topic 3 - enzymes Flashcards
how many amino acids do we have
~20
what do amino acids do
building blocks of proteins
encoded by genetics
what are amino acids made of
central carbon (alpha carbon)
carboxyl group (COO-)
amino group (H3N+)
R group
how do peptide bonds between amino acids form
dehydration reaction between 2 amino acids (new bond formed and water released)
where is peptide bond found
on backbone between a C double bonded to a O and N
what is a peptide made up of
backbone - same repeated pattern of atoms
N terminus and C terminus
variable R groups
how to tell if a R group is hydrophobic
lots of non polar bonds
when present on protein - they will be away from water on the inside of the protein
how to tell if a R group is hydrophilic
more polar covalent bonds
able to form bonds with water
when present on protein - they will face out towards water
some R groups have +/- charges and can form electrostatic interactions with each other
what is the difference between peptide, polypeptide, and protein
peptide = polymer (multiple) of amino acids
polypeptide = >10 amino acids joined together
protein = polypeptide folded into 3D shape
what is primary structure
sequence of amino acids in the polypeptide
what are the two types of secondary structure
helices and sheets
what are helices
stabilised by H bonds
each carbonyl group in the backbone forms a H bond with an amide 4 residues (amino acids) away
regular repeat of H bonds to stabilise the helix
what are sheets
adjacent strands can run in the saem direction or opposite direction (antiparallel)
H bonds can form between carbonyl groups in one polypeptide and amide groups in a different part of the polypeptide
main chain stabilised into sheets through H bonds
what is tertiary structure
secondary structure folded into the 3D protein shape
due to multiple levels of interaction between the R groups
shape is stabilised through H bonding, ionic interactions (+/- charged R groups), van der waals interactions, R groups with sulphur form covalent bonds (disulphide bond between cysteines)
what is quaternary structure
multiple polypeptides folded into 3D shapes (subunits) that interact with each other
gives the protein an overall shape and function
what is a subunit
has tertiary structure - within a protein
what is the difference between homotrimer and heterotrimer
homotrimer = 3 subunits with the same primary structure
heterotrimer = 3 subunits with different primary structure
what is the activation energy
energy barrier that must be overcame before the reaction can proceed
- energy destabilises the bonds in the reactants which allows (under the right conditions) for the formation of bonds that generate the products
what is the summit of activation energy
point where bonds in the reactants are breaking and bonds in the products are forming (transition state)
what are the ways to speed up a chemical reaction
- increase the temp so that reactants have more energy when they collide with each other
- increase the concen of the reactants so they collide with each other more often
- add a catalyst (enzyme = protein catalyst, ribozyme = RNA catalyst)
all decrease Ea
what effect does an enzyme have on delta G
no effect
- no change in delta G, just Ea
- can’t make an endergonic reaction exergonic
what is an enzyme
typically large molecule
made of 1+ polypeptide chains folded into a very specific 3D shape
shape determined by sequence of amino acids
what is the active site
region that interacts/binds with a specific substrate (reactant)
what is the induced fit model (interaction betwen active site and substrate)
- ES (enzyme-substrate) complex forces the reactants into the transition state (can change shape to help break bonds in the substrate)
- by forcing the transition state - enzyme reduces the need for as much Ea
- products are then released and enzyme shape returns to original (ready to bind with next substrate)
what does hexokinase do
catalyse a coupled reaction
(hydrolysed ATP and P is being transferred to glucose (in active site))
- speeds up a exergonic reaction (increases reaction rate)
how does an enzyme speed up a reaction
- bring reactant molecules close together in the correct orientation
- charge interations - expose reactants to charged environments
- physically distort or strain substrate molecules
what does the rate of an enzyme reaction (enzyme kinetics) depend on
temp
concen of substrate
pH
enzyme concen
how do cells control/regulate enzyme kinetics
change enzyme concen
increase concen of substrate
cells produce inhibitors / activators (small molecules that bind to enzyme to speed up or turn it off)
what is the relationship between enzyme concen and rate
linear relationship
what is the relationship between substrate concen and rate
non linear
- reaches saturation level and plateaus (when enzyme concen is constant)
- max velocity of reaction rate (Vmax)
what is denaturation
loss of protein structure
- can be partial (reversible) or complete (irreversible)
- caused by heat or pH
what is inactivation
loss of protein activity
- often due to denaturation
- can be reversible or irreversible
- highest activity at optimal temp (decrease on both sides of that temp)
what is reversible competitive inhibition
- inhibitor is chemically like the substrate
- non covalently binds to the enzyme at the active site (competes with the substrate to bind)
- molecules with the highest concen will outcompete the other
what is reversible non competitive inhibition
- inhibitor is not like the substrate
- inhibitor non covalently binds to the enzyme at a different point (away from active site)
- high concen of substrate will not outcompete the inhibitor
- max rate of enzyme reaction will be less than the inhibited rate of the reaction
what are allosteric activators
bind to the enzyme away from the active site which will change shape to a more active form
- stabilises the active form of the enzyme to increase activity
what are allosteric inhibitors
bind to the enzyme which will change shape to a less active form (bind away from active site) and decrease activity
- stabilises the inactive form of the enzyme
what is feedback inhibition
final product of a pathway inhibits an enzyme early in the pathway
