The Molecular Logic of Live

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Chapter 1Chapter 1

The Molecular Logic of LifeThe Molecular Logic of Life Biochemistry explains diverse formsBiochemistry explains diverse forms

of life in unifying chemical terms.of life in unifying chemical terms.


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figure 1-1Some characteristics of

living matter.

Chemical complexity;

Use energy;

Biological reproduction


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gure -

Diverse living

organisms sharecommon chemical

features.Same basic

structural units(cells)

Same kinds ofmacromolecules

(DNA, RNA,proteins)


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figurel-3Monomeric

subunits in linearsequences can

spell infinitelycomplex message


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All macromolecules are constructedAll macromolecules are constructed

from a few simple compoundsfrom a few simple compounds All living organism build moleculesAll living organism build molecules

from the same kinds offrom the same kinds of monomericmonomericsubunits.subunits.

The structure of a macromoleculesThe structure of a macromoleculesdetermines specific biological function.determines specific biological function.

Each genus and species is defined byEach genus and species is defined byits distinctive set of macromolecules.its distinctive set of macromolecules.


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Energy production andEnergy production and

consumption in metabolismconsumption in metabolism


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figure 1-4

Living organisms are

not at equilibriumwith their

surroundings.


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he dynamic steady state. A dynamic steady state

sults when the rate of appearance of a cellular

omponent is exactly matched by the rate of its

figure l-5


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Organisms transform energy andOrganisms transform energy and

matter from their surroundingmatter from their surrounding BioenergeticsBioenergetics

Universe: system and surroundingsUniverse: system and surroundings System: closed, isolated, openSystem: closed, isolated, open

A living organism is an open system.A living organism is an open system.


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Living organisms create and maintainLiving organisms create and maintain

their complex, orderly structurestheir complex, orderly structuresusing energy extracted from fuels orusing energy extracted from fuels or

sunlight.sunlight.


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figure l-6

During metabolic

transductions, the

randomness of the system

plus surroundings(expressed quantitatively

as entropy) increases as

the potential energy ofcomplex nutrient

molecules decreases.


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The first law of thermodynamicsThe first law of thermodynamics

In any physical or chemical change, theIn any physical or chemical change, the

total amount of energy in the universetotal amount of energy in the universeremains constant, although the form of theremains constant, although the form of the

energy may change.energy may change.

Th fl f l id


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The flow of electrons providesThe flow of electrons provides

energy for organismsenergy for organisms

-


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Sunlight is the ultimate source of

all biological energy.Thermonuclear reactions in the su

produce helium from hydrogen an

release electromagnetic energy,

which is transmitted to the earth a

light and converted into chemicalenergy by plants and some algae

and bacteria.


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figure l-8

hotosynthetic organisms are the ultimate providers of

- - -


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Energy coupling

in mechanical

and chemical

processes.

figure 1-9


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Free energy (G):Free energy (G): the amount of energythe amount of energy

available to do workavailable to do work Free Energy Change (G): is the

portion of the total energy change whichis available to do work as a reaction

proceeds to equilibrium at constanttemperature and pressure.


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The sign of the free energy change in a process

tells us whether that process or its reverse isthermodynamically favorable.

G

0 exergonic reaction G0 endergonic reaction

G of a spontaneously reacting system is

always negative

At equilibriumG0


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denosine triphosphate (ATP). The removal ofe terminal phosphoryl of ATP (shaded pink) is

ighly exergonic, and this reaction is coupled toany endergonic reactions in the cell as in the

figure l-10

nzymes promote sequences of chemical reactions


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ner y chan es durin a chemical reaction.

gure 1-11

nzymes promote sequences of chemical reactions


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n enzyme increases the rate of a specific chemicalaction.

figure l-12


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A linear metabolic pathway.

figure 1-13


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ATP is the shared

chemical intermediatelinking energy- releasing

to energy-requiring cell

processes.

figure l-14

Metabolism is regulated to achieve balance and


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eedback inhibition. Regulation byeedback inhibition in a typical

ynthetic (anabolic) pathway.

figure l-15

Metabolism is regulated to achieve balance and

economy


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Biological Information TransferBiological Information Transfer

Genetic continuity is vested in DNAGenetic continuity is vested in DNA

molecules.molecules. The structure of DNA allows for its repairThe structure of DNA allows for its repair

and replication with nearand replication with near--perfect fidelity.perfect fidelity. Changes in the hereditary instructionsChanges in the hereditary instructions

allow evolution.allow evolution.


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The complementary

structure of DNA.Complementarity between

the two strands accounts

for the accurate replicationessential for genetic

continuity.

figure 1-17


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gure 1-18

ole of mutation in evolution. The gradual accumulation

f mutations overlong periods of time results in new


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figure l-19


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figure l 19

The linear

sequence in DNA

encodes proteins

with three-

dimensional

structures.


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NoncovalentNoncovalent interactionsinteractions

stabilize threestabilize three--dimensionaldimensionalstructuresstructures

The Molecular Logic of Live

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