BIOCHEMISTRY LECTURE

REVIEW OF ORGANIC CHEMISTRY USE OF ORGANIC CHEMISTRY IN DAILY LIFE

CONCEPTS AND PRINCIPLES
- Part of the food: vitamins, fats, proteins, and
carbohydrates
ORGANIC CHEMISTRY
- Medicine/drugs: aspirin, Tylenol,
Decongestants, sedatives, and insulin
- Study of the structure, properties,
- Common products: alcohol, caffeine, nicotine
composition, reactions and synthesis of
- Products for Sale: Plastics, nylon, rayon, and
organic compounds
polyester
- Molecules with covalent bond carbon and
- Neurotransmitters, dopamine, serotonin and
hydrogen atoms (C-H Bonds)
adrenaline
- Different organic molecules may also contain
- Genetics: RNA and DNA
other elements such as oxygen, nitrogen and
phosphorus
- Not all compounds containing C and H are
ORGANIC VS. INORGANIC COMPOUNDS
organic ORGANIC INORGANIC
- EX: Carbon dioxide (CO2) is not an organic
chemical since it lacks of hydrogen, water - All are carbon - Contain metals
(H2O) contains no carbon, salt doesn’t contain compounds in salts and
either carbon or hydrogen - All have oxides
Covalent bonds - All have ionic or
- All have low polar bonds
HISTORY OF ORGANIC CHEMISTRY melting points - All have high
- All have low melting points
- 1777 boiling points - All have high
- Swedish chemist Carl Wilhelm Scheele - Most burn in boiling points
discovered that organic compounds contain oxygen - Few burn in
carbon and oxygen - Most are oxygen
soluble in - Most are
- 1828
non-polar soluble in polar
- German chemist Friedrich Wöhler solvents solvents
synthesized an organic compound, urea, from - Most are - Many are
inorganic materials non-electrolytes electrolytes
- During this period, scientists began to - All can have - All are usually
realize that organic compounds were different large molecules small with few
from inorganic compounds, and that organic with many atoms
atoms
chemistry was a instinct field of science
- 1855
- French chemist Auguste Laurent CARBON
discovered the first organic acid, formic acid
- 1858 - Unique in the sheer number of compounds
- Russian chemist Alexander Butlerov that it can form
proposed the idea of a carbon-based structure - Ability to form single, double and triple bonds
- 1860’s - CATENATION - Property of atoms to form
- German chemist Freidrich kekulé and bonds with itself through covalent bonds
August Wilhelm von Hofman developed the to form long chain, branch off, and or ring
structural theory of organic chemistry, which - Carbon completes its octet by sharing
provides a framework for understanding the electrons and not by forming ions
structures of organic compounds and how they - Small radius of carbon allows it to approach
react another carbon atom closely, giving rise to
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short and strong covalent bonds and stable 5. Electrical Conductivity
compounds - Electrical conductivity gauges a
- Carbon can form more compounds than material’s capacity to carry an
any other element in the periodic table electric current
- Organic compounds, mainly
PHYSICAL PROPERTIES OF ORGANIC consisting of carbon and
COMPOUNDS hydrogen, usually demonstrate low
electrical conductivity due to the
1. Solubility absence of freely mobile charged
- Refers to the ability of a substance particles
to dissolve in another substance
to form a homogeneous mixture, HYDROCARBONS
often called a SOLUTION
- The ability of a substance to dissolve - Organic compound consisting entirely of
in another substance to form a Hydrogen and Carbon only
homogeneous mixture - By far the most prevalent constituents of
2. Melting and Boiling Points crude oil, processed petroleum
- Melting and boiling points or organic hydrocarbons like gasoline, diesel,
compounds are key properties that kerosene, fuel oil and lubricating oil
reflect intermolecular forces and
molecular forces
- Affected by factors like molecular
weight, shape and types of
intermolecular forces
- Larger, complex molecules tend to
have higher melting and boiling
points
3. Color and Smell
- Certain organic compounds have
unique colors and odors attributed
to chromophores and functional
groups
- Color results from electronic
structure and chromophores that
absorb specific light wavelengths
4. Density ALIPHATIC
- Organic Compounds can have - Open-chain molecules with a linear or
densities either lower or higher branching structure
than water influenced by molecular
weight and structure 1. SATURATED
- Density quantifies mass per unit - Alkanes: Single bond
volume and is affected by factors - General formula: CnH2n+2
like molecular arrangement and - n = number of atoms in 1 molecule
functional groups of alkane, alkene and alkyne
2. UNSATURATED
- Alkenes: Double bond
- General formula: CnH2n
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- Alkynes: Triple bond
- General Formula: CnH2n-2
ALKANES/PARAFFINS/C-C
ALKENES/OLEFINS/C=C
ALKYNES/ACETYLENES/C≡C
- ETHYNE: Simplest alkyne
AROMATIC HYDROCARBON:
- Also known as Arenes frequently (but not
always) have distinguishing scents (odors)
- Hydrocarbons that contains atleast one
aromatic ring
- Cyclic, planar compounds that resemble
benzene in electronic configuration and
chemical behaviour
ISOMERISM
ILLUSTRATING AND NAMING
HYDROCARBONS
IUPAC NOMENCLATURE
(INTERNATIONAL UNION OF PURE AND
APPLIED CHEMISTRY)
- System used for the naming of organic
compounds
- General rule: the name should end with the
last syllable of the family or group where
it belongs
- All alkanes will end in “ane”, alkenes with
“ene”, alkyne with “yne” and so on
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NAMING BRANCHED ALKANE:

