TRANS: MODULE 1 (THE LIFE AND WORKS OF RIZAL)

LESSON 1.1: proteins, scientists can better

INTRODUCTION TO BIOCHEMISTRY understand immune responses and
BIOCHEMISTRY develop vaccines or treatments to
Biochemistry: The study of the chemical enhance disease resistance.
processes and substances in living organisms.
Purpose: Understands how life works at a 4. Pharmacology and Pharmacy: How drugs
molecular level, including cellular functions and interact with the body at a molecular level.
responses.  For instance, paracetamol reduces fever
Biochemical Reactions: The chemical by interfering with the biochemical
reactions that occur within biological systems, pathways that produce hormones
essential for life processes. responsible for raising body
temperature. Similarly, antacids like
It helps answer questions such as: magnesium hydroxide and aluminum
1. How is the food we eat digested, absorbed, hydroxide neutralize stomach acid by
and converted into energy or used to build reacting with it to form water and salt.
and repair the body?
2. How are metabolic processes in the body 5. Toxicology: Biochemical effects of toxins
connected and regulated? and how the body responds.
3. What roles do genes play in controlling  When alcohol is consumed, the body
various biological functions? releases enzymes that convert ethanol,
4. What are the molecular mechanisms the active ingredient in alcohol, into
behind the immune response, and how harmless substances like water. This
does the body recognize and defend detoxification process is vital for
against pathogens? preventing the buildup of harmful
substances in the body, showcasing the
BIOCHEMISTRY IN LIFE SCIENCES
importance of biochemical pathways in
1. Genetic: Understanding the chemical basis
protecting our health.
of heredity and gene expression.
 It explains how genes are expressed,
6. Pathology: The chemical changes
allowing traits to be passed from one
associated with diseases and disorders.
generation to the next. By studying DNA
 For example, lactose intolerance occurs
and the processes involved in gene
when the body lacks the enzyme
expression, biochemists can uncover
lactase, which is responsible for
the molecular basis of genetic disorders
breaking down lactose, a sugar found in
and develop potential treatments.
milk. Another example is diabetes, a
Ex: DNA
disorder where the body doesn't
- carriers of genes
produce enough insulin, a hormone
- it has ribonucleic acid
crucial for regulating blood sugar levels.
- if something is wrong with this there is
a possible abnormality
7. Microbiology: The role of chemical
- contains biomolecule acid that is
processes in microorganisms and their
important for heredity engine
impact on health.
expression
 Through biochemical processes and
reactions, scientists can detect specific
2. Physiology: How biochemical processes
markers or substances produced by
enable the functions of living organisms.
these microorganisms, aiding in the
 When we breathe, oxygen is used in
diagnosis and treatment of infections.
cellular reactions to produce energy and
This highlights the role of biochemistry
carbon dioxide is expelled as a waste
in understanding and combating
product. Biochemical reactions are
microbial threats to human health.
essential in converting the oxygen we
inhale into energy. BIOCHEMISTRY AND MEDICINE
Understanding and maintenance of health
3. Immunology: The biochemical include studying metabolic processes,
mechanisms behind immune responses nutritional needs, and the molecular
and disease resistance. mechanisms that keep the body functioning
 For example, antibodies are proteins properly. It helps in diagnosing diseases,
that identify and neutralize harmful developing treatments, and understanding how
invaders like bacteria and viruses. By lifestyle choices and medications impact health
studying the biochemical nature of these at the molecular level.

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 Metabolism (Both Anabolism and

Role of Biochemistry in Medicine: Catabolism)
 Anabolism: This is the process in which
cells build complex molecules from simpler
ones. It requires energy and is involved in
the growth, repair, and maintenance of
cells.
 Catabolism: This is the process in which
cells break down complex molecules into
NORMAL BIOCHEMICAL
PROCESSES ARE KEY TO HEALTH:
simpler ones, releasing energy in the
According to the World Health process. An example is the breakdown of
Organization (WHO), health is more than just glucose in cellular respiration to produce
the absence of disease. It involves complete ATP.
physical, mental, and social well-being.
Types of Cells
Biochemical processes in the body Modern Cell Theory
are essential for maintaining this overall state  Cells make up all living things.
of health.  All cells come from pre-existing cells.
 Genetic information is passed from one
Biochemistry helps us understand how generation to the next through cells.
certain foods can impact our health by  Metabolism (both Anabolism & Catabolism)
influencing hormone levels. For instance,
bananas are rich in potassium, which plays a Prokaryote Eukaryote
role in regulating stress hormones like  Smaller in size 1 to  Larger in size 10 to
cortisol. When cortisol levels rise due to 10 8 100 μm
stress, potassium helps to moderate this  Mainly unicellular  Mainly multicellular
response, potentially reducing the production single membrane- (with few exceptions)
of cortisol. By including potassium-rich foods surrounded
like bananas in our diet, we can support the  Rigid cell wall.  Lipid bilayer
body’s biochemical pathways in managing membrane
stress, thereby promoting better health and w/proteins; Do not
well-being. have a cell wall
because they rely on
BIOCHEMICAL VIEWPOINT ON HEALTH: a flexible
cytoskeleton for
shape and support.
Health involves Disruptions in  Anaerobic or aerobic  Aerobic
maintaining all biochemical processes  Not well defined  Nucleus well
biochemical processes can lead to health nucleus, only a defined, 4 to 6 μm in
and reactions necessary issues, highlighting the nuclear zone with diameter; contains
for the proper need for balance and DNA DNA and is
functioning of the body. regulation. surrounded by a
LESSON 1.2:
perinuclear
THE CELL membrane.
FUNDAMENTAL UNIT OF LIFE  Histones absent; a  Histones present; a
Modern Cell Theory: protein that provides protein that provides
 Cells make up all living things. structural support for structural support for
 All cells come from preexisting cells. a chromosome. a chromosome.
 Cytokinesis is the process that happens  Cytoplasm contains  Membrane-bound
at the end of cell division, where the no cell organelles cell organelles are
cell's cytoplasm splits into two new cells. present
Cytokinesis ensures that one cell  Ribosomes  Ribosomes are
divides to create two new cells, each presently free in present; studded on
with its own set of organelles and cytoplasm outer surface of ER
genetic material. This shows how new  Golgi apparatus  Golgi apparatus
cells are made from existing ones, absent storage presents flattened
following the principle of cell continuity. granules with single membrane
 Genetic information is passed from one polysaccharides vesicles.
generation to the next through cells.

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 Lysosomes absent  Lysosomes present envelope where ribosomal RNA (rRNA) is

– single membrane synthesized and ribosome assembly
vesicles containing begins.
packets of hydrolytic
enzymes. 5. Nucleoplasm: It contains various enzymes,
 Cell division is  Cell division through such as DNA polymerases and RNA
usually by fission, mitosis. polymerases for mRNA and tRNA
not mitosis.  Cytokinesis divides synthesis.
the cytoplasm to
form two daughter How is genetic material/information transferred
cells after mitosis or to another cell?
meiosis. “Genetic material is transferred to another cell
 Cytoskeleton absent  Cytoskeleton like a chef following a recipe to make a dish.
present First, the recipe (DNA) is copied onto a
 RNA and protein are  RNA synthesized. notepad (mRNA) in a process called
synthesized in the transcription. The notepad is then taken to the
same compartment. kitchen (ribosome), where the chef (tRNA)
 Ex: Bacteria,  Ex: Yeast, Oak reads the instructions and gathers the
cyanobacteria & trees, & dogs ingredients (amino acids) to cook up the final
Rickettsia. dish (protein) in a process called translation.
This "dish" is then used by the cell or passed
CELL ORGANELLE: THE NUCLEUS on to another cell to continue life's processes.”
 It contains more than 95% of the cell’s DNA
(DNA Storage) and is the control center of Functions of DNA Polymerases and RNA
the cell. Polymerases
 The organelle that contains the main
genetic apparatus in eukaryotes. DNA Polymerases
They are enzymes responsible for
Functions of the Nucleus synthesizing new DNA strands during DNA
1. DNA Replication replication. They add nucleotides to a growing
 Exact copy of the genetic materials DNA strand, ensuring accurate copying of
during cell division. genetic information, and also have
 Replicating DNA ensures the accurate proofreading abilities to correct errors during
transmission of genetic information to replication.
daughter cells during cell division.
2. RNA Transcription RNA Polymerases
 It converts DNA into RNA and occurs in They are enzymes that synthesize RNA
the nucleus. First step in gene from a DNA template during the process of
expression. transcription. They bind to specific regions of
DNA and transcribe the genetic information
Anatomy of the Nucleus into messenger RNA (mRNA), which carries
1. Nuclear Envelope: A double membrane the instructions for protein synthesis from the
that separates the nucleus from the cytosol. nucleus to the ribosome.
It helps to maintain the shape of the DNA Directs Protein Synthesis
nucleus and assists in regulating the flow of 1. Double-stranded DNA in the cell nucleus
molecules including the RNA into and out of unwinds and unzips to expose the gene
the nucleus through nuclear pores. sequence.
2. Nuclear Pore complexes: Embedded in 2. Messenger RNA (mRNA) is synthesized
the nuclear envelope, controlling the from the DNA template in a process called
movements of the proteins, RNA, and other transcription.
molecules between the nucleus and the 3. The mRNA exits the nucleus and enters the
cytoplasm. cytoplasm.
3. Chromatin 4. Ribosomes read the mRNA sequence and
 Loosely coiled chromosomes translate it into a specific protein sequence.
 Composed of deoxyribonucleic acid 5. Transfer RNA (tRNA) brings the
(DNA) and protein appropriate amino acids to the ribosome,
 Aggregate of DNA and protein where they are assembled into a protein.

