MARISOL A.

LAGUARDIA
Teacher-in-Charge
myra_laguardia @ yahoo.com
BIOCHEMISTRY
the study of the chemical composition
of living matter

the study of the biochemical processes

that underlie life activities during
growth and maintenance.

Seeks to describe the structure,

organization, and functions of living
matter in molecular terms.
 3 Principal Areas:
1. structural chemistry of the components
of living matter and the relationships of
biological function.

2. study of metabolism (totality of chemical

reactions that occur in living matter).

3. molecular genetics (chemistry of

processes and substances that store and
transmit biological information) to
understand heredity and the expression of
genetic information in molecular terms.
 Development of
Biochemistry
Living matter was generally believed
as composed of substances
qualitatively different from those found
in nonliving matter, substances that
did not behave according to the known
laws of physics and chemistry.

VITALISM held that living things are

endowed with a mysterious and divine
life force.
 Mid 18 th
century
investigations of the chemical composition of plant
and animal tissues
Friedrich Wohler showed that urea (of biological
origin) could be synthesized in the laboratory from
the inorganic compound ammonium cyanate.
O
II
NH4+NCO- H2N – C – NH2
Ammonium cyanate urea
 Late 18th and early 19th
Century
studies of respiration, fermentation and quantitative analysis
of naturally occurring substances.
1875- chromosomes were discovered by Walter Fleming
and identified as genetic elements by 1902.
1896- Friedrich Miescher isolated nucleic acids, but their
chemical structures were poorly understood and were
regarded as simple substances.
1897 - Eduard and Hans Buchner found that extracts
from broken and thoroughly dead yeast cells could carry out
the entire process of fermentation of sugar to ethanol.
 This discovery opened the door to analysis of biochemical
reactions and processes in vitro (Latin, “in glass”) in a test
tube, rather than in intact living matter (in vivo).
 Late 18th and early 19th
Century
1900- genes are found in chromosomes.

1903 – Carl Neuberg was the first to formally introduce

biochemistry.
1920s
 isolation, determination of other chemical structure
 synthesis of vitamins and certain hormones
 concepts of the essential amino acids in citric acid cycle
 elucidation of metabolic pathways by means of isotope tracers

1926- J.B. Sumner showed that protein urease (enzyme from

jack beans) could be crystallized, like any organic compound.
 Mid-19th Century
genes were discovered as the unit
of hereditary information as derived
from the works of Gregor Mendel.
1940s-1950s- DNA is the bearer of
genetic information.
 Early 1950s
 development of new and improved research techniques
and equipment
 1932- 1950 - development of electron microscope
providing a whole new level of insight into cellular
structure (mitochondria and chloroplasts).
 1953- James Watson and Francis Crick described
the double-helical structure of the DNA.
 Scientists who pioneered the study of
biochemistry
 Priestly
 Lavoisier
 Liebig
 Berzelius
 Bernard
 Their studies were concerned with the whole animals
and gross tissue samples answering the “what” type of
questions
 Later Advances in
Biochemistry involves:
Modern refinement of
biochemical techniques
Development of more
sophisticated and sensitive
instrumentation
 Ultracentrifuge by Svedberg –
made possible the investigation at
cellular levels
 Made possible the exploration of
chemical mechanisms involved in
the development and
differentiation of cells
 Made possible the study of the
physiology and mechanisms
within the cell.
 Later Advances in
Biochemistry involves:
 Biochemical elucidation of the
structures of deoxyribonucleic acid
(DNA) and ribonucleic acid (RNA)
 Provide fuller understanding of the
structure of genes and the
transmission of genetic information

 Study of the precise mechanism

involved in the metabolic reactions
in cells
 Studies on the chemical transformation
by which glucose, amino acids and
lipids derived from foods are
transformed into essential body
components (anabolism) by way of
metabolic pathways or are used for
energy (catabolism) in cells.
 Later Advances in
Biochemistry involves:
Visualization of changes in molecular transformation
by x-ray diffraction techniques

Discovery of the use of:

 isotropic tracers in metabolic pathways
 chromatographic procedures in isolating intermediates
involved in the metabolic reactions
 radioimmunoassay techniques in determining quantities of
certain biomolecules such as insulin and hormones
DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER
1. They are complicated
and highly organized.
Their cells possess
intricate internal
structures containing
many kinds of
molecules.
(a) Microscopic complexity and
They occur in an organization are apparent in this
enormous number of thin section of vertebrate muscle
different species with tissue, viewed with the electron
structural organization. microscope.
DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER
2. They undergo constant renewal of
a highly ordered structure, often
accompanied by an increase in the
complexity of that structure by
creating an elegant molecular order
within them and pass a pattern of
that order on to descendent
organisms.
DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER

