Introduction to Biotechnology

breadloafvariousΒιοτεχνολογία

20 Φεβ 2013 (πριν από 4 χρόνια και 6 μήνες)

105 εμφανίσεις

Chapter 9

Introduction to Metabolism

An Overview of Metabolism

Metabolism

is the total of all chemical reactions in
the cell and is divided into two parts


catabolism


energy
-
conserving reactions that also
generate a ready supply of electrons (reducing
power) and precursors for biosynthesis E.g break
down of glucose to release energy in the form of ATP
in the mitochondria.


anabolism


the synthesis of complex organic
molecules from simpler ones e.g formation of starch
from carbondioxide

Anabolism

Anabolism

are reaction which requires
energy E.g Photosynthesis in chloroplast


Catabolism

are reaction where energy is
released E,g Cellular respiration in
mitochondria

Energy and Work


Energy

is defined as the
capacity to do
work or to cause particular changes

Types of Work Carried out by
Organisms

Chemical work


Synthesis of complex molecules from simpler
precursors (i.e anabolism). Here energy is needed to
increase the complexity of a cell.

Transport work


Take up of nutrients, elimination of wastes, and
maintenance of ion balances i.e energy is needed to
transport molecules and ions across a cell membrane
against a gradient.

Mechanical work


Energy is needed for cell motility and movement of
structures within cells

The Laws of Thermodynamics


To understand how energy is conserved
in ATP and how ATP is used to do work
in a cell, one has to understand the law
of Thermodyanamics.

Thermodynamics


a science that analyzes energy changes in
a collection of matter called a system (e.g.,
a cell or a plant)


all other matter in the universe is called
the surroundings

….The Laws of Thermodynamics

Thermodynamics
focuses on the energy
difference between the initial state and
final state of a system and not the rate
of the process from one state to
another

e.g boiling of water: cold liquid

hot
-
vapor
i.e energy moves from one state to
another ( thermodyanmics is not
concerned with the rate at which the
water is boiling.

First Law of Thermodynamics

Two laws of Thermodynamics:


First Law
: energy can be neither created
nor destroyed



total energy in universe remains constant
however, energy may be redistributed
either within a system or between the
system and its surroundings

..First Law of Thermodynamics


Example in some reaction energy is
released and in some it is absorbed..Why?



We need the
second Law of Dynamics

to
explain why?

Second Law of Thermodynamics

Entropy
is a condition of matter and the

amount of
randomness (disorder) in a system


The second law of Thermodynamics

state that
physical and chemical processes proceed in such
a way that the disorder of the universe ( the
system and its surroundings) increases to the
maximum possible.


The greater the disorder the greater is the
entropy of the universe, however, the entropy of
a system varies: increases, decreases or remain
constant.

Energy Units


calorie (cal)


amount of heat energy needed to raise 1
gram of water from 14.5 to 15.5
°
C


joules (J)
-
amount of energy can also be
expressed in joules


units of work capable of being done


1 cal of heat is equivalent to 4.1840 J of
work


Refer pg 170 for
Kilo joule

and
Kilo calorie

Free Energy and Reactions


The first and Second Law of Thermodynamics

can be combined as follows:

Free energy change,

G

=

H

-

T

S



to expresse the change in energy that can
occur in chemical reactions and other
processes



to indicate if a reaction will proceed
spontaneously

Where,


G

=

H

-

T

S



G


free energy change


amount of energy that is available to do work at
constant temperature and pressure



H


change in
enthalpy

(heat content)/change in the
total energy during the reaction


T


temperature in Kelvin (
0
C +273)



S


change in entropy occurring during the reaction (
entropy is randomness/disorder)

Chemical Equilibrium

The change in the free energy has a definite and
concrete relationship to the direction of chemical
reactions.

Equilibrium:

consider the chemical reaction

A + B


C + D


reaction is at equilibrium when rate of forward
reaction = rate of reverse reaction

Equilibrium constant (
K
eq
)


expresses the equilibrium concentrations of
products

and
reactants
to one another. No further changes
occur in the products or reactants

Chemical Equilibrium





Equilibrium Constant:




(
K
eq
) = (C) (D)/(A)(B)

The equilibrium constant (
K
eq
) of a reaction
is directly related to its change in free
energy.




Standard Free Energy Change

(

G
º
)


Standard Free Energy Change

is when free
energy change is determined at standard
conditions of concentration, pressure,
temperature, and pH



G
º

symbol used to indicate
standard free
energy change

at pH 7 (close to pH of living
cells) and is directly related to
K
eq (
equilibrium
constant)


Relationship between

G
º

&
K
eq :




G
º
´

=
-
2.303RT
•log
K
eq


Where,
R is the gas constant(1.9872 cal/mole
-
degree) 7 T is
absolute temperature



Types of energy driven reactions


Exergonic reaction
-

reactions in a cell when
energy is released from energy source and
standard free energy change
(

G
´
) is

negative
&

Equilibrium constant

(
K
eq)

is greater than one.


