Principles of Structural and Cell Biochemistry

8/6/2019 Principles of Structural and Cell Biochemistry

http://slidepdf.com/reader/full/principles-of-structural-and-cell-biochemistry 1/28

Some insights into Principles of structural

and cell biochemistry (PSCB)

PIRES, Jorge Guerra

Universita' Degli Studi Dell'Aquila, L'Aquila, Italy.

17/06/11

Matricula: 203337

Double Diploma: Italy/Poland

Advanced Computational Methods in Material Science

[email protected]

“The road to equilibrium is down the free energy hill”

1. Introduction............................................................................................................... 6

2. Free energy ................................................................................................................ 8

3. Enzyme....................................................................................................................... 9

3.1 Specificity of the Enzymes................................................................................ 93.2 The enzyme substrate complex ........................................................................ 9

3.3 Factors affecting enzyme activity .................................................................. 11

3.4 The Michaelis – Menten Equation................................................................. 133.5 Enzyme inhibitors ........................................................................................... 14

3.6 Enzyme kinetic ................................................................................................ 14

3.7 Enzyme inhibitors and Enzyme kinetic ....................................................... 18

The role of protein structure...................................................................................... 26

The main metabolic pathways ................................................................................... 26

Bilirrubin ..................................................................................................................... 27

REFERENCE: ..................................................................................................................... 27

INDEX ................................................................................................................................ 28



PIRES, Jorge Guerra

Universita' Degli Studi Dell'Aquila, L'Aquila, Italy

Some insights into Principles of structural and cell biochemistry (PSCB) 2

NOTE. By no means the present file has the aim of introducing new ideas, defend a

point of view or similar action. The only aim is to gather in a coherent way the

information available in the files referred in the end of the same. All of them are text in

Principles of structural and cell biochemistry.



PIRES, Jorge Guerra



Abstract

Enzyme is probably the most well-known and important protein that may be found innature. This is assertion is posed having in mind that most of the reactions quite

important for our biological systems happen in a too low rate, what would make the

natural processes useless. Enzymes are catalysts proteins that speed up reactions. It is

worthwhile to point out that there are some catalysts that are not enzymes, they are RNA,

the difference is just the building blocks the composition. Due to this characteristic,

enzyme finds also a wide rage of application in industry.

There are two main points of enzyme that must be pointed out in order to

highlight the main properties of enzyme: a) it doesn’t not make the reaction possible, just

speed it up, it means that the reaction would happen even without the enzyme b) the

enzyme is not consumed by the reaction. This function of speeding up reactions is made

through a creation of an alternative way for the reaction happens, a “shortcut”. This is

done using the “hill” of the reaction, in order words, activation energy. Many reactions,

even releasing energy in the end, need a ‘’impulse’’ to start. It means that the reaction

happens just if an enough amount of molecule has a minimal energy to come over a

determined barrier. There are two ways to make a reaction happens: increase the

temperature or decrease the activation energy. The former effect all the system while the

latter, a specific reaction. The latter is done through enzyme.

Enzyme has a peculiarity; it works as “lock and key”. This means that enzyme is

specific for its “client”. The “client” is called substrate. Enzyme can be too specific or

more general, but still being specific. It may work on a group of substance, on a bond, on

a specific molecule and son on.

Since enzyme is a protein, it suffers the same problems that may face an ordinary

protein. One of the main point is the three dimensional shape, what plays a central hole in

the function of the protein, mainly in the creation of the active site, the “tiny” part of the

protein that really works. It means that enzyme may be affected by the temperature. It

happens because the “job” of the enzyme is done through a region called activity site. As

we know, the protein has its three dimension shaped determined by the sequence of

amino acids, or residues, what creates the secondary structure. This structure may be



PIRES, Jorge Guerra



broken down by the temperature, that increases the vibration of the molecules and giving

enough energy to escape to the electromagnetic field that keeps the structure.

