C1.1 enzymes and metabolism Flashcards
what is this crap
what are enzymes?
Enzymes are catalytic proteins - speeding up a reaction without being consumed by the reaction
What is metabolism?
The complex network of interdependent and interacting chemical reactions in organisms.
examples of anabolic and catabolic reactions
Anabolic (Forms a product):
- formation of macromolecules from monomers by condensation. e.g. protein synthesis, glycogen formation, photosynthesis (ATP)
Catabolic (Breaks down reactants):
- hydrolysis of macromolecules into monomers. e.g. digestion, oxidation of substrates during respiration.
Describe the general structure of enzymes and their active sites
- globular proteins, where the specificity of the enzyme results from its amino acid sequence.
- active sites are composed of a few amino acids only, but the interaction btwn these amino acids and the overall 3-dimensional structure of the enzyme ensures that the active site has the properties needed for catalysis.
Describe induced-fit binding
- active site adjusts to fit shape of substrate
- substrate adjusts to fit shape of active site
The distortion of both enzyme and substrate:
- puts substrate into transition state = the change in shape of the substrate puts stress on its chemical bonds = bonds become destabilised, which favours rxns and increase rxn rates.
- better orients substrate for reaction
- chemical groups of the active site are brought into positions that enhance their ability to catalyse the rxn
- directly promotes catalytic events
Types of enzyme specificity + examples
Absolute: Catalyses one type of rxn for a single substrate
- Urease catalyses only the hydrolysis of urea
Group: Catalyses one type of rxn for similar substrates
- Hexokinase adds a phosphate group to hexoses
Linkage: Catalyses one type of rxn for a specific type of bond
- Chymotrypsin catalyses the hydrolysis of peptide bonds
Effect of enzymes on activation energy
Energy required to initiate a chemical rxn = activation energy (EA)
Enzymes lower EA, providing an alternate pathway for the rxn where less EA is required
What must happen for a rxn to occur? (substrate and enzyme)
The moving particles (substrate and enzyme) must have sufficient energy and the correct orientation when they collide.
More specifically, the enzyme must collide with the active site of the enzyme with sufficient energy
What factors affect rate of collisions/rxn rate in enzymes? (4)
- Temperature: as temperature increases = particles move faster = substrates more likely to collide with active site of the enzyme with sufficient energy
- Substrate conc: as substrate conc. increases, chances of substrate colliding with active site..
- Immobilisation of substrates: Large substrates, such as proteins or starch, can be immobilised for repeated hydrolysis to monomers
- Immobilisation of enzymes in membranes: Some enzymes are immobilised in membranes, keeping them in close proximity to the substrates it catalyses. The membrane also provides stability to the enzyme.
Describe denaturation of an enzyme due to changes in temperature and pH
Temperature: increase in temperature increases the kinetic energy of the enzyme, putting stress on the intramolecular bonds. The weaker ionic and hydrogen bonds break = shape of active site is lost = no longer functional
pH: change in pH alters the ionic charges of the acidic and basic r-groups of the amino acids in the active site, disrupting bonding = active site no longer functional
Differences between and examples of intracellular and extracellular enzyme-catalysed reactions
Intracellular (Glycolysis, Krebs cycle):
- enzymes for use inside the cell
- synthesised by free ribosomes in cytoplasm
- most enzymes needed for aerobic respiration produced in mitochondria, likewise for photosynthesis
Extracellular (Chemical digestion in gut by enzymes):
- enzymes for use outside of cell = released from cell and used outside
- synthesised by ribosomes attached to RER
- e.g. digestive system - exoenzymes catalyse the breakdown of larger macromolecules to monomers
Why is heat generation a consequence of metabolism?
Metabolic reactions are not 100% efficient energy transfer (products of metabolism have lower energy than reactants) = excess energy converted to heat
Endotherms (organisms that maintain body temperature at a metabolically favourable temperature, e.g. humans, polar bears) DEPEND on the release of heat from metabolic reactions to maintain body temp.
