Week 2 Enzymes Flashcards
Recap: Enzymes are biological catalysts
What does a catalyst do?
Increases the rate of a reaction, without being consumed by the reaction.
How does it do it?
By lowering the activation energy.
Burning” glucose for fuel: Cellular respiration
Enzymes in the body
Lots of digestive enzymes break down food.
Releases nutrients that make up our bodies and energy we need to exercise.
Enzymes catalyse just about every reaction that happens in cells.
Enzymes in industry and agriculture
Rennet is a mix of enzymes used in cheesemaking: Pepsin breaks down proteins, Chymosin curdles milk, Lipases break down fats
Invertase breaks down hard sugars into soft sugars – used to make soft-centred chocolates
Phytases added to animal feed make minerals more bioavailable.
What are enzymes and why are they necessary?
Enzymes are usually proteins and their activity depends on the integrity of their three-dimensional structure.
A denatured or dissociated enzyme usually won’t work.
Some enzymes require nothing other than their amino acids to function, but many enzymes require cofactors and/or coenzymes.
Uncatalysed reactions in biology tend to be slow—most biological molecules are quite stable in the neutral-pH, mild-temperature, aqueous environment inside cells.
Many biological reactions are chemically unfavourable so need enzymes.
Enzymes are usually much better (specific and efficient) than catalysts in chemistry.
If human enzymes don’t work properly it can lead to disease.
Ribozymes: RNA enzymes
RNA molecules can have complex tertiary structures and so can be catalytically active.
Example: Hammerhead ribozymes promote site- specific cleavage of RNA molecules.
The RNA world hypothesis: very early in the evolutionary history of life RNA acted as both a storage molecule for genetic information and a catalyst for reactions.
Not all enzymes exclusively use amino acid functional groups
Amino acids, with their various R-groups, can take part in lots of chemical reactions.
But some enzymes need extra molecules to function, these are often coenzymes and cofactors.
Cofactors: metal ions
Cofactors are extra molecules or ions that are needed for the activity of some enzymes.
Very commonly these are metal ions like Fe2+ or Zn2+.
They are often found in enzymes that catalyse redox reactions (recall that Oxidation is loss of electrons, Reduction is gain of electrons). They also affect bonding, and can have a structural role.
More complex organic cofactors are called coenzymes.
The Zn2+ cofactor in carboxypeptidase A stabilises negatively charged groups in the amino acids surrounding it.
Many metal ions are used as enzyme cofactors
Coenzymes
Coenzymes are complex organic molecules needed for enzyme function.
They are often derived from vitamins.
They often act as transient carriers for functional groups.
Nicotinamide Adenine Dinucleotide (NAD) is very commonly used in redox reactions: it carries a hydride ion (:H-) and exists in reduced (NADH) and oxidised (NAD+) forms.
Many types of coenzymes exist
Some enzymes need both a coenzyme and a metal cofactor
Example: Alcohol dehydrogenase
Prosthetic groups
Prosthetic groups (like haem) bind tightly or covalently to a protein, and act as structural elements. What we commonly call coenzymes bind more loosely. There are some inconsistencies in usage of the terms.
Cofactors-coenzymes. - prosthetic groups, cosubstrates
- metal ions.
Holoenzymes and apoenzymes
Apoenzyme. Coezyme =. Substrate
(Protein portion) + Cofactor Holoenzyme
Inactive (Nonprotein portion). Whole enzyme
Activator Active
Classifying enzymes
Many enzymes’ names end in –ase. E.g. urease breaks down urea.
Others have names derived from their roles. E.g. pepsin comes from the Greek word for digestion.
Some have several names or ambiguous names, so an international agreement has been made to sort enzymes into classes and sub-classes.
Enzymes have active sites
An enzyme-catalysed reaction takes place in a pocket of the enzyme called the active site.
A substrate molecule binds in the active site and is acted upon by the enzyme.
The surface of the active site is lined with amino acid residues that allow the substrate to bind and catalyse its chemical transformation.
Often, the active site encloses a substrate, sequestering it completely from solution.
Enzymatic reactions: Overview
A simple enzymatic reaction might be written:
E + S ⇌ ES ⇌ EP ⇌ E + P
Where E = enzyme, S = substrate, P = product.
Enzymes affect the rate of a reaction but do not affect its equilibrium. i.e.
They speed up the conversion of S→P they don’t make more P.
What’s important in enzymatic reactions is energy, in particular Gibbs Free Energy (G).
Recall: G = H – TS
(Gibbs free energy combines enthalpy, temperature and entropy).
Normally we compare the difference in free energy between systems, we write this as ΔG.
Energy in reactions (uncatalysed)
As reaction progresses substrates (S) are converted into products (P). This leads to a change in Gibbs free energy of the system (ΔG).
In reactions old bonds are broken (uses energy) and new bonds are formed (gives out energy), S and P are different energy levels.
The energy level of “resting” S or P is called the ground state.
