E.4 Protein function and intro to enzymes Flashcards
name the different protein complexes in increasing order
monomer, dimer, trimer, tetramer, multimer
what are the two types of dimers?
homodimer (two identical monomers) and heterodimer (two different monomers)
what is a dimer and trimer?
dimer- complex made up of two protein monomers
trimer- complex formed from three molecules of a monomer
what is a tetramer and multimer?
tetramer- a protein made up of four subunits that are identical or similar
multimer- a protein molecule made up of two or more polypeptide chains, or monomers, that are linked together by covalent or non-covalent bonds
Haemoglobin function?
transports oxygen in the blood- erythrocytes. It is tetrameric (tetramer).
Myoglobin function?
stores oxygen in muscles- skeletal and cardiac
myoglobin is monomeric, what does that mean?
a molecule that can react with other monomer molecules to form a larger polymer chain
structure of myoglobin?
single polypeptide chain of 153 amino acids folded forming 8 alpha helixes
structure of haemoglobin?
4 polypeptide chains- 2 alpha chains of 141 amino acids, 2 beta chains of 146 amino acids; each chain folds to form 8 alpha helixes
similarities between structure of haemoglobin and myoglobin?
-both have haem prosthetic group- protoporphyrin IX, with central Fe2+ atom. This is where oxygen binds.
-3D structure of polypeptide chains are very similar
Describe the bonding of oxygen to haemoglobin
cooperative: binding to one subunit causes a conformational change from a tense (T) to relaxed state (R) and increases ease of binding of oxygen to the other subunits – this is called allostery; Haemoglobin is an allosteric protein (protein which changes shape due to binding)
Does myoglobin or haemoglobin have a higher affinity for binding with oxygen?
Myoglobin as haemoglobin binds oxygen in the lungs and releases it in the capillaries and to myoglobin in the muscle for storage.
Describe the conformational change when oxygen binds to the haem group in haemoglobin
-oxygen binding pulls the Fe2+ into the haem plane (without oxygen, Fe2+ is out of plane)
-oxygen binding also pulls histidine F8 ligand and F helix.
How does haemoglobin lower its affinity for oxygen when blood enters the tissues? (bohr effect)
-CO2 produced by metabolism in tissues is converted into carbonic acid catalysed by carbonic anhydrase
-dissociation of carbonic acid produces protons which react with amino acids in haemoglobin causing conformational changes that promote the release of oxygen
what are the different functions of proteins?
-structural proteins for cytoskeleton
-transport and store molecules
-enzymes catalyse biochemical reactions
-membrane transport proteins for ions and molecules
-regulatory and signalling proteins to control activities of other proteins and coordinate cellular responses
-motor proteins move intracellular complexes
are all enzymes proteins?
most but some are RNA (e.g peptidyl transferase involved in protein synthesis on ribosomes)
Describe enzymes
-lower the energy of the transition state of a chemical reaction
-works under physiological conditions
-highly specifics
-active site can use functional groups, coenzymes or metal ions
what is a transition state?
an unstable chemical form, part- way between substrate and product. It has the highest free energy in reaction pathway
What is Gibbs free energy of activation?
difference in free energy between the substrate and transition state. triangleG‡
How does an enzyme increase rate of reaction?
stabilises the transition state and lowers gibbs free energy of activation
(Entropy, Orientation, Distortion, Solvation)
Describe the Michaelis-Menten kinetics or saturation kinetics model
-Initial substrate, [S] and enzyme [E] concentrations are known
-all these sites may be occupied by substrates - the enzyme is saturated
-A plot of V against [S] gives a hyperbolic curve
Describe saturation kinetics
-Enzyme combines with substrate to form enzyme- substrate complex
-The E-S complex can dissociate again to form E+S OR form E and the product P
what is Vmax and Km?
Vmax = the maximum reaction rate (represents when reaction is saturated, all in E-S state)
Km= substrate concentration where V= Vmax/ 2
describe the michaelis- menten equation?
V0 = Vmax [S] /Km +[S]
-At low [S], a doubling of [S] will lead to a doubling of initial velocity V0 - linearly proportional
the lower the Km…
the higher the affinity of the enzyme for the substrate
Describe the Lineweaver-Burk plots (to linearize Michaelis-Menten)
-The reciprocal of both sides of the Michaelis-Menten equation generates an equation that has the form of straight line (y = mx + c)
-y=I/V0; m=Km/Vmax; x=1/[S]; c=1/Vmax
(more info on one note)
what are the varied ways in which an enzyme lowers activation energy and achieves transition state intermediates
-Acid –Base (proton donation/abstraction)
* Temporary covalent bond formation
* Redox effects
* Electrostatic effects
* Orientation/proximity effects and straining effects.
what are cofactors
non-protein molecules that are required for a reaction to take place in addition to the enzyme and substrate. can be organic or inorganic.
what are coenzymes
cofactors that bind loosely and are chemically altered by the enzyme. They are recycled for participating in the same reaction
what is a apoenzyme
enzyme without cofactor
what is holoenzyme
enzyme with cofactor
where do we get our cofactors?
minerals and vitamins
what ways can enzyme activity be regulated?
-competitive inhibition (reversible or irreversible)
-covalent modification
-allosteric regulation
-Rate slows as product accumulates
-Rate depends on substrate availability
-Genetic controls - induction and repression of the enzyme
-Zymogens, isozymes and modulator proteins may play a role
Explain covalent modification as a way of regulating enzyme activity
-chemical modification of amino acid residues which can lead to an increase or decrease of enzyme activity
-common type of normal cellular regulation
-some drugs work this way
Describe allosteric regulation of enzyme activity
-non covalent binding away from active site which causes conformational change leading to increase or decrease of enzyme activity
why are enzymes common drug targets?
they affect large numbers of substrate molecules; small changes in enzyme activity leads to large change in product concentration
what is used to treat HIV/AIDS
Anti-retroviral protease inhibitors
what do statins do
inhibit enzymes involved in cholestrol metabolism
what do non-steroidal anti-inflammatory drugs (NSAIDs) do?
modulate pain and inflammation by inhibiting cyclooxygenases
what do antibiotics do
block enzymes involved in assembling the bacterial cell wall
how are potential drug targets identified
- By studying the mechanism of action of existing drugs
- By studying the differences between diseased and normal cells or organisms
- By finding mutations that make normal cells like disease cells or the other way around