Since the part of the enzyme that really takes place in the process of catalysis is a

tiny part, the rest of the enzyme may be faced as a “ physical support” for create the

shape of the active site, the effect of key-lock.

The bind of the enzyme to the substrate is done through collision. It means that

the higher the temperature, the higher is the collisions, the higher the rate of the reactions.

It happens until the optimal temperature, where the three dimensional shape starts to be

lost and in case the high temperature is not cut off in a maximum time, the “deformation”

is permanent, it means, the three dimensional shape is lost and do so the function of theenzyme. That optimal temperature varies from species to species. This variation makes

possible life in extreme conditions. Once the enzyme is a protein that is coded to the

DNA that may suffer mutations, evolution is always possible, once a small change in the

promoter of the DNA may cause a high change on the protein.

The most famous mathematical model for kinetic enzyme is the Michaelis-

Menten model . It is the simplest model for kinetic enzyme and it studies the system in

early times, that means, in the beginning where the amount of product is quite small and

one may suppose that the last reaction will flow just for one direction. Since the slowest

reaction is always the bottleneck, this will determine the overall reaction rate.

Enzyme is not stopped just for temperature, also there are some enzyme

inhibitors, that may be others enzymes or special molecules. One may gather all the

inhibitor into two huge groups: non-specific or specifics. Branching specifics, one finds

irreversible and reversible. The former makes covalent bond with the substrate while the

latter, non-covalent bonds. The reversible may be branched more competitive and

noncompetitive. The former bind to the enzyme, making it “out of game”, while the latter

goes just to the complex enzyme-substrate, or even to both, complex or enzyme. The

competitive inhibitor change the constant Km, that is the concentration of substrate to

achieve half of the maximum velocity, and the noncompetitive alters the “velocities”, the

Vm and Vmax ( Half of the maximum velocity and Maximum velocity). Also may be

found the rare case, the uncompetitive, this alters all the constants of the kinetic.



PIRES, Jorge Guerra



Figure 1. Reactions with and without catalyst ............................................................... 8

Figure 2. Cellular respiration .......................................................................................... 8

Figure 3. Enzyme in a reaction ........................................................................................ 9

Figure 4. Effect of the temperature in the reaction ..................................................... 15

Figure 5. Michaelis –Menton model .............................................................................. 10

Figure 6. Effect of the enzyme concentration in the enzyme activity ......................... 11

Figure 7. Reaction with two step ................................................................................... 12

Figure 8. Step reaction with catalyst............................................................................ 12

Figure 9. Graphic for the Michaelis-Menten model ................................................... 13

Figure 10. Competitive inhibitors................................................................................. 19

Figure 11. noncompetitive inhibitors ........................................................................... 20

Figure 12. The main methabolic pathways ...................................................................... 26



PIRES, Jorge Guerra



1. Introduction

If the chemical reactions involved in our body were reversible, we would convert our

DNA back into food in a short period of time without eat! The chemical reactions in our

body are called Metabolic pathways, that is defined as a series of biochemical reactions,

irreversible. In a scheme:

It is worth noting that the two irreversible arrays is a quite important characteristic

of the metabolic pathway, it endowed the body with a “key” to control the amount of

substance in the body, for example, the acid level in the blood, that suppose to be kept

constant.

One has

In biochemistry, metabolic pathways are a series of chemical reactions

occurring within the cells. Enzymes catalyze these reactions. The set of

metabolic pathways forms a metabolic network.

As an example one has the homeostasis1, it is done through pathways. Many of those processes has as main processes the catabolic and anabolic processes.

The best-known role of proteins in the cells is as enzymes. Enzymes are catalyst

proteins that speed up the rate of a chemical reaction without being consumed in the

process2. It means that the amount of Enzyme have to be the same in the end of the

reaction as in the beginning. The enzyme achieves their effect by temporarily binding to

the substrate lowering the activation energy, providing a lower energy pathway

between the reactants and the product. This is done creating intermediate substances. In

a scheme, one has:

Where: A = substrate, E = enzyme, and P= product .