3. Each component part appears to

have a specific purpose or function.
DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER
4. They have the
capacity to
extract and
transform energy
from their
The lion uses organic compounds
environment by obtained by eating other animals to
interacting with fuel intense bursts of mus­cular
activity. The zebra derives energy
their from com­pounds in the plants it
surroundings. consumes; the plants derive their
energy from sunlight.
 DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER
5. They have the capacity
for precise self-
replication by passing
on information
describing the
organism’s structure
from one generation to
the next.
Biological reproduction occurs
with near-perfect fidelity.
WHY DOES THE LIVING ORGANISM
APPEAR TO BE MORE THAN THE SUM OF
ITS INANIMATE PARTS?

1. VITALISM- living things are endowed with a

mysterious and divine life force.

2. MECHANICS- the living body is a complex

machine capable of producing energy to do
work.
WHY DOES THE LIVING ORGANISM
APPEAR TO BE MORE THAN THE SUM
OF ITS INANIMATE PARTS?

3. BIOCHEMISTRY- collections of
inanimate molecules interact with
each other to constitute, maintain,
and perpetuate the living state.
governed by set of principles
called the molecular logic of the
living state.
 Complete Definition of LIFE in
Molecular Terms
Molecular Biology- Biochemistry-
study of nucleic structure,
acids structure and organization,
function and the
genetic aspects of and functions of
biochemistry. living matter in
molecular terms.
 MOLECULAR LOGIC OF
LIFE
1. All living organisms have the
same kinds of monomeric
subunits.
2. There are underlying patterns
in the structure of
biological macromolecules.
3. The identity of each organism
is preserved by its possession of
distinctive sets of nucleic acids
and of proteins.
Two most powerful research
techniques used by
biochemists:

x-ray diffraction
electron
Precise 3-dimensional
microscopy- structures of huge biological
molecules.
 remarkable
details of cellular
structure.
 USES OF
BIOCHEMISTRY

1. On human and animal

nutrition, it relates the dietary
requirements of an animal to the
metabolic utilization and fates of
a nutrient. (e.g. why vitamins are
essential to health)
 USES OF
BIOCHEMISTRY
2. On clinical chemistry, biochemical
measurements reveal clues to
diagnoses of illnesses or allow
monitoring responses to treatment.
(e.g. detection of certain enzymes in
blood serum is a clue to internal
damage to a tissue, which released
that enzyme from its cells.)
 USES OF
BIOCHEMISTRY
3. On pharmacology and
toxicology, it is concerned with
the effects of external chemical
substances on metabolism. (e.g.
drugs and poisons act by
interfering specific metabolic
pathways)
 USES OF
BIOCHEMISTRY
4. On environmental science, it is
involved in the understanding the
actions of herbicides and pesticides,
in trying to increase their
selectivity, and in understanding
and dealing with mechanisms by
which target organisms become
resistant to agents.
 USES OF
BIOCHEMISTRY
5. On manufacturing, the dissection
of the structures of enzymes reveals
general mechanism by which
proteins catalyze reactions, speeding
them up enormously under mild
reaction conditions. (e.g.
development of new synthetic or
semi-synthetic catalysts, either
protein or non-protein in nature)
 BIOMOLECULES/
MACROMOLECULES
found in living matter with very
large molecular weights, which
are composed of simple, small
building block molecules strung
together in long chains.
 Kinds and their identical
functions in all species of cells:
1. nucleic acid- store and transmit genetic
information.
2. proteins- direct products and effectors of gene
action, structural elements, and have specific
catalytic activity and functions as enzymes
3. polysaccharides- storage forms of energy fuel
for cell activity and as extracellular structural
elements (cellulose)
4. lipids- structural components of membranes and
storage form of energy- rich fuel.
 Primordial
Biomolecules
simplest ancestors from which all other organic
biomolecules have been derived during the
course of biochemical evolution.

Grouped according to their chemical structure:

amino acids- building blocks of proteins
pyrimidines, purines, and D-ribose-
precursors of nucleic acids.
D-glucose- precursor of many polysaccharides.
Glycerol, choline, and palmitic acid- building
blocks of lipids
 ORIGIN OF
BIOMOLECULES
 Many different organic compounds occurred in relatively high
concentrations (warm soup) in the surface waters of the
ocean wherein the first living cells arose.
 A.I. Oparin (Soviet biochemist) in the 1920s suggested that:
 natural chemical and physical processes could have led to the
spontaneous formation of simple organic compounds (amino acids
and sugars) from CH4, NH4+, and H2O vapor, which he postulated to
be components of the primitive atmosphere.

