Enzymes Flashcards
What are enzymes?
Proteins that catalyse specific chemical reactions
What functions are enzymes involved in?
Digestion, blood clotting, defence, movement, nerve conduction
List 5 properties of allosteric enzymes
They’re multisubunit complexes.
They have regulatory sites and catalytic sites on different subunits.
Regulation occurs via conformational changes.
They exhibit non-Michaelis-Menten kinetics- V vs S plots are sigmoidal.
They’re involved in feedback inhibition of metabolic pathways
Give an example of how an enzyme can be a drug target for antibiotic treatment
Penicillins inhibit cell wall synthesis by inhibiting the enzymes that make pentapeptide links
Give an example of how an enzyme can be a drug target for anti-inflammatory agents?
Aspirin blocks prostaglandin
Give an example of how an enzyme can be a drug target for anticancer drugs
Methotrexate is a folate analogue which interferes with synthesis of DNA precursors
Give the general 5 properties of enzymes
Increase reaction rate by up to 10 billion times
Enzymes show specificity
They remain unchanged at the end of the reaction
They do not alter reaction equilibrium
They facilitate reactions by decreasing free energy of activation of the reaction
What’s the name of the point of the reaction where free energy is highest?
The transition state
What are active sites?
3D cavities that bind substrates using electrostatic, hydrophobic, and hydrogen bonding and van Der Waal’s interactions.
What are 4 ways in which enzyme activity is regulated?
Control of gene expression
Compartmentation
Allosteric regulation
Covalent modification
What’s allosteric regulation of enzymes?
The regulation of an enzyme by binding an effector molecule at a site other than the active site, termed an allosteric site
What are the 2 types of allosteric regulators?
Allosteric inhibitors and allosteric activators
What is Michaelis constant?
KM is the substrate concentration where the rate is Vmax divided by 2, hence being where half the active sites are bound by substrate
What enzyme cleaves fructose 1,6-bisphosphate in glycolysis and what into?
Aldolase cleaves fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate
What converts dihydroxyacetone phosphate into glyceraldehyde 3-phosphate?
Triosephosphate isomerase (TIM)
Give a definition for a perfect enzyme
One for which the rate of the reaction it catalyses is limited by diffusion rate, not by the enzymes activity
What are the 4 categories of proteases?
Serine proteases, cysteine proteases, aspartyl proteases and metalloproteases
What allows serine proteases to function?
They have a very reactive serine amino acid which is able to directly participate in peptide bond hydrolysis
What are 3 important serine proteases?
Chymotrypsin, trypsin (pancreas) and elastase (lungs)
How does chymotrypsin affect peptide hydrolysis?
The very reactive serine attacks peptide bonds to form acyl-enzyme intermediates, which are much more prone to hydrolysis
What makes the serine amino acid so reactive in serine proteases?
There’s a catalytic triad of serine, histidine and aspartic acid in sequence. A proton is removed from the serine onto the histidine side chain, and then a proton on a nitrogen of the histidine can be moved away onto the negatively charged aspartic acid carboxyl group. This makes the serine oxygen very nucleophilic.
What amino acids does trypsin work specifically on?
Lysine and arginine
Why does trypsin work specifically on lysine and arginine?
Trypsin has a negatively charged pocket which accommodates the positive side chain of lysine and arginine, which gives tighter binding
What amino acids is chymotrypsin specific to?
Phenylalanine, tryptophan and tyrosine
Why is chymotrypsin specific to phenylalanine, tryptophan and tyrosine?
Chymotrypsin has a hydrophobic pocket that accommodates the aromatic, hydrophobic side chains of these amino acids
What amino acids is elastase specific to?
Amino acids with small side chains
Why is elastase specific to amino acids with small side chains?
Elastase has a narrow pocket
How are serine proteases structurally similar and different?
They have a conserved 3D structure with a charged-relay system, but their primary structures are very different, apart from the catalytic triad
How many active sites does rotary ATP synthase have?
3 active sites activated by a rotating spindle
How does ATP catalysis in mitochondria start?
ATP catalysis begins when protons pass through the part of the ATP synthase that lies in the cell membrane, causing it to turn. The central core of ATP synthase then rotates inside the top half of the enzyme. This region holds an ATP molecule and pulls in ADP and Pi. As the core rotates, the subunit with ATP loosens and the section holding ADP closes. The original ATP molecule is released, and a new one is formed from ADP. This cycle repeats.
What is topoisomerase II?
An enzyme that untangles chromosomes before they’re pulled to opposite poles of the cell in mitosis. It takes 2 interlocked DNAs and can make a transient double-stranded break in one of them to allow the other DNA chromosome to go through in an active process
Describe the mechanism of action of topoisomerase II in detail
Topoisomerase II is a dimeric clamp that binds the DNA from one of the chromosomes, called the gate (G-segment). Then in the presence of ATP, the clamp closes to capture the DNA from the other fragment, which is called the transported segment (T segment). This is an active trapping process. Once it’s trapped the DNA from the second chromosome, it passes it through a double-stranded break and out through the other side. The break is then resealed before another gate opens in the enzyme to free the chromosome out through the other side
