Lecture-1 Summary (brief notes)

Science is to know. Scientific knowledge can be obtained through conducting systematic

experiments and analysis.
Engineering is to make and is the application of science to invent and improve new findings.
Technology is to use the engineering and scientific findings for practical purposes.
Biochemistry is the chemistry of organic molecules from living systems, which involves
aqueous reactions (aqueous means containing water). Although biochemical reactions occur
at mild conditions, they cause extreme chemical changes: strong reactions (e.g., digestion of
food in our stomach by various proteins).
Organic molecules are generally carbon- and hydrogen-containing molecules.
99% of the human body consists of oxygen, carbon, nitrogen, calcium and phosphorous.
Approximately 1% consists of other elements. All of these elements are essential for life.
Valence number is the number of electrons in the outermost shell/energy level of an atom.
A covalent bond is a chemical bond that involves the sharing of electron pairs between
atoms.
The cell is the basic structural and functional unit of all living system. Cells are the building
blocks of living systems.
A cell consists of approximately 70% water, ~15% proteins, ~10% lipids and ~1% sugars.
Plant and animal cells are eukaryotic cells. Bacteria are examples of prokaryotic cells.
Prokaryotes (e.g., bacteria) were the only form of life on earth for millions of years. Later on,
the more complicated eukaryotes evolved.
The main difference between eukaryotes and prokaryotes: Only eukaryotes comprise
endoplasmic reticulum (ER), nucleus, membrane, mitochondria and Golgi apparatus.
Eukaryotic cells also tend to be bigger in size than prokaryotes.
Larger biological systems are assembled from smaller components: molecules
organelles cells tissues organs organism.
Bioengineering is the application of engineering methods on biological findings or the
translation of scientific findings into applications.
Biotechnology has a wide range of applications in agricultural, medical (clinical diagnostic,
therapeutics) and environmental sectors.
Beer is an example of an ancient biotechnological product.
Genetically modified organisms (GMOs) help produce huge amounts of biotech products.
Several mega countries use a large proportion of their land for biotech-based crop
production.
Drugs that arise from biotech research predominate in the pharmaceutical market.

Brief Notes (Summary) - Lecture 2

Oil is a chemical substance. Plant oils are liquid fat, mostly highly viscous, and nonpolar in nature.
Lipids are fat and fat-like compounds that are soluble in organic solvents and have minimum or no solubility in water.
Palm and soybean oils are the most widely produced and consumed oils in the tropical regions of the world (approx.
40 million tonnes/year). Natural oils are triglycerides of fatty acids. Palmitic acid and oleic acid are the two major
fatty acids in most of the natural oils.
Triglycerides are formed by the combination of glycerol with three fatty acid molecules. Fatty acids are the carboxylic
acids of aliphatic hydrocarbon chains (aliphatic means liner chain; aromatic means closed ring, i.e., cyclic). Fatty acids
contain 424 carbon atoms in their chain.
In saturated fatty acids, all the bonds between the carbon atoms are single, whereas, in unsaturated fatty acids, there
is at least one double/triple bond between the carbon atoms.
Liquid hydrocarbons are generally known as oils. These hydrocarbons are attracted by weak forces; e.g., van der
Waals interactions (also known as London dispersion forces).
The number of carbon atoms (i.e., chain length) will determine the phase of the hydrocarbon. Hydrocarbons that
contain fewer carbon atoms are in a gaseous phase, with the molecules showing a greater degree of separation.
Hydrocarbons that contain more carbon atoms are closer together and in a liquid phase, and hydrocarbons with an
even higher number of carbon atoms become solids.
The distribution of electrons within molecules is not static: electrons move around and produce small charge
differences, and this dynamicity renders the atoms as transient dipoles. The weak interactions between these dipoles
are van der Waal interactions.
Electronegativity is the electron attracting power of an atom in a covalent bond. In general, elements with a smaller
atomic radius will have higher electronegativity.
A Hydrogen bond is a weak bond between two molecules (intermolecular) or within a single molecule (intramolecular;
for example, DNA) resulting from an electrostatic attraction (dipoledipole) between hydrogen in one molecule and
a highly electronegative atom in the other.
Emulsion is the mixture of two unmixable fluids. The hydrophobic effect and surface tension separate fluids. For
example, oil and water, whole fat milk.
Detergent is a surfactant. The hydrophilic head group of a detergent interacts with water molecules and reduces the
surface tension. The reaction between a fatty acid and a base produce fatty acid salt, i.e., soap. Soap is a detergent: its
hydrophobic group interacts with the stain while its hydrophilic group interacts with water to first solubilize and then
remove the stains.
Homogenization is a process used to make the droplets small and of even size. Homogenization decreases the diameter
of the droplets and increases the droplet density.
Lipids systematically assemble into several shapes (e.g., spheres, cylinders, liposomes, sheets): these assemblies are
very extensive, have no edges, and are self-sealing. Lipids and detergents have similar structures and properties. The
three major types of membrane lipids are phospholipids, glycolipids, and cholesterol lipids. Cholesterol lipid is unique,
bearing an embedded cholesterol molecule in the lipid bilayer. Lipids can be used as liposomes to encapsulate a drug
to prolong its lifetime and for targeted drug delivery.

