Chapter 1: Outline
The 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
1P2-1
1.3 Biochemical Processes
Metabolism 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.
1P2-2
Bio Rxns: By Mechanism-1
Nucleophilic Substitution-acyl
O
O
R C CH2C SCoA + CoA-SH
O
O
R C SCoA + CH3C SCoA
Sulfur nucleophile attacks C=O
1P2-3
Bio Rxns: By Mechanism-1
Nucleophilic Substitution-alkyl
O
C O
+
H3N CH
O
+
CH2 O C CH3
HSO
C O
O
+
H3N CH
+ CH C O
3
CH2 SH
Sulfur nucleohile attacks alkyl C
1P2-4
Bio Rxns: By Mechanism-2
Addition: two molecules combine to give one.
One molecule usually multiple bonded.
O
C O
HC
HO
+
C H H2O
C O
O
Addition occurs at C=C
O
C O
CH
CH2
C O
O
1P2-5
Bio Rxns: By Mechanism-3
Elimination- a molecule loses atoms usually
in the form of a small molecule like water.
O
C O
2H C OPO3
CH2 OH
O
C O
2C OPO3
CH2 +H O
2
Water is lost to form
phosphoenolpyruvate
1P2-6
Bio Rxns: By Mechanism-4
Isomerization: molecule rearranges
atoms
O
O
C O
C O
2H C OPO3
H C OH
2CH2 OH
CH2 OPO3
3-phosphoglycerate to 2-phosphoglycerate
1P2-7
Bio Rxns: By Mechanism-5
Hydrolysis: water cleaves (splits) a
covalent bond and inserts itself.
O
CH2 O C R
O
H C O C R + 3 H2O
O
CH2 O C R
CH2 OH
H C OH
CH2 OH
O
+ 3 HO C R
Hydrolysis of a fat
Hydrolysis is a variant of acyl substitution.
1P2-8
Bio Rxns: By Redox Nature
Redox 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.
1P2-9
Bio Rxns: By Redox Nature-2
In 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.
1P2-10
Bio Rxns: By Redox Nature-3
Oxidation
O
C O
H C OH
CH3 NAD+
lactate
O
C O
C O
CH3
NADH + H+ puruvate
Lactate is oxidized.
NAD+ is oxidizing agent.
1P2-11
Bio Rxns: By Redox Nature-4
Reduction
O
CH3CH CH C S-ACP
NADPH + H+
NADP+
O
CH3CH2CH2C S-ACP
The double bond
is reduced.
NADPH is the
reducing agent.
1P2-12
Quiz
Classify the reactions: by mechanism
and by redox character.
O
CH3CH CH C S-ACP Mech: addition
Not redox
O
OH
(add
2H
and
1
O)
CH3CH CH2C S-ACP
O
OH
CH3CH CH2C S-CoA
O
O
CH3C CH2C S-CoA
Mech: elimination
Oxidation
(remove 2H)
1P2-13
Energy
Energy 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.
1P2-14
Metabolism
Metabolism is the sum of all the enzymecatalyzed 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.
1P2-15
Biological Order
Processes 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 phosphoanhydride bonds of ATP.
1P2-16
Biological Order-2
2. 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 movement
Examples include cell division,
organelle movement and even
movement of enzymes along a DNA
strand.
1P2-17
Biological Order-3
4. 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.
1P2-18
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).
1P2-19
Information Flow
DNA
RNA
Protein
Transcription: RNA is made on a DNA
template
Translation: Protein is synthesized
from AAs and the three RNAs.
1P2-20
Transcription
RNA polymerases and proteins copy the
coded instructions in genes into RNA
molecules.
1P2-21
Translation
The nucleotide base code of messenger
RNA binds to ribosomes where it is
decoded into the amino acids
sequence of proteins.
1P2-22