4. Nucleolus: A second dense structure mass CELL ORGANELLE: MITOCHONDRIA

closely associated with the inner nuclear “The Cellular Energy Generator”

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Function: Produces ATP through oxidative surface area for ATP production and to
phosphorylation; site of ATP production efficiently facilitate the energy-generating
processes of cellular respiration.
Process: Electrons from NADH and FADH2
move through the electron transport chain, Mitochondria Dynamics
creating a proton gradient that drives ATP Resting State: The inner mitochondrial
synthesis via AIP synthase. membrane is folded into cristae.

Number: Varies by cell type; more in energy- Respiring State: During respiration, the inner
demanding cells. membrane unfolds and shrinks, increasing the
volume of the intermembrane space for more O2.
Size: Typically 0.2 to 0.8 μm in diameter, 0.5 to
1.0 μm in length. Mitochondrial Structure
 Intermembrane Space:
Shape: Dyanamic change with metabolic - Located between the outer and inner
conditions. membranes.
- Similar ionic composition to the cytosol
Protein: Contain various proteins, involved in due to the outer membrane's permeability.
the electron transport chain and ATP synthase,
which are crucial for ATP production through  Mitochondrial Matrix
oxidative phosphorylation. - Enclosed by the inner membrane.
- Contains enzymes for the citric acid cycle
Other Roles: and fatty acid oxidation.
 Apoptosis – Programmed cell death; life - Includes circular DNA, ribosomes, and
span of RBCs is 120 days enzymes for protein synthesis coded by
 Calcium storage –Sequesters and the mitochondrial enzyme.
regulates intracellular calcium levels, crucial
for cellular signaling and energy production. Mitochondrial Functions
 ROS production - Generation of highly 1. Metabolism
reactive molecules, such as superoxide  Hosts enzymes for carbohydrate, fatty
anions, hydrogen peroxide, and hydroxyl acid, and nitrogen metabolism.
radicals, typically during cellular respiration
in the mitochondria. Responsible for cell 2. Energy Production
signaling and defense against pathogens.  Houses enzymes for electron transport
and oxidative phosphorylation.
Inner and Outer Mitochondrial Membranes
A. Outer Membrane: 3. Oxidation
 Composed mainly of phospholipids and  Specializes in the rapid oxidation of
cholesterol. NADH and FADH2 from glycolysis, the
 Contains the protein Porin, which forms citric acid cycle, and fatty acid oxidation.
channels that allow molecules smaller than
10,000 Daltons to pass through. 4. ATP Synthesis
 Other proteins are involved in fatty acid and  Converts energy from oxidation into ATP,
phospholipid synthesis and carry out the main energy currency for the cell.
oxidation reactions.
Important Enzymes in the Mitochondria
B. Inner Mitochondrial Membrane: Outer Membrane Intermediate
Composition: Rich in proteins, with a lipid-to- Space
protein ratio of 0.27:1. Contains a high  Cytochrome b5  Adenylate kinase
proportion of the phospholipid cardiolipin.  Cytochrome b5 reductase  Sulfite oxidase
 Fatty Acid CoA synthase  Nucleoside
Permeability: Virtually impermeable to polar  FA elongation system diphosphokinase
and ionic substances; they enter through  Phospholipase A
specific transport proteins.  Nucleoside
diphosphokinase

Cristae: The inner membrane is highly folded Inner Membrane Matrix

into structures called cristae, coated with  Cytochrome b, C1,  Pyruvate
proteins, including enzymes involved in the C, a and a3 dehydrogenase
electron transport chain, to maximize the

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 NADH complex (PDH)  Involved in key cellular functions: protein

dehydrogenase  Citrate synthase synthesis, transport, modification, storage,
 Ubiquinone  Aconitase and secretion.
 Electron-transferring  Isocitrate
flavoproteins dehydrogenase Characteristics:
 Vector ATP (ICD)  Varies in shape, size, and amount within
synthase (F0F1)  α-oxoglutarate different cells.
 Β-OH-butyrate dehydrogenase  Extends from the cell membrane to the
dehydrogenase  malate nucleus.
 Carnitine palmityl dehydrogenase  Surrounds mitochondria.
transferases  FA oxidation system  It often connects directly to the Golgi
 All translocases  Ornithine apparatus.
transcarbamylase
 Carbamoyl Structure:
phosphate  Comprised of membranes and aqueous
synthetase I channels called cisternae.

Clinical Aspects of Mitochondrial Diseases Functions:

1. Luft's Disease  Protein Synthesis: Ribosomes on the RER
 A rare disorder involving defective synthesize proteins, especially those
mitochondrial energy transduction. destined for secretion, membrane insertion,
2. Mitochondrial DNA Damage or lysosomes.
 Free radicals can damage mitochondrial  Protein Folding and Modification:Newly
DNA, leading to age-related degenerative synthesized proteins enter theRER lumen,
diseases, such as Parkinson's Disease where they fold into their proper shapes
& Cardiomyopathy and may undergo post-translational
3. Parkinson's Disease modifications (eg. glycosylation).
 Involves mitochondrial dysfunction  Transport: Proteins are packaged into
contributing to neurodegeneration. vesicles and transported to the Golgi
4. Cardiomyopathy apparatus for further processing and
 Mitochondrial damage affects heart sorting.
muscle function.  Membrane Production: Synthesizes
5. Leber's Hereditary Optic Neuropathy membrane components, including lipids
(LHON) and proteins, which are then used for cell
 A condition that leads to sudden vision membrane expansion and maintenance.
loss due to mitochondrial DNA mutations.
6. Mitochondrial Myopathy Types of Endoplasmic Reticulum
 Muscle weakness and exercise A. Rough Endoplasmic Reticulum
intolerance are caused by mitochondrial Structure:
defects in muscle cells.  A surface covered with ribosomes gives it a
7. Mitochondrial Encephalomyopathy, "rough" appearance under a microscope.
Lactic Acidosis, and Stroke-like  Composed of interconnected, flattened
episodes (MELAS) membranous sacs called cisternae.
 A disorder affecting the brain, nervous
system, and muscles, caused by Functions:
mitochondrial mutations.  Protein Synthesis: Ribosomes on the RER
8. Kearns-Sayre Syndrome synthesize proteins, especially those
 A multisystem disorder involving eye, destined for secretion, membrane insertion,
muscle, and heart problems, resulting or lysosomes.
from deletions in mitochondrial DNA.  Protein Folding and Modification: Newly
synthesized proteins enter the RER lumen,
where they fold into their proper shapes
and may undergo post-translational
modifications (eg., glycosylation).
 Transport: Proteins are packaged into
CELL ORGANELLE: ENDOPLASMIC vesicles and transported to the Golgi
RETICULUM (ER) apparatus for further processing and
Description: sorting.
 A network of interconnected membrane  Membrane Production: Synthesizes
complexes. membrane components, including lipids

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and proteins, which are then used for cell

membrane expansion and maintenance. Biochemical Functions:
 Protein Modification: Glycosylation and
B. Smooth Endoplasmic Reticulum phosphorylation.
Structure:  Protein Sorting & Packaging: Prepares
 Lacks ribosomes, giving it a smooth proteins for transport to cell membrane,
appearance. lysosomes, or secretion
 Consists of a network of tubules and  Lipid Transport: Modifies and sorts lipids
vesicles. for membrane formation.
 Lysosome Formation: Packages enzymes
Associations: for lysosomes
 Works closely with the rough ER,  Protein Selection
contributing to membrane and lipid  Processes proteins with specific signals.
production.  Unprocessed proteins remain in the
 Interacts with the Golgi apparatus and other cytoplasm.
cellular organelles for the distribution of
lipids and other synthesized molecules. ER Relationship
 Works closely with the ER for protein
Functions processing and transport.
 Lipid Synthesis: Produces lipids, including
phospholipids and cholesterol, essential for Golgi Apparatus: Protein Processing and
membrane formation and maintenance Transport
 Detoxification: Involved in detoxifying 1. Cis Side (Proximal):
drugs, alcohol, and harmful substances,  Receives newly synthesized proteins from
particularly in liver cells. the endoplasmic reticulum(ER) via
 Calcium Storage: Stores and regulates transfer vesicles.
calcium ions, crucial for muscle contraction
and other cellular processes. 2. Golgi Lumen (Medial Region):
Calcium - Bone and teeth formation,  Site of post-translational modifications.
muscle contraction, blood clotting, nerve  Carbohydrates and lipid precursors are
transmission, cell signaling & hormonal added to proteins, forming glycoproteins
secretion and lipoproteins.
Crucial for osteocytes and osteoblasts
because these bone cells rely on controlled 3. Trans Side (Distal):
calcium release to regulate bone formation  Releases processed proteins through
and remodeling. Osteoblasts, build bone, secretory vesicles.
and use calcium to mineralize the bone  These vesicles fuse with the plasma
matrix, while osteocytes, which maintain membrane, expelling their contents via
bone tissue, help regulate calcium levels exocytosis.
within the bone through signaling that
depends on intracellular calcium stores. CELL ORGANELLE: LYSOSOMES
Heparin: Affects calcium levels, as an  Cell organelles are found in cells that
anticoagulant, it can bind to and reduce contain packets of enzymes.
calcium levels because it has a strong  Size:
affinity for calcium ions. - Mean diameter is approximately 0.4 μ
 Carbohydrate Metabolism: Plays a role in (varies in between that of microsomes
the metabolism of carbohydrates, and mitochondria). They are surrounded
particularly in the liver where it helps in by a lipoprotein membrane.
glucose regulation  Lysosomes are found in all animal cells,
except erythrocytes, in varying numbers
and types.

