Enzymes Flashcards
What are enzymes and what do they do
Biological catalysts (proteins) that increase rates of reactions without undergoing permanent change themselves (without being used up in the process)
Name the classes of enzymes
oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases
What do oxidoreducatses do? give an example
transfer of electrons (H+). Eg: alcohol dehydrogenase
What do transferases do? give example
transfer a functional group from one molecule to another. Eg: hexokinase
what do hydrolases do? give example
Break down a molecule using water. Eg: alkaline phosphate
what do lyases do? give example
add or remove groups without hydrolysis usually to double bonds. Eg: citrate lyase
what do isomerases do? give example
transfer of groups within molecules. Eg: phosphoglycerate mutase
what do ligases do? give example
join 2 substrates. Eg: pyruvate carboxylase
what is the most abundant enzyme in living organisms? and what class is it part of?
RuBisCO (lyase class)
What is an isoenzyme (isozyme)
different forms of the same enzyme within an organism, they catalyse the same reaction, have similar AA sequences and share a common evolutionary origin
What type of proteins are enzymes?
globular proteins, have hydrophobic internal residues, hydrophilic external residues.
what is the active site?
3D cleft where substrates are bound, usually extends to the internal hydrophobic pocket where the reaction occurs, contains catalytic groups that participate in the making and breaking of bonds
What are coenzymes/cofactors
Cofactors can be organic molecules (coenzymes - derived from vitamins weakly bound to the enzyme, can act as co-substrates and are converted into products) or inorganic metal ions. cofators/coenzymes that are tightly bound are called prosthetic groups
What is a vitamin
organic compounds essential for normal growth and nutrition that cannot be synthesized by the body. (many vitamins are precursors for coenzymes)
GIven vitamin (niacin) name: coenxyme - reaction catalysed - deficiency
NAD+, NADP+ - Oxidation - Pellagra
NADH, NADPH - Reduction
What is the international unit of enzyme activity
one I.U: amount of enzyme required to catalyse the conversion of 1umol of substrate (or product) per minute at 25C
What is special about enzymes (what makes them work well)
They work under mild conditions of temp and pH, they are highly specific for substrates and for reaction catalysed, have immense catalytic power (can increase reaction rates up to 10^12 fold), they can be regulated
What does the pH profile of an enzyme depend on?
charge state of enzyme and/pr substrate due to ionisation of amino acids or substrate, enzyme denaturation at extreme pH
what are thermophilic organisms?
enzymes that are very resistant to denaturation at high temp.
what temp range do psychrophiles like?
low temp <15C
what temp do mesophiles like?
midrange temperature
what is the lock and key hypothesis
large enzyme with active site (lock), small molecule substrate (key)
what is the induced-fit hypothesis
substrate binding results in conformational change in enzyme
what is transition state binding
enzyme active site binds subtrate but has greater affinity for the transition state intermediate in the reaction pathway - thus drives reaction
define absolute specificity and give example
the enzyme will catalyse only one reaction. eg: maltase only acts on maltose
define group specificity and give example
the enzyme will act only on molecules that have specific functional groups. eg: tyrosine kinase
define linkage specificity and give exmaple
the enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure. eg: amylase clease alpha 1-4 glycosidic bonds in starch
define sterochemical specificity and give example
the enzyme will act on a particualr steric or optical isomer. eg: D-amino acid oxidase acts only on D-amino acids
enzyme catalysis
enzymes increase rate of reaction by lowering the activation energy barrier. no change in overall thermodynamics. no change in enzyme (true catalyst)
what are the 6 ways enzymes achieve rate enhancement
1) proximity and orientation effects, 2) acid/base catalysis, 3) electrostatic interactions, 4) covalent catalysis, 5) transition state stabilisation, 6) metal ion catalysis
What is proximity and orientation
enzyme acts as a template to bring reactants close together and ina favourable orientation for reaction to occur (not a chance encounter between molecules in solution)
what is acid/base catalysis
side chain groups of some amino acids in active site can act as acids or bases by donating/accepting protons from substrates or intermediates OR one aa side chain acts as an acid and another as a base simultaneously to facilitate reaction (concerted acid-base catalysis)
what is covalent catalysis
amino acid side chains can react with substrate to form a covalent intermediate (usually nucleophilic attack on substrate C)
what is transition state binding
enzyme active site promotes formation of transition state intermediates. TS - highly unstable intermediates where bonds are made/broken
what are electrostatic/environment effects
enzyme active site excludes H2O - allows electrostatic stabilization of transition states through favourable charge distributions
what is metal ion catalysis
metal ion is held in place by specific residues (usually His). charge can stabilise intermediates and can polarize substrates to make them more reactive.
What is carbonic anhydrase important for
enzyme important for maintaining the pH of blood and other tissues. Found in RBC’s. The bicarbonate ion product is the major form of transport for CO2 in the blood. one of the fastest known enzymes
what is the mechanism of carbonic anhydrase
1) zinc polarises and deprotonates water generating a hydroxide ion, 2) CO2 substrate binds to the active site and it positioned for optimal interaction with -OH, 3) the hydroxide ion (nucleophile) attacks the carbonyl C of CO2, converting it to bicarbonate ion HCO3-, 4) enzyme is regenerated and the bicarbonate ion is released
what is lysozyme important for?
cleaves the polysaccharide in bacterial cell wall, binds 6 sugar units in a long active site cleft, cleaves the glycosidic bond between residues 4 and 5
what is enzyme kinetics
effect of substrate concentration on initial ratesof enzyme catalysed reactions
