CHEM 015
TOPIC 3: INTRO TO BIOCHEMISTRY
& BIOTECHNOLOGY
DR. GLORINA P. OROZCO
LEARNING OUTCOMES
1. Review the biomolecules and inorganic substances
comprising living systems
2. Describe the Carbon as the backbone and molecules of
life.
3. Integrate Biochemistry with Engineering Chemistry
4. Discuss some chemistry applications on the present
Covid 19 pandemic.
Important Substances in the Living State
INORGANIC COMPOUNDS: WATER
1. A Polar molecule: a Universal
Solvent
2. Has high heat capacity: minimizes
abrupt temperature change
3. Has high heat of evaporation: w/ H+ and OH−
great cooling effect participate in
chemical
4. Permits capillary processes reactions
INORGANIC COMPOUNDS: WATER
• Solvent
• Polar substances
dissociate, forming
solutes
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.5
ACIDS, BASES, AND SALTS
• An acid is a substance that
dissociates into one or more
H+ .
HCl → H+ + Cl−
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.6a
ACIDS, BASES, AND SALTS
• A base is a substance that
dissociates into one or more
OH−.
NaOH → Na+ + OH−
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.6b
ACIDS, BASES, AND SALTS
• A salt is a substance that
dissociates into cations and
anions, neither of which is H+ or
OH−.
NaCl → Na+ + Cl−
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.6c
ACID-BASE BALANCE
• The amount of H+ in a solution is expressed as pH.
• pH = −log[H+]
• Increasing [H+], increases acidity.
• Increasing [OH−] increases alkalinity.
• Most organisms grow best between pH 6.5 and 8.5.
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ACID-BASE BALANCE
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.7
ACTION OF BUFFER SOLUTION
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ORGANIC COMPOUNDS
• The chain of carbon atoms in
an organic molecule is the
carbon skeleton.
• Functional groups are
responsible for most of the
chemical properties of a
particular organic compound.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Table 2.3.1
ORGANIC COMPOUNDS
• Small organic molecules can combine into large macromolecules.
• Macromolecules are polymers consisting of many small repeating molecules.
• The smaller molecules are called monomers.
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ORGANIC COMPOUNDS
• Monomers join by dehydration synthesis or
condensation reactions.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.8
ORGANIC COMPOUNDS:
THE 4 BIOMOLECULES
1. 1. Carbohydrates = hydrated carbon compounds
2. (CH2O)n
3. 2. Proteins= polypeptides containing polymers of amino
acids
4. 3. Nucleic Acids = polymers of nucleotides
5. 4. Lipids = heterogenous class of compounds grouped
together due to their solubility in fat solvents
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CARBOHYDRATES
❖Are important for structure and as energy sources.
❖Consist of C, H, and O with the formula (CH2O)n
❖Functions:
1. Primary source of energy
2. Form structural components of cells
3. Backbone of other molecules
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.8
CARBOHYDRATES
• Building blocks: Monosaccharides - simple sugars with 3 to 7 carbon atoms.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.8
CARBOHYDRATES
• Disaccharides are formed when two monosaccharides are joined in a
dehydration synthesis.
• Disaccharides can be broken down by hydrolysis.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.8
CARBOHYDRATES
• Oligosaccharides consist of 2 to 20 monosaccharides.
• Polysaccharides consist of tens or hundreds of
monosaccharides joined through dehydration synthesis.
• Starch (in cereals), glycogen (animal starch) and cellulose
(in plant cell wall) are polymers of glucose that are
covalently bonded differently.
• Chitin is a polymer of two sugars found in the exoskeleton
of insects
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
LIPIDS
• Are the primary components of cell membranes.
• Consist of C, H, and O.
• Are nonpolar and insoluble in water.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
FATS (TRIGLYCERIDES)
• Composed of three fatty acids bonded to a glycerol
molecule
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2.14
FATTY ACIDS
• Saturated: only single covalent bonds between carbons
• Unsaturated: one or more double covalent bonds between
carbons
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2.15
SIMPLE LIPIDS
• Called fats or triglycerides contain glycerol and fatty acids; formed by
dehydration synthesis.
• Unsaturated fats have one or more double bonds in the fatty acids.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.9c
COMPLEX LIPIDS
• Contain C, H, and O + P, N,
or S.