 pH:
CELL ORGANELLE: - pH inside the lysosomes is lower than
GOLGI COMPLEXES/APPARATUS that of cytosol. The lysosomal enzymes
Structure: have an optimal pH of around 5.
 Stacked, membrane-bound compartments - Acid phosphatase is used as a marker
(cisternae). enzyme for this organelle.
 Organized into cis, medial, and trans
regions. Types of White Blood Cells (WBCs)

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1. Neutrophils: The most abundant WBCs,

first responders to infection, engulfing and Biomedical Importance of Lysosomes
destroying bacteria and other pathogens. Autophagy: Lysosomes digest cellular
organelles like mitochondria and ER during
2. Lymphocytes: Includes T cells and B cells, autophagic processes.
which are crucial for adaptive immunity,
recognizing specific pathogens and creating Cell Death: During cell death, lysosomal
memory cells for long-term immunity. enzymes cause autolysis by breaking down
cellular components.
3. Monocytes: Differentiate into macrophages
and dendritic cells, engulf pathogens, and Bacterial Digestion: White blood cells use
present antigens to lymphocytes to initiate lysosomes to digest engulfed bacteria.
an immune response.
a. Macrophages: Large phagocytic cells, Reproductive Role: The acrosome in sperm,
that engulf and digest pathogens, dead a specialized lysosome, aids novum
cells, and debris, and also present penetration.
antigens to T cells to initiate and
regulate immune responses. CELL ORGANELLE:
PEROXISOMES (MICROBIOLOGY)
b. Dendritic Cells: Specialized antigen- Structure:
presenting cells that capture and  Small organelles, ~0.5 pm in diarneter.
process antigens from pathogens or  Present in eukaryotic cells.
damaged cells, then migrate to lymph
nodes to activate T cells and initiate Functions:
adaptive immune responses.  Subcellular respiratory organelles.
 Lack of energy-coupled electron transport
4. Eosinophils: Primarily combats parasitic systems.
infections and allergic reactions, releases
enzymes that break down parasites and Formation:
modulate inflammatory responses.  Likely formed by budding from the smooth
5. Basophils: The least common WBCs, they endoplasmic reticulum (ER).
release histamine and other chemicals
during allergic reactions and play a role in Functions of Peroxisomes
the body's defense against parasites.  Oxidation Reactions: Carry out oxidation
reactions, producing toxic hydrogen
Lysosomal Enzymes peroxide (H2O2).
1. Proteolytic Enzymes  Detoxification: Hydrogen peroxide (H2O2) is
 Cathepsins (Proteinase) destroyed by the enzyme catalase
 Collagenase  Fatty Acid Oxidation: In liver cells,
 Elastase peroxisomes perform B-oxidation of long-
chain fatty acids (C16 % C18 or longer).
2. Nucleic Acid Hydrolyzing Enzymes  Unique Enzyme: β -oxidation starts with a
 Ribonucleases flavoprotein,"acyl-CoA oxidase."
 Deoxyribonucleases - Reaction Acyl-CoA + O2 → α , β
unsaturateCoA + H2O2
3. Lipid Hydrolyzing Enzymes - H2O2 Breakdown: The produced H2O2 is
 Lipases immediately broken down by catalase.
 Phospholipases
 Fatty acyl-Esterases
COMPARISON OF PEROXISOMES
AND LYSOSOMES
4. Carbohydrate splitting Enzymes Aspect Peroxisomes Lysosomes
 A-glucosidase
Primary Oxidation & Digestion &
 B-galactosidase
Function detoxification waste
 Hyaluronidase
breakdown
 Aryl sulfatase
Ezyme Oxidative Hydrolytic
Types enzymes (eg., enzymes (e.g.,
5. Other Enzymes
catalase, acyl- proteases,
 Acid phosphatase
CoA oxidase) lipases,
 Catalase

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nucleases) and serves as a storage site for amino

Formation Likely formed Formed from acids, ions, and essential molecules.
by budding the Golgi  Buffering: The cytosol helps maintain the
from the apparatus cell's pH and ionic balance, ensuring a
smooth ER stable environment for cellular processes.
Targeted Fatty acids, Biomolecules
Substance amino acids, (proteins, CELL ORGANELLE: CELL MEMBRANE
(FUNCTION & IMPORTANCE)
s toxins nucleic acids,
Separation from Environment: This
pathogens)
membrane separates the cell's internal
Presence
contents from the external environment, acting
of Energy-
as a crucial barrier.
Coupled No No
Electron
Selective Permeability: Regulates the flow of
Transport
molecules and ions into and out of the cell,
Role in Involved in lipid Not directly
allowing essential nutrients and waste products
Metabolism metabolism involved in
out.
and β -oxidation metabolism

CELL ORGANELLE: CYTOSOL

Cellular Recognition & Communication: This
Simplest Structure: Organelle-free fluid contains specific molecules that enable the cell
portion of the cytoplasm. to recognize and communicate with other cells,
facilitating various cellular processes.
Metabolic Hub: Site of metabolic reactions,
facilitating enzyme-substrate interactions. How do Phagocytes & T Cells recognize
bacteria?
Protein-Rich: Supports protein synthesis on Phagocytes recognize bacteria through
the rough ER by supplying cofactors and pattern recognition receptors (PRRs) on their
energy. surface, which detect specific molecules called
pathogen-associated molecular patterns
Free Ribosomes: Contains free ribosomes (PAMPs) that are commonly found on bacterial
(polysomes) for cytosolic protein synthesis. surfaces, such as lipopolysaccharides,
peptidoglycans, and flagellin. This recognition
Dual Role in Protein Synthesis: Assists in triggers the phagocyte to engulf and destroy
protein production on the rough ER and within the bacteria.
the cytosol.
T cells recognize bacteria through the
Biochemical Functions of the Cytosol interaction of their T-cell receptors (TCRs) with
(Preparatory Step Reactions) antigens presented on the surface of infected
 Metabolic Reactions: Site for numerous cells or antigen-presenting cells. These
metabolic pathways, including glycolysis, antigens are displayed on major
gluconeogenesis, and the pentose histocompatibility complex (MHC) molecules,
phosphate pathway, where substrates and with MHC class I presenting antigens to
enzymes interact. cytotoxic T cells (CD8+), and MHC class II
 Protein Synthesis: Free ribosomes in the presenting antigens to helper T cells (CD4+).
cytosol synthesize proteins that function This recognition activates the T cells, leading
within the cell, such as enzymes, structural to an immune response against the bacteria.
proteins, and signaling molecules.
 Cofactor Supply: Provides essential
cofactors, such as ATP, ions, and
coenzymes, necessary for enzymatic Chemical Composition of Membranes
reactions and energy production.  Key Components: Membranes are
 Signal Transduction: Acts as a medium primarily composed of lipids, proteins, and
for intracellular signaling, where second carbohydrates.
messengers like calcium ions and cyclic  Relative Content:
AMP (CAMP) transmit signals from the cell - Lipids: Constitute approximately 40% of
membrane to target molecules within the the membrane's dry weight.
cell. - Proteins: Make up about 60% of the
 Transport and Storage: It facilitates the membrane's dry weight.
transport of molecules and ie within the cell

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- Carbohydrates: Account for 1% to 10%

of the membrane's dry weight, 3. Cholesterol
depending on the membrane type.  A significant component of animal cell
 Attachment: All carbohydrates present in membranes, but not present in plant and
the membrane are covalently attached to prokaryotic membranes.
proteins or lipids, forming glycoproteins and  Cholesterol molecules are oriented with
glycolipids. their hydrophilic heads exe membrane,
while their hydrophobic regions are buried
CELL ORGANELLE: within cholesterol helps regulate
CELL MEMBRANE (LIPIDS) membrane fluidity in animal cells.
 Lipids are the basic structural components
of cell membranes. Formation of Lipid Bilayer
 Lipid molecules have a 'polar' or ionic 1. Criteria for Bilayer Formation:
head, hence hydrophilic, and the other  Lipids can form bilayers only if the
end is 'non-polar' and hydrophobic, hydrophobic tail and hydrophilic head
allowing them to form bilayers that are have roughly equal cross-sectional areas.
crucial for membrane structure and  Glycerophospholipids and
function. Sphingolipids meet this criterion,
allowing them to form bilayers.
Types of Lipids Present in Bio Membranes
1. Fatty Acids 2. Lipids That Don't Form Bilayers:
 Major components of most membrane  Lysophospholipids: Have only one fatty
lipids. acyl group, making their polar heads too
 The nonpolar tails of membrane lipids are large to form a bilayer
typically long-chain fatty acids attached to  Cholesterol: Its rigid ring system and
polar head groups, such as glycerol-3- large nonpolar tails prevent it from forming
phosphate. bilayers.
2. Saturation
 About 50% of the fatty acid chains are 3. Forces Behind Bilayer Formation:
saturated, containing 16 to 18 carbon  The hydrophobic effect and solvent
atoms. entropy drive the formation of lipid
 The other 50% are unsaturated or bilayers.
polyunsaturated fatty acids.
3. Common Unsaturated Fatty Acids 4. Characteristics:A lipid bilayer is extremely
 Oleic Acid: Most abundant. thin, about 6 nanometers across, and
 Others: Arachidonic acid, linoleic acid, behaves like a two-dimensional fluid.
and linolenic acid
4. Membrane Fluidity CELL ORGANELLE:
 The degree of unsaturation of the fatty CELL MEMBRANE (PROTEINS)
acids directly impacts the fluidity of the Integral (Intrinsic) Membrane Proteins
membrane. More unsaturated fatty acids  They are proteins that are deeply
lead to greater membrane fluidity. embedded within the cell membrane.
 Portions of these proteins contact the
Types of Lipids in Biomembranes membrane's hydrophobic (water-repelling)
1. Glycerophospholipids regions through Van der Waals forces,
 Common examples include which help stabilize their position within the
phosphatidylethanolamine (cephalin), membrane.
phosphatidylcholine (lecithin), and
phosphatidylserine. Peripheral Membrane Proteins (Extrinsic
 These lipids are major components of Proteins):
biological membranes.  Attachment: These proteins are weakly
bound to the membrane sun ace through
2. Sphingolipids ionic interactions or hydrogen bonds with
 It is found predominantly in the tissues of the polar heads of membrane lipids. They
the nervous system. may also interact with integral membrane
 Types include sphingomyelin, proteins.
cerebrosides, and gangliosides.  Peripheral proteins can be removed from
 Gangliosides constitute about 6% of the the membrane without disrupting its
membrane lipids in the grey matter cells structure.
of the brain.

