8b Flashcards
1
Q
what are enzymes
A
biological catalysts
theyre needed for biochemical processes
2
Q
how many amino acids make up an enzymes catalytic site
A
2-4 amino acids
3
Q
what are catalytic sites next to
A
theyre next to 1+ binding sites
4
Q
whats a binding site on an enzyme
A
where residues orient a substrate into its proper position
aka they position the substrate in the correct orientation
5
Q
the active site is made up of what
A
the catalytic and the binding site
6
Q
what is the active site
A
the place a substrate binds to
7
Q
okay so an enzyme has its active site made up of the binding and catalytic site but what is the rest of it
A
the remaining part of the enzymes serves to maintain the orientation and dynamics of the active site.
8
Q
what are cofactors
A
cofactors are extra chemical compounds that enzymes require for their activities
non protein compounds // metallic ions that enzymes require for their activity
9
Q
name the 2 types of cofactors
A
- co enzymes ( organic cofactors )
- metal ions ( inorganic cofactors)
10
Q
what are the diff types of coenzymes
A
- co substrate (transient bonding to benzyme)
- prosthetic group (permanently bound to enzyme + changes enzymes activity)
11
Q
name types of cosubstrates ,, aka coenzymes that bind to an enzyme temporarily
A
acetyl coenzyme A
ATP
12
Q
the transfer of a phosphate group needs what co factor
A
the metal ion Mg,, aka an inorganic cofactor
13
Q
Cu 2+ cofactor is used by what enzyme
A
cytochrome oxidase
14
Q
Mg2+ cofactor is used by what enzyme
A
glucose-6-phosphatase
15
Q
Zn 2+ cofactor is used by what enzyme
A
DNA polymerase
16
Q
what can the cofactor Zn2+ be displaces by
A
Hg2+ and Ca2+ bc theyre in the same periodic group
17
Q
what are coenzymes again
A
organic cofactors
either cosubstrates or prosthetic groups
18
Q
where are coenzymes normally derived from
A
theyre normally derived from vitamins
19
Q
what do coenzymes do to an enzyme
A
they bind to them reversibly by acting as substrates
20
Q
when a coenzyme is bound to an enzyme loosely,, what is it called
A
cosubstrate
21
Q
whats a holoenzyme // holoprotein
A
when u have the coenzyme x enxyme
coenzyme bound enzyme
22
Q
whats a coenzyme
A
a cofactor that is chemically changed by the enzymatic reactions and must returnn to its original state to complete the catalytic cycle.
22
Q
whats an apoenzyme // apoprotein
A
coenzyme unbound enzyme
23
Q
what is transaminase
A
an enzyme that is used to transport nitrogen
24
describe a apoenzyme and a coenzyme
the apoenzyme has the incorrect active site for the substrate
the coenzyme binds to the active site and changes it.
aka the coenzyme chnages the active site of the apoenzyme - it goes from being an inactive enzyme to an active one
25
name 2 coenzymes
TPP : thiamine pyrophosphate
PLP: pyridoxal phosphate
26
what does coenzyme,, tPP aka thiamine pyrophosphate do
it cleaves CC bonds
27
what does coenzyme PLP,, aka pyridoxal phosphate do
group transfer of amino acids
its the active form of b6.
28
b6 is a mix of how many compounds
its the mix of 3 different compounds
29
name the 3 compounds that make up b6,, and what coenzyme are these related to
thyere related to PLP : pyridoxal phsophate,, group transfer of amino acids
- pyridoxine: PN (OH)
- pyridoxal: PL (aldehyde)
- pyridoxamine: PM ( NH2 )
30
describe the main structure of the b6 coenzymes and how they differ
PLP : phosphate group,, aldehyde
PN = OH instead of phosphate and OH
PL: OH instead of phosphate and aldehyde
PM: OH instead of phosphate and NH2
31
once the vitamin b6 enters the cell what must occur
u must add a phosphate group to it,, this group is negatively charged and so are cell membranes
this means that the PLP remains in the cell!! its concentration is regulated
32
whats another cofactor of the transaminase enzyme
PLP
phosphate group and aldehyde
33
in PLP what are the
- aldehyde
- OH
- NH
- CH3
useful for
- aldehyde = key for binding to the enzyme
- OH = intermediate stabilisation
- NH = e- sink = stabilises all negative charge
- CH3 = hydrophobic ,, helps bind to the enzyme
34
how many of the 20 amino acids do human synthesise themselves
11 out of the 20 amino acids humans can synthesise themselves
the other 9 we must get from external sources such as our food
35
what can we do from some amino acids
we can recycle some amino acids from protein degradation using proteases
36
what are the 2 main problems u get from aa synthesis. clock that its amino acid synthesis and not protein synthesis
- we need a source of nitrogen for the amine group
- how do we make the alpha carbon the correct stereochemistry,, aka how do we form an L alpha carbon
37
how do we normally get nitrogen
- harbor process : aka from fertiliser to plants to animals to us
- bacteria call also fix N into NH3
38
whats the equation that nitrogen fixing bacteria do to get from N to NH3
N2 + 8e- + 16ATP + 16H2O --> 2NH3 + H2 + 16ADP + 16Pi + 8H+
39
okay so now that we have a source of nitrogen in the form of NH3 what do we do
we take alpha - ketoglutarate
and we attack the alpha ketone with the NH3 to form an imine,, we then reduce this using NADH
to form an amine at the alpha position.
this forms a glutamate!!!!
this process is called reductive amination
40
what enzyme is used when NH3 from the harbor process attacks the alpha keto glutarate and then undergoes reductive amination in order to form glutamate,, aka the same molecule but with a NH2 where the alpha keto was before
we use glutamate dehydrogenase
this is a stereoselective enzyme meaning it always makes L glutamate isomer!!!