INCASE:
- Two alkyl groups, are attached to the parent
chain, name each and locate each with a
number
- The alkyl names are assembled in
NAME OF ALKANES AND ALKYL GROUP alphabetical order. Again use a hyphen to
separate the number from the words
- Consider the longest continuous chain
(Parent chain) of the carbon in the
structure and the alkyl group
- Alkyl group - Alkane minus one of its
hydrogen atoms

NAMING ALKENE:

INCASE:
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- Alkene has two or more double bonds, the
prefixes di, tri, tetra, penta and so on are
used as part of the parent name

ALCOHOL:

ALDEHYDES
- Compounds where an atom of carbon has
three single bonds: one with hydrogen, one
with oxygen,and one with another atom or
group of atoms
NAMING ALKYNES:
- The rule in naming alkynes is the same as
those in alkanes and alkenes but should end
with the suffix “yne”

NAMING CYCLIC STRUCTURES

- Cyclic structures are circular
KETONES
- Have “CYCLO” in name
- Organic compounds known as ketones has
- Same rules apply
a carbonyl group, which is made up of
- The number 1 is not usually written
carbon atom covalently linked to an oxygen
unless there are multiple double or triple
atom. The final two bonds (R) are to
bonds
hydrocarbon radicals or other carbon atoms

FUNCTIONAL GROUP
- Defined as an atom or group of atoms
within a molecule that has similar
chemical properties whenever it appears in
various compounds
- Every molecule that contains a particular
functional group generally exhibits the
same chemical behaviour
CARBOXYLIC ACIDS
- Contain the functional group of carboxyl.
Carboxyl group’s carbon atom can be joined
to either a hydrogen atom or a carbon chain
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AMINES
- Organic substances that have a lone pair of
nitrogen atoms in them

ESTERS
- Have a carbonyl + connecting oxygen
function with two linked alkyl or aromatic AMIDE
groups - Joined to the carbonyl Group
- Esters are utilized as ingredients and other - Simple amides are referred to as carboxylic
products that have a pleasant aroma acid derivatives
- Often used as organic solvents

ACID HALIDES
ETHER - Organic compounds created from carboxylic
- Oxygen sandwiched between two alkyl acids by substituting a halide group for a
groups hydroxyl group
- They have the formula R-O-R
- Alkyl groups represent the R’s
- These substances are utilized industrially, in
dyes, fragrances, oils and waxes
- Alkoxyyalkanes are a term for ethers

