Chemistry 501 Handout 1 The Foundations of Biochemistry Chapter 1

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Chemistry 501 Handout 1The Foundations of
BiochemistryChapter 1
Lehninger. Principles of Biochemistry. by Nelson
and Cox, 5th Edition W.H. Freeman and Company
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• Distinguishing features of living organisms
• A high degree of chemical complexity and
  microscopic organization.
• Systems for extracting, transforming, and using
  energy from the environment.
• A capacity for precise self-replication and
  self-assembly.
• Mechanisms for sensing and responding to
  alterations in their environment.
• Defined functions for each of their components
  and regulated interactions among them.
• - A history of evolutionary change.

Diverse living organisms share common chemical
features
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Cells are the structural and functional units of
all living organisms
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There are three distinct domains of life
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Organisms can be classified according to their
source of energy (sunlight or oxidizable chemical
compounds) and their source of carbon for the
synthesis of cellular material.
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Common structural features of bacterial cells
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Subcellular fractionation of tissue
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The cytoplasm is organized by the cytoskeleton
and is highly dynamic
The three types of cytoskeletal filaments
Actin filaments (red) Microtubules (green)
Intermediate filaments (red) Microtubules (green)
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Cells build supramolecular structures
Structural hierarchy in the molecular
organization of cells
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The organic compounds from which most cellular
materials are constructed
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Elements essential to animal life and health
Only about 30 of the more than 90 naturally
occurring chemical elements are essential to
organisms
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Biomolecules are compounds of carbon with a
variety of functional groups
Geometry of carbon bonding
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Some common functional groups of biomolecules
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Several common functional groups in a single
molecule
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Representations of molecules
Perspective form
Ball-and-stick model
Alanine
Space-filling model (van der Walls radius)
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Three-dimensional structure is described by
configuration and conformation
Configuration is conferred by (i) double bonds,
around which there is no freedom of rotation
(ii) chiral centers, around which substituent
groups are arranged in a specific sequence.
Configurations of geometric isomers (cis-trans
isomers)
Configurational isomers cannot be interconverted
without temporarily breaking one or more
chemical bonds (covalency defines configuration)
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Initial event in light detection (vertebrate
retina)
250 kJ mol-1
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Molecular asymmetry chiral and achiral molecules
Enantiomers (stereoisomers)
Stereoisomers molecules with the same chemical
bonds but with different stereochemistry That
is, different configuration, the fixed spatial
arrangement of atoms.
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Two types of stereoisomers
A molecule with n chiral C-atoms has 2n
stereoisomers.
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Nomenclature the D, L system based on the
absolute configuration of glyceraldehyde
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Nomenclature the RS system
rectus
sinister
Decreasing priority
Lowest priority pointing away from the viewer
To each group attached to a chiral C atom is
assigned a priority e.g. -OCH3 gt -OH gt -NH2
gt -COOH gt -CHO gt -CH2OH gt -CH3 gt -H
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Stereochemistry distinguishable by smell and
taste in humans
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Distinct from configuration is molecular
conformation (The spatial arrangement of
substituent groups that, without breaking any
bonds, are free to assume different positions in
space because of the freedom of rotation about
single bonds)
Ethane Conformations
Eclipsed
Staggered
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Interactions between biomolecules are invariably
stereospecific (the fit in such interactions
must be stereochemically correct i.e. the
combination of configuration and conformation)

• e. g.
• - reactant with enzymes
• hormone with its receptor on
• the cell surface
• - antigen with its specific antibody

Complementary fit between a macromolecule and
a small molecule
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Living cells and organisms must perform work to
stay alive and to reproduce themselves (which
requires the input of energy)
Some energy interconversions in living organisms
Living organisms exist in a dynamic steady
state, never at equilibrium with their
environment
Organisms transform energy and matter from their
surroundings
A flow of electrons provides energy for organisms
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Energy coupling links reactions in biology
Cell function depends largely on molecules, such
as proteins and nucleic acids, for which the free
energy of formation is positive. To carry out
these thermodynamically unfavorable reactions,
cells couple them to other reactions that
liberate free energy, so that the overall process
is exergonic.
The usual source of free energy in coupled
biological reactions is the energy released by
hydrolysis of phosphoanhydride bonds, such as
those of adenosine triphosphate (ATP).
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Energy coupling in mechanical and chemical
processes
DG DGo RT ln Q
DG DH - TDS
DG gt 0 ---gt nonspontaneous process
(endergonic) DG lt 0 ---gt spontaneous process
(exergonic) DG 0 ---gt equilibrium (DGo -
RT ln Keq)
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Energy changes during a chemical reaction
Enzymes catalyze reactions by lowering the
activation barrier
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The central role of ATP in metabolism
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Genetic continuity is vested in single DNA
molecules
Complementarity between the two strands of DNA
A deoxyadenylate G deoxyguanylate C
deoxycytidylate T deoxythymidylate
The single DNA molecule of the bacterium E. coli
contains about 10 million characters
(deoxyribonucleotides)
The structure of DNA allows for its replication
and repair with near-perfect fidelity
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The linear sequence of DNA encodes proteins with
three-dimensional structures
Protein folding into its native conformation is
often aided by molecular chaperones, which
catalyze the process by discouraging incorrect
folding.
Once in its native conformation, a protein may
associate noncovalently with other proteins, or
with nucleic acids or lipids, to form
supramolecular complexes such as chromosomes,
ribosomes, and membranes.
DNA to RNA to protein (hexokinase)
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Changes in hereditary instructions allow evolution

Mutations can be harmful or even lethal to the
organism. Occasionally a mutation better equips
an organism or cell to survive in its
environment.
Survival of the fittest under selective pressure
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RNA or related precursors may have been the
first genes and catalysts.
Biomolecules first arose by chemical evolution.
To simulate lightening
To simulate primitive atmospheric conditions
Abiotic production of biomolecules
A possible RNA world scenario
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Landmarks of evolution of life on earth
Eukariotic cells evolved from prokariotes in
several stages
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Evolution of eukariotes through endosymbiosis
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