BIOCHEMISTRY PRELIMS

LECTURE NOTES
in hemoglobin being vulnerable to
oxidation that makes the urine
TOPIC 1: INTRODUCTION TO darken or black in color.
BIOCHEMISTRY - PNH is an acquired form of genetic
abnormality
b. Pathways occur simultaneously. The
1. Biochemistry speaks of biodiversity; different molecules participate in different
pathways. There are molecules that have
- a variety of lifeforms on earth that are
one function and others have multiple
interrelated for having similar
functions.
biomolecules
- Despite the genetic, species and
ecosystem variation, the biomolecules of Speaks about structure and organization
all organisms use the same constituents
- atoms > molecules > macromolecules>
- H20, CH4, CO2, N2, H2
organelles > cells> tissues > organs > organ
system > organism
Speaks of diverse biochemical pathways
- Understanding at the molecular level Biochemistry and organic chemistry
regarding activities and pathways within
- Life is held by vital forces (molecules of
the cell allows effective treatment.
living organisms); known as vitalism and
- Example is the PAROXYSMAL
cannot be prepared in vitro.
NOCTURNAL HEMOGLOBINURIA which is
- Molecules found in living organisms are
an abnormality in RBC
only exclusive to them.
a. PAROXYSMAL (chills, fever, and sweating)
- Friedrich Wohler in 1828 disproved the
NOCTURNAL HEMOGLOBINURIA
idea of vitalism by synthesizing Urea from
(hemoglobin present in urine), when RBCs
Ammonium cyanate. (NH4OCN ->
are destroyed and does not last until 120
H2NCONH2)
days, the person experiences black urine,
chills and sweating. PIG-A gene is
OrgChem: study of carbon and hydrogen and
important for synthesis of GPI link protein
their derivatives
which is an anchor protein.
- CD55 (Decay Accelerating Factor);
CD59 (Membrane inhibitor of Biochemistry and biomolecules
reactive lysis); GPI acts as - Biomolecules are composed of biologically
identification of the cell. Without important functional groups.
GPI, there’s no CD55 and CD59. - Biomolecules are dependent on the
- No GPI = activation of MACC functional group present in their structure
(membrane attack system of that is significant for how the molecules
complement cascade) which react or behave.
attacks the RBC that causes - Formation of ATP, most important
hemolysis. Happens at night due to biochemical processes in species.
complement systems becoming Phosphoric acid esters and anhydrides.
active at lower pH where CO2
increases due to hypoventilation
which causes high acidity of the
body.
- Hemoglobin is removed from the
circulation when RBC. This results
 BIOCHEMISTRY PRELIMS
LECTURE NOTES

- Recent works suggest RNA, not proteins,

are the first genetic molecules.
- There is a possibility to synthesize
nucleotides from simpler molecules using
precursors that are not sugar nor a
nucleobase.
a. Chemicals in earth before life
i. 2-aminooxazole (a fragment
consisting of sugar and a
base; a highly volatile
molecule) condensed to
give amounts of materials
which lead to;
ii. Arabino Oxazoline bind with
phosphate
Biochemistry and origin of life iii. Gives rise to RNA nucleotide
iv. Intense UV light destroyed
- Earth came to life due to the big bang
previous RNA nucleotides
theory in which a primordial fireball
resulting in wrong
expands forces.
combinations
- Composed of hydrogen, helium, and
v. After longer exposure to UV
lithium.
rays, the existing RNA has
- Proposed formation of other
been formed.
elements: 1) thermonuclear
Living cells consists of assembly of very large
reactions, 2) in explosion of stars,
molecules: (building blocks -> large molecules)
and 3) action of cosmic rays
1. Amino acids -> peptides -> proteins
2. Nucleotides -> Nucleic acids
Biochemistry and biomolecules (cont.) 3. Monosaccharides -> Polysaccharides
4. Glycerol and three fatty acids -> lipids
Gasses present in the atmosphere of the early
a. Monomers - small molecules that
earth include: NH3, H2S, CO, CO2, CH4, N2, H2, and
may bond to form a polymer
H2O.
b. Polymers - large
Formation of biomolecules happened
molecules/macromolecules that
abiotically (in contrast with vitalism);
are formed through the bonding of
- Miller-Urey experiment; simple molecules
smaller units
such as H2, CH4, and NH3 combined with
water are bombarded with electric charge
Informational macromolecules are a sequence
yielding formaldehyde and hydrogen
of monomeric units that contains information.
cyanide. These (F and HC) are products
Examples are strands of DNA as it provides the
when amino acids are formed.
sequence for synthesizing proteins.
 BIOCHEMISTRY PRELIMS
LECTURE NOTES