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Types of Proteins functions, including transport, and

1. Integral Proteins: Involved in energy maintaining the membrane's integrity.
production and electron transport chain in
mitochondria.
Ex: ATP synthase & Cytochrome c oxidase
2. Peripheral Proteins: Provide structural
support and help anchor the cytoskeleton to
the membrane.
Ex: Spectrin & Ankyrin
3. Transmembrane Proteins: Act as
receptors for hormones, neurotransmitters,
and signaling molecules, facilitating cellular
communication.
Ex: Insulin receptor G-protein coupled
receptors (GPCRs)

CELL ORGANELLE:
CELL MEMBRANE (CARBOHYDRATES)
Composition: Approximately 5% of the weight
of cell membranes consists of carbohydrates in
the form of glycoproteins and glycolipids.
Example:
 Glycophorin: A major integral membrane
glycoprotein found in human erythrocytes
(red blood cells). It has 130 amino acid
residues and spans the lipid membrane,
with polypeptide regions extending
outside both the external and internal
(cytoplasmic) surfaces. The carbohydrate
chains are attached to the amino-terminal
portion on the external surface of the cell.
Microheterogeneity: The carbohydrate chains
of many glycoproteins show structural variation
from one molecule to another, a phenomenon
known as microheterogeneity. This variation
contributes to the diversity of glycoproteins on
cell surfaces, which can affect cell recognition
and signaling.

Fluid Mosaic Model of Membrane Structure

 Proposed by Singer and Nicholson
(1972): This model has become the widely
accepted explanation of how biological
membranes are structured.
 Key Concept:
- The membrane is composed of a fluid
phospholipid bilayer, where membrane
proteins are embedded and float.
- Intrinsic (integral) proteins are deeply LESSON 2:
embedded within the lipid bilayer. MODERN ATOMIC THEORY
- Peripheral proteins are loosely attached AND THE PERIODIC TABLE
to the surface of the membrane. A BRIEF HISTORY OF ATOMIC THEORY
 Analogy: The model can be compared to  Greeks were the first to suggest that matter
icebergs floating in seawater, where the is made up of atoms.
proteins represent the icebergs, and the  Earty chemists performed experiments.
fluid phospholipids represent the seawater.  Their experiments led to Daton's Atomic
 Importance: The fluidity of the membrane Theory.
allows for dynamic movement of proteins,  Limitations of Dalton's model led to the
which is essential for various cellular Thompson and Rutherford models of the
atom.

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 While these models work reasonably well The color of the light emitted corresponds to
their limitations have led to more modern one of the lines of the hydrogen spectrum.
theories as to the nature of the atom. The space in atoms is called the electron
cloud.
DIFFERENCE OF IONIC BONDS
AND MOLECULAR BONDS
 Ionic bonding occurs when The first four principal energy levels of the
atoms transfer electrons, creating hydrogen atom.
oppositely charged ions (cation & anion)
that attract each other.
 Molecular bonding (or covalent bonding)
happens when atoms share electrons to
achieve stability.
 Ionic bonds are generally stronger but
form between metals and nonmetals, while Within sublevels the electrons are found in
covalent bonds form between nonmetals. orbitals.
An s orbital is spherical in
Why do elements have charges? shape.
Elements have charges due to the loss The spherical surface
or gain of electrons. Atoms become positively encloses a space where
charged (cations) when they lose electrons and there is a 90% probability
negatively charged (anions) when they gain that the electron may be
electrons, as they strive to achieve a stable found.
electron configuration, usually similar to that of
a noble gas. An atomic orbital can hold a maximum of two
VALENCE ELECTRONS
electrons.
 Valence electrons are the outermost
An electron can spin in one
electrons in an atom.
of two possible directions
 They determine an element's chemical
represented by ↑ or ↓.
properties and its ability to bond with other
elements.
The two electrons that
 Atoms with similar numbers of valence
occupy an atomic orbital
electrons exhibit similar chemical behavior.
must have opposite spins.
 Valence electrons participate in forming
This is known as the Pauli Exclusion Principal.
chemical bonds, such as ionic or covalent
bonds.
A p sublevel is made up of three orbitals.
 The number of valence electrons
influences an atom's reactivity; elements
with a nearly full or nearly empty valence
shell are more reactive.

OCTET RULE
 The octet rule states that atoms tend to  Each p orbital has two lobes.
gain, lose, or share electrons to achieve a  Each p orbital can hold a maximum of six
full valence shell of 8 electrons. electrons.
 This rule is based on the stability observed
in noble gases, which naturally have 8
valence electrons (except helium, which
has 2). A p sublevel is made up of five orbitals.
 The octet rule explains the formation of
most ionic and covalent bonds.
 It applies mainly to main-group elements
and may have exceptions, especially
among transition metals and molecules with
an odd number of electrons.
 Atoms that follow the octet rule achieve  The five d orbitals all point in different
greater stability and lower energy. directions.
 Each p orbital can hold a maximum of 10
THE BOHR ATOM
electrons.

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RULES OF ELECTRON CONFIGURATION  It is the basic component of ALL ORGANIC

COMPOUNDS.

What then makes Carbon so special that it is

the subject of interest of this course?
Versatility in Bonding: Carbon can form four
Arrangement of electrons within their covalent bonds, allowing it to create a diverse
respective sublevels. range of structures, from simple molecules to
complex macromolecules like proteins and
RULES OF ELECTRON CONFIGURATION
DNA.
1. Pauli Exclusion Principle
Unique Hybridization: Carbon’s ability to
 No more than 2 electrons can occupy a
undergo hybridization leads to various bonding
single orbital, and they must have geometries, crucial for the stability and function
opposite spins. of organic compounds.
Foundation of Organic Chemistry: Carbon is
2. Aufbau Principle the central element in organic chemistry, which
 Electrons occupy the lowest energy is fundamental to understanding biological
orbitals first before filling higher energy processes, materials science, and numerous
orbitals (e.g., 1s before 2s, 2s before 2p). other fields.
3. Order of Orbitals (s, p, d, f)  Carbon is always an excited state. Based
 Electrons fill orbitals in the following order on its position in the periodic table, let's
based on increasing energy: 1s, 2s, 2p, explore its electronic configuration: 1s 2s?
3s, 3p, 4s, 3d, 4p, 5s, 4d, etc., with "s" 2p?".
orbitals filling first, followed by "p," "d,"  Carbon is always on excited state, making it
and "f." want the maximum reactions.
4. Hund's Rule  Carbon as a part of IV-AFamily has four
 Each orbital within a sublevel (e.g., p, d,
valence (outer) electrons; it can share all
or f sublevel) is singly occupied by one
the valence electrons, forming strong
electron before any orbital is doubly
COVALENT BONDS.
occupied. Electrons in singly occupied
 Carbon atoms can bond with one another,
orbitals have parallel spins.
forming long chains and even rings.
Note: Atomic number of an element is equal to
 Of all other elements, carbon alone has the
the number of protons and electrons.
ability to form an immense diversity of
compounds.
Electron Config of the First 18 elements
Hydrogen (H): 1s¹, ↑ WHY STUDY ABOUT CARBON?
Helium (He): 1s², ↑↓  Understanding carbon's properties and its
Lithium (Li): 1s² 2s¹, ↑↓ ↑ reactions with other elements is crucial.
Beryllium (Be): 1s² 2s², ↑↓ ↑↓  Carbon has long been a mysterious 'vital
Boron (B): 1s² 2s² 2p¹, ↑↓ ↑↓ ↑ force' that puzzled scientists for centuries.
Carbon (C): 1s² 2s² 2p², ↑↓ ↑↓ ↑ ↑  Carbon is the foundation of all organic
Nitrogen (N): 1s² 2s² 2p³, ↑↓ ↑↓ ↑ ↑ ↑ compounds that comprise your body.
Oxygen (O): 1s² 2s² 2p⁴, ↑↓ ↑↓ ↑↓ ↑ ↑  From your cells to the food you eat, carbon
Fluorine (F): 1s² 2s² 2p⁵, ↑↓ ↑↓ ↑↓ ↑↓ ↑ is essential.
Neon (Ne): 1s² 2s² 2p⁶, ↑↓ ↑↓ ↑↓ ↑↓ ↑↓  The aroma of coffee, the taste of fresh
Sodium (Na): 1s² 2s² 2p⁶ 3s¹, ↑↓ ↑↓ ↑↓ ↑↓ ↑↓ ↑↓ apples, and even your emotions are linked
Carbon undergoes hybridization to to carbon-containing compounds.
achieve a more stable configuration by
rearranging its valence electrons. This process UNDERSTANDING THE NATURE OF
allows carbon to form four equivalent covalent ORGANIC COMPOUNDS
bonds, maximizing bonding capacity and Why study Organic Chemistry?
resulting in a more stable molecule, such as in Simple: You need it to pass your subect.
methane (CH₄).
 First things first, let’s ask ourselves: What
LESSON 3: is Organic Chemistry?
ORGANIC CHIEMSTRY  Organic Chemistry is the study of carbon-
WHAT IS CARBON? containing compounds. It explores the
 It is the head of the Carbon Family (IV-A) in nature of carbon, its compounds, and its
the periodic table. reactions.

