1 | The Foundations of
Biochemistry
© 2017 W. H. Freeman and Company
CHAPTER 1
The Foundations of Biochemistry
Learning goals:
• Distinguishing features of living organisms
• Structure and function of the parts of the cell
• Roles of small and large biomolecules
• Energy transformation in living organisms
• Regulation of metabolism and catalysis
• Coding of genetic information in DNA
• Role of mutations and selection in evolution
Biochemistry Is
the Chemistry of Living Matter
Living matter is characterized by:
• a high degree of complexity and organization
• the extraction, transformation, and systematic use of
energy to create and maintain structures and to do
work
• the interactions of individual components being
dynamic and coordinated
• the ability to sense and respond to changes in
surroundings
• a capacity for fairly precise self-replication while
allowing enough change for evolution
Complexity and Organization
Living Organisms Must Intake and Transform
Nutrients into Energy
Living Organisms Must
Accurately Reproduce
Three Distinct Domains of Life Defined by Cellular
and Molecular Differences That Evolved over Time
Six Kingdoms of Life Defined by
Organism, Cellular, and Molecular Differences
Six kingdoms
Cellular organization
• Archaea
• Bacteria
• Protista
• Fungi
• Plantae
• Animalia
Unicellular prokaryote
Unicellular prokaryote
Unicellular eukaryote
Uni- or Multicellular eukaryote
Multicellular eukaryote
Multicellular eukaryote
Cell: The Universal Building Block
• Living organisms are made of cells.
• The simplest living organisms are unicellular (singlecelled).
• Larger organisms are multicellular (many-celled),
with different functions for different cells.
• Cells have some common features but can contain
unique components for different organisms.
All Cells Share Some Common Features
Bacterial Cell Structure
Components of Bacterial Cell
Structure
Composition
Function
Cell wall
Cell membrane
Nucleoid
Ribosomes
Pili
Flagella
Cytoplasm
Carbohydrate + protein
Lipid + protein
DNA + protein
RNA + protein
Protein
Protein
Aqueous solution
Mechanical support
Permeability barrier
Genetic information
Protein synthesis
Adhesion, conjugation
Motility
Site of metabolism
Eukaryote Cells: More Complexity
• Have membrane-bound nucleus by definition:
– protection for DNA; site of DNA metabolism
– selective import and export via nuclear membrane pores
• Have membrane-enclosed organelles:
– mitochondria for energy in animals, plants, and fungi
– chloroplasts for energy in plant
– lysosomes for digestion of un-needed molecules
• Compartmental segregation of energy-yielding and
energy-consuming reactions helps cells to maintain
homeostasis and stay away from equilibrium.
Animal and Plant Cells
Contain Unique Components
Animal and Plant Cells
Contain Unique Components
Animal and Plant Cells
Contain Identical and Unique Components
Plant
Both
Animal
Chloroplast
Vacuole
Glyoxysome
Plasmodesma
Cell wall
Membrane
Nucleus and Nucleolus
Mitochondria
Rough and Smooth ER
Ribosomes
Golgi
Cytoskeleton
Lysosome
Peroxisomes
Cytoplasm and Cytoskeleton
• Cytoplasm is a highly viscous solution where many
reactions take place.
• Cytoskeleton consists of microtubules, actin
filaments, and intermediate filaments.
– cellular shape and division
– intracellular organization
– intracellular transport paths
– cellular mobility
The Cytosol Is Very Crowded
Folded proteins
Translated peptide
Cytoskeleton Maintains
Cellular Organization
Cellular Organization Is Dynamic,
Changing Drastically at Different Stages
Biochemistry is
the Chemistry of Living Matter
•
The basis of all life is the chemical reactions that take place
within the cell.
