BIOCHEMISTRY
Lecturer: Dr. Don Abrina
I. INTRODUCTION TO BIOCHEMISTRY
II. CELL BIOLOGY
III. PROPERTIES OF WATER
I. INTRODUCTION TO BIOCHEMISTRY
BIOCHEMISTRY: DEFINITION
 science concerned w/ various molecules that occur
in living cells & organisms w/ their chemical
reactions
 2 central concerns:
 understanding and maintenance of health
 understanding and effective treatment of
disease (an imbalance of the different chemical
reactions in the body)
Health - state of complete physical, mental, social
well-being and not merely the absence of disease or
infirmity (according to WHO)
BIOCHEMISTRY: PREVENTION & DIAGNOSIS OF DISEASES
1. VITAMINS
 Organic complex molecules which humans need
to ingest to maintain health
 Not produced by our body
SCURVY: lack of vitamin C (purpura or ecchymoses)
RICKETS: lack of vitamin D (bow legged, stunted
growth)
Vitamin D: important in mineralization of bones
2. AMINO ACID
 Building blocks of proteins
KWASHIORKOR: malnutrition of people
who depend on plants, lacking in essential
amino acids that one can get from animal
sources
*Patient/s with KWASHIORKOR (swollen
abdomen & edema on the lower extremities,
moon face). Patient/s with MARASMUS (old
man facies, wasting)
3. FATTY ACID
 Building blocks of lipids
 Diet rich in polyunsaturated fatty acids
 Found in fish oils -> low plasma cholesterol
levels -> low incidence of atherosclerosis -> low
incidence of heart disease
JFSM BATCH 2020
4. ENZYMES
 Proteins needed in various chemical reactions
in the body
PHENYLKETONURIA: disease where there
is low enzyme, phenylalanine hydroxylase,
converting phenylalanine to tyrosine (severe
mental retardation in infancy)
5. GENES
CYSTIC FIBROSIS: genetic disease of
exocrine glands and of the eccrine sweat glands
(increase Cl-, sweat and absence of three bases
in gene)
CFTR gene: gene which creates proteins
that remove salt and water out of the cell. If
there is a dysfunction with this gene, will lead
to accumulation of Cl-
6. BACTERIA
CHOLERA: caused by toxin produces by
vibrio cholera (patients present with massive
diarrhea)
7. PLASMODIA
 Parasites that cause MALARIA w/ mosquito as
vector
COMMON QUESTIONS ASKED BY BIOCHEMISTS:
 What are the chemical structures? Ex. Different chemical
structures of the carbohydrates, proteins, lipids.
 How do the interactions of these components give rise
to cells, tissue and organisms? Ex. Carbon can
accommodate bonds. If carbon can bond itself to
another carbon and bond itself to another. Then, it will
be able to give rise to a deeper organism.
 How does living matter extract energy from its
surroundings in order to remain alive? Ex. Krebs cycle,
oxidative phosphorylation
 How do organisms store and transmit the information it
needs to grow and reduce itself? Ex. DNA and RNA
 What chemical changes accompany the reproduction,
aging, and death of cells and organisms?
 How are chemical reactions controlled?
THREE (3) PRINCIPAL AREAS OF BIOCHEMISTRY
a) Structural Chemistry - relationship of the components
and living matter
b) Metabolism - totality of chemical reaction that occur in
living matter
c) Chemistry of processes and substances that store and
transmit biological function (DNA, RNA)
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 BIOLOGICAL MOLECULES

ROOTS OF BIOCHEMISTRY BUILDING

BIOMOLECULE FUNCTION
BLOCKS
Before 19th century: substances in living matter is
different in non-living
1828: Friedrich Wohler discovered that urea can be 1. DNA Deoxynucleotide Genetic material
synthesized from an inorganic compound, ammonium
cyanate Template for
Vitalism: Biological reactions took place through a 2. RNA Ribonucleotide protein
mysterious “life force” ; reactions are for living matter synthesis
only
1897: Edward and Hans Buchner found out that extracts Perform
from broken and dead yeast cells could still carry out 3. PROTEINS Amino Acids
work/enzymes
the process of fermentation (sugar -> ethanol)
Short-term
4. POLYSACCHARIDE Glucose
BIOCHEMISTRY AS CLINICAL SCIENCE storage

