BIOCHEMISTRY
BIOCHM LEC
BACHELOR OF MEDICAL LABORATORY SCIENCE | PRELIMS
TOPIC 1: Basics of Biochemistry
1. Biochemistry speaks of Biodiversity
 variety of different lifeforms on earth, not only in
humans
 DIVERSITY: genetic variation, ecosystem, species
variation.
 INTERRELATED: due to the similarity in
biomolecules that makes up their existence. All
together, we use energy.
 H2O, CH4, CO2, NH3, N2, H2
2. Biochemistry speaks of diverse biochemical pathways
 Biochemistry is versatile and diverse.
 Attracts a multitude of disciplines in the scientific
community.
 The understanding of the Molecular activities and
pathways within the cells allowed medical
practitioners to EFFECTIVELY TREAT DISEASES.
 Pathways occur simultaneously: some molecule
have a single role while others have multiple roles.
5.
Biochemistry and Biomolecules
 Biomolecules are composed of biologically
important “Functional Groups”.
 Formation of ATP is one of the most important
biochemical processes in species.
 Gases present in the atmosphere of the earth
included: NH3, H2S, CO, CO2, CH4, N2, H2, and
H2O.
 Formation of biomolecules happened
ABIOTICALLY.
PAROXYSMAL NOCTURNAL HEMOGLOBINURIA
Paroxysm: sweating, chills, fever
Nocturnal: paroxysm occurs at night
Hemoglobinuria: Hemoglobin (protein in RBC) is present in urine.
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If there is an early damage in RBC, hemoglobin will be
released in the circulation.
RBC will be destroyed, chills and fever at night, black urine at
morning (occurs at night because compliment proteins are
more active at acidic ph.)
Small survival rate
Deadly disease
Caused by acquired membrane mutation
↑CO2 increase because of Hyperventilation during sleep
Urine appears black because it is oxidized because it spends more
time in the Urinary bladder.
3.
4.
Biochemistry speaks about structure and organization
 Cascading formation from SIMPLE → COMPLEX.
Biochemistry and ORGANIC CHEMISTRY
 They used to believe that life is held by a vital force
(Vitalism)
 Molecules that are found in living organisms are
exclusively found among living organisms and do not
arise from non-living particles. (Old belief)
 ORGANIC CHEMISTRY: The study of compounds of
carbon, especially of carbon and hydrogen and their
derivatives.
 Side Note: It was previously thought that in the 19th
century, vital forces (molecules unique to living things
cannot be prepared/ made “in vitro”)
 Theory (above) was disproved by Friedrich Wohler in
1828
 he was able to synthesize urea from ammonium cyanate
in the laboratory.
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MILLER- UREY EXPERIMENT
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The formation of polymerization of monomers have a
sense of “Directionality” which comprises a cascade of
events.
↓ all building blocks have a head and a tail.
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The effect of monomer sequence affects the properties
of polymers Therefore, dictating its biological function.
ENZYME: increases the rate of chemical reaction →
Catalytic activity
CATALYSIS: Depends on the sequence of amino acids.
Miller-Urey Experiment: proved that biomolecules happened
abiotically.
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Recent works suggest that RNA, not proteins, as the
first genetic molecules.
The possibility to synthesize nucleotides from simpler
molecules using a Precursor that is not a sugar nor a
nucleobase.
Chemicals in earth
befpre life (2aminooxazole)
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Arabinooxazoline
(Phosphate)
RNA nucleotide
2-aminooxazole:
- A fragment consisting of a sugar and a part of a base.
- Highly volatile molecules (Easily vaporized)
- Condensed to give back pockets of pure materials
↓ produces Arabinooxazoline
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Nucleotides present before was destroyed because of excessive
amount of UV Rays.
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Living cells consists of assembly of Very Large Molecules:
WHAT DICTATES THESE SEQUENCE OF AMINO ACIDS?
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1) Amino Acids → Peptides → Proteins
2) Nucleotides → Nucleic Acids
3) Monosaccharides → Polysaccharides
4) Glycerol and Three Fatty Acids → Lipids
MONOMERS: small molecules that may bonds to form a
polymer.
POLYMERS: large molecules/macromolecules that are
formed through bonding of smaller units.
INFORMATIONAL MACROMOLECULES: sequence of
monomeric units that contains information.
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Amino Acid Sequence is based on the Nucleotide sequence.
The DNA serves as the storage of all information needed to
synthesize protein in the body. Decoded by mRNA. mRNA is
processed by ribosomes. Translation process happens in
ribosomes, different sequences of amino acids are created
using the different information found in the DNA.
Ribosomes: Site of protein synthesis.
From Molecules to Cells:
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If there is a mistake in the sequence of DNA, it will have a
repercussion in the sequence of amino acid and it will
alter the functionality of the protein.
If the functionality of the protein is altered, it will have an
impact to the entire system of the set. Impairing its
general function.
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Past Theory: It was though that catalytic activity is limited
with proteins.
Recent Developments: RNA is capable of catalyzing its
own reaction (RNA WORLD THEORY)
Key point: Formation of membranes that separated the cells
from their environment.
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This membrane makes communication and internal pathway
processes more efficient within the cell.
WARM SIDE OF THE POND:
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DOUBLE ORIGIN THEORY:
1.
2.
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Rise of aggregates of molecules for catalysis
Rise of nucleic acid based coding system
Protocell moves to the warm side where the strand
separates.
The membrane incorporates more lipid molecule to the
strand.
The protocell divides with a single stranded RNA in each daughter
cell and repeats the cycle.
6.