1See http://en.wikipedia.org/wiki/Homeostasis

2This process of catalysis might also be made by RNA, but in some special situations. The only different is

the building block of them.

A + E P + E

A B C ... PPPP



PIRES, Jorge Guerra



Take the following set of reactions:

C is a catalyst!

As an example, takes the hydrogen peroxide that turns into water and oxygen:

OO H O H 222222 +→

This reaction is affected by the presence of manganese dioxide.

One may accept for all reactions that stability is the answer for everything, for

example the process of oxidation of the iron left in an opened place for a long time.

The catalysis may be homogeneous or heterogeneous. For the former, both the

substrate and enzyme are in the same phase while in the latter they ate in different phases.

Enzymes are usually highly specific and accelerate only one or a few chemical

reactions.

Although enzymes can consist of hundreds of amino acids, only a small portion

is involved in the process of catalysis and is smaller the amount that really react. This

part is called active site. It means that the fact of the enzyme be huge molecules goes

beyond just the catalysis in a restrict sense. The main function of the huge structure is

form the shape of the active “place”. One may use the follow metaphor: the body is a

huge structure that mainly “feed” the brain, the really active area of the body, all the other

part is support, the muscles get food to get oxygen and send to the brain that “thinks”.

As a principle, one may accept:

Enzymes bind temporarily to one or more of the reactants – the substrate-

lowering the activation energy.

X + C XCY + XC XCY

XCY CZ

CZ C + Z

X + Y Z



PIRES, Jorge Guerra



In a scheme:

Figure 1. Reactions with and without catalyst

2. Free energy

It is energy that can be harnessed to do work. “The road to equilibrium is

down the free energy hill”

When water is used to generate energy, one is using the free energy of the water,

that is, the potential energy. In the nature there are many types of potential energy, such

as electric potential, mechanical potential and so on. After Lavoisier3

, a French scientist,

the humankind started to understand that in natural every existence of energy changes

from a shape to another: in the nature nothing is lost, everything is converted into other existence.

We do the same when we eat, we use the chemical energy kept in the bond of the

molecules, such as glucose. In a scheme:

Figure 2. Cellular respiration

As exposed in previous lines, the secret of the catalysts is the activation energy.

3See http://it.wikipedia.org/wiki/Antoine-Laurent_de_Lavoisier

C6H12O6 + 6O2 -> 6CO2 + 6 H2O, ∆ G = -686 kcal.

Glucose

mitochondria

CELLULAR RESPIRATION



PIRES, Jorge Guerra



Activation energy is defined as the energy that must be overcame in order

to a chemical reaction occurs

Let’s work a little more into enzymes.

3. Enzyme

Enzymes are special protein molecules whose function is facilitate or

otherwise accelerates most of the chemical reactions in cells.

See picture that follows.

Figure 3. Enzyme in a reaction

3.1 Specificity of the Enzymes

One of the properties of the enzymes that makes them so important as

diagnostic and research tools is the specificity they exhibit relative to the

reaction they catalyze.

3.2 The enzyme substrate complex

The enzyme works as following:

E + S ES

ES P + E

S P



PIRES, Jorge Guerra



Where: E stands for Enzyme, S stands for substrate, ES stands for intermediate

complex, P stands for product of the reaction

Figure 4. Michaelis –Menton model

Using this graph, one may infer:

o Curves of the substrate concentration (Pink) and product (green)

has an inverse behavior in relation to each other. This due to the conservationmass law, once the total mass o substrate is converted into product as the reaction

evolves;

o The curves of the complex (light pink) and enzyme has a behavior

of inverse functions. Furthermore, the amount of enzyme is recovered at the end

of process at the same that the complex falls;

One point should be mentioned about enzyme:



PIRES, Jorge Guerra



Enzyme catalyzes both forward and backward.