Endergonic reactions
-
reactions in a cell when
energy is trapped and the energy captured by
cell is used to drive reactions to completion,
hence standard free energy change
(

G
´
)

is
positive &
(
K
eq)

is less than one.


The Relationship…

Figure 9.1 Relationship between Equilibrium constant and Free Energy
Change.

Assignment on Adenosine 5’
triphosphate (ATP) (SL.19
-
27) for
next lecture!!

Adenosine 5’ triphosphate


For all metabolic reactions (exergonic &
endergonic) energy in the form of ATP
drives the processes in a cell


Some reactions earn ATP and some
process spend ATP


ATP serves as a link between exergonic &
endergonic reactions


ATP also referred as
Energy Currency of the Cell.

..Role of ATP in Metabolism


Endergonic e;g
reactant (A+b) to
give product (C+D)


Exergonic breakdown
of ATP to ADP is
aiding an endergonic
reactions to make
them more favorable

Figure 9.3 ATP as a coupling agent

..Adenosine
-
5'
-
triphosphate

(
ATP
)


Adenosine
-
5'
-
triphosphate

(
ATP
) is a
multifunctional
nucleotide


"
molecular unit of currency"

of intracellular energy
transfer



In this role, ATP transports chemical energy




….Adenosine
-
5'
-
triphosphate

(
ATP
)


ATP is made from
adenosine diphospahate

(ADP) or
adenosine monophosphate

(AMP), and its use in metabolism converts
it back into these precursors.



ATP is therefore continuously recycled in
organisms, with the human body turning
over its own weight in ATP each day


..Adenosine
-
5'
-
triphosphate


This conversion of
ATP to ADP

is an
extremely crucial reaction for the
supplying of energy for life processes.


Just the breaking of one bond with the
accompanying rearrangement is sufficient
to liberate about 7.3 kilocalories per mole
= 30.6 kJ/mol.


This is about the same as the energy in a
single peanut!!

Adenosine
-
5'
-
triphosphate


Living things can use ATP like a
battery.




The ATP can power needed reactions by losing one of its
phosphorous groups to form ADP



One can use food energy (cellular respiration) in the
mitochondria to convert the ADP back to ATP so that the
energy is again available to do needed work




In plants, sunlight energy can be used to convert the
less active compound (CO2) and water back to the
highly energetic form ( to starch )







..Structure of Adenosine 5’
-
triphosphate
(ATP)

Energy Currency of the Cell

Figure 9.2
-

Pyrimidine ring with carbon atoms in a ribose attached to 3 phosphate
group, adenine and an amino group.

..Adenosine 5’ triphosphate


Structure of ATP has a carbon compound as a
backbone


Part which is really critical is the phosphorous
part
-

the triphosphate.


Three phosphorous groups are connected by
oxygens to each other, and there are also side
oxygens connected to the phosphorous atoms.


Each of these oxygens has a negative charge &
the negative charges repel each other.Highly
charged



These bunched up negative charges, want to
escape
-

to get away from each other, so there
is a lot of potential energy here.

The Cell’s Energy Cycle

Figure 9.4 Cell Energy Cycle

Oxidation
-
Reduction Reactions
and Electron Carriers


many metabolic processes involve
oxidation
-
reduction reactions
(electron
transfers)


electron carriers are often used to transfer
electrons from an
electron donor

to an
electron acceptor

Oxidation
-
Reduction (Redox)
Reactions

can result in energy release, which can be
conserved and used to form ATP


E.g Acceptor + e
-

=donor



The acceptor and the donor makes a couple and
called a
redox couple



In a reversible reaction, the acceptor becomes
the donor until an equilibrium is reached called
Standard Reduction Potential (E
0
)


..REDOX


The term

redox

comes from the two concepts
of
red
uction and
ox
idation. It can be explained
in simple terms:


Oxidation

describes the

loss

of
electrons

/
hydrogen

or
gain

of
oxygen




Reduction

describes the
gain

of
electrons

/
hydrogen

or a
loss

of
oxygen


Redox


This can be either a simple
redox

process
such as the
oxidation

of
carbon

to yield
carbon dioxide
or


the
reduction

of
carbon

by hydrogen to
yield
methane

(CH
4
),



or it can be a complex process such as
the oxidation of
sugar

in the human body
through a series of very complex electron
transfer processes.