• Membranes are made of
phospholipids
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.10a
OTHER LIPIDS
• Phospholipids: modified triglycerides with two fatty
acid groups and a phosphorus group
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CELL MEMBRANE STRUCTURE
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COMPLEX LIPIDS: STEROIDS
Consist of four carbon rings,
with an –OH group attached
to one ring.
Are part of membranes
Types:
a) Cholesterol
b) Sex Hormones
c) Bile salts
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.11
OTHER LIPIDS
• Eicosanoids: 20-carbon fatty acids found in cell membranes
• Steroids: flat molecules with four interlocking hydrocarbon
rings
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
PROTEINS
❖ Biomolecules containing
❖Examples:
CHON&PS 1. Enzymes - are proteins that
❖ Also called polypeptides speed chemical reactions.
2. Antibodies –
❖Building blocks:
immunoglobulin proteins;
Amino Acids “soldiers of the body”
❖ Functions: 3. Hemoglobin – blood
pigment protein
1. Build & repair body tissues 4. Keratin – protein in skin,
2. Are essential in cell hair, nails
structure and function 5. Myoglobin – muscle
3. Secondary source of
protein
energy
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
PROTEINS
• Are essential in cell structure and function.
• Enzymes are proteins that speed chemical reactions.
• Transporter proteins move chemicals across
membranes.
• Flagella are made of proteins.
• Some bacterial toxins are proteins.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
PROTEINS
• Consist of subunits called amino acids.
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PROTEINS
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PEPTIDE BONDS
• Peptide bonds between amino acids are formed by dehydration synthesis.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.14
PROTEINS
• Macromolecules
• Contain C, H, O, N, and some S
• Composed of 20 basic types of amino acids
bound together with peptide bonds
• Dipeptide: Two amino acids
• Tripeptide: Three amino acids
• Polypeptide: Many amino acids
• Proteins are polypeptides of hundreds of amino
acids
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
AMINO ACIDS (AA)
• Building blocks of proteins
• Organic acids containing
• amino group (-NH2)
• a carboxyl group (COOH)
• a hydrogen atom
• a side chain designated by the
symbol R attached to the same
carbon atom as the hydrogen
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
STRUCTURAL LEVELS OF PROTEIN
STRUCTURE
• Primary: determined by the number, kind, and
arrangement of amino acids
• Secondary: results from folding or bending of the
polypeptide chain caused by the hydrogen bonds
between amino acids (helices and pleated sheets)
• Tertiary: results from the folding of the helices or
pleated sheets and the hydrogen bonds formed with
water
• Quaternary: spatial relationships between two or
more proteins that associate to form a functional unit
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FIG. 2.19AB
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
FIG. 2.19CD
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
CONJUGATED PROTEIN
• Conjugated proteins consist of amino acids and other
organic molecules:
• Glycoproteins
• Nucleoproteins
• Lipoproteins
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
PROTEINS
• Functions
• regulate chemical reactions (enzymes)
• structural proteins provide the framework for many of the
body’s tissues
• responsible for muscle contraction
• Fibrous proteins
• Extended and strand-like proteins
• Examples: keratin, elastin, collagen, and certain contractile fibers
• Globular proteins
• Compact, spherical proteins with tertiary and quaternary structures
• Examples: antibodies, hormones, and enzymes
• Denaturation
• Disruption of hydrogen bonds, which changes the shape of
proteins and makes them nonfunctional
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
CHARACTERISTICS OF ENZYMES
• Speed up chemical reactions by lowering the activation
energy
• Most are globular proteins that act as biological catalysts
• Are chemically specific
• Frequently named for the type of reaction they catalyze
• Names usually end in -ase
• Chemical events of the body are regulated primarily by
mechanisms that control
• concentration of enzymes
• activity of enzymes
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ENZYME ACTION
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
ENZYMES
• Enzymes bind to reactants
according to the lock-and-
key model
– The shape of both the enzyme
and reactants are critical to the
function of the enzyme
– By bringing the two reactants
close to each other it reduces the
activation energy for the reaction
– Each enzyme catalyzes only one
type of chemical reaction
– After each reaction the enzyme is
released and can be used again
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
NUCLEIC ACIDS
❖Consist of nucleotides (building blocks)
❖Nucleotides consist of a:
1. Pentose
2. Phosphate group
3. Nitrogen-containing (purine or pyrimidine) base
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.16
DNA
• Has deoxyribose
• Exists as a double helix
• A hydrogen bonds
with T
• C hydrogen bonds
with G
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.16
RNA
• Has ribose
• Is single-stranded
• A hydrogen bonds
with U
• C hydrogen bonds
with G
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.17
ATP
• Has ribose, adenine, and 3 phosphate groups
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings Figure 2.18
ATP
• Is made by dehydration synthesis.
