CHAPTER I: BIOCHEMISTRY AND THE

ORGANIZATION OF CELLS
1.1
BASIC THEMES
How does biochemistry describe life
processes?
Humans down to individual cells
are complex, but one unifying
feature for all living things:
- All use the same types of
biomolecules, all use energy (so
they can be studied via chem
and physics)
- Lol 19th century bio: Vital
forces
Multidisciplinary nature allows it to
use results from many sciences to
answer questions about the
molecular nature of life processes
- Important in medical field
How did living things originate?
Atoms > molecules > macromolecules
> organelles > cell > tissue > organ >
body system of organism
1.2
CHEMICAL FOUNDATIONS OF
BIOCHEMISTRY
Organic chemistry study of carbon
compounds, especially carbon and
hydrogen and their derivatives
Can a chemist make the molecules of
life in a laboratory?
Friedrich Wohler, 1828, synthesized
urea from ammonium cyanate

What makes biomolecules special?

Most of the functional groups in
biomolecules contain oxygen and
nitrogen, highly electronegative,
polar
ATP (Adenosine triphosphate), a
molecule that is the energy
currency of the cell, contains both
ester and anhydride linkages
involving phosphoric acid
1.3
THE BEGINNINGS OF BIOLOGY:
ORIGIN OF LIFE
The Earth and its age
How and when did the Earth come to
be?

Most widely accepted theory: Big

Bang, a cataclysmic explosion
- All matter was confined to a
small volume, explosion,
primordial fireball expanded
- Extremely hot: 12x109 K
- Coz of expansion, cooling
universe, formation of stars and
planets
- Hydrogen, Helium and Lithium
yung predominant
- The rest are formed by (1)
thermonuclear reactions that
normally take place in stars (2)
explosions of stars (3) the
action of cosmic rays outside
the stars since the formation of
the galaxy
- C, O, N, P, S their isotopes
have particularly stable nuclei,
produced by nuclear reactions
in first generation stars
- Many first generation stars were
destroyed by supernovas, their
material being recycled to
produce second-generation
stars like our Sun
- Radioactive dating (decaying
unstable nuclei) makes out our
Earth to be 4-5 billion years old
- In the early stages of the Earth
walang oxygen
- Walang ozone layer, and laging
naiiirradiate ng UV rays
- Under these conditions,
chemical reactions produced
simple biomolecules
- Gases in early atmosphere: NH3,
H2S, CO, CO2, CH4, N2, H2, H2O
- Sabi nung una CH4 yung carbon
source
- But 3.8 billion years ago,
madami na daw CO2 oldest
rock kasi ganun yung age tapos
carbonate siya, produced from
CO2
- NH3 must have dissolved in
oceans leaving N2 for the
formation of proteins and
nucleic acids
Biomolecules
How were biomolecules likely to have
formed on the early Earth?

Miller-Urey experiment abiotic

synthesis
Trial: electric discharge (lightnigh)
is passed through a closed system
that contains H2, CH4 and NH3 in
addition to H2O
- Products: formaldehyde (HCHO)
hydrogen cyanide
(HCN) which are simple organic
molecules, and then also amino
acids (building blocks of
proteins)
Theorized that the reactions either
occurred in the early oceans, or on
the surfaces of clay particles that
were present in the early earth
Mineral substances similar to clay
can serve as catalysts in many
types of reactions
Recent theories focus on RNA, not
proteins, as the first genetic
molecules
Recent experiments: possible to
synthesize nucleotides from simple
molecules that includes a precursor
that is neither a sugar nor a
nucleobase, but a fragment consisting
of a sugar and a part of a base
- Fragment: 2-aminooxazole
o Highly volatile
o Can vaporize and
condense so as to give
rise to pockets of pure

material in reasonably
large amounts
o In turn, phosphates
released by volcanic
action can react with the
2-aminooxazole to
produce nucleotides
o Products include
nucleotides that are not
part of present-day RNA,
but intense UV light,
which was present on the
early earth, destroyed
those, leaving those
found in RNA today
Monomers: hundreds or thousands of
smaller molecules which can be linked
to produce polymers
- Monomers include amino acids,
nucleotides, and
monosaccharides (sugar
monomers)
- Amino acids are the monomers,
polymerize to form proteins
- Nucleotides are monomers,
polymerize to form nucleic acids
- Sugar monomers aka
monosaccharides produce
polysaccharides
- Polymerization expts on amino
acids have produced protein-like
polymers nucleotides and
monosaccharides also, but they
are less ready to polymerize