REACTIONS OF ORGANIC COMPOUNDS

1. SUBSTITUTION
- Replaced by another functional group
or atom
- EX: Chlorination of methane
2. ADDITION
- Two or more reactants combine to
form a single product molecule
- EX: Hydrogenation of alkenes to form
a saturated compound
3. ELIMINATION
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- Molecule loses atoms of groups of
atoms to form a new molecule
- EX: Dehydration of alcohols where
the water is removed from the
molecule to form an alkene
4. OXIDATION-REDUCTION
- Involves transfer or electrons
between reactants
- OXIDATION: Atom or molecule loses
electrons resulting in an increase in
its oxidation state
- EX: Browning of cut apple when
exposed to air
- REDUCTION: Atom or molecule
gains electrons leading to decrease
in its oxidation state
- EX: Caramelization of sugar
5. HYDROLYSIS
- Reaction when a molecule reacts
with water, leading to the breakdown
of bonds and the formation of new
compounds
- EX: Saponification reaction which
involves the hydrolysis of an ester to
form a carboxylic acid and an alcohol
- SAPONIFICATION: Process used to
produce soap from fats and oils
6. CONDENSATION
- Two or more molecules combine to
form a single, larger molecule with
the simultaneous release of a smaller
molecule, typically water or another
simple compound
- EX: Peptide bond formation is an
example of condensation reaction
- Involves reaction between two amino
acids
7. ESTERIFICATION
- Reaction involves the formation of an
ester by the reaction between a
carboxylic acid and an alcohol
- EX: Use of ethyl acetate with a fruity
aroma that is often found in fruits and
used as a flavoring and fragrance
agent
- Synthesized through the
esterification reaction between acetic
acid and ethanol
CELLS
BIOSPHERE
- Regions of the Earth’s crust, waters and
atmosphere inhabited by living things
ECOSYSTEM
- A community plus the environment
COMMUNITY
- Interacting populations in a particular area
POPULATION
- Several organisms of the same kind in a
particular area
ORGANISM
- An Individual: Complex individuals contain
organ systems
ORGAN
- Composed of a number of tissues and
organized for a particular task
TISSUE
- Group of cells with a common structure and
function
CELL
- Smalles unit of a living thing
MOLECULE
- Smallest unit of a compound that still has the
properties of the compound
ATOM
- Smallest unit of a molecule
WHAT ARE LIVING THINGS MADE OF?
- Some organism are made up of only one cell
and are called uni-cellular
- Others are made up of lots of cells and are
called multi-cellular
FROM CELL TO ORGANISM
- All living things are made of cells
THE CELL - STRUCTURES AND
THEIR FUNCTIONS
GENERAL FEATURES OF CELL
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PROKARYOTIC 3. GOLGI APPARATUS/GOLGI
- Unicellular organisms that thrives in a range COMPLEX/GOLGI BODY
of environment - Group of Organelles that prepare
- EX: Vents, dead sea, ice caps certain protein compounds for
EUKARYOTIC diespersal from the cell
- (Eu - true, karyon - nut) - These protein chemicals are
- Includes all animals, plants, fungi and enclosed in small membrane for
protists journey
- Eukaryotes may be unicellular (One-celled) 4. LYSOSOMES
or multicellular (many celled) organism - Small, sac-like structures
- Members of the domain Eukarya have true - Contains digestive enzymes, w/c are
nucleus used to dissolve large food
BACTERIA molecules and to break up old or
- (Bacterium-singular) damaged structures
- Single or Colonial microorganism that are 5. ENDOPLASMIC RETICULUM
often associated with diseases of human, - Provides space for important
animal and even plants chemical reactions and help move