 All forms of life is constructed of the same chemical Membrane

elements
 Chemistry of living matter is similar throughout the
biological world
 Chemical elements of living matter carbon, hydrogen,
oxygen, nitrogen (important to life because of their
strong tendencies to form covalent bonds)
 The stability of C-C bonds and the possibility of forming
a single, double, triple bonds (carbon’s versatility)
II. CELL BIOLOGY
17th century: Robert Hooke observed cells in a piece
of cork
1869: Friedrich Meischer = nucleic acids
1875: Walter Fleming = chromosomes
1930 - 1950: electron microscope
Mid - 19th century: Gregor Mendel = gene is the unit
of hereditary information
1940 - 1950: DNA is the house of genetic information
1953: James Watson and Francis Crick = described
the structure of DNA; as a double helical structure
CELL : as the fundamental unit of biologic activity
ELEMENTS FOUND IN ORGANISMS
 1ST TIER: Carbon, Hydrogen, Nitrogen, Oxygen
 2ND TIER: Calcium, Chlorine, Magnesium, Potassium,
Phosphorous, Sodium, Sulfur
 3RD TIER: Cobalt, Copper, Iron, Manganese, Zinc
 4TH TIER: Aluminum, Boron, Flourine
5. LIPIDS Fatty Acids
components
 DNA, RNA, PROTEINS, POLYSACCHARIDES
- Bipolymers: made up of repeating units of
their building block or monomers
 CELLULOSE - Polysaccharide (polymer of simpler sugar)
- homopolymer (identical monomeric units)
 NUCLEIC ACID & PROTEINS
- Polymers made from number of different
kinds of monomers (heteropolymers)
 NUCLEIC ACID
- Polynucleotides
 PROTEINS
- Are assembled from combinations of 20
different amino acids
- 10 essential amino acids (arginine,
histadine, isoleucine, leucine, lysine,
methionine, phenylalanine, threonine,
tryptophan and valine)
TWO CLASSES OF ORGANISMS
A. PROKARYOTES (Greek "before nucleus")
 Always unicellular
 Surrounded by plasma membrane and cell wall
 Cytoplasm contains cytosol and does not have
compartments
 Genetic information is in the form of one or more
DNA molecules that exists free in cytosol
 Surface may have pili of flagella

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B. EUKARYOTES ( "true" nucleus) 2. Bound water
 Multicellular plants and animals - Combined with other substances with reduced
 Unicellular and simple multicellular organisms activity of water molecule
(protozoa, fungi, algae) - More constant in tissues
 10x larger than prokaryotes - Less activity of water
 compartmentalized organelles:
- mitochondria: oxidative phosphorylation COMPARTMENTS OF WATER
- rER: rich in ribosomes
a. Intracellular (ICF) – 70%
- sER: without ribosomes
- fluid inside the cell
- Golgi Complex: secretion & intracellular shuttling
b. Interstitial (ISF) – 20%
of new proteins
- fluid between tissues
- Nucleus: genetic information of cell
c. Blood Plasma (BP) – 7%
- (animal cells): lysosomes; plasma membrane
d. Others (Intestinal lumen, CSF, etc.) – 3%
- (plant cells): chloroplasts; cell wall
Chemical composition: controlled by homeostasis
(maintained at constant level)
 CYTOSOL: Glycolysis, gluconeogenesis, protein synthesis
*take note of the similar yet sharp differences:
 LYSOSOME: Cathepsins, hexosaminidase A,
sphingomyelinase  PROTEINS: ICF>Plasma>ISF
 MITOCHONDRIA: Kreb’s cycle, B-oxidation of fatty acids; - 4% higher than Blood Plasma
oxidative phosphorylation - Least amount found in Interstitial Fluid
 NUCLEUS: DNA replication, RNA processing  K+, Mg+: ICF (majority are cations)
 PEROXISOMES: metabolizes hydrogen peroxide via  Na+: BP and ISF
catalase and peroxidase  HPO4- , SO4-: ICF
 PLASMA MEMBRANE: houses insulin/glucagon,  Cl-, HCl, Bicarbonate: BP and ISF (majority are
lipoprotein receptors, ATPase anions)
 SMOOTH ER: phospholipid synthesis
 ROUGH ER: protein synthesis Differences:

III. PROPERTIES OF WATER
WATER AND ITS COMPOSITION
WATER
- Universal solvent
- most abundant constituents whereas it is
considered a major compartment of fluid with
a total of 75-85% of body’s weight
- an excellent nucleophile (as a
reactant/product)
- Bicarbonate and other buffers maintain ph
between 7.35 and 7.45
- Acidosis : blood ph < 7.35
 causes: diabetic ketosis, lactic acidosis
- Alkalosis : blood ph > 7.45
 results to vomiting of gastric contents
 Membrane permeability
 Active transport mechanisms
e.g. Na+ pump maintains lower level of intracellular
and higher level of extracellular Na+
EDEMA / accumulation of Sodium inside the cell
 Cell Burst and Lysis
 Metabolite activities in different body areas
CLINICAL CORRELATIONS
- Failure in balance: dehydration/ overhydration
- Causes of water depletion:
↓ intake – comatose patients
↑loss – severe sweating, severe diarrhea/ cholera,
Diabetic Patient
- Causes of water excess:
↑ intake – excess administration of IV fluids
↓ excretion of fluids – nutrients with severe renal failure

TYPES OF WATER IN TISSUE/BODY FLUIDS
1. Free water
- Substances may dissolve in this
- May pass back and forth in and out of the cell
- Vary in diet and activity
Electrolyte – changes in content, the ECF bear brunt in
fluctuations
Metabolite water – water produced inside living organism
through metabolism

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WATER AND ITS MOLECULAR STRUCTURE
 2 H atoms shared e- with unshared O2
 H2O molecule – irreg. tetrahedron w/ oxygen atom
central
 2 bonds of H point towards 2 corners
 Unshared on 2 hybridized orbitals of
oxygen and occupy 2 other corners
 Angle between 2 H atoms is 104.6 / 105°
(whereas 109.5° is a normal tetrahedral)
 ‘skewed’ tetrahedral structure, not uniformly
distributed; electron charged
 water is dipole in nature with electrons unequally
distributed
 the area around the hydrogen atom is electro
positive
 the area around the oxygen atom is electro positive
http://www.earthsurfaceprocesses.com/3E-
WaterStructureFig1D.jpg
ASSOCIATIONS BETWEEN WATER MOLECULES
 Molecule ordering of water occur in liquid water
and ice
 In solid state: 4 other molecule associated with
 In liquid state: transient association less than 3.5
 Half-life for association-dissociation of liquid water
bonding is 1 millisecond
 Dipole nature to form H-bonds, electrostatic
interaction between H of 1 water molecule and
another shared electron. They are not restricted to
water molecule e.g. alcohol + water. They are
weaker than covalent bond.
 Covalent bonds are stronger because they share
electrons.
 Although individually weak, when taken together
many of these hydrogen bonds play a significant
structure on dipolar molecules (ex: water, alcohol,
DNA, proteins, etc)
 The bonds between bases and DNA are formed by
hydrogen bonds.
DISSOCIATION OF WATER
 water exhibit a slight but physiologically important
tendency to ionize water to become H+ and OH-
1.) Water molecules
H+ and OH- e.g. H2O ↔ H++OH-
(reversible dissociation)
 Hydrogen ions should be balanced by hydroxyl ions,
because of this, water acts both as an acid and a
base
 Acid/base – proton donors/acceptors
2.) Free ions, involves H+ (hydrated proton)
(tendency of water to dissociate)
 A Hydrogen proton never exists in an aqueous
solution as a free ion, they are always associated
with one or more water molecule.
The formula for water dissociation is:
K = [H+] + [OH-]/ [H2O]
where K is dissociation constant and considered a reversible
equation. At 25°C, the value of K is 1.8x10-16 moles/L.
e.g.
[H] & [OH] = 1X10-7 moles/L
[H2O] = 55.56 M
In product of water, Kw is 55.56 H2O. Kw is constant for
aqueous solution with dissolved acids and bases.
K = [H+] + [OH-]/ [H2O] = 1.8x10-16 moles/L
Kw= [K][ H2O] = [H][OH] = (1.8x10-16 moles/L) (55.56
moles/L) = 1x10-14 (moles/L)2
If H ions added to pure water, the OH concentration
decreases thus the temperature of 25° C remains constant in
the 1x10-14 value of Kw
pH IS THE NEGATIVE LOG OF HYDROGEN ION
CONCENTRATION
calculate pH:
pH = -log[H+]
1. Calculate hydrogen ion concentration [H+]
2. Calculate the base 10 logarithm of [H+]
3. pH is the negative of the value found in step 2
if: ↓ pH -↑ ion concentration
↑pH- ↓ ion concentration
Normal value of pH is 7.35-7.45
CLINICAL CORRELATIONS:
pH <7.35 – leads to alkalosis
pH>7.35 – leads to acidosis