41
what does glutamate dehydrogenase have a high affinity for
it has a high affinity to NH3
42
in plants and bacteria ,, what reaction is favoured,, the one going from alpha-keno-glutarate to glutamate
or glutamate to alpha-keto-glutarate
the one going to glutamate
aka the recutive amination reaction is favoured
however in animals both reactions can occur,, aka the synthesis of glutamate and its catabolism
43
what is the role of glutamate,, why is it so important
it has a key role in the synthesis of amino acids as its the source of N
bc we used NH3 from harbor process to attack the alpha keto-glutarate
to form glutamate ,, meaning theres an NH3 on the glutamate
via the transamination reaction!!! using transaminase enzyme
44
what dos transaminase do
it transports an amino group from the SM --> other molecules.
it can either make or degrade amino acids.
it catalyses the redistribution of 'N' between amino acids and corresponding oxoacids
45
what do we need to think about when we think of transaminase
think of an amine and a keto // aldehyde group on separate molecules
then think of these switching place
the direction of this reaction depends on the concentration of each molecule.
aka u have A-amino and B-keto//aldehyde <---> B-amino + A.keto//aldehyde
46
what does the enzyme that can either make or break amino acids need as a cofactor
it needs PLP!!!
it needs PLP in order to help it transport amin ogroups between diff molecules
PLP = pyridoxal phosphate
47
what is plp and what does it look like,, and what uses it
- PLP = pyridoxal phosphate
- coenzyme // cofactor
- phosphate, OH, aldehyde, CH3 substituent on a pyridine ring.
- transaminase needs it
- its used in the transfer of amino groups between diff molecules
48
okay so we have the glutamate with the COOH with NH2 on the adjacent carbon,, what happens when we use E-PLP on it.. and what is E-PLP
- E-PLP = enzyme - pyridoxal phosphate . that enzyme being transaminase.
we have the amine on the glutamate and when it reacts with E-PLP the haloenzyme transports the amine onto itself for a bit,, and forms a ketone where NH2 was on glutamate.
aka u had glutamate - NH2 AMINO DONOR and now u have glutamate- ketone ALPHA KETO ACID
and instead of the haloenzyme E-PLP u have E-PMP (pyridoxamine) aka u have the phosphate, NH2, OH, CH3
the top groups on the coenzyme switch places.
49
whats E-PMP used as
its used as a temporary carrier of NH2
50
amino donor + E-PLP --->
alpha keto 1 + E-PMP
51
once u form the alpha keto 1 and E-PMP what happens
another alpha keto comes,,, diff R group to the first one and this reacts with E-PMP
to form an amino acceptor,, aka its carbonyl accepts the NH2 from the E-PMP and forms E-PLP again!!!
the ketone and the amine switch again
52
okay give a summary of the transaminases reaction
amino donor (NH2) + E-PLP ---> alpha keto ( c=o ) + E-PMP
then E-PMP + alpha keto acid (c=o) --> amino acceptor (NH2) + E-PLP
the top groups keep switching with the coenzyme
53
what else does PLP react with
amino acids!! but when they're charged on the NH3 and COO-
and on the coenzyme u get an immine with the rest of the aa joined on where the aldehyde used to be!!!
transaminases then kives u an alpha keto again
54
how is PLP normally bound to a transaminase
its normally bound covalently to transaminase via forming an imine with a lysene side chain.
55
what is the lysine side chain
long hydrocarbon chain with NH2 at the end
56
how does PLP bind to the enzyme, transaminase using lyses
bc the NH2 at the end of lysine chain can attak the aldehyde and kick off water once the O is protonated twice to give an imine.
the separate OH on PLP then forms a H bond between its O and the H of NH immine snd this provides stabilisation of the imine cation
57
once u havr the immine formrmed when ureact PLP with lysene,, what happens
u react it with an amino acid
the NH2 of the amino acid attacks the C of the C=N of the imine PLP
then transimination occurs where the amino acid remains bound to the PLP,, so u have an imine and bound to the N of the imine is the R,H and COOH of the AA.
u also have lysine as a side product.
this is the new schiff base!! but its just a normal imine tbh.
58
once u have the PLP with the amino acid u reacted with it bound as the immine,, what do u do
the H of the AA is easiky removed
the NH+ at the bottom helps stabilise any (-) of the molecule.
so u deprotonate the H of the AA and resonate the e- onto the NH+ at the bottom.
u then use the lone pair of the N at the bottom and use this to protonate the imine double bond (C=N) OF THE CYCLIC STRUCTURE,, not the amino acid souble bond. aka u protonate the cofactor.
u then hydrolyse the amino acid imine by attacking it with a H2O.
this kicks off all the AA accept the N!! which remains on the cofactor. and forms PMP ( pyridoxamine phosphate )
the alpha keto leaves and then a new one joins!!
the PMP NH2 of the previous aa attacks the carbonyl of thr alpha ketone and then the reverse occurs to get back to PLP.
