Introduction to Biochemistry

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Introduction to Biochemistry
Contrary to what I once thought, scientific
progress did not consist simply in observing, in
accumulating experimental facts and drawing up a
theory from them. It began with the invention of
a possible world, or a fragment thereof, which
was then compared by experimentation with the
real world. And it was this constant dialogue
between imagination and experimentation that
allowed one to form an increasingly fine-grained
conception of what is called reality.
Francois Jacob
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Learning Objectives
Define dynamic steady-state and
homeostasis. Describe the three major
characteristics that distinguish living from
non-living systems. Identify the universal
carrier of metabolic energy. Describe the process
of information transfer in biological
systems. Describe the molecular logic of life.
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Periodic Table of the Elements
Alkali metals
Alkali earth metals
Rare earth metals
Transition metals
Other metals
Halogens
Nobel gases
Other non-metals
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C
H
O
Element abundances
N
in humans
Ca
Log ppb
(by weight)
Atomic Number
(ppb parts per billion)
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The most abundant elements in living organisms C
carbon O oxygen N nitrogen H
hydrogen
The vast majority of biochemically important
compounds are constructed from these elements.
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On a daily basis, our bodies requireon
averagemore than 100 mg of the major minerals
Minor or traceminerals B boron Cr chromium C
u copper I iodine Va vanadium Zn zinc Fe iron
Mn manganese Mo molybdenum Se selenium Si sili
con
Ca2 calcium P phosphorus (PO43-) K potassium Na
sodium Cl- chloride Mg2 magnesium S sulfur
(SO42-)
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Living organisms are composed of lifeless
molecules. Yet living organisms possess
extraordinary attributes not exhibited by any
random collection of molecules.
What distinguishes living organism from inanimate
objects?
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Inanimate matter usually consists of mixtures of
relatively simple chemical compounds. Living
organisms have a high degree of chemical
complexity and organization.
Thin section of vertebrate muscle tissue viewed
with the electron microscope.
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Living organisms extract, transform, and use
energy from their environment.
A prairie falcon acquires nutrients by consuming
a smaller bird.
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Living organisms have the capacity for precise
self-replication and self-assembly, a property
that is the quintessence of the living state its
most essential principle.
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All macromolecules are constructed from a few
simple compounds.
All living organisms (on earth) build molecules
from the same kinds of monomers.
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Living organisms are not at equilibrium with
their surroundings.
Proteins, nucleic acids, sugars, and fats are
present in living organisms but are essentially
absent from the surrounding medium, which contain
only simpler molecules such as carbon dioxide,
molecular oxygen, and water. Only by continuously
expending energy can an organism establish and
maintain its constituents at concentrations
distinct from those of the surroundings.
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The concentration of certain chemical components
in an organism may remain relatively constant
through time, but the population of these
molecules is far from static. Molecules are
synthesized and broken down by continuous
chemical reactions, involving a constant flux of
mass and energy through the system. The constancy
of concentration is the result of a dynamic
steady state.
steady state a nonequilibrium state of a system
through which matter is flowing and in which all
components remain at a constant concentration.
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When r1 r2 r3 r4, then the concentration
of glucose in the blood is constant.
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Blood glucose levels in normal individuals
Fasting state (after an overnight fast) 80-100
mg/dL (5 mM)
Fed state after a high carbohydrate meal, blood
glucose levels rise to 120-140 mg/dL (8
mM). Within two hours after a meal, blood glucose
levels return to 80-100 mg/dL, the fasting state
level.
homeostasis the maintenance of a dynamic
steady-state by regulatory mechanisms that
compensate for changes in external circumstances.
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Organisms transform energy and matter from their
surroundings.
Living cells and organisms must perform work to
stay alive and to reproduce themselves. The
continual synthesis of cellular components
requires chemical work. The accumulation and
retention of salts (Na, K, Cl-, Ca2) and
various organic compounds against a concentration
gradient involves osmotic work. The contraction
of a muscle or the motion of a bacterium
flagellum represents mechanical work.
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A living organism is an open system it exchanges
both matter and energy with its surroundings.
Living organisms use either of two strategies to
derive energy from their surroundings (1) they
take up chemical fuels from the environment and
extract energy by oxidizing them (catabolic
metabolism) (2) they absorb energy from sunlight
(photosynthesis)
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Nearly all living organisms derive their energy,
directly or indirectly, from the radiant energy
of the sun.
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Photosynthetic organisms are the ultimate
providers of fuels reduced, energy-rich
compounds.
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The flow of electrons provides energy for
organisms.
Photosynthetic cells absorb light energy and use
it to drive electrons from water to carbon
dioxide, forming energy-rich products such as
starch and sucrose, and release molecular oxygen
into the atmosphere. Nonphotosynthetic cells and
organisms obtain energy by oxidizing the
energy-rich products of photosynthesis and then
passing electrons to atmospheric oxygen to form
water, carbon dioxide, and other end products,
which are recycled in the environment.
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Energy coupling links reactions in biology
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Enzymes promote sequences of chemical reactions
Virtually every cellular chemical reaction occurs
at a measurable rate only because of the presence
of enzymes, biocatalysts that greatly enhance the
rate of specific chemical reactions without being
consumed in the process.
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Enzymes lower the activation energy between
reactant and product
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Stored nutrients
Complex biomolecules
The overall network of enzyme-catalyzed pathways
constitutes cellular metabolism.
Ingested foods
Mechanical work
Osmotic work
ATP (adenosine triphosphate) is the major
connecting link, the shared intermediate, between
the catabolic and anabolic components of this
network.
Catabolic reaction pathways
ADP
Anabolic reaction pathways
ATP
ATP is the universal carrier of metabolic energy.
CO2
NH3
H2O
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Metabolism is regulated to achieve balance and
economy
Regulation by feedback inhibition in a typical
synthetic (anabolic) pathway.
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Genetic continuity is vested in DNA molecules
The single DNA molecule of E. coli, seen leaking
out of a disrupted cell, is hundreds of times
longer than the cell itself, and contains all of
the encoded information necessary to specify the
cells structure and functions.
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The structure of DNA allows for its repair and
replication with near-perfect fidelity.
DNA is the only molecule that is repaired.
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Information transfer
The linear sequence in DNA encodes proteins with
three-dimensional structures
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Noncovalent interactions stabilize
three-dimensional structures.
These include hydrogen bonds, ionic interactions
among charged groups, van der Waals interactions,
and hydrophobic interactions among nonpolar
groups.
Three-dimensional biological structures combine
the properties of flexibility and stability.
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The Molecular Logic of Life
A living cell is a self-contained,
self-assembling, self-adjusting,
self-perpetuating, constant-temperature system of
molecules that extracts free energy and raw
materials from its environment. The cell uses
this energy to maintain itself in a dynamic
steady state, far from equilibrium with its
surroundings. The many chemical transformations
within cells are organized into a network of
reaction pathways, promoted at each step by
specific catalysts called enzymes, which the cell
itself produces. A great economy of parts and
processes is achieved by regulation of the
activity of key enzymes.
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Self-replication through many generations is
ensured by the self-repairing, linear
information-coding system. Genetic information
encoded as sequences of nucleotide subunits of
DNA and RNA specifies the sequence of amino acids
in each distinct protein, which ultimately
determines the three-dimensional structure and
function of each protein. Many weak (noncovalent)
interactions, acting cooperatively, stabilize the
three-dimensional structures of biological
macromolecules while allowing sufficient
flexibility for biological actions.