7.
Biochemistry and Origin of Life
 We are the only life sustaining planet in the
Universe.
 The Big Bang Theory: A tremendous explosion
happened. A “primordial fireball” started to expand
with great force.
 Composed of: Hydrogen. Helium, and Lithium
 Proposed formation of the other elements:
(1) Thermonuclear reactions
(2) In explosion of stars
(3) Action of cosmic rays
Evolution of Replication
8.
Biomolecules to Single Cell Organisms
CLAY PARTICLES
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Clay particles dictated the process of replication and the
formation of protocells.
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Protocells exist in a pond with two sides: Cold and Warm
side of Pond.
COLD SIDE OF THE POND:
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Double stranded polynucleotide on a single stranded
template
JOURNEY TO THE MODERN CELL
After life got started, competition among lifeforms fueled the
drive toward ever more complex organisms. We may never know
the exact details of early evolution, but there is a plausible
sequence of some of the major events that led from the first
protocell to DNA-based cells such as bacteria.
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1)
EVOLUTION STARTS
The first protocell is just a sac of water and RNA and
requires an external stimulus (such as cycles of heat and
cold) to reproduce. But it will soon acquire new traits.
2)
RNA CATALYSTS
Ribosomes – folded RNA molecules analogous to proteinbased enzymes- arise and take on such jobs as speeding up
reproduction and strengthening the protocells membrane.
Consequently, protocells begin to reproduce on their own.
3)
METABOLISM BEGINS
Other ribozymes catalyze metabolism – chains of chemical
reactions that enable protocells to tap into nutrients from
the environment.
4)
PROTEIN APPEAR
Complex systems of RNA catalysts begin to translate strings
of RNA letters (gene) into chains of amino acids (proteins).
Proteins later prove to be more efficient catalysts and able
to carry out a variety of tasks.
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6)
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A Comparison of Prokaryotes and Eukaryotes
Organelle
Prokaryotes
Eukaryotes
Nucleus
No definite
Present
nucleus: DNA
present but not
separate from rest
of cell
Cell Membrane
Present
Present
(Plasma
Membrane)
Mitochondria
None; enzymes for Present
oxidation reactions
located on plasma
membrane
Endoplasmic
None
Present
Reticulum
Ribosomes
Present
Present
Chloroplasts
None;
Present in Green
photosynthesis (is
plants
present) is
localized in
chromatophores
PROKARYOTES
PROTEINS TAKE OVER
Proteins take on a wide range of tasks within the cell.
Protein-based catalysts, or enzymes, gradually replace most
ribozymes.
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THE BIRTH OF DNA
Other enzymes begin to make DNA. Thanks to its superior
stability, DNA takes on the role of primary genetic
molecule. RNA’s main role is now to act as a bridge
between DNA and proteins.
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BACTERIAL WORLD
Organisms resembling modern bacteria adapt to living
virtually everywhere on earth and rule unopposed for
billions of years, until some of them begin to evolve into
more complex organisms.
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EUKARYOTES
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Prokaryotes and Eukaryotes
Prokaryotes
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Closely linked to primitive cells are the
“PROKARYOTES.”
Greek derivation: “Karyon” = kernel. Nut. Literally
means “Before the nucleus”.
Comprises of two organisms: Bacteria and
Cyanobacteria
Eukaryotes
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Modern, complex, that can be multicellular or singlecelled (yeasts and paramecium).
Means “true nucleus.”
Eukaryotes has a nuclear membrane.
Fact: eukaryotes evolved from eukaryotes about 1.5
billion years ago.
Has a nuclear region contained genetic material and has the
essentially the same function as the nucleus in a Eukaryotic
Cell.
Nuclear region: single, closed, circular molecule of DNA
(Attached to the Cell Membrane)
One Copy of the DNA is passed to the two daughter cells.
Cytosol: has a slightly granular appearance due to the
presence of ribosomes (also known as ribonucleoprotein
particles)
The only kingdom is MONERA.
UNICELLULAR
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Has subcellular organelles; Important: nucleus,
mitochondrion, *chloroplast (plants).
Chloroplast: found in green plants and green algae, sites of
photosynthesis.
NOTE: Mitochondria and Chloroplasts contain DNA. Have
their own transcription and ability to synthesize proteins.
MULTICELLULAR
ORGANELLES
1.) Nucleus
 MOST IMPORTANT ORGANELLE
 Surrounded by a “nuclear membrane.”
 Rich in RNA
2.) Mitochondrion
SECOND most important
organelle
Outer Membrane: Smooth
Inner Membrane: Cristae
SPACE within these two
membranes is called the
Matrix.
Powerhouse of the cell
Processes of ATP
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3.) Endoplasmic Reticulum
 Single membrane system throughout the cell
 Attached to both nuclear and cellular
membrane.
4.) Golgi Apparatus
 Found close to the smooth endoplasmic
reticulum.
 Secretion of proteins in the cell.
 Important for cellular content packaging.
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A better understanding in the mechanism of nucleic
acids gives us further understanding of genetic diseases.
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Protein gives us understanding diseases of diseases
which give rise to protein errors such as sickle cell
anemia.
Understanding the lipids gives us better understanding
of atherosclerosis.
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Carbohydrates gives us better understanding of
Diabetes Mellitus.
CLASSIFICATION OF ORGANISMS
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Different organisms are classified into different
kingdoms.
BIOCHEMISTRY AND MEDICINE
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Knowledge of the biochemical topics has clarified our
understanding of the diseases. Conversely, analyses of
the diseases have casted light on many areas of
biochemistry.
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