chemicals to their proper destination
PROKARYOTES VS. EUKARYOTES 6. RIBOSOMES
- Smallest organelles
- Found either in the ER or Floating
freely in the Cytoplasm
- They synthesis protein used to create
parts of the cell
7. MITOCHONDRIA
- Oval-shaped structure
- Contains enzymes that aid the cell in
drawing energy from glucose
- Energy released in glucose is stored
COMMON STRUCTURES IN PLANT AND in ATP
ANIMAL CELLS
UNIQUE STRUCTURES IN PLANT
1. CYTOPLASM AND ANIMAL CELLS
- Holds the organelles inside the cell
2. NUCLEUS CELL STRUCTURE - ENERGY PRODUCTION
- Controls all the chemical activities of
AND WASTE MANAGEMENT
the cell
- Deoxyribonucleic acid
- Ribonucleic acid
3. ENDOMEMBRANE SYSTEM
1. ROUGH ENDOPLASMIC RETICULUM
- Protein processing
2. SMOOTH ENDOPLASMIC RETICULUM
- Synthesis of lipids
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UNIQUE STRUCTURES IN PLANT
1. CHLOROPLAST
- Contains pigment
2. CHLOROPHYLL
- Site for photosynthesis
3. CELL WALL
- Solid structure framing the cell
membrane
- Composed mainly of complex
carbohydrate
4. LARGE VACUOLES
- Bag-like structures
- Stores water and other materials for
use by the cell
- Smaller in animal cells compared to
plant cells
CELL STRUCTURE: STRUCTURE, SUPPORT
AND MOBILIZATION
1. CELL MEMBRANE
- Thine semi-permeable membrane
that surrounds the cytoplasm of a cell
- Function is to protect the integrity of
the interior of the cell by allowing
certain substances into the cell, while
keeping other substances out
2. CYTOSKELETON & RELATED
STRUCTURES
- Dense network of protein fibers that
support the shape of the cell and
anchors organelles such as nucleus
to fixed location
3. CENTROSOME
- Definition, structure, function, Cell
division
4. CILIA
-Short eyelash like filament that is
numerous on tissue cells of most
animals
- Back and front seating
5. FLAGELLA
- Propeller like motion
CHEMICAL COMPOSITION OF CELL
- Made up of water, inorganic ions and organic
molecules
- Water molecules mediate the chemical
interactions inside the cell
- Inorganic substances like sodium (Na+),
potassium (K+), Magnesium (Mg2+),
Calcium (Ca2+), Phosphate (HPO42-),
Chloride (Cl-), and Bicarbonate (HCO3-)
regulates cellular activities and are crucial
cell metabolism
- Macromolecules such as lipids, proteins,
carbohydrates, and nucleic acids form the
cellular components and are utelized by the
cell as raw materials or products of cellular
activity
TYPES OF CELL
STEM CELL
- Unique cells of the body in that they are
unspecialized and have the ability to develop
into specialized cells for specific organs or to
develop into tissues
BONE CELL
- Composed of a matrix of collagen and
calcium phosphate minerals
BLOOD CELL
- Transporting oxygen throughout the body to
fight infection
- Produced by bone marrows
MUSCLE CELL
- Muscle tissues which is important for bodily
movement
1. SKELETAL MUSCLE
- Attached to the bones
enabling voluntary movement
2. CARDIAC MUSCLE
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- Form involuntary cardiac METABOLIC REACTIONS FUNCTIONS:
muscle
FAT CELL
- Called Adipocytes, are the major cell
component of adipose tissue
- Contain droplets of stored fat (Triglycerides)
that can be used for energy
SEX CELL (GAMETES)
- Reproductive cells produced in male and
female gonads
SKIN CELL
- Composed of a layer of epithelial tissue
(Epidermis) that is supported by a layer of
connective tissue (Dermis) and an
underlying subcutaneous layer
NERVE CELL (NEURONS)
- Basic unit of the nervous system METABOLIC PROCESSES:
- Consists of two major parts: Cell body and
Nerve processes
CANCER CELL
- Result from the development of abnormal
properties in normal cells

