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Course:

Type:

Total Units:

No. of Lectures:

Lecturers:

CELL BIOCHEMISTRY (BOM 113/4)

Minor

3 (3 x 1 h lecture per week)

21 (Part II)

Assoc. Prof. Dr. K. Sudesh Kumar

Room 402, Block G09A School of Biological Sciences

Tel: 04-6534367

Objectives:

Introduction to cells, organelles, molecules; structure & function relationship; working of a cell

Course contents are divided into 4 major sections:

1. Concept of a cell: Prokaryote, Eukaryote, Animal and Plant Cells; cellular organelles

2. Cell components (Structure & Function):

Water and buffer, amino acids and protein, fatty acids and lipid, monosaccharide and carbohydrate, nucleotides and DNA, RNA, membrane and membrane transport

Objectives:

3. Enzymology: Enzyme as catalysts, enzyme kinetics, inhibitor effects, enzyme regulations, allosteric

enzymes

4. Energetics and metabolisms:

Bioenergetic principles, carbohydrate metabolisms (glycolysis), TCA cycle, pentose

phosphate pathway,

gluconeogenesis and photosynthesis, fatty acid oxidation

Course evaluation: Test/Quiz/Assignment/Practical: 30% Final Exam: 70%

Learning Objectives

The basics of metabolism, enzymes as catalyst of metabolic pathways and energetics principles in general.

Details on vital metabolic pathways and processes such as glycolysis, fermentation of sugars, pentose phosphate pathway, gluconeogenesis, citric acid cycle, electron transport chain, oxidative phosphorylation, fatty acid

oxidation and biosynthesis, photosynthesis as well as their

regulation will be covered in detail.

ENERGY FLOW

Thermodynamics

“Thermodynamics is a

funny subject. The first time

you go through it, you don't understand it at all. The second time you go through

it, you think you understand

it, except for one or two small points. The third time you go through it, you know

you don't understand it, but by that time you are so used to it, it doesn't bother

you any more.”

-Arnold Sommerfeld-

it doesn't bother you any more.” -Arnold Sommerfeld- Arnold Johannes Wilhelm Sommerfeld ( December 5 ,

Arnold Johannes Wilhelm Sommerfeld (December 5, 1868 April 26, 1951) was a German theoretical physicist who pioneered developments in atomic and quantum physics, as

well as educated and groomed a large number of

students for the new era of theoretical physics. He

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introduced the fine-structure constant into quantum

Energy

Defined as capacity to do work

Two types of energy: Kinetic (movement) and

Potential (stored) energy

To understand energy flow, we need to know two things: the quantity of available energy and the usefulness of the energy: these are described in the laws of thermodynamics

emphasizes causation

emphasizes change

Kinds of changes made by living cells

A. Changes in chemical bonds:

1) biosynthesis 2) growth of new cells 3) maintenance of existing cells:

i) large molecules are easily damaged

ii) most large molecules are recycled

(a)

protein-->amino acids-->protein-->…

(b)

DNA/RNA -->nucleotide-->DNA/RNA-->…

iii) Synthesis of large molecules needs some energy

iv) cell needs change with time

(a)

different proteins needed during mitosis

(b)

food change, need different enzymes

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Kinds of changes made by living cells

4) synthesis of small molecules

i) 6CO 2 + 6H 2 O ---> glucose + 6O 2

(a)

requires 18 ATP (chemical energy)

(b)

requires 12 NADPH (reducing power)

ii) major fraction of cell energy used here for the synthesis of small molecules

Kinds of changes made by living cells

Kinds of changes made by living cells B. Mechanical work (changes in location) 1) move cell

B. Mechanical work (changes in location)

1) move cell relative to environment; examples:

i) flagellated cell (sperm)

ii) ciliated epithelium in bronchial tubes

iii)

iv) movement of chromosomes

muscles

http://en.wikipedia.org/wiki/Spermatozoon

v) cyclosis in plant cells

vi) movement mRNA relative to ribosome

vii) movement of plant parts (venus flytrap)

http://en.wikipedia.org/wiki/Venus_Flytrap

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Kinds of changes made by living cells