3.3 Factors affecting enzyme activity

The first factor that may affect enzyme activity is the enzyme concentration. One may

accept that the higher is the concentration, the higher is the activity. Even though, there is

a limitation. Once Enzyme needs to bind to the substrate in order to work, there is a

saturation point. Thus, the law is accepted under huge amount of substrate.

In a graph:

Figure 5. Effect of the enzyme concentration in the enzyme activity

Another factor that may affect the activity of the enzyme is the enzyme specificity. One

has:

Reaction with more than one step has one step that determines the

reaction velocity. Therefore, when a step of a reaction is slower, it

becomes the step of the reaction.

Below follows a scheme of a reaction with two step:



PIRES, Jorge Guerra



See graphic below more insights.

Figure 6. Reaction with two step

One may rethink of the graph of enzyme and activation energy as above:

Figure 7. Step reaction with catalyst



PIRES, Jorge Guerra



3.4 The Michaelis – Menten Equation

In biochemistry, Michaelis–Menten kinetics is a model of enzyme kinetics. In

particular, the Michaelis–Menten equation describes the rate of

irreversible enzymatic reactions by relating reaction rate V to

the concentration of The substrate[S]4.

Above follows a graphic

Figure 8. Graphic for the Michaelis-Menten model

One of the most basic enzymatic reactions, as first proposed by Michaelis and

Menten in 1913,[1] involves an enzyme E reversibly binding to a substrate S to form a

complex ES, which in turn is converted into a product P and the enzyme.

As a first step of the reaction one has:

This is the transformation of the enzyme into the substrate in reversible

process. Thus:

4From: http://en.wikipedia.org/wiki/Michaelis%E2%80%93Menten_kinetics



PIRES, Jorge Guerra



In overall, we have the process of catalysis done by the enzyme.

3.5 Enzyme inhibitors

Basically, one may gather the inhibitor of enzymes in two groups: irreversible and

reversible inhibitors. Furthermore, into the group of the reversible, one may branch it in

competitive, noncompetitive and uncompetitive.

The difference between reversible and irreversible is the way they attach to the

target; the former does a covalent bind while the latter, non-covalent. Loosely saying, the

reversible inhibitor does not change the target chemically, while irreversible does.

The competitive inhibitor binds to the same place as the substrate, the same active

site. In the other hand, the noncompetitive binds to some place else, other site than the

one that the substrate uses. Having it in mind, the noncompetitive just reduce the catalytic

power of the enzyme, while competitive make the enzyme “out of game”. The

uncompetitive binds only to the complex-conjugate (ES).

One may accept

Competitive inhibitor binds to the enzyme (E), not to the complex (ES)

A interesting characteristic of the competitive inhibitor is that it does not

change Vm, but in the other hand, changes Km . One knows that Km is the

substrate concentration that is necessary to achieve half of Vm, Since the

competitive makes the bound enzyme not available anymore, it will be necessary

a higher concentration to increase the probability of the enzyme attach to the

substrate and form the complex.

Noncompetitive inhibitor binds to either the enzyme (E) or the complex (ES)and enzyme (E).

3.6 Enzyme kinetic

The glucose in the presence of oxygen is thermodynamically unstable5, in the other hand,

it is stable kinetically6 .

5See http://en.wikipedia.org/wiki/Chemical_stability



PIRES, Jorge Guerra



C6 H12 O6 + 6O2 6CO2 + H2O

There are mainly two ways to accelerate a reaction rate:

o Increasing the temperature in order to have sufficient molecules with enough

energy to come over the barrier that stop the reaction;

o Lower the activation energy.

For temperature, see picture below, for enzyme, go back to previous picture.

Figure 9. Effect of the temperature in the reaction

The difference of the two approaches are mainly that by increasing the

temperature all the system is effected. For enzyme, just the target. Imagine if one has to

increase the temperature of the blood in order the Bilirrubin7

, for instance, be processed.

