BIOL2220 Lecture 3 (coenzyme)

What is the difference between cofactors and allosteric modulators?

Cofactors bind to the active site or close to catalytic area for the chemical reaciton.
Allosteric modulators bind to the regulatory site that won’t involve in the chemical reaction

What are the major divion of cofactors?

Essential ions: metal ions that serve as cofactors

Coenzymes: orgnaic molecules that provide reactive groups not present on the active site

What are the types of essential ions?

1. One serve for metal-activated enzymes: Serve for enzymes that require stimulation of metal ions, which are loosely bound

2. One serve of metalloenzymes: serve for enzymes that contain metal ions that are firmly bound at their active site

Why we require some intake of trace elements?

metal-activated enzymes and metalloenzymes need metal ions as cofactors to run the chemical reactions

Why heavy metals are toxic?

They replace the essential ions in active site, reducing the activity of the enzymes.

What are the types of coenzymes?

1. Cosubstarte: loosely bound to active site. it will cheicamlly change after a reaction then being released. FInally regenerate to oringla state in another reaction

2. Prosthetic groups: Tightly bound to active site, even it is chemically changed during the reaction, it will regenrate to orginal state after the reaction is completed

Metabolite coenzymes and vitamins-dervied coenzymes are further divsion of cosbustrate and prosthetic groups.

How does ATP work as a cofactor?

It is a a coenzymes, more specifically, a metabolite cosubstrates.

It helps transfering Pyrophosphoryl group in different number : P, PP, even directly a AMP
E.g: It provide the sourves of Phosphyl group for hexose kinase, and regenerate from ADP with the help from pyruvate kinase and phosphoenolpyruvate)

Does regeneration of ATp in another reaction?

Yes, as it is a cosubstrate but not a prosthetic groups

How does SAM work as a cofactor?

it is a coenzyme, more speficifally, a metabolite cosubstrate

IT helps transfer of a methyl group that joined to a sulphur atom (SAM → SAH)

It can regenerated from SAH to SAM via methionine cycle

How does nucleotide sugar phosphates work as cofactor?

it is a coenzyme, more specifically, a metabolite cosubstrate

It helps a trasnfer of a glucose unit that links to a phosphate group of a nucleotide
e.g: UDp-glucose → UDP + glucose-substrate

It regenerates from UDP in 2 reactions:
1. UDP + ATP → UTP + ADP (with the help of NDP kinase)

2. UTP + glucose 1-phosphate → UDP-glucose + ppi (with the help of UDP-glucose pyrophosphorylase)

Why we need to obtain vitamins from our diet, while plants and microorganisms don’t?

We cannot synthesize vitamisn on our own, while plants and microorganisms can
Vitam can be structurally modified to become coenzymes that are crucial for the funcion of enzymes

How many Vitamin B-derived coenzymes are there from 1to12

only 8, B5, B8,B10,B11 can be synthesized by human, so they are no longer classified as vitamins

How does Vitamin b1 work as a cofacotr?

It will first be modifiend by adding 2 phosphate groups into Thiamine diphosphate (TDP)
Then it can be used as Vitamin B-derived Prosthetic group in coenzymes for carboxyl group transfer (N=C-H)

How Pyruvate decarboxylase and TDP works together?

The catalytic amino acid Enz-B: of pyruvate decarboxylase and TDP take part in the chemical change of pruvate to acetaldehyde. After that both of them returns to ther original states.

How does vitamin B2 work as a cofactor?

It will be modified by adding phosphate gorup and a nucleotide A / H to form FAD and FMN respectively
Then it can be used as a vitamin derived prosthetic groups of coenyzmes for redox reacitons

How E3 enzyme work with FAD?

E3 enzyme and FAD will bound tightly, then it help oxidize reactants by accepting hydrogen to form E3-FADH2

It can return to its oringal form by reacting with NAD+, This will prdouce E3-FAD, NADH, H+

How B3 vitamin work as a cofacotr?

iT first be modified by adding 2 nucleotide to form NAD+, if another phosphate gorup join, it will turn into NADP
Then, it can be used as vitamin derived cosubstrate of coeznyme for redox reaction

How B3 vitamin and b2 vitramin relates together as cofactor?