There is an activation energy barrier (ΔG‡) to overcome before the reaction can occur.
The transition state (‡) is the activated form of the molecules at the top of the “energy hill”, at this precise point decay back to S or progress to P is equally likely.
The higher the activation energy, the slower the reaction.
Enzymes lower activation energy
In enzymatic reactions intermediates are introduced: Enzyme-substrate complex (ES) and enzyme-product complex (EP).
The activation energies required to produce these intermediates is lower and the transition state is at a lower energy level, so the rate of the reaction increases.
ΔG‡cat is lower than ΔG‡uncat.
Enzymes are not used up in the reaction, which is why we call them catalysts.
Enzyme activity is affected by pH
If an enzyme is outside its optimum pH range, the amino acid side-chains will be incorrectly ionised leading to loss of function.
Pepsin is an endopeptidase, it hydrolyses peptide bonds to break down proteins into smaller peptides. It is found in the stomach.
Glucose 6-phosphatase hydrolyses glucose 6-phosphate to produce glucose and free phosphate. It is found in the liver.
Cofactor
An inorganic ion or a coenzyme required for enzyme activity.
Coenzyme
An organic cofactor required for the action of certain enzymes; often has a vitamin component.
Prosthetic group
A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity.
Holoenzyme
A catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors.
Apoenzyme
The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.
Classifying enzymes
Many enzymes’ names end in –ase. E.g. urease breaks down urea.
Others have names derived from their roles. E.g. pepsin comes from the Greek word for digestion.
Some have several names or ambiguous names, so an international agreement has been made to sort enzymes into classes and sub-classes.
Enzymes have active sites
An enzyme-catalysed reaction takes place in a pocket of the enzyme called the active site.
A substrate molecule binds in the active site and is acted upon by the enzyme.
The surface of the active site is lined with amino acid residues that allow the substrate to bind and catalyse its chemical transformation.
Often, the active site encloses a substrate, sequestering it completely from solution.
Chymotrypsin is an example of an enzyme
Chymotrypsin is a protease that catalyses the hydrolysis of peptide bonds. It is specific for peptide bonds next to aromatic amino acids (Trp, Phe, Tyr).
Primary structure: 3 peptide chains linked by disulphide bridges. Important residues are highlighted.
Polypeptide backbone showing α-helices and β- sheets.n
Space-filling model. Binding pocket is yellow. Residues in active site are red.
Close-up of active site with substrate bound.
Enzymatic reactions: Overview
A simple enzymatic reaction might be written:
E + S ⇌ ES ⇌ EP ⇌ E + P
Where E = enzyme, S = substrate, P = product.
Enzymes affect the rate of a reaction but do not affect its equilibrium
. i.e. They speed up the conversion of S→P they don’t make more P.
What’s important in enzymatic reactions is energy, in particular Gibbs Free Energy (G).
Recall: G = H – TS
(Gibbs free energy combines enthalpy, temperature and entropy).
Normally we compare the difference in free energy between systems, we write this as ΔG.
Energy in reactions (uncatalysed)
As reaction progresses substrates (S) are converted into products (P). This leads to a change in Gibbs free energy of the system (ΔG).
In reactions old bonds are broken (uses energy) and new bonds are formed (gives out energy), S and P are different energy levels.
The energy level of “resting” S or P is called the ground state. There is an activation energy barrier (ΔG‡) to overcome before the reaction can occur.
The transition state (‡) is the activated form of the molecules at the top of the “energy hill”, at this precise point decay back to S or progress to P is equally likely.
The higher the activation energy, the slower the reaction.
Enzymes lower activation energy
In enzymatic reactions intermediates are introduced: Enzyme-substrate complex (ES) and enzyme-product complex (EP).
The activation energies required to produce these intermediates is lower and the transition state is at a lower energy level, so the rate of the reaction increases.
ΔG‡cat is lower than ΔG‡uncat.
Enzymes are not used up in the reaction, which is why we call them catalysts.
Enzyme activity is affected by pH
If an enzyme is outside its optimum pH range, the amino acid side-chains will be incorrectly ionised leading to loss of function.
Pepsin is an endopeptidase, it hydrolyses peptide bonds to break down proteins into smaller peptides. It is found in the stomach.
Glucose 6-phosphatase hydrolyses glucose 6-phosphate to produce glucose and free phosphate. It is found in the liver.
Cofactor
An inorganic ion or a coenzyme required for enzyme activity.
Coenzyme
An organic cofactor required for the action of certain enzymes; often has a vitamin component.
Prosthetic group
A metal ion or organic compound (other than an amino acid) covalently bound to a protein and essential to its activity.
Holoenzyme
A catalytically active enzyme, including all necessary subunits, prosthetic groups, and cofactors.
Apoenzyme
The protein portion of an enzyme, exclusive of any organic or inorganic cofactors or prosthetic groups that might be required for catalytic activity.