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 Why is it important? certain manner the time an "attack" of

- Organic Chemistry is important another molecule comes.
because it provides a foundation for
understanding the complex structures THE CARBON ATOM: BONDING AND SHAPE
that make up living organisms and  The carbon atom is central to all organic
materials. compounds.
- It touches every aspect of life, and  A carbon atom usually forms four covalent
understanding organic chemistry gives bonds.
insights into more complex structures - Single bonds
such as cells, viruses, bacteria, and Ex: H3C-CH3 in ethane
even ourselves. - Double bonds
Ex: H2C=CH2 in ethene
ORGANIC CHEMISTRY VS INORGANIC CHEMISTRY - Triple bonds
Organic Chemistry Inorganic Chemistry Ex: HC≡CH in ethyne (acetylene)
 Studies Carbon  Studies any
compounds. compound.  An organic compound is classified as
 Compounds studied  Compounds studied saturated if it contains only single bonds.
mostly derived from are mostly derived Ex: H,C-CH, in ethane
living sources. from minerals.  An organic compound is classified as
 Compounds can  Compounds are unsaturated if the molecules possess one
decompose decompose through or more multiple carbon-carbon bonds.
naturally. energy Ex: H,C=CH, in ethene
HC≡CH in ethyne (acetylene)
WHAT ARE ORGANIC COMPOUNDS? THE SHAPES OF CARBON-CONTAINING
 Carbon-containing compounds COMPOUNDS
 Naturally occurring: mostly of life origin, and Valence Shell Electron Pair Repulsion
nature based. theory (VSEPR)
- However, not all organic compounds are  VSEPR theory states that electron pairs
not derived from living organisms, of repel each other because they have liek
course. Newly discovered organic charges.
compounds were merely synthesized even  The electron pairs will try to spread far as
derived from non-organic compounds, or possible around an atom
products of laboratory tests.
 Exceptions: CO2, H2CO3, CO3, CN-
 Of all the hundred plus elements in the
periodic table Organic Chemistry is mostly
concerned only for ten! Okay so Carbon is
given. The other nine are: Figure 19.1 Shows the tetrahedral structure of
Hydrogen: H carbon: (a) a regular tetrahedron; (b) a carbon
Carbon Group: C, Si atom with tetrahedral bonds; (c) a carbon atom
Nitrogen Group: N, P within a regular tetrahedron; (d) a methane
Oxygen Group: O, S molecule, CH4
Halogen Group: F, CI, Br, I
 There are about 37 million known organic
molecules.
 However, nature follows specific 'rules,'
allowing us to understand these molecules Figure 19.2 (a) Lewis structure for C 2H4. (b)
by focusing on small combinations of Shape of a molecule with a carbon-carbon
atoms. double bond. The hydrogens and carbon form
 Instead of studying 37 million compounds the vertices of a triangle. The bond angles are
individually, we can group them into a 120°.
dozen families with predictable chemistry."
In a triple bond, the carbon has only two
FUNCTIONAL GROUPS regions for shared electrons. To be placed as
 A group of atoms within a larger molecule far apart as possible, a linear arrangement is
with a characteristic chemical behavior. required.
 Simpler: a particular group or part of a 180 o
molecule that has a specific function. That
H:C:::C:H
function is to react, and behave in a
MOLECULAR MODELS

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 Models are often used in organic chemistry

to illustrate molecules.

Figure 19.3 shows molecular models of

methane: (a) ball-and-stick model; (b)
spacefilling model

Figure 19.4 Models of ethane shows (a) Lewis

structure; (b) bond-line drawing; (c) ball-and-
stick model; (d) spacefilling model

CLASSIFYING ORGANIC COMPOUNDS

Functional Groups
 Organic compounds with similar structures
are grouped into classes.
 Members of each class contain a
characteristic atom or group of atoms
known as the functional group.
 A functional group:
- is part of a larger molecule.
- is composed of an atom or group of
atoms that have characteristic chemical
behavior.
- Chemically, a given functional group
behaves in nearly the same way in
STRUCTURAL FORMULAS every molecule it’s part of.
 In a structural formula, the arrangement of
atoms within the molecule is clearly shown. Hydrocarbons
 These structural formulas are often  Hydrocarbons are compounds that are
shortened into condensed structural composed entirely of carbon and hydrogen
formulas. atoms bonded to each other by covalent
-e.g. CH3CH2CH3, & CH3-CH2-CH3 bonds.
 Fossil fuels - natural gas, petroleum and
coal - are the principal sources of
hydrocarbons.
 Hydrocarbons are classified into two major
categories, aliphatic and aromatic.
- aliphatic (do not contain benzene ring)
Ex. Alkanes, alkenes, alkynes, cycloalkanes
- aromatic (contain a benzene ring)

Hydrocarbon
(Contain only hydrogen and carbon)

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Figure 19.7 The tetrahedral nature of sp3

orbitals:
(a) a single sp3-hybridized orbital;
(b) four sp3-hybridized orbitals in a tetrahedral
arrangement; (c) sp3 and s orbitals overlapping
to form C-H bonds in methane.

SIGMA () BOND

 A C-C and C-H single bond result from the
SATURATED HYDROCARBON: ALKANE overlap of sp3 orbitals.
 The alkanes, also known as paraffins or  This type of bond is called a sigma ()
saturated hydrocarbons, are straight or bond.
branched-chain hydrocarbons with only  A sigma bond exists if the electron cloud
single covalent bonds between the carbon formed by the pair of bonding electrons lies
atoms. on a straight line drawn between the nuclei
CH3CH2CH2CH2CH3 of the bonded atoms.
straight-carbon chain
The valence bonds or points of attachment
may be represented in structural formulas by a
(CH3)2CHCH2CH2CH3
corresponding number of dashes attached to
each atom:
branched chain of carbon atoms
 When each member of a series differs from
the next member by a CH2 group, the series
is called a homologous series.
 The members of a homologous series are
similar in structure, but have a regular
difference in formula.

CnH2n + 2
General formula for open-chain alkanes  Alkane molecules are non-polar.
- Carbon-carbon bonds are non-polar,
since they are between like atoms.
- Carbon-hydrogen bonds are only slightly
polar.
- The bonds in an alkane are symmetrically
directed toward the corners of a
tetrahedron.
- In virtue of their low polarity, alkane
molecules have relatively low boiling
points compared with other organic
compounds of similar molar mass.
Carbon Bonding in Alkanes

Figure 19.6 Schematic hybridization of Figure 19.8 Ball-and-stick models illustrating

2s22px12pz0 orbitals of carbon to form four sp3 structural formulas of methane, ethane and
electron orbitals. propane.

ISOMERISM
It is possible to write two structural formulas
corresponding to the molecular formula C4H10:

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 This is the only four-chain compound that

can be written.

For the third isomer, start with a three-carbon

 The phenomenon of two or more chain, attach the other carbon atoms to the
compounds having the same molecular central carbon atom, and complete the
formula but different structural structure by adding 12 hydrogen atoms:
arrangements of their atoms is called
Isomerism.
 The various individual compounds H are
called Isomers.
- e.g. There are two isomers of CH no:

No more isomers of C5H12 can be written.

NAMING ORGANIC COMPOUNDS

IUPAC System for Naming Organic
Compounds
 The method recommended by the
International Union of Pure and Applied
Figure 19.8 Ball-and-stick models illustrating Chemistry is systematic, generally
structural formulas of butane and isobutane. unambiguous, and internationally accepted.
 Some trivial or common names are still
Isomers are compounds that have the same used.
molecular formula, but different structural
formulas. ALKYL GROUPS
 Alkyl groups have the general formula
There are three isomers of pentane, CAH,2. CnH2n+1 (one less hydrogen than the
Write structural formulas and condensed corresponding alkane).
structural formulas for these isomers.  The name of the group is formed from the
name of the corresponding alkane by
1. Write the carbon skeleton of the compound simply dropping -ane and substituting a -yl
containing the longest continuous carbon ending.
chain. CH4 = methane -CH3 = methyl
C-C-C-C-C  The letter R is often used in formula of the
many possible alkyl group
2. Complete the structure by attaching
hydrogen atoms around each carbon. Table 19.3
H H H H H Names and Formulas of elected alkyl Groups

H C C C C C H CH3CH2CH2CH2CH3

H H H H H

Isomers of Pentane, C5H12 (continued)

For the next isomer; start by writing a four-
carbon chain and attach the fifth carbon atom
to either of the middle carbon toms - do not use
the end ones. Add 12 hydrogens to complete
the structure.

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4. When the same alkyl-group branch chain

occurs more than once, indicate this by a
prefix (di-, tri-, tetra-, etc.) written in front of
the alkyl group name (e.g. dimethy/
indicates two methyl groups). The numbers
indicating the positions of these alkyl
groups are separated by a comma, followed
by a hyphen, and placed in front of the
name.
CH 3
H2
Primary (1°), Secondary (2°), and Tertiary (3°) C 3 C 5 CH 3
1
Carbon Atoms H3C 2 CH 4 C 6
H2
primary CH 3
CH 3

2,2,3-trimethylhexane
CH3 When several different alkyl groups are
primary attached to the parent compound, list them in
primary H2 alphabetical order (e.g. ethyl before methyl as
CH C in 3-ethyl-4-methyloctane).

H3C C CH3
tertiary H2
secondary
IUPAC RULES FOR NAMING ALKANES
1. Select the longest continuous chain of
carbon atoms as the parent compound, and
consider all alkyl groups attached to it as
branch chains that have replaced hydrogen Name the following alkane:
atoms of the parent hydrocarbon. The
name of the alkane consists of the name of
the parent compound prefixed by the
names of the branch-chain alkyl groups
attached to it.