C. Concentration work (changes in concentration across membrane)

1. move molecules or ions against chemical gradient

i)

[glucose] in cell >[glucose] outside cell

(a)

must pump glucose in

ii)

pumping H + , Na + , Ca 2+ etc

iii)

eg: light driven accumulation of H + in thylakoid lumen

(b) pumped in against concentration and electron gradient

iv) at rest, cell's energy used to pump substances

Kinds of changes made by living cells

D. Electrical work (changes in cell's potential)

i) cell membranes have electrical potential (~70mV inside neg.)

ii) move ions against electron gradient

iii) must consider both the concentration and the electron grad.

iv) electron gradient drive ATP synthesis in bacteria, chloroplasts &

mitochondria

v) ATP used to make electrical potential

(1)

example: electric eel has electric organ

(a)

layers of cells called electroplaxes

(b)

each cell has potential of 0.15 V

(c)

cells are in series

(d)

total potential generated: >400 V

http://en.wikipedia.org/wiki/Electric_eel

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Kinds of changes made by living cells

E. Heat energy

i) homeotherms (birds & mammels)

a) must maintain relatively constant temperature

b) heat production is the major use of food energy

F. Bioluminescent work

i) fireflies, some bacteria

ii) can be large energetic drain

(1)

large energy output indicates important function

Which part of you consumes the most amount of energy?

http://en.wikipedia.org/wiki/Brain#Brain_energy_consumption

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Brain energy consumption

Although the brain represents only 2% of the body weight, it

receives 15% of the cardiac output, 20% of total body oxygen

consumption, and 25% of total body glucose utilization.

The energy consumption for the brain to simply survive is 0.1 Calories per minute, while this value can be as high as 1.5

Calories per minute (100W) during crossword puzzle-solving.

The demands of the brain limit its size in many species. Molossid bats and the Vespertilionid Nyctalus spp. have brains that have been reduced from the ancestral form to invest in wing-size for

the sake of maneuverability.

This contrasts with fruit bats, which require more advanced neural structures and do not pursue their prey.

Using Energy

A. Environmental energy available at earths surface:

Energy Source

Cal/cm 2 /yr

Solar radiation

260,000

Lightening

4

Radioactivity

0.8

Volcanoes

0.13

Photosynthesis

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Only source of large amounts of Energy = light

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Our main source of energy! 17 http://www.solarviews.com/eng/sun.htm

Our main source of

energy!

Our main source of energy! 17 http://www.solarviews.com/eng/sun.htm

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http://www.solarviews.com/eng/sun.htm

Using Energy

B.

Many organisms capture light energy

1. Plants, Photosynthetic bacteria, Photosynthetic protists

1. Plants, Photosynthetic bacteria, Photosynthetic protists 2. Called "phototrophs" a. use light energy to make

2. Called "phototrophs" a. use light energy to make all molecules required for life from inorganic precursors like CO 2 and H 2 O b. function as chemotrophs in dark

i) use chemical energy stored in light (starch)

C. Chemotroph organisms get energy from source other than light

1. All animals, fungi, many protists and most bacteria are chemotrophs

2. Release energy from compounds they take up (via fermentation, glycolisis, respiration)

Flow of energy in biosphere

1) Begins with nuclear fusion reactions in sun

2) Light

3) Small amount captured by phototrophs and "stored" as molecules [some energy lost as heat/entropy (S)]

4) Chemotrophs release energy captured by phototrophs

and stored as chemical [Some energy lost as heat/entropy during conversion] 5) Flow is: from sun light (+heat/S) --> molecules of phototrophs (+heat/S) --> molecules of chemotrophs (+heat/S) --> heat/S

Flow of matter in biosphere

1) Energy usually stored as chemical bonds 2) Flow of matter accompanies energy flow 3) Energy enters without matter (light)

4) Energy leaves without matter (IR radiation/S)

5) In biosphere, energy mainly in the form of chemical bonds associated with matter:

i) matter cycles between phototrophs and chemotrophs

a.

carbon

b.

oxygen

c.

nitrogen

d.

hydrogen

e.

etc.

ii) two groups (phototrophs & chemotrophs) live in symbiotic relationship 6) Ecology deals with macroscopic energy cycles

7) Cell biochemistry deals with microscopic energy transactions at cellular

and molecular level

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The Laws of Thermodynamics

ALL processes that occur in the universe are subject to the 3 basic laws of thermodynamics. These laws

define the basic properties and behavior of energy.