The formation of monomers has a sense of FROM MOLECULES TO CELLS

directionality which comprises a cascade of - Catalytic activities is limited with proteins
events; meaning they have a head and a tail. - Recent: RNA is capable of catalyzing its
own reaction
- RNA world Theory
● Aside from being an intermediate
processor, it can catalyze its own
reaction
● Used as a basis by scientists as it is
observed in viruses; they have RNA
and synthesize to multiply
themselves.
● Original catalyst is RNA
● RNA created subgroups
specializing in storing information;
and other gives rise to proteins
(enzymes)

Evolution of Replication
- A catalytic RNA catalyzing its own
replication, synthesizes RNA as a group
The effect of monomer sequence affects the and more catalytic RNA evolves that give
properties of polymers, therefore, dictating its rise to existing RNA functions due to
biological function. DNA sequence should be adaptor mechanism.
transferred correctly as it would affect the
biological function of the protein along with the
cell’s total activity.

Enzymes increase the rates of chemical reactions

-> CATALYTIC ACTIVITY. (Enzymes act as
catalysts)

Catalysis depends on the sequence of

amino acids. If there is a mutation in the
FROM MOLECULES TO CELLS
sequence of codes, it would arise in diseases.
- Formation of membranes that separates
the cells from their environment
Based on the nucleotide sequence where
- Membrane makes communication and
it is stored in the DNA, decoded by mRNA, and
internal pathway processes more efficient
then processed by ribosomes along with tRNA, a
within the cell.
sequence of amino acids is created.
 BIOCHEMISTRY PRELIMS
LECTURE NOTES
3. Metabolism begins
DOUBLE ORIGIN THEORY a. Other ribozymes catalyze
- Development of catalysis is different from metabolism allowing protocells to
coding systems. Combination of the two tap nutrients from the
gives rise of: environment.
1. Aggregates of molecules for 4. Proteins appear
catalysis a. Complex systems of RNA translate
2. Nucleic acid based on the coding RNA letters (genes) to chains of
system amino acids (proteins).
5. Proteins take over
a. Protein-based catalysts, or
enzymes, gradually replace
ribozymes
6. Birth of DNA
a. Other enzyme begin to make DNA.
DNA takes on the role of primary
genetic molecule due to its
stability. RNA becomes the bridge
CLAY PARTICLES between DNA and proteins.
- Dictated the process of replication and the 7. Bacterial world
formation of protocells a. Organisms resembling modern
- Coding material of clay surface > ions adapt living on earth which evolve
present on the surface and serve as the to more complex organisms.
code > crystallization is responsible for
replication process > DNA and RNA
formed on the clay surface. RNA molecules
are released in the surface enclosed by a
lipid sac that forms the protocell.

MODERN THEORY
1. Evolution starts
a. First protocell is a sac of water and
RNA
2. RNA catalysts
a. Ribozymes (folded RNA molecules Prokaryotes and Eukaryotes
analogous to protein based
enzymes) speeds up reproduction Primitive cells are mostly prokaryotes.
and strengthen protocells’ From the Greek word “Karyon” which is kernel,
membranes resulting in producing nut that means before the nucleus. Has two
other protocells. organisms
 BIOCHEMISTRY PRELIMS
LECTURE NOTES
a. Bacteria
b. Cyanobacteria In hematopoietic blood cells the size of the
nucleus shrinks as it matures and until the
Eukaryotes “true nucleus” are cells that nucleus is rejected for the cell to move efficiently
have a nuclear membrane. A more modern and change size.
complex, that can be multicellular or single-celled
(yeasts and paramecium). MITOCHONDRION
- Second most important organelle
- Smooth on the outside membrane; cristae
in the inside
- Space between the outer and inner
membrane is called the matrix.

Prokaryotes
Has nuclear region (not nuclear
membrane) contains the genetic material.
Nuclear region is a single, closed, circular
molecule of DNA attached to the cell membrane.
One copy of DNA is passed through the daughter
cell.
Cytosol (the fluid in cytoplasm) has a
granular appearance due to ribosomes a.k.a
ribonucleoprotein particles.

Prokaryotes
Has subcellular organelles: Nucleus,
mitochondrion, and chloroplast (found in plants,
sites of photosynthesis). Mitochondria and
Chloroplasts contain their own DNA and is
capable of own transcription

Organelles
NUCLEUS
- Nucleolus is rich in RNA
- Surrounded by Nuclear membrane ENDOPLASMIC RETICULUM
- Histones help organize the DNA A single membrane system throughout the cell
- Coils to make chromatin which contains that is attached to both nuclear and cellular
DNA and histone proteins
- Chromosomes a condensed structure of
DNA (condensed chromatins)
- Chromatids are a copy of chromosome
combined together with the centromere
 BIOCHEMISTRY PRELIMS
LECTURE NOTES
membranes.

GOLGI APPARATUS
Found close to the smooth endoplasmic
reticulum. Helps in secretion of proteins in the cell
and is important in cell packaging.

Classification of organisms

BIOCHEMISTRY AND MEDICINE