 These gases were activated by the radiant energy of sunlight or by

lightning discharges to react with each other to form simple organic
compounds condensed and dissolved in the primitive ocean, which
gradually became enriched in variety.

 He postulated that the 1st living cell arose spontaneously from this
warm, concentrated solution of organic compounds.
 ORIGIN OF
BIOMOLECULES
J.B.S. Haldane in England
independently put forward
the same view of Oparin.
 ORIGIN OF
BIOMOLECULES
Stanley Miller
 (in 1953) carried out experiments on the abiotic origin
of organic molecules.

 subjected mixtures of gases (methane, ammonia,

water and hydrogen believed to be predominant in the
primitive atmosphere) in a closed flask at 800C to
electric sparking across a pair of electrodes, to
stimulate lightning, for periods of a week or more.
Abiogenesis: Evolution of
Life
 ORIGIN OF
BIOMOLECULES
Then he collected and analyzed the contents of
the system which were as follows:
A. GAS PHASE B. DARK-COLORED CONDENSATE

1. CO 1. Glycine
2. CO2 2. alanine α -amino acids
3. N2 3. aspartic acid
4. glutamic acid
5. formic acid
6. acetic acid
7. propionic acid organic acids
8. lactic acid
9. succinic acid
 Chemical Reactions in
Spark Discharges:
1. CH4 + NH3 HCN + 3 H2

2. C2H4 + HCN CH3CH2CN (a nitrile)

3. CH3CH2CN + NH3 CH3CH2COOH

(propionic acid) + NH3

4. CH3CHOHCN + NH3 CH3CHNH2CN

(aminonitrile) + H2O

5. CH3CHNH2CN + 2 H2O CH3CHNH2COOH

(alanine) + NH3
WHICH CAME FIRST, DNA OR PROTEIN?
 HIERARCHY OF THE MOLECULAR
ORGANIZATION OF CELLS
1. Precursors from the environment
(mol. wt. 18-44) CO2, H2O, NH3, N
- very simple, low molecular weight

2. Metabolic Intermediates (mol. wt. 50-250)

- converter sequences of precursors into building Pyruvate, citrate, malate, glyceraldehyde
block molecules 3-phosphates

3. Building Blocks (mol. wt. 100-350)

- organic compounds of somewhat larger molecular Nucleotides, amino acids,
weight. monosaccharides, fatty acids, glycerol

4. Macromolecules ( mol. wt. 103-104)

- covalently linked chains of building block Nucleic acids, Proteins, Polysaccharides,
molecules with relatively high molecular weight Lipids

5. Supramolecular Assemblies (mol. wt. 106-

109) Lipoproteins, Ribosomes, Enzyme
- association of macromolecules of different Complexes, Contractile systems,
classes. Microtubules
6. Cell Organelles
- highest level of organization in the cell structure. Nucleus, Mitochondria, Chloroplasts,
Golgi Bodies
 Comparison of some properties of
.

prokaryotic and eukaryotic cells

Properties Prokaryotic Cells Eukaryotic Cells
Size 0.2—5 µ m in diameter Most are 10-5- µ m in
diameter
Containment of Free in cytoplasm as nucleoid In nucleus, condensed with
DNA proteins into multiple
chromosomes

Ploidya Usually haploid Almost always diploid or

Polyploid
Mechanism of cellSimple division following DNAMitosis in somatic cells,
replication replication meiosis in gametesb

Internal No Yes, with different kinds of

compartmentation organelles

a-The term ploidy refers to the number of copies of the genetic information carried by each cell. Haploid cells have one copy, diploid cells two,
polyploid cells more than two.
b- In mitosis the diploid state is retained by chromosome duplication. This occurs in most somatic, or "body," cells of organisms. In the gametes (cells
that lead to sperm or ova) there is a somewhat different process called meiosis, which leads to a haploid state
Subcellular fractionation of Tissue.
A tissue such as liver is first mechanically
homogenized to break cells and disperse
their contents in an aqueous buffer. The
sucrose medium has an osmotic pressure
similar to that in organelles, thus preventing
diffusion of water into the organelles, which
would swell and burst.

The large and small particles in the suspensi

can be separated by centrifugation at differe
speeds.
The particles of different density
can be
separated by isopycnic
centrifugation.
A centrifuge tube is filled with a
solution the density of which
increases from top to bottom; a
solute such as sucrose is
dissolved at different
concentrations to produce the
density gradient. When a mixture
of organelles is layered on top of
the density gradient and the tube
is centrifuged at high speed,
individual organelles sediment
until their buoyant density
exactly matches that in the
gradient. Each layer can be
collected separately.