1st law: Energy can neither be created or destroyed (law of conservation of energy)

2nd law: ALL naturally occurring processes proceed in a

direction that leads to a minimum potential energy level (or maximum entropy) (means that, when energy is converted from one form to another, the amount of

useful energy decreases)

3rd law: At absolute zero temperature (0° K) the entropy is zero

First Law of Thermodynamics

1. Energy cannot be created or destroyed, only converted

from one form to another

a. for a given system:

(1)

energy out = energy in - energy stored, or

(2)

energy stored = energy in - energy out

b. amount energy stored in a system/molecule = E

c. not concerned with actual value of E

d. very concerned with "changes in E"

e. E = E 2 - E 1 = E in - E out

First Law of Thermodynamics

2. Example:

a. C 6 H 12 O 6 + 6O 2 --> 6CO 2 + 6H 2 O + energy b. Burn 1 mole glucose; 673 kcal energy released i) 1 mole glucose has 673 more kcal energy than 6 moles of CO 2 + 6 moles of H 2 O ii) reaction has E = -673 kcal iii) negative E => a decrease in internal energy of molecules as glucose & O 2 converted to CO 2 & H 2 O

First Law of Thermodynamics

c. The reverse reaction

i)

6CO 2 + 6H 2 O + energy --> C 6 H 12 O 6 + 6O 2

ii)

this reaction: E = +673 kcal

iii)

positive E => internal energy when CO 2 & H 2 O converted to glucose & O 2

(a) glucose + O 2 has internal energy released to CO 2 + H 2 O

d. So: amount of internal energy released when glucose is burned is exactly equal to amount of energy stored in glucose when

the sugar is synthesized (energy neither created nor destroyed = 1 st Law of Thermodynamics)

Second Law of Thermodynamics

1. The value of S (entropy) in the universe is positive for

every real process or reaction

2. Universe becomes more random with every reaction that occurs

3. But, not always convenient to deal with predicting the spontaneity of reaction in the test tube in terms of universal entropy

4. Use G (free energy) to predict spontaneity of reaction in closed systems

Lets look at the concept of entropy first…

The concept of entropy, S

Entropy, represented by the symbol S, is a measure of the randomness or orderliness of the energy and matter in a system.

The more random, disordered, disorganized, or

chaotic the system, the higher the entropy.

Only organized, non-random/focused/concentrated energy is useful (can be made to do work)

Entropy of a substance increases with its volume. (eg.

gas molecules in occupying all the volume available to it maximizes its entropy) (What will happen to our universe?)

Entropy and the 2 nd law of thermodynamics

“Disorder spreads

through the universe,

and life alone battles against it”

“Disorder spreads through the universe, and life alone battles against it” G. Evelyn Hutchinson (1903-1991) 27

The Concept of Free Energy Arises from

a Combination of the First & Second

Laws

Free energy (G) - energy available to do work; defined by J. Willard Gibbs, American chemist (1878)

Together the 1 st & 2 nd laws of thermodynamics show that the energy of the universe is constant, but that entropy (S) continues to increase toward a maximum

Gibbs combined concepts inherent in 1 st & 2 nd Laws to get equation:H = G + TS where:

1. G is the change in free energy (the change during a process in energy available to do work)

2. H - change in enthalpy (total energy content of system;

equivalent to E for our purposes)

3. T - absolute temperature ( ° K; ° K = ° C + 273)

4. S - change in entropy of system

H = G + TS

Total energy change = sum of changes in useful energy available (G) & unavailable (TS) for work

Rearrange to G = H - TS; can predict direction in

which, process will proceed & the extent to which the

process will occur

Spontaneous process has - G (exergonic) & proceeds toward state of lower free energy; such a process is thermodynamically favored

Non-spontaneous process, +G (endergonic); cannot

occur spontaneously; it is thermodynamically

unfavorable; make it go by coupling to high -G (energy- releasing) reaction.