2. Number the carbon atoms in the parent

carbon chain from one end to the other,
starting at the end closest to the first carbon
atom that has a branch chain.
3. Name each branch-chain alkyl group and
designate its position on the parent carbon
by a number.

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Write the formula for 3-ethylpentane Addition reactions

H2 H2  Two reactants adding together to form a
1 C 3 C 5 single product is called an addition reaction.
H3C 2 CH 4 CH 3  An addition reaction can be thought of as
the reverse of an elimination.
CH 2
H3C
Write the formula for 2,2,4-trimethylpentane
CH 3 CH 3

1 C CH
2 3 5
H3C C 4 CH 3
REACTIONS OF ALKANES
H2 Combustion of Alkanes
CH 3 Alkanes, as well as other hydrocarbons,
undergo combustion with oxygen with the
INTRODUCTION TO THE REACTIONS OF CARBON evolution of large amounts of heat energy.
One of the most important carbon reactions is
oxidation reduction. CH4(g) + 2O2 (g)  CO2(g) + 2H2O(g) + 802.5 Kj

Oxidation When CO2 is formed, the alkane has

 When carbon atoms are oxidized, they undergone complete oxidation.
often form additional bonds to oxygen.
Aside from their combustibility, alkanes
are relatively sluggish and limited in reactivity.
With proper activation, such as with high
temperature or catalysts, alkanes can be made
to react in a variety of ways.
Reduction Some Important Noncombustion Reactions of
 When carbon atoms are reduced, they Alkanes
often form additional bonds to hydrogen.  Halogenation
- A substitution reaction; A halogen is
substituted for a hydrogen atom.

Substitution reactions
 If, in a reaction, one atom in a molecule is
exchanged by another atom or group of
atoms, a substitution reaction has taken
place.  Dehydrogenation
- An elimination reaction; Hydrogen is lost
from an organic compound.

 Cracking
- Breaking up large molecules to form
Elimination reactions smaller ones
 An elimination reaction is a reaction in
which a single reactant is split into two
products, and one of the products is
 Isomerization
eliminated.
- Rearrangement of molecular structures
 Elimination reactions form multiple bonds. catalyst,
pressure,
CH3CH2CH2CH2CH3 heat CH3CH2CHCH3

CH3

Sources of Alkanes

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 The two main sources of alkanes are

natural gas and petroleum.
- Natural gas is formed by the anaerobic
decay of plants and animals.
- Petroleum, also called crude oil, consists
of a mixture of hydrocarbons and is formed
by the decomposition of plants and animals
over millions of years.

GASOLINE: A MAJOR PETROLEUM PRODUCT Reactivity of Cyclopropane and

Figure 19.9 Uses of petroleum Cyclobutane
 There is a greater reactivity in cyclopropane
and cyclobutane because the carbon-
carbon bond angles in these substances
deviate substantially from the tetrahedral
angle.
 Their carbon-carbon bonds are strained
and therefore weakened.

Conformations of Cyclohexane
 The conformation of a molecule is its three-
dimensional shape in space.

CYCLOALKANES
 Cycloalkanes have the formula CnH2n.
 Their names are formed by adding the
prefix cyclo- to the name of the alkane with
the same number of carbon atoms. Figure 19.12 Conformations of cyclohexane:
(a) chair conformation; (b) boat conformation.
Axial hydrogens are shown in blue in the chair
conformation.

NAMING CYCLOALKANES
 Substituted cycloalkanes are named by
identifying and numbering the location of
the substituents) on the carbon ring,
followed by the name of the parent alkane.
 With the exception that follows for CH3
cyclopropane and cyclobutane,
cycloalkanes are generally similar to open
chain alkanes in both physical properties
and chemical reactivity. methylcyclohexane
 Cycloalkanes are saturated hydrocarbons:  When a cycloalkane has two or more
they contain only single bonds between substituted groups, the ring is numbered
carbon atoms. (clockwise or counterclockwise) to give the
location of the substituted groups the
smallest numbers.

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LESSON 4: The carbon-carbon pi () bond is much weaker

UNSATURATED HYDROCARBONS and, as a consequence, much more reactive
INTRODUCTION than the carbon-carbon sigma () bond.
Unsaturated hydrocarbons enhance our lives in
many ways:
1. Polyethylene plastic bags and bottles
2. Polystyrene Styrofoam cups
3. Plastic wraps
4. Essential oils in plants contain multiple
bonds between carbon atoms.
– Cosmetics, medicines, flavorings,
perfumes
5. Hydrocarbons also form rings of carbon
atoms (aromatics)
– Detergents, insecticides, and dyes
The formation of a triple bond between
BONDING IN UNSATURATED HYDROCARBONS carbon atoms, as in acetylene, CHCH, may
The unsaturated hydrocarbons consist of three be visualized as shown below.
families of homologous compounds that
contain multiple bonds between carbon atoms.
 Alkenes contain carbon-carbon double
bonds.
 Alkynes contain carbon-carbon triple
bonds.
 Aromatic compounds contain benzene
rings.
NOMENCLATURE OF ALKENES
The four orbitals available for bonding in The general formula for alkenes is:
alkenes are three sp2 orbitals and one p orbital. CnH2n

IUPAC Rules for Naming Alkenes

1. Select the longest continuous carbon-
carbon chain that contains the double bond.
2. Name this parent compound as you would
Schematic hybridization of 2s22px12py1 orbitals an alkane, but change the –ane ending to –
of carbon to form three sp2 electron orbitals and ene.
one p electron orbital
3. Number the carbon chain of the parent
compound starting with the end nearer to
the double bond. Use the smaller of the two
numbers on the double-bonded carbon
atoms to indicate the position of the double
bond. Place this number in front of the
alkene name.

(a) A single sp2 electron orbital and (b) a side

view of three sp2 orbitals all lying in the same
plane with a p orbital perpendicular to the three 4. Branch chains and other groups are treated
sp2 orbitals. as in naming alkanes, by numbering and
assigning them to the carbon atom to which
they are bonded.

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How would we write the structural formula for Condensed & Line formulas
4-methyl-2-pentene?
The name indicates:
– Five carbons in the longest chain
– A double bond between carbons 2 and 3
– A methyl group on carbon 4

Condensed & Line formulas GEOMETRIC ISOMERISM IN ALKENES

 Compounds containing a carbon-carbon
double bond (pi bond) have restricted
rotation about that double bond.
 This restricted rotation in a molecule gives
rise to a type of isomerism known as
geometric isomerism.
 Isomers that differ from each other only in
the geometry of their molecules and not in
the order of their atoms are known as
geometric isomers.
Write a structural formula for: - They are also called cis-trans isomers.
7-methyl-2-octene
 Octene indicates an 8-carbon chain Trans is a Latin noun or prefix, meaning
 The chain contains a C=C between carbons “across”, “beyond” or “on the opposite side”.
2 and 3.
 There is a –CH3 group on carbon 7 Cis is a Latin prefix, meaning “on the same
side [as]” , “on this side [of]”, or “near side [of]”.

Condensed & Line formulas

An alkene shows cis-trans isomerism when

each carbon atom of the double bond has two
different kinds of groups attached to it.

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Draw a structure for cis-5-chloro-2-hexene PROPERTIES OF ALKENES

The compound contains 6 carbons with A. Cracking
a C=C between carbons 2 and 3, and a Cl  Cracking, or pyrolysis, is the process in
atom on carbon 5. which saturated hydrocarbons are heated
to very high temperatures in the presence
of a catalyst (usually silica-alumina):

Alkane (CnH2n+2)  Mixture of alkenes + Alkanes + H2 (g)

2CH3CH2CH3  CH3CH=CH2 + CH2=CH2 + CH4 + H2

B. Dehydration of Alcohols
Dehydration involves the elimination of a
molecule of water from a reactant molecule.
H H
Condensed cis-5-chloro-2-hexene conc. H2SO4
H H

H3C C C CH 3 H3C C C CH 3 + H2O

heat
H OH

Physical Properties of Alkenes

Very similar to the corresponding alkanes.

Is the compound below the cis or trans isomer?

trans-3-methyl-2-pentene CHEMICAL PROPERTIES OF ALKENES

Addition Reactions of Alkenes
Condensed trans-3-methyl-2-pentene  Addition at the C=C bond is the most
common reaction of alkenes.
– H2
– Br2 and Cl2
– HBr, HCl
– H2O
CYCLOALKENES
 As the name implies, cycloalkenes are cyclic Addition of H2
compounds that contain a C=C in the ring.  Hydrogenation
 The carbons of the double bond are
assigned numbers 1 and 2.