The equilibrium of the reaction is not effect by enzyme action.

By the activation energy:

6See

http://chemwiki.ucdavis.edu/Physical_Chemistry/Chemical_Equilibrium/Kinetically_vs_Thermodynamically_Stable 7

See the appendix



PIRES, Jorge Guerra



Figure 10. Effect of the catalysis in the reaction

One may say that there are two ways of make reaction happens faster, or one may

move all the energy distribution of system or move the activation energy: move a line or

a “mountain”.

The simplest model for enzyme kinetic is the Michaelis- Menten model. This

studies the model basically in the beginning. It brings as advantage the fact that, since the

product is still in small concentration, the reaction happens just forward in the last step,

the release of the enzyme. For this model:

Figure 11. The Michaelis Menten Model

For this model, the reaction velocity is given by:

][2 ESk v =

Since the substrate concentration is difficult to measure, let’s seek a formula in term of

some easy to measure quantities. The balance mass of the enzyme in the system is,

supposing a close system:

][][][ ES E E total +=

E + S E + PES

K1

K-1

K2



PIRES, Jorge Guerra



The formation of ES is given by:

]]][[][[]][[ 11 S ES E k S E k v total ES −==

And the breakdown:

])[(

][][

12

12

ESk k v

ESk ESk v

ES

ES

−−

−−

+=

+=

In equilibrium:

112

1

112

][][][][

]]][[][[])[(

)()(

k Sk k S E k ES

S ES E k ESk k

breakdown formation

total

total

++

=

−=+

=

−

−

Remembering ][2 ESk v = :

112

1

2][

][][

k Sk k

S E k k v total

++

=

−

Finally:

][

][][

1

12

2

Sk

k k S E k v total

++

=

−

Suppose the concentration of S much bigger than the concentration of E, one has:

][][ ES E total =

Hence:

total ESk v ][2max=

And define:

1

12

k

k k k m

−+

=

Therefore:



PIRES, Jorge Guerra



][

][max

Sk

Svv

m +

=

This is the Michaelis-Menten equation.

3.7 Enzyme inhibitors and Enzyme kinetic

An enzyme inhibitor is a molecule that binds to enzymes and decreases

their activity.8

The inhibitor may be reversible in irreversible. Furthermore, it may be

competitive, noncompetitive or uncompetitive inhibitor.

Reversible inhibitors bind to enzymes with non-covalent interactions such

as hydrogen bonds, hydrophobic interactions and ionic bonds, while Irreversible

inhibitors usually covalently modify an enzyme, and inhibition cannot therefore

be reversed.

Irreversible inhibition is different from irreversible enzyme inactivation.

Irreversible inhibitors are generally specific for one class of enzyme and do

not inactivate all proteins; they do not function by destroying proteinstructure but by specifically altering the active site of their target. For

example, extremes of pH or temperature usually cause denaturation of

all protein structure, but this is a non-specific effect.9

For the competitive inhibitors:

8From http://en.wikipedia.org/wiki/Enzyme_inhibitor

9From http://en.wikipedia.org/wiki/Enzyme_inhibitor



PIRES, Jorge Guerra



Figure 12. Competitive inhibitors

It is inferred by the scheme that a third way, a sort of “sink” of enzyme, appears. It

decreases the amount of enzyme available.

Let’s seek an equation for the reaction velocity.