Standard Reduction Potential
(E
0
)


Equilibrium constant for an oxidation
-
reduction reaction and is measured in
volts (unit of electric potential)


Hence redox couples are a potential source
of energy


A measure of the tendency of the reducing
agent to lose electrons


Redox couple with more
negative

E
0
(Std
reduction potential)



better
electron
donor

i.e reducing agent has tendency to
lose more electrons


Redox couple with more
positive E
0
(Std
reduction potential)



better electron
acceptor



Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

33

Electron Transport Chains

(ETC)


Also
known as electron transport system
(ETS)


ETC comprises of electron
carriers
such as
co
-
enzymes,
NAD

(
Nicotinamide

adenine
dinucleotide
), or
FAD

(
Flavin

adenine
dinucleotide
) and others


E.g

when glucose ( C
6
H
12
O
6
) is
oxidised

during cellular respiration, many electrons
are released and these are accepted by
NAD
which is converted/reduced to
NADH


..ETC



During
Cellular Respiration
:


C
6
H
12
O
6

+ 6O
2

––
> 6CO
2
+ 6H
2
O + energy
ATP),

NADH transfers electrons to Oxygen via a
series of electron carriers with varying
redox potential (
E
0)
which is organised
into a system called
electron transport
system.






Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

35

Electron Carriers


NAD


nicotinamide

adenine
dinucleotide



NADP


nicotinamide

adenine
dinucleotide

phosphate

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

36

…Electron
Carriers


FAD


flavin

adenine
dinucleotide



FMN


flavin

mononucleotide

Figure 9.8

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

37

…Electron
Carriers


cytochromes


use iron to transfer electrons


iron is part of a
heme

group

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

38

…Electron
Carriers


coenzyme Q (
CoQ
)


a
quinone


also called
ubiquinone

Figure 9.9

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

39

…Electron
Carriers


nonheme

iron proteins


e.g.,
ferredoxin


use iron to transport
electrons

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

40

Enzymes


Enzymes are critically important for cells
to speed up reactions. They act as
catalysts


catalyst


substance that increases the rate of a
reaction without being permanently altered


substrates


reacting molecules


products


substances formed by reaction

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

41

Enzyme Structure

Many enzymes are composed of only
proteins. However many enzymes are
composed an

Apoenzyme

which is


protein component of an
enzyme
and a

Cofactor


nonprotein

component of an enzyme


prosthetic group


firmly attached


coenzyme



loosely attached


Holoenzyme

is a complete enzyme
i.e

Holoenzyme
=
apoenzyme

+ cofactor

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

42

Coenzymes


Coenzymes
often
act as
carriers,
transporting
substances
around the
cell

Figure 9.11
-

Coenzyme as a carrier

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

43

The Mechanism of Enzyme
Reactions

a typical
exergonic

reaction


A + B


AB




C + D


transition
-
state complex



resembles both the substrates and the
products

Copyright
© The McGraw
-
Hill Companies, Inc. Permission required for reproduction or display.

44


Activation
energy
(E
a)


energy required to
form transition
-
state
complex



enzyme speeds up reaction by lowering
E
a



Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

45

How Enzymes Lower
A
ctivation
energy (
E
a)


by increasing concentrations of substrates
at
active site
of enzyme


by orienting substrates properly with
respect to each other in order to form the
transition
-
state complex

Copyright
© The McGraw
-
Hill Companies, Inc. Permission required for reproduction or display.

46

Lock and Key Model of Enzyme Function

Figure 9.13
Lock and Key Model of Enzyme Function


Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

47

The Effect of Environment on
Enzyme Activity


Rate of enzyme
activity is significantly
impacted by substrate concentration,
pH, and temperature

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

48

Effect of [substrate]


rate
increases

as [substrate]
increases


no further
increase occurs
after all enzyme
molecules are
saturated
with
substrate

Figure 9.15

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

49

Effect of pH and Temperature


Each
enzyme has
specific pH
and
temperature optima


Denaturation


loss of enzyme’s structure and activity when
temperature and pH rise too much above
optima

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

50

Enzyme Inhibition

Competitive inhibitor

Microorganisms can be poisoned
with
enzyme inhibitors
/
competitive
inhibitor

which directly competes
with binding of substrate to active
site


Noncompetitive inhibitor


binds enzyme at site other than
active site; changes enzyme’s shape
so that it becomes less active

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

51

Metabolic Channeling


Metabolic Channeling
-
differential
localization of
enzymes and
metabolites



compartmentation


differential distribution of enzymes and metabolites
among separate cell structures or organelles

Copyright
© The McGraw
-
Hill Companies, Inc.
Permission required for reproduction or display.

52

Chemotaxis


An
example of a complex behavior that is
regulated by altering enzyme activity


system involves a number of enzymes and
other proteins that are regulated by
covalent modification
e.g

Chemotaxis

response of
E. coli


Bibliography



Lecture
PowerPoints

Prescott’s Principles of
Microbiology
-
Mc
Graw

Hill Co.


http://en.wikipedia.org/wiki/Scientific_metho
d


https://files.kennesaw.edu/faculty/jhendrix/bi
o3340/home.html


http://hyperphysics.phy
-
astr.gsu.edu/Hbase/biology/atp.html