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

• Biomolecules

• 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

• Biomolecules (Cont’d)

• Functional group: an atom or group of atoms that shows characteristic physical and chemical
properties

• 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

• Gases present in the atmosphere of the early earth included NH 3, 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

• 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

• 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

• Biomolecules (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

• 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

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