- excess heat requires mechanisms like sweating and evaporative cooling, shivering
Examples of linear and cyclical metabolic pathways
All chemical reactions in both linear and cyclical require specific enzymes
Linear:
Glycolysis
Cyclical:
Krebs cycle
Calvin cycle
HOW is ENZYME ACTIVITY regulated in a metabolic pathway? (3)
There would be chemical chaos if a mechanisms metabolic pathways were not tightly regulated.
- genes that encode for specific enzymes can be switched on/off by the cell
- Specific localisation of enzymes bring order to metabolic pathways.
- e.g. some enzymes act as structural components of membranes. In specific organelles, e.g. mitochondria, enzymes for cellular respiration are located. - Regulation and modification of co-factors (non-proteins, co-enzymes)
- Many enzymes require co-factors to carry out catalytic activity, such as for chemical processes like electron transfers which cannot be easily carried out by the amino acids of the enzyme.
Differences btwn competitive and non-competitive inhibition (4)
Competitive:
- binds to active site
- close structural resemblance to substrate
- Increasing substrate conc. lowers inhibition of rxn rate = at high substrate conc. effects of inhibitor are not observed
- Maximum rate of rxn can be achieved with high substrate conc.
Non-competitive:
- binds to allosteric site
- no structural resemblance to substrate
- Increasing substrate conc. does not affect inhibition of rxn rate = at high substrate conc. effects of inhibitor are still observed
- Maximum rate of rxn cannot be achieved
Describe non-competitive inhibition
- inhibitor binds to the allosteric site of the enzyme
- binding causes interactions within an enzyme which causes conformational changes = active site is altered, catalysis no longer possible
- binding is REVERSIBLE
Describe competitive inhibition, giving an example
- inhibitor binds REVERSIBLY to the active site, competing with the substrate
statins inhibit cholesterol production = used to treat high blood cholesterol - compete with the substrate HMG-CoA due to structural similarities
- binds to the active site of enzyme HMG-CoA reductase (which catalyses the rate-limiting step of the production of cholesterol in liver cells)
How does feedback inhibition regulate METABOLIC PATHWAYS? + 1 example
- the end product of the metabolism shuts down the pathway
- prevents a cell from wasting products by synthesising too much of what is needed
ISOLEUCINE (helps to make haemoglobin) PATHWAY:
- Initial substrate (threonine) binds to the enzyme 1 (threonine deaminase)
- goes through a chain of metabolic reactions
- isoleucine as the end product is produced
- isoleucine binds to the ALLOSTERIC site of enzyme 1 (threonine deaminase), switching off the pathway as the active site has changed shape.
Mechanism-based inhibition + 2 examples
- competitive inhibitors that PERMANENTLY COVALENTLY bond to the active site of an enzyme = creates a stable inhibitor-enzyme complex
- IRREVERSIBLE = substrate can no longer enter the active site
Heavy metals (e.g. mercury and lead):
- non-specific inhibitors that bind irreversibly to -SH groups in the amino acid cystine (involved in disulfide bridges) = very toxic to body, dangerous pollutants
Penicillin:
- binds to the active site of transpeptidases involved in the production of peptidoglycan cell walls of bacteria.
- prevents bacteria from forming cell walls
- However, the enzyme that breaks cross-links in the bacteria cell wall still continues functioning but transpeptidase enzyme can not work to reform these links = cell wall is weakened, bacteria lyses and dies.
IMPT: transpeptidase (and other bacteria) have evolved to have resistance against penicillin, where their active site no longer binds to penicillin
Why is non-competitive inhibition by binding to allosteric site reversible?
- When a non-competitive inhibitor binds to allosteric site, the bonds of the active site are “stressed” = alters its shape, stops catalytic activity
- When the non-competitive inhibitor releases from allosteric site, the bonds are not broken = stressed bonds return to their original positions and active site functions normally once again