Josiah Willard Gibbs

Josiah Willard Gibbs

and mathematician. One of the greatest American scientists of all time, he

devised much of the

theoretical foundation for chemical thermodynamics as well as physical chemistry.

http://en.wikipedia.org/wiki/Josiah_Willard_Gibbs

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Gibbs free energy (G) - energy available to do work at constant temperature and pressure

-G

High Energy

+G

-G

Low Energy

+G

-G

High Energy

+G

Low Energy

The coupling of energy-producing reactions and energy-requiring reactions is a central feature in the metabolism of all organisms. In

catabolism, oxidative reactions are coupled to the endergonic

production of ATP by phosphorylation of ADP.

In anabolism, the exergonic hydrolysis of the high-energy bond of

ATP releases the energy needed to drive endergonic reductive

reactions.

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ATP functions as

energy currency in processes that release energy

and processes that use energy

ATP functions as energy currency in processes that release energy and processes that use energy 32

Free energy changes in

chemical reactions

All cell chemical reactions are reversible, so

one must consider forward & reverse reactions at the same time

Law of Mass Action - reaction rate proportional to reactant concentration

(Ex.: A + B <> C + D)

1. Forward reaction rate - proportional to A & B concentrations (k 1 [A][B]); k 1 : forward rate constant 2. Reverse reaction rate - proportional to C & D concentrations (k 2 [C][D]); k 2 : reverse rate constant

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All reactions proceed toward equilibrium (can

be slow), where forward & reverse rates are equal 1. At equilibrium, the same number of A & B molecules are converted into C & D molecules per unit time as are formed from them

2. k 1 [A][B] = k 2 [C][D] at equilibrium - allows

calculation of equilibrium constant (K

combining k 1 & k 2 into K eq (K eq = k 1 /k 2 = [C][D]/[A][B])

) by

eq

3. Gives predictable ratio of product to reactant

concentrations at equilibrium & allows prediction of reaction direction (forward or reverse) under given set of conditions

4.

Ratio can be determined experimentally by

measuring product & reactant concentrations at equilibrium

5.

If K eq > 1 & initial concentration ratios = 1 > products increase at expense of reactants

6.

If K eq < 1 & initial concentration ratios = 1 > reactants increase at expense of products

7.

Net direction in which, reaction is proceeding at any moment depends on relative

concentrations of all participating molecules & can be predicted if K eq is known.

Free energy changes in

chemical reactions

-G favors product formation; +G favors reactant formation; a greater - G reaction is farther from equilibrium & the system can

perform more work

- G when total free energy of reactants > total free energy of products (+G - vice versa)

As reaction proceeds, difference in free energy

content between reactants & products decreases (G gets less negative)

At equilibrium, no further work can be obtained & the free energy difference, G is 0

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Standard States for Free-Energy Changes

1.

2.

3.

4.

5.

G for a given reaction depends on the reaction mixture present at a given time, thus it is not useful for comparing the energetics of various reactions

To allow such comparisons & various types of calculations, scientists began to consider reactions under standard conditions

G 0 : G at standard conditions, in which the concentration of all reactants in solution is set at 1 M. Can be related to the equilibrium constant of a reaction by the equation:

G 0 = -RT ln K eq

G 0 - modified standard states (for biochemical applications) ; 25° C [298° K], 1 atm pressure, reactant/product concentrations, 1 M, pH 7 [H + ion concentration at 10 -7 M])

’prime indicates a modified standard state, where [H] is changed from 1M to 110 -7 M)

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Relationship between K eq & G 0

(G 0 : spoken as ‘delta G zero prime’)

G 0 = -RT ln K eq = - 2.3 RT log K eq

1. R = gas constant (1.987 cal/mol/ ° K or 8.31 J/mol/° K); T = absolute temperature ( ° K)

2. G 0 & K' eq indicate that standard conditions include pH7 (for biological conditions), while G 0 & K eq indicate standard conditions in 1 M H + (pH = 0.0!)

