Chapter One

Biochemistry and the

Organization of Cells
Some Basic Themes

• All living things make use of the same types of biomolecules,

and all use energy
• as a result, all living things can be studied using the
methods of chemistry and physics

• The fundamental similarity of cells of all types makes it

interesting to speculate on the origins of life
• both cells and the biomolecules of which they are made
must have arisen ultimately from very simple molecules,
such as H2O, CH4, CO2, NH3, N2, and H2

• Field of Biochemistry draws many disciplines

• allows us to answer questions related to molecular nature
of life
Bio-molecules

• Organic chemistry: the study of the compounds of

carbon
• the cellular apparatus of living organisms is made up
of carbon compounds
• biomolecules are part of the subject matter of organic
chemistry
• the reactions of biomolecules can be described by the
methods of organic chemistry
• The experiment of Friedrich Wöhler in 1828
Levels of Structural Organization in the
Human Body
Bio-molecules (Cont’d)

• Functional group: an atom or group of atoms that shows

characteristic physical and chemical properties
ATP and The Reactions for its Formation
Origins of Life
• The “big bang” theory
• all matter was originally confined in a very small space
• as the result of an explosion, it started to expand with great
force; temperature approx. 15 x 109 K
• the average temperature of the universe has been decreasing
ever since
• in the earliest stages of the universe, the only elements present
were H, He, and Li
• other elements formed by
• thermonuclear reactions in stars
• explosions of stars
• the action of cosmic rays outside the stars
Relative Abundance of Important Elements
Bio-molecules (Cont’d)

• Gases present in the atmosphere of the early earth included

NH3, H2S, CO, CO2, CH4, N2, H2, and H2O but not O2

• Experiments have demonstrated that important biomolecules,

such as proteins and nucleic acids, could have arisen under
abiotic (nonliving) conditions from reactions of these simple
compounds
• in the earth’s oceans
• on the surface of clay particles
Bio-molecules (Cont’d)

• Living cells include very large molecules, such as proteins,

nucleic acids, polysaccharides, and lipids
• these biomolecules are polymers (Greek: poly + meros, many +
parts)
• they are derived from monomers (Greek: mono + meros, single
+ part)
--amino acids --> proteins
--nucleotides --> nucleic acids
--monosaccharides --> polysaccharides
--glycerol and 3 fatty acids --> lipids
Informational Macromolecules
Bio-molecules (Cont’d)

• Enzymes: a class of proteins that are biocatalysts

• the catalytic effectiveness of a given enzyme depends on its
amino acid sequence
• Genetic code: the relationship between the nucleotide
sequence in nucleic acids and the amino acid sequence in
proteins
• theories of the origin of life consider how such a coding system
might have arisen
Bio-molecules (Cont’d)

• Which came first…the chicken or the egg?

• catalytic activity associated with proteins
• coding associated with nucleic acids
• It has been discovered recently that certain types of RNA have
catalytic activity and are capable of catalyzing their own
further processing (See Figure 1.7 p.12)
• RNA is now considered by many scientists to have been
the original coding material
• it still serves this function in some viruses
The “RNA World”

• The appearance of a form of RNA capable of coding

for its own replication was the pivotal point in the
origin of life

• This original RNA both encoded for and catalyzed its

own replication

• In time, this system evolved to encode for the

synthesis of protein catalysts

• Even later, DNA became the primary genetic

material, and RNA took on only an intermediary role
in the synthesis of proteins
Stages in the Evolution of Self-replicating
RNA Molecules
Theories on the Origin of Life

• A key point in the development of living cells is the

formation of membranes that separate cells from their
environment
• Some theories of the origin of life focus on proteins
• according to one model, proteinoids aggregated to
form microspheres
• Double-Origin theory: the development of a coding
system and the development of catalysis came about
separately
• a combination of the two later in time produced life as
we know it.
Prokaryotes and Eukaryotes

• Prokaryote: Greek derivation meaning “before the

nucleus”
• single-celled organisms
• include bacteria and cyanobacteria
• Eukaryote: Greek derivation meaning “true nucleus”
• contain a well-defined nucleus surrounded by a
nuclear membrane
• can be single celled, such as yeasts and Paramecium,
or multicellular, such as animals and plants
Comparison of Prokaryotes and Eukaryotes
A Comparison of a typical animal cell, plant
cell, and prokaryotic cell

• Important organelles
listed in table 1.3
Comparison of Prokaryotes and Eukaryotes
Five Kingdoms, Three Domains

• 5-kingdom system takes into account differences

between prokaryotes and eukaryotes

• Provides classification for eukaryotes that are neither

plants nor animals

• Kingdoms are: Monera, Protista, Fungi, Plantae, and

Anamilia
Five Kingdoms, Three Domains
What is source of energy in cells?

• Light from the sun is the ultimate source of energy for

all life on earth
• photosynthetic organisms use light energy to drive the
energy-requiring synthesis of carbohydrates
• non-photosynthetic organisms consume these
carbohydrates and use them as energy sources
• The energetics of a chemical reaction
• if the change in free energy is negative (free energy
decreases), the reaction is spontaneous as written
• if the change in positive (free energy increases), the
reaction will not occur as written unless energy is
supplied from an external source
How are energy changes measured?

Thermodynamics- branch of science that answers questions

about processes that are energetically favorable
Spontaneity in biochemical reactions
• Free Energy of a System
 G < 0 spontaneous exergonic- energy released
 G= 0 Equilibrium
 G > 0 Nonspontaneous endergonic- energy required
• Life and Thermodynamics
 G=H-TS
 H is heat of a reaction at constant pressure
 S is the change in entropy
 G is the change in free energy
• T is the temperature