][2 ESk v =

According to mass conservation:

][][][][ E ES EI E total ++=

Also:

][

]][[

11

11

ESk v

S E k v

−−=

=

In equilibrium:

sk ES

S E

k

k

ESk S E k

vv

==

=

=

−

−

−

][

]][[

][]][[

1

1

11

11

In the same way, one find:

i

i

i k EI

I E

k

k ==

−

][

]][[



PIRES, Jorge Guerra



From the mass balance:

][]][[]][[

][ E k

I E

k

S E E

istotal

++=

And:

)1][][(

][][

1][][

][

][]][[]][[

]][[

][]][[]][[

][

][

2

22

2

++

=

++

=

++

=

++

=

is

s

total

is

s

is

s

is

total

k

I

k

Sk

S E k v

k

I

k

S

k

Sk

E k

I E

k

S E

k

S E k

E k

I E

k

S E

ESk

E

v

Finally:

][)1][

(

][max

Sk

I k

Svv

i

s ++

=

Comparing to the Michaelis-Menten, one sees that km changes.

And, for a noncompetitive:

Figure 13. noncompetitive inhibitors

Making the comparison with the previous case, a forth “sink” is created having

communication with the previous one in dynamical system.



PIRES, Jorge Guerra



The kinetic is given by, making the supposition above:

o The rates of formation of EI and ESI from I are the same : k i;

o The rates of breakdown of ESI and EI having I as final product are the same: k -i;

o The rate of formation of ES and ESI from S is the same : k 1;

o The rate of breakdown of ESI and ES having S as final product are the same: k -1;

Now the mass balance gives:

][][][][][ ESI E ES EI E total +++=

And:

][

]][[

11

11

ESk v

S E k v

−−=

=

In equilibrium:

sk k

k

ES

S E

vv

==

=

−

−

1

1

11

][

]][[

In a similar manner:

][

]][[

EI

I E k i =

As a consequence of our suppositions:

sk k

k

EIS

S EI ==

−

1

1

][

]][[

][

]][[

ESI

I ESk I =

Note. Note that functional speaking, we assume ][][ EIS ESI = . The difference is that for

the former the inhibitor bind to the complex enzymatic and the latter the substrate

reaction to the “inhibitor complex”.



PIRES, Jorge Guerra




][][][][][ ESI E ES EI E total +++=

Using the relation:

sk

S E ES

]][[][ =

ik

I E EI

]][[][ =

I k

I ES ESI

]][[][ =

sk

S E ES

]][[][ =

+++=

+++=

+++=

I ssitotal

I ssi

total

I

s

si

total

k k

I S

E k

S

k

I

E E

k k

I S E E

k

S E

k

I E E

k

I k

S E

E k

S E

k

I E E

]][[

][

][][

][][

]][][[][

]][[]][[][

][]][[

][]][[]][[

][

Calculating :

][

][][1

]][[1

][][

][

]][[1

][][

][][

]][[1

][][

][

]][[1

][][][

]][[

]][[1

][][][

][

][

max

max2

2

2

2

Sk

S

k

I

v

k k

I S

k

S

k

I k

Sv

k k

I S

k

S

k

I k

S E k v

k k

I S

k

S

k

I k

Sk

k k

I S

k

S

k

I E

k

S E k

k k

I S

k

S

k

I E

ESk

E

v

s

i

I ssi

s

I ssi

s

total

I ssi

s

I ssi

s

I ssi

total

+

+

=

+++

=

+++

=

+++

=

+++

=

+++

=



PIRES, Jorge Guerra



][

][][1

max

Sk

S

k

I

v

s

i

+

+

As one may see, the maximum velocity is affected by the presence of a noncompetitive

inhibitor, as well as the half-maximum velocity.

For the uncompetitive case:


][][][][ ESI E ES E total ++=

Therefore:

][

]][[

][

]][[

ESI

I ESk

ES

S E k

s

s

=

=

As consequence:

+++=++=++=

ississi

s

s

totalk k

I S

k

S E

k k

I S E E

k

S E

k

I k

S E

E k

S E E

]][[][1][

]][][[][

]][[][

]][[

][]][[

][

And:



PIRES, Jorge Guerra



++

=

++

=

iss

s

iss

s

total

k k

I S

k

Sk

Sk

k k

I S

k

S E

k

S E k

E

v

]][[][

][

]][[][!][

]][[

][

2

2

+++

=

iss

s

total

k k

I S

k

Sk

S E k v

]][[][1

][][2

++

=

i

sk

I Sk

Svv

][1][

][max

Finally:

][][

1

][][

1

max

S

k

I

k

S

k

I

v

v

i

s

i

+

+

+

=

NOTE. Basically, the difference between the models of kinetic for the diverse inhibition

process lies in the conservation mass equation.