3. If K eq > 1, then G 0 negative (spontaneous) & if K eq < 1, then G 0 positive (nonspontaneous) under standard conditions

4. So, G predicts the spontaneity of a reaction.

5. G predicts only direction of reaction, NOT reaction rate!

Sample calculation 1

Hydrolysis of ATP at pH 7, 25°C, yields ADP, monohydrogen phosphate ion (P i ) and H +

ATP + H 2 O ADP + P i + H +

The value for K’ eq for this reaction is 2.23 10 5

G 0 = -RT ln K eq

= - (8.31 J/mol/ ° K)(273+25° K)(12.32)

= - 3.05 10 4 J/mol

= - 30.5 kJ/mol

= - 7.29 kcal/mol (because 1 kJ = 0.239 kcal)

-G 0 indicates that the hydrolysis reaction of ATP to ADP is a spontaneous process in which energy is

Sample calculation 2

The G 0 for a reaction at 25 ° C is -15 kJ/mol. What is the equilibrium constant for the reaction? (R=8.314;

T=273)

K eq = e -G°/RT

= -[-15,000/(8.314)(298)]

e

= 6.05

e

= 426

Facts of Origins of Life

Life originated 600 million years ago and continental drift occurred

200 million years ago creating five continents.

Mammals evolved 140 million years ago, Hominids that is the

human type, evolved 26 million years ago but modern humans only

arrived on the scene some 200,000 years ago.

Humans migrated and colonized the world only in the last 50,000 years.

The spoken language is some 10,000 years old while writing evolved only a few thousand years ago.

All this phenomenal progress has been achieved only within the

short span of 200 to 400 generations, that is in just 10,000 to 5,000

years.

………from Dr. APJ Abdul Kalam’s Convocation Acceptance Speech at the Universiti Sains Malaysia, Penang 30/Aug/2008 : Pinang, Malaysia“Evolution of Enlightened citizenship”

B

B

I

I

O

O

E

E

N

N

E

E

R

R

G

G

E

E

T

T

I

I

C

C

S

S

The Cell is a Open System

No exchange of matter or energy

Exchange of energy may occur

Exchange of matter and/or energy may occur

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Bioenergetics

LIFE requires constant supply of ENERGY & MATERIAL

Derived from the food that we consume

Involves a series of biochemical reactions

Electron donors transfer energy to electron

acceptors

Oxidation-reduction reactions are fundamental to the extraction of energy from

our food

METABOLISM

The molecules of carbohydrates, fats, and proteins taken into an organism are

processed in a variety of ways.

This is called METABOLISM, which is the sum total of the chemical reactions

of biomolecules in an organism.

Metabolism consists of two processes:

CATABOLISM and ANABOLISM

CATABOLISM

The breakdown of large molecules to smaller

ones

Is an oxidative process that releases energy

Free energy in substrate/reactant is greater

than the free energy in product (exergonic)

Electrons are transferred to various acceptor molecules

3 stages:

1) Macromolecule-->monomer (eg. Starch to glucose)

Energy is produced!

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2) Monomer --> acetyl-CoA

3) Acetyl-CoA --> CO 2 and H 2 O

ANABOLISM

The process of building macromolecules from

small molecules

Is a reductive process that requires energy

The free energy in reactants are less than the free energy in product (endergonic)

Involves acceptance of electrons from a variety of donors

3 stages:

1. CO 2 + H 2 O + energy --> acetyl-CoA 2. Acetyl-CoA --> monomers (fatty

acid/sugar/amino acid)

Energy is used!

3. Monomers --> macromolecules (eg. Polymers

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and complex molecules)

Nutrients (fats, carbohydrates, proteins) taken into an

organism are processed in a variety of ways

Nutrients (fats, carbohydrates, proteins) taken into an organism are processed in a variety of ways 50

Oxidation and Reduction Transfer of

Electrons

Oxidation - reduction (redox) reactions must occur simultaneously

Involve change in the electronic state of reactants

Both oxidation & reduction are

reversible; both anabolic & catabolic

pathways involves redox reactions

Oxidation

Oxidation - reaction involving loss of one

or more electrons; ex.: metallic iron (Fe 0 ) to ferrous state (Fe 2+ ) via loss of electron pair; since an electron acceptor is

needed, it is accompanied by reduction

The molecule oxidized is called a reducing agent & becomes more positive

Reaction is reversible; oxidized molecule can pick up electrons & return to earlier state (Fe 2+ -> Fe 0 )