Chemistry allows for:
•
a high degree of complexity and organization
•
the extraction, transformation, and systematic use of energy
to create and maintain structures and to do work
•
the interactions of individual components to be dynamic and
coordinated
•
the ability to sense and respond to changes in surrounding
•
a capacity for fairly precise self-replication while allowing
enough change for evolution
Organisms Can Also Be Classified by
Different Energy and Carbon Sources
Living Systems Extract Energy
• From sunlight
– plants
– green bacteria
– cyanobacteria
• From fuels
– animals
– most bacteria
• Energy input is needed in
order to maintain life.
The Molecular Logic of Life
We look at the chemistry that is behind the:
• initiation and acceleration of reactions
• organization and specificity of metabolism and
signaling
• storage and transfer of information and energy
The Molecular Hierarchy of Structure
Biochemistry: Unique Role of Carbon
30 Elements Essential for Life
• Other than carbon, elements H, O, N, P, and S are also common.
• Metal ions (e.g., K+, Na+, Ca++, Mg++, Zn++, Fe++) play important roles
in metabolism.
Common Functional Groups of Biological Molecules
Biological Molecules Typically Have
Several Functional Groups
The ABCs of Life
The Function of Molecules Strongly
Depends on Three-Dimensional Structure
Cis vs. Trans
Cis vs. Trans
Enantiomers and Diastereomers
Diastereomers (non-mirror images)
Enantiomers and Diastereomers
Interactions Between
Biomolecules Are Specific
• Macromolecules fold into 3D structures with
unique binding pockets.
• Only certain molecules fit in well and can bind.
• Binding of chiral biomolecules is stereospecific.
Interactions Between
Biomolecules Are Specific
Organisms Perform Energy Transductions
to Accomplish Work to Stay Alive
Organisms Perform Energy Transductions
to Accomplish Work to Stay Alive
How to Speed Reactions Up
Higher temperatures
− stability of macromolecules is limiting
Higher concentration of reactants
− costly, as more valuable starting material is needed
Changing the reaction by coupling to a fast one
− universally used by living organisms
Lower activation barrier by catalysis
− universally used by living organisms
Equilibrium and ΔG°Measure
Spontaneity of a Reaction
Unfavorable and Favorable Reactions
Energy Coupling
• Chemical coupling of exergonic and endergonic
reactions allows otherwise unfavorable reactions.
• The “high-energy” molecule (ATP) reacts directly with
the metabolite that needs “activation.”
Catalysis
• A catalyst is a compound that increases the rate of a
chemical reaction.
‡
• Catalysts lower the activation free energy G .
• Catalysts do not alter G°.
• Enzymatic catalysis offers:
– acceleration under mild conditions
– high specificity
– possibility for regulation
Enzymes Lower the Activation Energy to
Increase the Reaction Rate
Series of Related Enzymatically Catalyzed
Reactions Forms a Pathway
Metabolic pathway
• produces energy or valuable materials
Signal transduction pathway
• transmits information
Pathways Are Controlled in Order to
Regulate Levels of Metabolites
Example of a negative regulation:
Product of enzyme 5 inhibits enzyme 1 to prevent
wasteful excess products.
Genetic and Evolutionary Foundations
• Life on Earth arose 3.5–3.8 billion years ago.
• The formation of self-replicating molecules was a
key step.
• Could it have been DNA?
• Could it have been proteins?
RNA World?
• RNA can act both as the information carrier and
biocatalyst.
• Some viruses use RNA as a primary means of genetic
information.
Complementarity in DNA Allows for
Replication with Near-Perfect Fidelity
The Central “Dogma” of Biochemistry:
DNA → RNA → Protein
Natural Selection
Favors Some Mutations
• Mutations occur more or less randomly in DNA and
RNA.
• Mutated polynucleotides may be transcribed and
translated into molecular machinery like proteins.
• Mutations that give organisms an advantage in a
given environment are more likely to be propagated.
Natural Selection
Favors Some Mutations
Evolution of Eukaryotes Could Also Be
Mediated Through Endosymbiosis
Chapter 1: Summary
In this chapter, we learned to:
• understand what defines living organisms
• relate structure and function of the cell
• realize that the structure of biomolecules
often gives them specific functions
• grasp principles of bioenergetics
• review the forces behind evolution