Tightly bound to enzyme can be artificial/poison/suicide
Describe specific inhibitors of enzyme activity
- Competitive
- Reversible
- Uncompetitive
- Non-competitive
Describe irreversible inhibitors
- Often tightly bound to enzyme, either covalently or non-covalently, e.g. Thiol group inhibitors like iodoacetamide
- Often artificial
- Often posions
- Include ‘suicide’ inhibitors
Describe reversible inhibitors
- Rapid dissociation of enzyme/inhibitor complex
- Usually specific
- 3 major categories
- Comp, uncomp., non-comp.
What is the difference between non-competitive and uncompetitive?
- Non-comp binds allosterically to the enzyme equally well whether substrate is bound or not
- Uncomp binds allosterically to the ES complex and not the free enzyme
Give examples of inhibitor use
- Alcohol poisoning
- NSAIDs
Describe alcohol metabolism
- Alcohol dehydrogenase converts ethanol to acetaldehyde
- Aldehyde dehydrogenase converts acetaldehyde to acetic acid
- Both of these enzymes are oxidoreductases
