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+NCOH2N 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.
They occur in an
enormous number of
different species with
structural organization.

(a) Microscopic complexity and

organization are apparent in this
thin section of vertebrate muscle
tissue, viewed with the electron
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
consumes; the plants derive their
surroundings.
energy from sunlight.

DISTINGUISHING CHARACTERISTICS
OF LIVING MATTER
5. They have the capacity
for
precise
selfreplication by passing
on
information
describing
the
organisms
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
Molecular Terms

LIFE in

Molecular Biology-

Biochemistry-

study

structure,

of nucleic
acids structure and
function and the
genetic aspects of
biochemistry.

organization,
and functions of
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:
electron
microscopy remarkable

details of cellular
structure.

x-ray diffraction
Precise

3-dimensional
structures of huge biological
molecules.

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-riboseprecursors 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
2. CO2
3. N2

1.
2.
3.
4.
5.
6.
7.
8.
9.

Glycine
alanine
aspartic acid
glutamic acid
formic acid
acetic acid
propionic acid
lactic acid
succinic acid

-amino acids

organic acids

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
(aminonitrile) + H2O

CH3CHNH2CN

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)
- very simple, low molecular weight

CO2, H2O, NH3, N

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. 106109)

- association of macromolecules of different
classes.
6. Cell Organelles
- highest level of organization in the cell structure.

Lipoproteins, Ribosomes, Enzyme

Complexes, Contractile systems,
Microtubules
Nucleus, Mitochondria, Chloroplasts,
Golgi Bodies

Comparison of some properties of

prokaryotic and eukaryotic cells
.

Properties
Size
Containment of
DNA
Ploidya
Mechanism of
replication

Prokaryotic Cells

Eukaryotic Cells

0.25 m in diameter

Most are 10-5- m in

diameter
Free in cytoplasm as nucleoid In nucleus, condensed with
proteins
into
multiple
chromosomes
Usually haploid

Almost always diploid or

Polyploid

cellSimple division following DNAMitosis in somatic

replication
meiosis in gametesb

Internal
No
compartmentation

cells,

Yes, with different kinds of

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.