Enzymes Flashcards
What are enzymes
biological catalysts
They increase the speed of specific chemical reactions
Not chemically changed by reation catalysed
Why are enzymes important
Because reactions like DNA synthesis, without enzymes, would take billions of years to occur
True or False?
The Majority of proteins are enzymes
True
But RNA enzymes also exist too
How can enzymes differ
In complexity e.g. how many subunits it has
How fast they operate
Where they are found
What reactions they catalyse
Enzymes have nomenclature
What do: oxidoreductase, transferase, hydrolase and lyase do?
Oxidise/reduce
Transfer chemical group
hydrolytic cleavage
Removal of a chemical group
Enzymes have nomenclature
What do: Isomerase, ligase and polymerase do?
Chemical rearrangement
Joining of two chemical
Polymer synthesis e.g. DNA
What is a substrate
The chemical that enzymes act upon
Substrate specificity is common, but doesn’t always occur
What is an Active site
A region of the ezymes that interact with the substrate
This close interaction allow the reaction to be sped up
Enzymes can bend, and have the ability to take on different configurations
Why is this an important characteristic of enzmes and how does it occur?
The tight, induced fit helps speed up the reaction
Charge on the active site, start to interact with charges on the substrate, and begin to pull electrons and bonds, which put the enzyme in an increased tension state. The likelihood of undergoing a reaction increases
Describe the enzyme cycle
- The substrate interacts with the active site of the enzyme, through diffusion and collision
- Once bound, the enzyme holds the substrate tighly, as the binding triggers a change in the enzyme conformation
- The bond between the two subunits begins to be put under tension and streched, causing the charges of the enzymes active site to act upon the charges in the substrate
- The enzyme is more likely to interact with water and split apart into its constituent pieces
- When it does so, the produces are released because the chemical configuration and balance of charges changes, which changes the configuration of the active site and the enzymes opens up
- The cycle can now begin again
Glucose is an important source of energy which the body breaks down using enzymes, without enzymes why would this reaction not at normal body temperature
Gluose has higher energy state, where it has more energy stored within it than in the products of carbon dioxide and water
The enzyme helps reduce this activation to go from gluose to its substituents
True or False?
Enzymes allow reaction to happen that would otherwise not occur
False
Most enzymic reaction can be done without enzymes
Reactions would happen without them, but slower
What is ‘inverting’ sugar and what are the two ways to do it
Hydrolysing polysaccharides and disaccharides into monosaccharides
Can be done through boiling or enzymatically
Industrially why would you use enzymes rather than boiling the invert sugar
Boiling: Easy, but energy expensive and industrially needs acid for effectivness
Enzymatic: Lower temperatures and doesn’t risk burning or colouring the sugar
Relating the the environment of where the enzymes are found, how can enzymes differ
Enzymes have optimal temperatures and pH ranges
This is because deviation from the optimum can affect the stability and speed of the enzyme
What is the issue with using enzymes as target drugs
They can be inhibited by other substrates
When using enzymes for certain drugs, what are the two ways they can be obtained
Human vs microbial protein in medical treatment
Sometimes recombinant enzymes can also be used
What is the benefit of using some enzymes in medical setting
They are extremely specific and can inhibit, or activate a certain reaction to occur
What are the benefits are using enzymes industrially
Allow reactions to occur at lower temperatures
Allow complex reactions to occur
Why may enzymes be used in the lab
To increase the sensetivity of assays
Copy and join pieces of DNA in PCR
Streptokinase is an enzymes which comes from a bacteria which acts as a clot-buster-dry
What is the issue with using it
As a foreign protein, it can induce immune reponse or allergy
Because of this, it has now largely been replaced by recombinant tPA (tissue plasminogen activator) which is a humanised enzyme product and is not recognised for foregin
Rennet is extracted from calves stomachs and is used to convert liquid milk to curds
What is the issue with this and how has it been overcome
Genetic modification of fungi allows production of vegetarian rennet - purified chymosin B
How have enzymes been used in cooking
Enzymes have been used to tenderise meats
What are biological washing agents
Enzymes which are added to help remove stains
Proteases, cellulases, amylases and lipases may be used
many are bacterial in origin
These enzymes are contains within a wax shell to protect them from the harsh environments before being put in the washing machine
Many drugs are enzyme inhibitors
There is two main classes: Reversible or irreversible
What is the difference between the two
Reversible - may be compete with substrate for active site, may also bind elsewhere and reduce function
Irreverisble - most covalently link to enzymes, often in/at active sites
Penicillin is an irreversible inhibitor
How does it work
Binds to bacterial transpeptidase active site and forms an ester linkage to the enzyme
Stops cross-linking of cell wall peptidoglycan
New cell wall is weak and fails, cell bursts
How have bacteria become resistant to penicillin
How can this be overcome
High-level resistance often is mediated by B-lactamases
These cleave the ring structure of penicillins
Clavuanic acids can enter the B-lactamase active site and covalently bond to it, it permently bond to the B-lactamase active site causing it to become inactivated
What is the issue with over or under expression of an enzyme
Can lead to cell dysfunction and disease
Hence enzymes are really important for the treatment and monitoring of diease
What is the substrate-binding site
Substrates bind to specific sites via interactions with the enzyme’s amino acids
Spatial geometry dictates specificity
What is the Active catalytic site
The region where the reaction occurs
Functional groups present include co-enzymes, metal ions, amino acid residues
What is the transition state
The high-energy intermediate which energy is need to form
Enzymes reduce the energy of this transition state
What are two ways to increase an enzymatically controlled reaction
Moving towards both optimum temperature and pH
How do enzymes affect equilibrium
Enzymes do not alter the position of equilibrium but rather accelerate its establishmentn
There is two models of substrate-binding
What are they and how do they differ?