B3 vitamin’s cofacotr NAD+ helps regeranted E3-FADH2 into its original state E3-FAD, which is the cofactor of B2 vitamin

How NADH regenerate back to NAD+?

From the reaction E3-FADH2 + NAD+ → E3-FAD + NADH + H+
NADH + H+ + pyruvate → L-lactase + NAD+

How does vitamin B5 work as cofacotr?

It first be modified into coenzyme-A, The -SH group can be used to attach acyl group into Acetyl-CoA (H₃ - C-C=O)
Then it can be used as vitamin-derived cosubstrate of coenzyme for acyl group transfer

How Acetyl CoA help citrate synthase?

It bind to the substrate, connecting the acetly group and substrate. then water molecules comes, leaving citrate with a deprotonated carboxylic gorup and HS-CoA and proton from water.

HS-CoA can return back to acetyl-CoA by reacting with pyruvate and NAD+ to form acetyl-CoA, Co2 and NADH

How vitamin B6 work as cofactor?

Different forms of B6, but all with the Carbon ring, will be modified into PLP by adding phosphate gorup and amino group
This can be used as vitamin-dervied prosthetic group of coenzyme for amino group transfer (H2-N) By attaching it to the branched CH next othe O- arom

How cofacotr of B6 help transaminase that catalyze the transamination?

The cofactor is a prosthetic group in active site that bound to Lys. When an amino acid arrive the acitve site. Cofactor will take away the amine gorup from amino acid, turning it into Keto acid, and leave.

Then another Keto-acid arrive, The cofacotr transfer the amine group to it, and form a new amino acid

this is a ping-pong mechanism.

how vitamin B7 work as cofactor?

It is called biotin, it covalently linked to a lysine
Then it is a prosthetic goup for enzymes in carboxyl group trasnfer by using its NH in its biotin ring further away from hte lysine.

How cofacotr of vitamin B7 work with pyruvate carboxylase?

the cofactor will bind to the carboxyl group donor, bicarbonate with the NH in its biotin ring furhet awat from the lysin
When enol pyruvate arrives the active site, the cofactor trasnfer the carboxyl group (O-C=O) to it and forming a oxaloacetate, while the cofactor regenerate to its original form

How vitamin B9 work as cofactor?

It is modified into THF
then it can be used as cosubstrate for enzyme in transfer of 1-carbon units by using the N-H bonds that pointing to the same direction with the double bonded O in the rings (N5) , and the one next to the discrete ring (N10)

How THF helps the transfer of 1-carbon units?

It has different derivatives
1. carbon unit bind to N5 (methyl group CH3 donor)

2. carbon unit bind to N5 and N10 (methylene gorup CH2 donor )

3. carbon unit bind to N10 (formyl group O=C-H donor )

what is the characteristic of vitamin B12?

1. it is the largest B vitamin

2. It has a corrin iring with cobalt cation

How does Vitamin B12 work as cofacotr?

It will be modified by adding a different group to the cobalt cation in corrin ring.
If a CH3 join to the coblat, then coenzyme methylcobalamin is formed

If a large ring nucleotide join to the cobalt, then it is adenosylcobalamin

Both of the coenzyme are vitamin dervied prosthetic group for enzymes in methyl group transfer or intramolecular rearrangement.

How vitamin B9 and vitamin B12 work together for homocysteine methyltransferase?

B9: cosubstrate

B12: prosthetic gorup
enzyme bound tightly with the B12 cofactor cobalamin, Then 5-MTHF ( cofactor of B9 ) donate the methyl group to the E-Cobalamin complex. This form into

E-Methylcobalamin + THF

E-Methylcobalamin trasnfer the methyl group to the homoctsteine, forming E-Cobalamin back and a methionine

THF can return back to 5-MTHF in 2 steps by reactaing with serine acting as a methyl-donor. Forming 5-MTHF + glycine