KINETIC EQUATION IN THE PRESENCE OF NONCOMPETITIVE INHIBITION

In summary, for noncompetitive inhibition:

Binding either to ES or E and ES;

Changes Vmáx and Vm , but k m;

Cannot be overcame by the increase of substrate concentration.

For inhibition one has:



PIRES, Jorge Guerra



Figure 14. Hierarchy for the enzyme categorization

ENZYME

INHIBITORS

NON-SPECIFIC SPECIFIC

Denaturation

Acids&Bases

Alcohol

Heavy Metal

Reducing agents

IRREVERSIBLE

COMPETITIVE

REVERSIBLE

NONCOMPETITIVE



PIRES, Jorge Guerra



APPENDIX

The role of protein structure

The function of a protein is determined by its shape, even thought, the shape of a protein

is determined by its primary structure that is the sequence of amino acids, that is

determined by the genes. Then one has:

DNA sequence function

It makes the evolution always possible, once the DNA is under mutation and evolution.

The main metabolic pathways

Figure 15. The main methabolic pathways



PIRES, Jorge Guerra



Bilirrubin

In the liver it is conjugated with glucuronic acid by the enzyme glucuronyltransferase,

making it soluble in water. Much of it goes into the bile and thus out into the small

intestine. Some of the conjugated bilirubin remains in the large intestine and is

metabolised by colonic bacteria tourobilinogen, which is further metabolized

to stercobilinogen, and finally oxidised to stercobilin. This stercobilin gives feces its

brown color. Some of the urobilinogen is reabsorbed and excreted in the urine along with

an oxidized form, urobilin.

REFERENCE:

• Note of course Principles of structural and cell biochemistry (PSCB), held byProf. M. Catarella ( main notes).

• http://en.wikipedia.org/wiki/Metabolic_pathway

• http://www.chem1.com/acad/webtext/thermeq/TE5.html

• http://en.wikipedia.org/wiki/Catalysis

•

file:///C:/Users/Jorge/Desktop/Principles%20of%20strutural%20and%20cell%20biochemistry/Enzymes.html

• http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BondEnergy.html#Gib

bs (Discussion on free energy)

• http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/DenaturingProtein.html (The Rules of Protein Structure)

• http://en.wikipedia.org/wiki/Order_of_reaction

• http://en.wikipedia.org/wiki/Enzyme_inhibitor

• http://en.wikipedia.org/wiki/Michaelis-Menten_kinetics

• http://themedicalbiochemistrypage.org/

• http://webcache.googleusercontent.com/search?q=cache:TKhHevJbr5cJ:en.wikip

edia.org/wiki/Egg_(food)+egg+protein&cd=2&hl=it&ct=clnk&gl=it&source=www.google.it (eggs)• Biochemistry. 5th edition. Berg JM, Tymoczko JL, Stryer L. New York: W H

Freeman; 2002. (Protein (chapters 3 & 4) and Enzymes (Chapters 8,9 and 10)

• ALON, Uri. An Introduction to systems biology: design principles of biological

circuits. Chapman & Hall/CRC. (discussion on proteins)



PIRES, Jorge Guerra



INDEX

activation energy, 3, 6, 7, 8, 12, 15

enzyme inhibitors, 4

kinetic enzyme, 4

Metabolic pathways, 6

Michaelis-Menten equation, 18

Michaelis-Menten model , 4, 5, 13

substrate, 3, 4, 6, 7, 9, 10, 11, 13, 14, 24

Documents

Principles of Structural and Cell Biochemistry