Addition of X2
 Bromination (Br2) or Chlorination (Cl2)

CH 3 CH 3
5 4
1 3

4 2 5 2

3 6 1
1-methylcyclopentene CH 3
1,3-dimethylcyclohexene
PREPARATION AND PHYSICAL

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Bromine changes from a CARBOCATION

red-orange (flask on the An ion in which a carbon atom has a positive
left) to colorless when charge is known as a carbocation.
added to an alkene as
shown in the flask on the H H C C
right.
H C C C C C C C

H H H C
o o
methyl primary (1 ) secondary (2 )
Addition of HX carbocation carbocation carbocation tertiary (3 )
o

 Hydrobromination (HBr) or carbocation

Hydrochlorination (HCl)
The order of stability of carbocations and
hence the ease with which they are formed is:

H H C C

H C C C C C C C

Addition of H2O H H H C
methyl primary (1o) secondary (2o)
carbocation carbocation carbocation tertiary (3o)
carbocation

increasing stability
Addition of HX to an Unsymmetrical Alkene
Write formulas for the organic products formed
when 2-methyl-1-butene reacts with:
a) H2, Pt/25°C
2-methyl-1-butene + H2, Pt/25 °C

2-methylbutane

b) Cl2
2-methyl-1-butene + Cl2

REACTION MECHANISM
1. A proton (H+) from HCl bonds to carbon 1 of
propene by utilizing the pi bond electrons.
The intermediate formed is a positively
charged alkyl group, or carbocation. The 1,2-dichloro-2-methylbutane
positive charge is localized on carbon 2 of
this carbocation. c) HCl
H H - 2-methyl-1-butene + HCl
H3C C CH2 + H-Cl H3C C CH2 + Cl
3 2 1
H
isopropyl carbocation

2. The chloride ion then adds to the positively 2-chloro-2-methylbutane

charged carbon atom to form a molecule of
2-chloropropane. d) H2O, H+
H - H 2-methyl-1-butene + H2O
H3C C CH2 + Cl H3C C CH2 CH 3 CH 3
+
H
H Cl H H2C C CH 2CH 3 + H2O H2C C CH 2CH 3

2-chloropropane
H OH
2-hydroxy-2-methylbutane

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MARKOVNIKOV’S RULE (VLADIMIR MARKOVNIKOV) • Acetylene can be prepared from calcium

When an unsymmetrical molecule such carbide and water.
as HX (HCl) adds to a carbon-carbon double – CaC2 + 2H2O  HCCH + Ca(OH)2
bond, the hydrogen from HX goes to the • Acetylene is also prepared by the cracking
carbon atom that has the greater number of of methane at 1500 °C.
hydrogen atoms. Simple terms: Hydrogens will – 2CH4  HCCH + 3H2
bind with the Carbon rich in Hydrogen.
PHYSICAL AND CHEMICAL
PROPERTIES OF ALKYNES
Physical Properties of Alkynes
 Acetylene is a colorless gas with little odor
when pure.
 Acetylene is insoluble in water and is a gas
at normal temperature and pressure.
This reaction proceeds via the formation of the
most stable carbocation intermediate (2°). Chemical Properties of Alkynes
• Alkynes undergo addition reactions rather
DIENES similar to those of alkenes.
 Many compounds have more than one – Cl2 and Br2
C=C. – HCl and HBr
 Compounds with two C=C are called – Positive reaction with Baeyer’s test.
dienes.
Bromination of Acetylene
HCCH + Br2  CHBr=CHBr
HCCH + 2 Br2  CHBr2-CHBr2

Tests for Unsaturation

1,3-butadiene
Compounds with three C≡C are called trienes.

OXIDATION
Oxidation at the C=C Bond
 Baeyer Test
Bromine Potassium permanganate
(Baeyer’s test)

HCl Addition to Unsymmetrical Alkynes

 This addition follows Markovnikov’s rule:
CH3CCH + HCl  CH3CCl=CH2
ALKYNES: NOMENCLATURE AND PREPARATION
CH3CCH + 2 HCl  CH3CCl2-CH3
IUPAC Rules for Naming Alkynes
LESSON 5:
The rules for naming alkynes are the AROMATIC HYDROCARBONS: STRUCTURE
same as those for alkenes, but the ending – BENZENE
yne is used to indicate the presence of a triple Benzene and all substances with
bond. structures and chemical properties that
CH3CH2C≡CH resemble benzene are classified as aromatic
1-butyne compounds.
Nomenclature of Common Alkynes

Representations of Benzene

BONDING IN BENZENE
PREPARATION OF ALKYNES

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 The electrons are not attached to particular

carbon atoms, but are delocalized and
associated with the entire molecule.
 This electronic structure imparts unusual
stability to benzene and is responsible for
many of the characteristic properties of
aromatic compounds.

Figure 20.5 (a)

sp2-sp2 orbital
overlap to form PHENYL GROUP
the carbon ring  The C6H5- group is known as the phenyl
structure. group, and the name phenyl is used to
name compounds that cannot easily be
named as benzene derivatives.

Figure 20.5 (b)

carbon-
hydrogen bonds
DISUBSTITUTED BENZENES
formed by sp2-s
 The prefixes ortho-, meta-, and para-
orbital overlap
(abbreviated o-, m-, and p-) are used to
and overlapping
name disubstituted benzenes.
p orbitals.

Figure 20.5 (c) pi electron clouds above and

below the plane of the carbon ring.

Dichlorobenzenes, C6H4Cl2
 The three isomers of dichlorobenzene have
different physical properties.

NAMING AROMATIC COMPOUNDS

Naming Substituted Benzene Compounds
 A substituted benzene is derived by
replacing one or more hydrogen atoms of
benzene by another atom or group of
atoms.
 Monosubstituted benzene has the formula
Disubstituted Benzenes
C6H5G, where G is the group replacing a
When the two substituents are different
hydrogen atom.
and neither is part of a compound with a
 Some Monosubstituted benzenes are
special name, the names of the two
named by adding the name of the
substituents are given in alphabetical order,
substituent group as prefix to word
followed by the word benzene.
benzene.
CH2CH3 Br

O2N Cl

nitrobenzene ethylbenzene chlorobenzene bromobenzene

 Certain monosubstituted benzenes have

special names.

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DIMETHYL BENZENES  Aromatic hydrocarbons are essentially

 The dimethylbenzenes have the special nonpolar substances, insoluble in water but
name xylene. soluble in many organic solvents.
 They are liquids or solids and usually have
densities less than that of water.
 Aromatic hydrocarbons burn readily,
usually with smoky yellow flames as a
result of incomplete carbon combustion.

CHEMICAL PROPERTIES OF
 When one of the substituents corresponds AROMATIC HYDROCARBONS
to a monosubstituted benzene that has a Substitution Reactions of Aromatic
special name, the disubstituted compound Hydrocarbons
is named as a derivative of that parent  Halogenation: Net addition of -Br or -Cl
compound. When benzene reacts with chlorine or
bromine in the presence of a catalyst such as
iron (III) chloride or iron (III) bromide, a Cl or Br
atom replaces an H atom to form the products.

POLYSUBSTITUTED BENZENES
 When there are more than two substituents
on a benzene ring, the carbon atoms in the
ring are numbered starting at one of the
substituted groups.  Nitration: Net addition of –NO2
 Numbering must be done in the direction When benzene reacts with a mixture of
that gives the lowest possible numbers to concentrated nitric acid and concentrated
the substituent groups. sulfuric acid at about 50C, nitrobenzene is
CH3 OH formed.
O2N 1 NO2 1 Cl
6 2 6 2

5 3 5 3
4 Br
4
NO2 5-bromo-2-chlorophenol
2,4,6-trinitrotoluene (TNT)  Alkylation: Net addition of –R (alkyl group)
Alkylation of benzene is known as the
POLYCYCLIC AROMATIC COMPOUNDS Friedel-Crafts reaction.
The alkyl group from an alkyl halide
(RX), in the presence of AlCl 3 catalyst,
substitutes for an H atom on the benzene ring.

Sources of Aromatic Hydrocarbons  Side-Chain Oxidation

 The aromatic hydrocarbons, such as Carbon chains attached to an aromatic
benzene, toluene, xylene, naphthalene, and ring are fairly easy to oxidize.
anthracene, were first obtained in
significant quantities from coal tar.
 Coal  Coke + Coal gas + Coal tar
 Because of the great demand for aromatic
hydrocarbons, processes were devised to
obtain them from petroleum.
LESSON 6:
Properties of Aromatic Hydrocarbons

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ALCOHOLS, ETHERS, PHENOLS, AND THIOLS  Polyhydroxy alcohols and polyols are
FUNCTIONAL GROUPS general terms for alcohols that have more
 The various classes of compounds are than one –OH group per molecule.
identified by the presence of certain  Polyhydroxy compounds are very
characteristic groups called functional important molecules in living cells, as they
groups. include the carbohydrate class of
 Through the chemical reactions of biochemicals.
functional groups, it is possible to create or
synthesize new substances. STRUCTURAL REPRESENTATIONS OF ALCOHOLS
 An alcohol such as 2-butanol can be written
in a single-line formula by enclosing the –
OH group in parentheses and placing it
after the carbon to which it is bonded.

CLASSIFICATION OF ALCOHOLS
 Alcohols are classified by the number of R
groups (i.e. carbon atoms) attached to the
hydroxyl carbon as shown here. APPLICATION TO BIOCHEMISTRY
Blood sugar (glucose) contains five
alcohol groups. Using the structure of glucose
shown here, label each group as 1°, 2°, or 3°.

O=CHCH(OH)CH(OH)CH(OH)CH(OH)CH2OH
primary (1 ) secondary (2 ) tertiary (3 )
Name CH3CH2CH2CH2OH
TESTS FOR ALCOHOLS
Lucas Test
 Addition of ZnCl2 in
concentrated HCl 1-butanol
forms a “turbid”
solution. Order of NOMENCLATURE OF ALCOHOLS
reactivity is 3o > 2o
>> 1o.

PHYSICAL PROPERTIES OF ALCOHOLS

 The physical properties of alcohols are
related to those of both water and alkane
hydrocarbons.
 An alcohol molecule is made up of a
waterlike hydroxyl group joined to a
hydrocarbonlike alkyl group.

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BOILING POINTS OF ALCOHOLS For example 2-butanol is branched and

 Alcohols have relatively high boiling points. has a b.p. of 91.5 C versus 118 C for 1-
 The boiling points of the normal alcohols butanol.
increase in a regular fashion with increasing
number of carbon atoms.
 Branched-chain alcohols have lower boiling
points than corresponding straight-chain 2-butanol
alcohols. (writ en as a single-line formula )
2-butanol
 Alcohols containing up to three carbon
atoms are infinitely soluble in water.
CHEMICAL PROPERTIES OF ALCOHOLS
 The –OH group on the alcohol molecule is
A. Chemical Properties
responsible for both the water solubility and
 If an alcohol is mixed with a strong acid, it
relatively high boiling points of the low-
will accept a proton (act as a Brønsted-
molar-mass alcohols.
Lowry base) to form a protonated alcohol or
HYDROGEN BONDING IN ALCOHOLS oxonium ion.