Lock & Key: Complementary 3-D surfaces recognises the substrate, binds by forming bonds. Can be prevented by steric hinderance and charge repulsion
Induced fit: As substrate binds, the enzyme undergoes conformational change and side chains of amino acid active site reposition
What happens when the transition state complex forms in an enzymatic vs non-enzymatic system
Unstable high-energy complex with strained electronic configuration
‘activation energy’ of formation is reduced compared to the non-catalysed reaction
What happens once the transition state is formed
The transition state is the point at which bonds become maximally strained
It decomposes to products
Enzyme returns to its original form and can bind to new substrates
What is activation energy and how does it affect the overall rate of reaction
Activation energy is the difference between substrate and transition-state complex
The overall rate of reaction is determined by no. of molecules aquiring the activation energy
Enzymes decrease the activation energy
What are co-factos/co-enzymes
Needed for enzymes to work
Catalytic properties often dependent on non-peptide molecules
NAD+, NADP+, FAD
TIghly bound cofactors are know as prosthetic groups: Mg2+, Fe2+, Zn2+ (often to stabilise negative charges)
If a singular enzyme becomes non-function, why is this problematic on a larger scale
Some enzymes promote consecutive reactions in a metabolic pathway
Associate to form a multi-enzyme complex
What are the benefits of multi-enzyme complexes
Transit time via diffusion is reduced
Less interference: products are acted upon by correct enzyme
What are Isozymes
Enzymes can catalyse the same reactions as one another, even if the majority of their sequence differs, due to interactions being due to 3D spatial arrangement
They can catalyse the same reactions but will have different properties to them e.g. different speeds of conc of substrate
In terms of enzyme kinetics, what does the value of k stand for
For most enzymes, inital rate varies hyperbolically with substrate concentration for a fixed enzyme concentration
This is expressed through which graph and equation
Michaelis-Mention Equation
On the Michaelis-Menten curve, what happens as we approach Vmas on the curve
We seen zero order or saturation kinetics
You reach a level of substrate, where if you add anymore the enzymes will not increase anymore in speed
What is the benefit of knowing Km of an enzyme
In many cellular environments, the concentration of substrates present in that environment are in the vicinity of Km
Hence by tweaking the amount of substrate present, e.g. a decrease would lead to a significant decrease in speed of enzyme, however an increase would only lead to a minor increase is speed
Before the updating of modern computers, it was difficult to work out what Vmax was (hence what Km was) because the Michaelis-Menten curve is an asymptote
How was this overcome?
The equation for the curve, could be rearranged and linearised
The curve can be converted into a straight line graph (forming the Lineweaver-Burk plot)
How can you use the Lineweaver-Burk plot to work out Km and Vmax
How would the lines on the Michaelis-Menten and Lineweaver plot change if a reversible inhibitor is added
How is the Michaelis-Menten and Lineweaver-Burk plot affected by non-competitive inhibitors
How do uncompetitive inhibitors affect the Michaelis-Menten curve and the Lineweaver-Burk graphs
How can substrate act as inhibitors
The substrate of some enzymes can act as an uncompetitve inhibitor
At very high substrate concentrations, substrate binds to second non-catalytic site
Not all but large majority of allosteric enzymes have a property called cooperativity, what is it?
Usually, a homotrophic effector functions as a positive effector …
When a substrate binds to one subunit it can enhance the catalytic properties of the other subunits - ‘positive co-operativity’
However, the opposite can also occur and a reduction in catalytic properties of other subunits can also occur - ‘negative co-operativity’
What is the sequential model
When a allotrophic effector binds, you get not only one of the subunits changing into th R state, but another subunit will also change into the R state, then another subunit etc
The R-state will have an enhanced ability for binding the substrate
