Enzymes 1 Flashcards
What are enzymes and why are they important?
what do they do?
various functions in human body? (5)
what are enzymes named after?
They speed up reactions
They are proteins that catalyze chemical reactions
They have various functions in the human body:
• digestion: carbohydrates, fats, proteins
• blood clotting: fibrin clot catalysed by thrombin
• defence: immune system, activation of complement
• movement: muscle actomyosin is an ATPase
• nerve conduction: membrane ion pumps for Na+, Ca2+
Each enzyme catalyzes a specific type of reaction
They are named after the type of reaction they catalyze
• nuclease: break down nucleic acids
• protease: break down proteins
• polymerase: put things together
• kinase: transfer phosphate groups
Enzymes - intracellular or secreted?
Enzymes can be intracellular (made in the cell and kept inside) or secreted (into lumen of intestine for example).
In general they catalyse a particular type of reaction. The type of reaction the enzyme catalyses is used to name the enzyme e.g. nucleases (breaks down nucleic acids), proteases (break down proteins), polymerases (put things together), kinases (transfer phosphate group)
Enzymes defects cause diseases
examples
phenylketunoria?
glycogen storage disease?
Tay-Sachs disease?
Enzyme defects can cause diseases
• phenylketunoria
- children cannot convert Phe to Tyr
- Phe gets converted to a toxic for the brain
- treatment is a low Phe diet
• glycogen storage disease
- unable to mobilize glycogen in liver
- difficulty in maintaining blood glucose levels
• Tay-Sachs disease
- membrane cerebroside
- it is a lipid disease
- inability to synthesize membrane lipids
Enzymes are drug targets
antibiotics? role? example?
anti inflammatory drugs? role? example?
anti cancer drugs? role? example?
• antibiotics
- block enzymes that produce cell walls eg penicillin
• anti inflammatory drugs
- inhibits prostaglandin eg aspirin
- prostaglandin is an important part of the inflammatory response
• anti cancer drugs
- methotrexate is a folic acid analog
- it acts as a competitive inhibitor to enzymes that use folic acid
- folic acid is converted to a co enzyme dihydrofolatereductase
- this co enzyme makes bases for DNA synthesis
- competitive inhibition by methotrexate reduces production of bases
Key Enzyme Properties (5)
what does free energy of activatio need to be? substrate vs product? what does enzyme do?
• Increase reaction rate by up to 10 billion fold!
• Show specificity
• Unchanged at end of reaction
• Do not alter reaction equilibrium
• Facilitate reaction by decreasing the free energy of
activation of the reaction (lowers activation energy)
• free energy of activation needs to be negative for a
reaction to be feasible
- the energy level of the product should be less than
the substrate
• this activation energy needs to be reduced so the
reaction can happen in the body
• enzymes reduce this free energy of activation
Free energy substrate + product graph
why is action feasible? how?
what needs to be put in? how does enzymes help?
Here it can be seen an enzyme reaction, the progress of a substrate to its product.
The substrate has a higher free energy than the product, so it releases free energy, which makes it favourable reaction.
However not all reactions will occur without enzymes even if there is release of energy, as first free energy has to be put in, free energy of activation (to get it to transition state). I
f this free energy of activation is reduced, the barrier the reaction has to get over is less. So enzymes reduce this free energy of activation. It is this way they catalyse the reaction.
How do enzymes reduce this free energy of activation?
what do enzymes have? what are they and what do they do?
- Enzymes have active sites
- These are 3-D cavities or clefts that bind substrate(s) using electrostatic, hydrophobic, hydrogen bonding and Van der Waals interactions
- Substrate binds to enzyme
- This binding energy is enough to distort and break substrate bonds reducing free energy of activation
X-ray Crystallography
what do you do to pure protein?
what is done to it and taken where?
what happens and recorded?
This has given evidence for active sites on enzymes
The process is as follows:
• enough pure protein is crystalized
• crystal is frozen in a wire loop
• it is taken to a synchrotron where it loses energy
• high intensity x-rays are produced
• beam of x-rays shot onto the crystal (wavelength of x-rays = average C-H bond)
• diffraction pattern is produced
Enzyme Models
what are the 2 models?
describe the both and which one enzymes work mostly like?
There are two main theories on how enzymes work
• lock and key
- the enzyme has a shape that is a direct complement to the shape of the active site
- most enzymes do not work in this way
• induced fit
- as the substrate binds, enzyme begins to change shape to something thats complementary to the shape of the substrate
- most enzymes work this way
How is substrate binding energy used to catalyze a reaction
what is approximation?
what does the binding energy do? (2)
what does the enzyme do in the transition state?
why does the enzyme eliminate water?
what does the enzyme do to lower free energy more?
how does enzyme use stress of binding to its adv?
example lysosyme - how does it break down cell wall? where does it strain bond? number?
• Enzymes bring substrates very close to each other
brings molecules together at the active site
this is called approximation
• The binding energy constrains the movement of the substrate
this stops the substrates from moving around and rotating too much
they are also aligned in a way they can react optimally
• Enzymes stabilize positive and negative charges in the transition state
the enzyme has residues that neutralize these charges
• Enzymes close over the substrate and eliminates water
making the reaction hydrophobic increases the reaction rate
• Enzymes break the reaction up into smaller steps
they use different pathways with lower free energy of activation
• Enzymes strain particular bonds in the substrate, making breakage easier.
the enzyme can use the stress of binding the substrate to break particular critical bonds
• reducing the free energy of activation
• the substrate is distorted to resemble the transition state
• eg lysozyme
- recognizes polysaccharides on bacterial cell wall
- hydrolizes cell wall, weakening the cell wall, bacteria pops open
- it has a crevice on the enzyme which binds 6 sugars, and changes the 4th sugar, straining the bond and making it susceptible to water
• Enzymes use co-factors to bring a different chemistry to the reaction
Enzyme Kinetics
what is recorded?
what is the label ofr the graph?
what is Km?
what does lower Km mean?
what is Vmax?
• This has also given proof for existence of active sites
• Purified enzyme is taken
• There is an increasing amount of substrate
concentration in a number of tubes
• Same amount of enzyme is added to the tubes
• Rate of the reaction is calculated
Rate against [S] is plotted
• Km is the Michaelis constant
- it tells how sticky relative substrates are
- the binding affinity of the enzyme
- lower the Km, tighter the binding of the substrate
• Vmax is the maximum possible velocity when all the
active sites are occupied
• The graph levels off at higher substrate levels
showing that active sites are a limiting factor
Vmax
The Vmax is the maximum possible velocity when all active sites are occupied
Vmax/2
Vmax/2 is half the max velocity when half of the active sites are occupied
Km
Km is the amount of substrate you would have to put in to half saturate the active site (tells you about the binding affinity of the enzyme)
Turnover number
what does it giv?
Turnover number = Vmax / [enz]total = Gives the turnover of a single enzyme when it is working full out.
