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Chapter 1: OutlineThe Living World

Bacteria, Archaea, Eukarya, (Viruses)

Biomolecules

Functional Groups

Major Classes of Biomolecules

Biochemical Processes (We are here.)

Reactions, Energy, Metabolism, Order

Genetic Information Processing

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1.3 Biochemical ProcessesMetabolism is the sum of all biochemical

reactions.

Functions of metabolism are:

1. Synthesis of biomolecules.

2. Transport of ions and molecules across cell membranes.

3. Production of force and movement.

4. Removal of metabolic waste and other toxic substances.

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Bio Rxns: By Mechanism-1Nucleophilic Substitution-acyl

R CO

CH2CO

SCoA

R CO

SCoA CH3CO

SCoA

CoA-SH+

+

Sulfur nucleophile attacks C=O

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Bio Rxns: By Mechanism-1Nucleophilic Substitution-alkyl

Sulfur nucleohile attacks alkyl C

OCO

CHOCH2 C

OCH3

NH3

+

OCO

CHSHCH2

NH3

+OC

OCH3

HS-+

+

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Bio Rxns: By Mechanism-2Addition: two molecules combine to give one.One molecule usually multiple bonded.

OCO

OCO

CC

HH

OCO

OCO

CCH2

HOH+ H2O

Addition occurs at C=C

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Bio Rxns: By Mechanism-3Elimination- a molecule loses atoms usually in the form of

a small molecule like water.

OCO

CCH2

HOH

OPO32-

OCO

CCH2

OPO32-

+H2OWater is lost to formphosphoenolpyruvate

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Bio Rxns: By Mechanism-4Isomerization: molecule rearranges

atoms

OCO

CCH2

HOH

OPO32-

OCO

CCH2

HOPO3

2-OH

3-phosphoglycerate to 2-phosphoglycerate

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Bio Rxns: By Mechanism-5Hydrolysis: water cleaves (splits) a

covalent bond and inserts itself.

CH2OHCCH2

HOHOH

COH RO

CO RO

CH2O

C

CH2

H O

CO RO

CO RO

+ 3 H2O

+ 3Hydrolysis of a fat

Hydrolysis is a variant of acyl substitution.

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Bio Rxns: By Redox NatureRedox reactions involve the transfer of

electrons.

Oxidation: a loss of electrons

Reduction: a gain of electrons

Oxidizing agent: the electron acceptor

Reducing agent: the electron donor

Note: Reactions may fall into both classification categories, mechanism and redox.

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Bio Rxns: By Redox Nature-2In biochemistry redox reactions are

usually recognized by the following changes:

Oxidation occurs when a molecule loses two hydrogens and/or gains an oxygen.

Reduction occurs when a molecule gains two hydrogens and/or loses an oxygen.

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Bio Rxns: By Redox Nature-3Oxidation

CCH OHCH3

OO

CC OCH3

OO

NAD+

NADH + H+lactate puruvate

Lactate is oxidized.NAD+ is oxidizing agent.

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Bio Rxns: By Redox Nature-4

Reduction

CH3CH CH CO

S-ACP

CH3CH2CH2CO

S-ACP

NADPH + H+

NADP+

The double bond is reduced.NADPH is the reducing agent.

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QuizClassify the reactions: by mechanism

and by redox character.

CH3CH CH CO

S-ACP

CH3CH CH2CO

S-ACPOH

Mech: additionNot redox (add 2H and 1 O)

CH3C CH2CO

S-CoAO

CH3CH CH2CO

S-CoAOH

Mech: eliminationOxidation (remove 2H)

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EnergyEnergy is the capacity to do work.

Cells generate most of their energy from redox reactions.

When electrons are transferred to an electron deficient molecule, energy is lost. Several redox reactions provide enough energy for ATP synthesis.

The ultimate source of energy used by most organisms on earth is the sun.

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MetabolismMetabolism is the sum of all the enzyme-

catalyzed reactions in a living organism.

In anabolic (biosynthetic) pathways large complex molecules are synthesized from smaller molecules.

In catabolic pathways large complex molecules are degraded into simpler products. A portion of the energy produced drive anabolic reactions.

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Biological OrderProcesses can be classified in the

following categories.

1. Synthesis of biomolecules

Many reactions are integrated into carefully regulated pathways. Energy is supplied either directly or indirectly by breaking phospho-anhydride bonds of ATP.

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Biological Order-22. Transport across membranes.

Cell membranes regulate the passage of ions and molecules from one compartment to another.

Much of this is accomplished by membrane bound proteins.

3. Cell movementExamples include cell division,

organelle movement and even movement of enzymes along a DNA strand.

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Biological Order-34. Waste removal

Excess CO2, H2O, and NH3 must be

removed. CO2 is exhaled, H2O is

excreted by the kidneys, and NH3 is

converted to urea.

Hydrophobic molecules such as the steroid hormones are converted to water soluble derivatives.

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1.4 Genetic Information“Central dogma” of molecular biology

The chemical information in a gene (DNA) directs the assembly of amino acids into polypeptides (proteins).

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Information Flow

DNA RNA Protein

Transcription: RNA is made on a DNA template

Translation: Protein is synthesizedfrom AAs and the three RNAs.

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TranscriptionRNA polymerases and proteins copy the

coded instructions in genes into RNA molecules.

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Translation

The nucleotide base code of messenger RNA binds to ribosomes where it is decoded into the amino acids sequence of proteins.