B. Acidic Properties
 Alcohols can also act as Brønsted-Lowry
acids.
 The resulting anion in the alcohol reaction
is known as an alkoxide ion (RO-).
Na+
H2 H2
2 H3C C O H + 2 Na 2 H3C C O + H2 (g)
sodium ethoxide

Reactivity of Alcohols with Na or K

 The order of reactivity of alcohols with
sodium or potassium is:
- primary > secondary > tertiary.
 Reactivity decreases with increasing molar
mass, since the –OH group becomes a
relatively smaller, less significant part of the
molecule.
Glucose is one of the most important
carbohydrates in biochemistry. It has six C. Oxidation Properties
carbons and five alcohol groups (molar mass =  Oxidation is the loss of hydrogen or the
180.2 g). How would you predict the water gain of bonds to oxygen by the organic
solubility of glucose to differ from that of 1- reactant.
hexanol?  Carbon atoms exist in progressively higher
stages of oxidation in different functional
EFFECT OF HYDROXYL GROUPS ON SOLUBILITY
groups.
Note the difference in solubility of
hexanol (only one –OH group) and glucose
( five –OH groups).

EFFECT OF BRANCHING ON BOILING POINT

A branched-chain alcohol will have a
lower boiling point than the corresponding
straight-chain alcohol.

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H O O
UTILITY OF THE HYDROXYL FUNCTIONAL GROUP
[O] [O]
R C OH R C H + H2O R C OH
aldehyde carboxylic
H acid
o
primary (1 )
alcohol
The –OH
R O
group gives an
[O]
R C OH R C R organic compound
ketone
H the capability of
o
secondary (2 )
forming an COMMON ALCOHOLS
alcohol
aldehyde, ketone, Three General Methods for Making Alcohols
R or carboxylic acid. 1. Hydrolysis of an ester.
[O] No reaction
R C OH
2. Alkaline hydrolysis of an alkyl halide (1° and
R 2° alcohols only).
o
tertiary (3 )
3. Catalytic reduction of aldehydes and
alcohol
ketones.
Common Oxidizing Agents
 KMnO4 Hydrolysis of an Ester
 K2Cr2O7  Hydrolysis is a reaction of water with
 O2 another species in which the water
molecule is split.
D. Dehydration
 Alcohols can be dehydrated with sulfuric
acid to form alkenes.
H H H H
96% H SO
H C C H heat 2 4 H C C H + H2O
Alkaline hydrolysis of an alkyl halide (1° and 2°
H OH alcohols only).
 For many alcohols, there is more than one
way to remove water. Therefore, the CH3CH2Cl + NaOH(aq)  CH2CH3OH + NaCl
double bond can be located in different
positions. Catalytic Reduction of Aldehydes and
 The major product in such cases is the Ketones
alkene in which the C=C bond has the  Produces primary and secondary alcohols.
greatest number of alkyl substituents on it  Chapter 23
(or the least number of hydrogens).
PREPARATION OF METHANOL
 Methanol is a common industrial solvent
prepared by the high-pressure catalytic
hydrogenation of carbon monoxide.
 The most economical nonpetroleum source
SAYTZEFF’S RULE
of carbon monoxide for making methanol is
During intramolecular dehydration, if
coal.
there is a choice of positions for the carbon-
Uses of Methanol
carbon double bond, the preferred location is
1. Conversion to formaldehyde (use in
the one that generally gives the more highly
manufacture of polymers).
substituted alkene – that is, the alkene with the
2. Manufacture of other chemicals, especially
most alkyl groups attached to the double-bond
various kinds of esters
carbons.
3. Denaturing ethyl alcohol
ESTERIFICATION
4. Industrial solvent
(CONVERSION OF ALCOHOLS TO ETHERS)
 An alcohol can react with a carboxylic acid PREPARATION OF ETHANOL
to form an ester and water.  Large quantities of ethanol are prepared by
fermentation.
- The conversion of simple sugars to
ethanol is accomplished by yeast.
 Industrially, ethanol is made by acid-
catalyzed addition of water to ethylene.

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Uses of Glycerol
 Each directly related to the three –OH
groups.
1. As a raw material in the manufacture of
Uses of Ethanol polymers and explosives (nitroglycerin).
1. An intermediate in the manufacture of other 2. As an emollient in cosmetics.
chemicals such as acetaldehyde, acetic 3. As a humectant in tobacco products.
acid, ethyl acetate, and diethyl ether. 4. As a sweetener.
2. A solvent for many organic substances.
3. A compounding ingredient for PHENOLS
pharmaceuticals, perfumes, flavorings, etc.  The term phenol is used for the
4. An essential ingredient in alcoholic class of compounds that have a
beverages. hydroxy group attached to an
aromatic ring.
PREPARATION OF 2-PROPANOL  The parent compound is also
(ISOPROPYL ALCOHOL)
called phenol, C6H5OH.
 2-Propanol is made from propene.
Naming Phenols
 Many phenols are named as derivatives of
the parent compound, via the general
methods for naming aromatic compounds.
Uses of 2-Propanol (Isopropyl Alcohol)
1. To manufacture other chemicals (especially
acetone).
2. As an industrial solvent.
3. As the principal ingredient in rubbing
alcohol formulations.

PREPARATION OF ETHYLENE GLYCOL (1,2-

ETHANEDIOL)
 Industrial synthesis
Derivatives of Phenol
Compounds of phenol are the active
ingredients in the essential oils of nutmeg,
thyme, cloves, and vanilla.

Uses of Ethylene Glycol (1,2-Ethanediol)

1. In the preparation of the synthetic polyester
fiber Dacron and film Mylar
2. As a major ingredient in “permanent-type”
antifreeze cooling systems
3. As a solvent in the paint and plastic Common Phenols
industries
4. In the formulations of printing ink and ink for
ballpoint pens.

PREPARATION OF GLYCEROL (1,2,3-

PROPANETRIOL)
 Glycerol (also known as Glycerine) is an
important trihydroxyalcohol.
 It is obtained as a by-product of the
processing of animal and vegetable fats to
make soap and other products.
 It is synthesized commercially from
propene.

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Production of Phenol
 Phenol is obtained from coal tar.
 Several commercial methods are used to
produce phenol synthetically.

ETHERS
 Ethers have the general formula below
where both R groups can be the same or
different.
 ROR′

Common Phenols/Alcohols

Naming Simple Ethers

Name each alkyl group in alphabetical
order followed by the word ether as shown
here.

Use a prefix if both alkyl groups are the same.

Herbicides produced by Phenols

Naming Ethers Using IUPAC Rules

1. Name the longest continuous carbon chain
corresponding to the parent alkane.
PROPERTIES OF PHENOLS 2. Change the –yl ending of the other
 Colorless, crystalline solid, mp = 41 °C hydrocarbon group to –oxy to obtain the
 Highly poisonous alkoxy group name.
 More acidic than alcohols and water 3. Combine the two names from Steps 1 and
2, giving the alkoxy name and its position
on the longest carbon chain first, to form
the ether name.
For

example…

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…would be named methoxyethane Preparation of Ethers by Intramolecular

Examples of Naming Alkoxy Groups Dehydration
 Ethers can be prepared by splitting out
water from two molecules of a primary
alcohol. This type of reaction is known as a
condensation reaction.

Examples of Naming Ethers

Williamson Synthesis of Ethers

 The alkyl halide, RX, may be a methyl or
primary group, but not a secondary or
tertiary alkyl group or an aryl group.
 The alkoxide, R’ONa, may be methyl,
primary, secondary, tertiary, or an aryl
Structures and Properties of Ethers
group.
 Ethers are somewhat more polar than
alkanes, but are much less polar than
alcohols.
 Ethers – especially diethyl ether – are
exceptionally good solvents for organic
THIOLS
compounds.
 Thiols or mercaptans, contains sulfur, are
similar to alcohols and contain a thiol (-SH)
group.
 They often have strong odors and are found
in cheese, onions, garlic, and oysters
 They are used to detect gas leaks
 They are named in the IUPAC system by
adding thiol to the alkane name of the
longest carbon chain.

Formation of Peroxides from Ethers

 Oxygen of the air slowly reacts with ethers
to form unstable peroxides that are subject
to explosive decomposition.

Properties of Thiols
1. Foul odors.
2. Oxidation to disulfides:

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Striped Skunk (Mephitis mephitis) Thiols

 For pets that have been sprayed, bathe the

animal in a mixture of 1 quart of 3%
hydrogen peroxide (from drug store), 1/4
cup of baking soda (sodium bicarbonate)
and a teaspoon of liquid detergent.
 After 5 minutes rinse the animal with water.
Repeat if necessary.
 The mixture must be used after mixing and
will not work if it is stored for any length of
time.
 DO NOT STORE IN A CLOSED
CONTAINER - it releases oxygen gas so it
could break the container. This mixture may
bleach the pet's hair.

Why tomato juice is believed to eliminate skunk

odor?
 Bathing an animal in tomato juice seems to
work because at high doses of skunk spray
the human nose quits smelling the odor
(olfactory fatigue).
 When this happens, the odor of tomato
juice can easily be detected.
 A person suffering olfactory fatigue to skunk
spray will swear that the skunk odor is gone
and was neutralized by the tomato juice.
 Another person coming on the scene at this
point will readily confirm that the skunk
spray has not been neutralized by the
tomato juice.

CHRISTIAN ACE G. BOBIS 33