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BIOCHEMISTRY

Biochemistry and the Organization of Cells

Some Basic Themes

Biomolecules

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

Organic chemistry: the study of the compounds of


carbon

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

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 Whler in 1828

Levels of Structural Organization in the


Human Body

Biomolecules (Contd)
Functional group: an atom or group of atoms that show
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 10 9 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

Biomolecules (Contd)
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 earths oceans
on the surface of clay particles

Biomolecules (Contd)

Informational Macromolecules

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

Biomolecules (Contd)

Biomolecules (Contd)

Enzymes: a class of proteins that are biocatalysts

Which came firstthe chicken or the egg?

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

The RNA World

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.11)
RNA is now considered by many scientists to have been
the original coding material
it still serves this function in some viruses

Stages in the Evolution of Self-replicating


RNA Molecules

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

Prokaryotes and Eukaryotes

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.

Prokaryote: Greek derivation meaning before the


nucleus

Comparison of Prokaryotes and Eukaryotes

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

A Comparison of a typical animal cell, plant


cell, and prokaryotic cell

Important organelles
listed in table 1.3

Five Kingdoms, Three Domains

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

What is source of energy in cells?

How are energy changes measured?

Light from the sun is the ultimate source of energy for


all life on earth

Thermodynamics- branch of science that answers questions


about processes that are energetically favorable

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

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 - TS
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