• Is broken by hydrolysis to liberate useful energy for the cell.
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
Copyright © 2004 Pearson Education, Inc., publishing as Benjamin Cummings
On Biotechnology
My Vaccine Research Story in UP Diliman
UP NATURAL SCIENCES RESEARCH INSTITUTE
My Vaccine Research Story
in UP Diliman
➢ I got a UP scholarship and pursued
MS MICROBIOLOGY major in
Immunology in UP Diliman.
➢ I became part of a Research Team of
a project entitled “The Biology of Free-
living Pathogenic Amoeba Naegleria
fowleri”
➢ An amoeba causing fatal Primary
Amoebic Minongoencephalitis (PAM)
in man, that can kill a human being in
6 days.
My Vaccine Research Story
➢ One day I saw my cultures dried up
& when I examined them they were
not moving anymore thinking they
were dead.
➢ I was about to wash my glassware
when I accidentally placed a drop of
water in it.
➢ When I examined them again I was
surprised they were active swimmers
again!
➢ I forgot about the aseptic protocols & I might
have contaminated the water tables of QC.
➢ My boss said we are handling a Biological
warfare!
My Vaccine Research Story
➢My research was about the Immunology
of the amoeba Naegleria fowleri
➢to determine if mice will produce
sufficient antibody titers against the
amoebae for vaccine production.
➢One time, my infected mouse bit me 2x,
it escaped & went to the director’s
office!
➢ However, my co-researcher
friend, a PhD student &
professor of UPLB, got sick and
died while finishing her
research.
➢ She was hospitalized April 15,
1990.
➢ Her graduation was April 21,
1990.
➢ She died April 28, 1990.
➢ Her marriage was set May 3,
1990.
➢ God spared my life!
Part III. Overview of Basic Concepts of
Immunology & Molecular Virology
❖ Resistance & Immunity
Immunity = ability to resist infection
Resistance= ability to maintain immunity
Antigen (atg)= any substance considered foreign by the body
eg. viruses, bacteria, toxins
Antibody (atb)= immunoglobulin proteins that fight antigens (5 types)
❖ Types of Immunity:
1. Innate Immunity = natural ability to resist infection [Link] atb
inbody secretions, phagocytosis, etc
2. Acquired Immunity =ability to develop powerful protective
mechanisms against invading antigens
eg. immunization
2a. Humoral Immunity or B-cell Immunity = development of
circulating antibodies capable of attacking invading antigens.
2b. Cell-mediated Immunity or T-cell Immunity =
Achieved by the form’n of large # of lymphocytes specifically designed to
destroy specific pathogens
BLOOD Cells
1. Red Blood Cells = Erythrocytes
2. Blood Platelets = Thrombocytes
3. White Blood Cells = Leucocytes
➢ Function: defend the body against infection; ~ 9,000/ ml
➢Types:
a. Neutrophil = w/ 3 or more lobules of nucleus; numerous fine granules
b. Eosinophil = w/ 2 lobules of nucleus; w/ bigger granules in the cytoplasm
c. Basophil= w/ S,T,U,V shaped nucleus; w/ few large granules
d. Monocyte = biggest WBC w/ bean shaped nucleus; becomes Macrophages
e. Lymphocyte = smallest WBC;
B- Lymphocytes for antibody production
T- Lymphocytes = Cytotoxic Killer; Helper; Suppressor
Overview of Adaptive Immune Response
Inflammatory Response
Acellular Infectious Agents: Viruses
Corona
Virus
400nm
Eukaryote vs Prokaryotic Cells
SARS COV-2 CENTERS FOR DISEASE CONTROL & PROTECTION
2021 [Link]
Protein Synthesis of mRNA
Viral Cycle
Molecular Pathway
of mRNA Vaccine
References:
[Link]
[Link]
[Link]
museums/[Link]
[Link]
[Link]
disease/jad200831
[Link]
Thank you for listening&
be ready for your Midterm
Exams next meeting!
MERRY CHRISTMAS & A
HAPPY NEW YEAR!!