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Reduction

Reduction - a reaction involving a gain of one or more electrons; ex.: Fe 2+ to Fe 0 ; The reduced molecule is called an

oxidizing agent;

Since electron donor is needed, it is accompanied by oxidation

Example: Fe 0 + Cu 2+ <> Fe 2+ + Cu 0 ; Cu 2+ is oxidizing agent, Fe 0 is reducing agent

Redox of organic compounds

The oxidation & reduction of organic compounds

during cellular metabolism involve carbon atoms that are covalently bonded to other atoms

When a pair of electrons is shared by 2 different atoms, the electrons are more strongly attracted to one of the 2 atoms of the polarized bond

In CH bonds, C pulls electron more strongly & is in reduced state

In CO & CN bonds, electrons are attracted by

electronegative atom, thus C is in oxidized state

Oxidation state of carbon atom

Carbon atom has a number of oxidation

states, since it can share a number of

valence electrons (4)

Ranging from CH 4 (fully reduced) to CO 2 (fully oxidized);

Oxidation state of a carbon atom in an organic molecule is a measure of the

molecule's free energy content

One can roughly determine oxidation state by counting number of H vs. O & N

atoms per C atom

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Capture & utilization of energy

Chemical fuels (hydrocarbons) are highly

reduced organic compounds; energy is

released when they are burned in presence of O 2 converting them to more oxidized states (CO, CO 2 )

As carbon is more reduced, more chemical work can be done in cell - fats (HCH) have more energy per unit weight than carbohydrates (HCOH)

The more H atoms that can be stripped from a

"fuel" molecule, the more ATP can be made

The role of coenzymes in biologically

important oxidation-reduction reactions

NADH: the reduced form of nicotinamide adenine dinucleotide

NADH is oxidized to NAD + , which is an electron acceptor in redox reactions

Important coenzyme in many reactions

Is a derivative of nicotinic acid (also called niacin),

one of the B-complex vitamins

Its structure has 3 parts: a nicotinamide ring, an adenine ring and two sugars. The phosphate groups of the two sugars are linked together.

NAD +

NADH

NAD + NADH The functional group involved in the reaction A similar compound is NADPH (the
NAD + NADH The functional group involved in the reaction A similar compound is NADPH (the

The functional group involved in the reaction

A similar compound is NADPH

(the oxidized form is NADP + ).

It differs from NADH by having

an additional phosphate group

attached to one of the ribose

sugars

58

Another important electron acceptor is FAD (flavin adenine dinucleotide), which is the oxidized form of FADH 2 . They contain the flavin group which are derived from vitamin riboflavin B 2 .

Oxidation of nutrients to provide energy for an

organism cannot take place without reduction of some electron acceptor such as NAD + and FAD.

The ultimate electron acceptor in aerobic oxidation is oxygen.

NAD + , FAD and

ATP are constantly recycled

Activation of metabolic pathways

and the role of coenzyme A

In order to produce and use energy efficiently and in a controlled manner, cells carry out multistep metabolic processes

We will see later that the partial anaerobic breakdown of glucose (glycolysis) and the complete aerobic breakdown of glucose to CO 2 and H 2 O requires many steps

A step frequently encountered in metabolism is the process of activation. This is to make the substrate/metabolite more reactive.

Coenzyme A is a compound that is used for this

purpose.

Thiol group is the

reactive portion of

CoA

High energy thioester/ covalent bond

Acetyl-CoA

Energy Changes and Electron Transfer in Metabolism

Learning Outcome: By now you should…

Know What Are Standard States for Free-Energy Changes

Know What Is a Modified Standard State for Biochemical Applications

Know What Is Metabolism

Know How Are Oxidation and Reduction Involved in

Metabolism

Know How Are Coenzymes Used in Biologically Important OxidationReduction Reactions

Know How Are the Production and Use of Energy Coupled?

To Know How Is Coenzyme A Involved in Activation of Metabolic Pathways?