Lecture 13 - Introduction to enzyme function Flashcards
What is the basic role of an enzyme?
To catalyse the conversion of substrates into products
What is meant by ‘biological catalyst’?
Enzymes speed up reactions without undergoing any permanent chemical changes.
Why do enzymes not change the position of equilibrium of a reaction?
Increase the forward and backwards reactions by the same rate
Describe the basic enzyme catalytic cycle.
A substrate molecule will bind to the active site of the enzyme. This forms an enzyme-substrate complex. Catalysis occurs. We then have an enzyme product complex. The product is then released from the enzyme.
S+E ⇌ES ⇋EP ⇆P+E
Substate + enzyme -> enzyme substrate complex -> enzyme product complex -> product + enzyme
The shape of a substrate is specific to….
shape of active site
What are the two models of catalysis called?
- lock and key
- induced fit
Describe lock and key.
Lock and key- the substrate fits into the active site like a key fit into a lock. The shape of the substrate is complementary to the active site.
Describe the induced fit model
The induced fit model – there is a change in the shape of the active site of the enzyme induced by the substrate, so that the substrate fits perfectly into the active site. This is a highly specific binding interaction.
It is important for multi-substrate enzymes –> The first substrate binds, triggering a conformational change to the shape of the active site, allowing the second substrate to bind.
Most enzymes work by lowering …. . Describe.
Activation energy.
By lowering activation energy, a greater proportion of substrates have energy equal to/above the activation energy so a large proportion of the substrates react to form product
Basically, lower activation energy= rate of reaction increases
Describe a way in which enzymes will lower activation energy.
The enzymes bring the substrates and reacting groups close together- entropic effect and reacting groups are orientated correctly with respect to each other. By doing this, the activation energy is reduced
List some of the enzyme strategies/ things that enzymes do during catalysis
- Reacting bonds are stretched or bent
- Active sites are usually rich in hydrophobic residues- can change the pKa of charged amino-acid sidechains and substrate groups
- Bulk solvent- water- is excluded from enzyme active sites- charged groups are not masked
- Ordered water molecules often participate in the reaction
- Protons can be donated or accepted by active site groups- acid/base catalysis.
- Nucleophilic catalysis (acyl-enzyme intermediates)
- Enzymes are usually stereospecific (chiral environment)
What is a cofactor?
- without cofactors some enzymes are inactive.
- cofactors are often metals, such as metal ions like Mg2+
- Binding of a metal to an enzyme alters the enzyme’s conformation so that it can react with the substrate.
What are Cosubstrates/Coenzymes?
- Coenzymes are organic molecules which participate as one of the substrates in the reaction.
- Coenzymes transfer small groups of atoms from one substrate to another
- Atoms transfer to the coenzymes in the reaction, and then can be transferred from the coenzyme to another substrate with the aid of a second enzyme. This second reaction converts the coenzyme back to its original form- it is unchanged.
What reactions use coenzymes?
reactions whereby atoms are either removed from or added to a substrate
Where do coenzymes come from? Give two examples.
coenzymes are derived from vitamins and minerals. For example, NAD+ from niacin and Coenzyme A from Vitamin B3
How does decreasing degrees of freedom affect rate of reaction?
rate of reaction increases by decreasing degrees of freedom.
Enzymes will lock the substrate into a fixed position into the active site.
Hydrolase
splitting of compounds using water
Nuclease
hydrolases DNA or RNA
Protease
hydrolyses protein peptide bonds
Kinase
adds phosphate groups
Phosphatase
removes phosphate groups
ATPase
Degrades ATP
Polymerase
produces polymers such as DNA and RNA
Synthase
synthesis
Oxidoreductase
redox reaction typically using nucleotide cofactors
Isomerase
interconversion of isomers
What is an acyl group?
R-C=O
What is an acyl substitution reaction?
An acyl substitution reaction is a reaction that occurs when a nucleophile replaces a leaving group attached to an acyl group. The nucleophile stacks the carbonyl carbon of an acyl group, forming a tetrahedral intermediate and then the leaving group departs.
Draw the basic mechanism for an acyl-substitution reaction, where X is the leaving group and Y- is the intermediate.
What are poor leaving groups? They often require ………. to make them better
oxygen, ester, amides. Require protonation
An acyl substitution reaction does not occur for aldehydes or ketones. Why?
hydrogen atoms, alkyl groups and aryl groups cannot leave
Three steps of an acyl-substitution reaction involving enzymes.
- Activation of the active site nucleophile by deprotonation
- Acyl substitution occurs using active site nucleophile
- Acyl substitution by water to regenerate enzyme
Enzymes that use the acyl-substitution mechanism
- Serine proteases (chymotrypsin)
- Cysteine proteases (papain)
- Penicillinases and other B-lactamases
- Lipases
- Esterase and thioesterases
most enzymes reactions are simple…
carbonyl chemistry
Draw the mechanism for stage one of enzyme chymotrypsin in an acyl-substitution reaction.
- Activation of the nucleophile in the active site by deprotonation
Draw the mechanism for stage two of enzyme chymotrypsin in an acyl-substitution reaction.
- Formation of the acyl-enzyme intermediate
- The deprotonated nucleophile adds to the carbonyl group
- The tetrahedral intermediate is transiently formed
- Leaving group is protonated and leaves
Draw the mechanism for stage three of enzyme chymotrypsin in an acyl-substitution reaction.
- hydrolysis of the acyl-enzyme intermediate to regenerate the enzyme
- This time water is the nucleophile and the enzyme- O- is the leaving group.