COMPARING CELL STRUCTURE

OVERVIEW ON BIOMOLECULES
METABOLIC PROCESSES
- Totality of chemical reactions that occur in a
cell of organism
- Reactions are controlled by enzymes
(Expression regulated by gene activation)
- Follows ANABOLIC (Build up) or
CATABOLIC (Break down) pathways
- These reactions involve organic molecules
or inorganic molecules
ANABOLIC REACTIONS:
- Anabolic reactions build up complex
molecules from simple ones
- Includes the formation of macromolecules
from monomers
- The synthesis of macromolecules involve
condensation reactions
- Monomers covalently joined and water
produced as by-product
- Anabolism synthesis of complex molecules
from simpler molecules by condensation
reactions
CATABOLIC REACTIONS
- Breaks complex molecules into simple ones
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- Includes the release of monomers from ORGANIC MONOMERS
macromolecules CARBOHYDRATES
- The break down of macromolecules involves
hydrolysis reactions
- Covalent bonds are broken via the
consumption of water
- Catabolism is the breakdown of complex
molecules from simpler molecules by
hydrolysis

ORGANIC COMPOUNDS

- Carbon containing molecules found in living

things LIPIDS
- Carbon Forms the bases of organic life due
to its capacity to form 4 covalent bonds
- Allows it to form a wide variety of large
complex stable molecules
- FOUR MAIN ORGANIC COMPOUNDS
1. CARBOHYDRATES (SUGARS)
2. LIPIDS (FATS AND OILS)
3. PROTEINS
4. NUCLEIC ACID
- These organic compounds are composed of
recurring subunits called monomers
- The exception is lipids, which may have
subunits but they are not recurring

PROTEINS

- Life is based on carbon compounds

including carbohydrates, lipids, proteins and
nucleic acid
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NUCLEIC ACID TRIGLYCERIDE

POLYPEPTIDES

POLYMERIZATION
- Organic compounds can form complex
macromolecules when simple subunits
(monomers) are joined together via
condensation reactions to form a polymer
- Lipeds are not composed of monomers but
triglycerides do have distinctive subunits

NUCLEIC ACID

ORGANIC POLYMERS

POLYSACCHARIDES

TYPES OF BIOMOLECULES
(PROPERTIES AND FUNCTIONS)
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DISACCHARIDE

CARBOHYDRATES
- Short term energy source
- Formula [CH2O]n
- French term: Hydrate de carbone meaning
Hydrates of carbon pr carbon with water
- Most abundant class of biomolecules
containing carbon, hydrogen and oxygen
atoms
- Known as the chief source of energy of
almost all living organism
- Storehouses of chemical energy

MONOSACCHARIDE POLYSACCHARIDE
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SIMPLE LIPIDS

TRIGLYCERIDES

LIPIDS
- Diverse group of water-insoluble primarily
nonpolar biological molecules composed
mostly of hydrocarbons
- Store of energy (triglycerides)
- Hormonal roles (steroids)
- Insulation (thermal)
- Protection of organs
- Structural roles (Cholesterol)

FATTY ACIDS
- Carboxylic acids usually with long aliphatic
tails
- Either saturated of unsaturated

COMPOUND LIPIDS
- Ester of fatty acids containing groups in
addition to alcohol and fatty acid
- Major component of the cell membrane
- Composed of 2 fatty acids, GLYCEROL
UNIT and PHOSPHATE GROUP and a polar
molecule
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STEROLS - Proteins are the macromolecules of amino
acids

CONSIDERED AS THE MOST VERSATILE

BIOMOLECULES SINCE THEY SERVE
NUMEROUS ESSENTIAL FUNCTIONS IN THE
BIOLOGICAL PROCESSES

1. Catalysts & Enzymes

2. Antibodies
3. Contractile proteins
- Actin
- Myosin
4. Hormonal proteins
- Insulin
AMINO ACIDS - Somatotropin
5. Structural proteins
- Keratin
- Collagen
6. Transport proteins
- Hemoglobin

PROTEIN STRUCTURE
- Polypeptides fold into unique shapes which
may be essential to their functions

PROTEINS
- Amino acids are the building blocks of
protein
- Joined by the peptide bond
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DNA VS. RNA

NUCLEIC ACID
- Molecular repositories for genetic inform
ation and are jointly referred to as the
“MOLECULES OF HEREDITY”

STRUCTURAL COMPONENT OF DNA

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STRUCTURAL COMPONENT OF RNA

SUMMARY

- Biological macromolecules are large

molecules, necessary for life that are built
from smaller organic molecules
- Four major classes of biological
macromolecules are CARBOHYDRATES,
LIPIDS, PROTEINS, AND NUCLEIC ACIDS
(found in DNA & RNA)
- Each of these four has their own unique
chemical structure and their own specific
function within living organisms