Brief Notes (Summary) Lecture 3

Rubber is a natural biomaterial; it is a sticky, elastic, solid product derived from a milky liquid
called latex (i.e., rubber in liquid form) that is obtained from trees or plants. Rubber is a
hydrocarbon polymer consisting of isoprene monomers. In rubber, the cross-link between the
polyisoprene chains confers elasticity. Vulcanization is a process that forms the sulfur crosslink between the polyisoprene chains. This cross-link increases the strength and elasticity of
rubber. Synthetic rubber is obtained as a petroleum byproduct.
Cotton is an example of natural cellulose. The cellulose fibers consist of macrofibrils
microfibrils chains of cellulose molecules (polymer). Cellulose is a polymer formed by the
condensation of beta-D-glucopyranose units. One beta subunit joins with another beta subunit
through a covalent bond between positions 1 and 4 to form a polymer chain. The hydrogen
bonding cross-links between the cellulose chains form the microfibrils. The crystalline region
of the cellulose fibrils has more ordered and complete hydrogen-bonding contacts than the
amorphous region, and the strength of the crystalline region will be higher than amorphous
region.
Cellulose can be chemically modified as cellulose acetate. Cellulose acetate has better
properties than cellulose, including improved solubility, toughness and transparency. These
properties are very useful for spinning, casting and molding for various applications.
Polycarbonate (PC) is another industrially important thermoplastic. The monomer of
polycarbonate is bisphenol A (BPA). PC is highly transparent, and has excellent toughness and
thermostability. PC is one of the most widely used thermoplastics, with uses from bullet-proof
windows to CD and DVDs. Filter membranes can be made from PC using the track-etched
method: this method uses/bombards the thin PC membrane with heavy ions to make small
holes (precise narrow pores) in the membrane.
All sugars are carbohydrates and are classified as simple and complex carbohydrates. Simple
carbohydrates are monosaccharides (one sugar molecule) or disaccharides (two sugar
molecules), whereas complex carbohydrates are polysaccharides (several sugar molecules).
Monosaccharides are the building blocks of polysaccharides. Monosaccharides are cyclic
molecules (i.e., containing a ring structure or closed-chain formation) and tend to have 5 to 6
carbon atoms. In nature, sugar molecules are present in closed-chain or open-chain form: the
closed-chain form is the most preferred form in cells, whereas the open-chain form is rarely
(less than 1%) observed.
Agar is a gelling agent or gel. At low temperature (<40C), gels are solid. Gels are elastic but
brittle, held together by hydrogen bonding cross-links. Agar is a mixture of two
polysaccharides (agaropectin and agarose). Both polysaccharides have the same galactosebased backbone; however, agaropectin is heavily modified with acidic side-groups, such as
sulfate and pyruvate. Agarose is a polymer made up of repeating units of galactose
disaccharides (monomers). Galactose disaccharides covalently bond to form agarose chains
hydrogen bonds between the agarose chains form dimer helices hydrogen bond cross-links
between dimer helices form agarose gels. Agarose gel has several applications, such as in gel
electrophoresis for protein and DNA separation.

Brief Notes (Summary) L4

Nucleotides are monomers that covalently bond to each other to form nucleic acids. DNA (deoxyribonucleic acid)
is a double-stranded, long molecule that carries genetic information. RNA (ribonucleic acid) is single-stranded
but may also present in double strands. RNAs are relatively shorter molecules than DNA. There are three types of
RNAs: transfer RNA (tRNA), ribosomal RNA (rRNA), and messenger RNA (mRNA). mRNA copies the genetic
message from DNA and binds with the ribosome, which translates the mRNA sequence into a polypeptide chain
(protein). The major difference between RNA and DNA is in the ribose (sugar) part of the nucleotide. In RNA, an
OH group is present in the 2 position, whereas it is absent in DNA. Another major difference is the base Uracil
(U) is present only in RNA, and the base Thymine (T) is present only in DNA.
Nucleotides consist of three parts: the phosphate group, the 5-carbon sugar, and the base. A phosphodiester bond
is a covalent bond that links two nucleotides between the pentose sugar OH group (position: 3) of one nucleotide
and the phosphate group (position: 5) of the other nucleotide to form a single strand.
Nucleotides comprise 5 different bases. These are grouped into purine and pyrimidines. Purines are two-ring
structures (adenine and guanine); pyrimidines are single-ring structures (thymine, cytosine and uracil). Nucleotide
monomers may consist of 1 or more phosphate groups (monophosphate, diphosphate and triphosphate). For
example, adenosine monophosphate (AMP), adenosine diphosphate (ADP) and adenosine triphosphate (ATP) are
independent nucleotides that are involved in various biological functions.
In polynucleotides, the 3 position of one nucleotide is attached to the 5 position of the other nucleotide. The
direction of the nucleic acid chain (strand) is from 5 3.
Hierarchy of nucleic acid structures: The primary structure is the linear order of nucleotides in nucleic acids.
Secondary structures are based on hydrogen bonding and hydrophobic interactions: this will lead to double helix
(duplex) and stem-loop structures. Duplexes are the self-assembly of DNA strands into a double standard helix.
The strands in duplexes run antiparallel and are complementary. Antiparallel means that the two stands are parallel,
but run in opposite directions (one is 5 3, other is 3 5). Complementary: If the sequence of one strand is
known, the other interacting strand sequence can be predicted. A purine will interact only with a specific
pyrimidine. For example: A with T and G with C.
Minor groove and major groove: Strand backbones (e.g., phosphate groups) are closer together on one side of the
helix than on the other. The major groove occurs where the backbones are further apart; the minor groove occurs
where they are closer together.
There are four major forces that govern the duplex formation: hydrogen bonding contacts, hydrophobic and van
der walls interactions between base pairs, and electrostatic repulsive force between phosphate groups.
In 1962, James Watson, Francis Crick, and Maurice Wilkins jointly received the Nobel Prize for the discovery of
the structure of DNA.
Nucleic acids can fold into various 3D shapes known as their tertiary structure. DNA and RNA may combine with
proteins to form large nucleoprotein complexes known as quaternary structures. The ribosome, the protein
producing machinery of the cell, is an example of an RNAprotein complex. Chromatin, which controls gene
expression and DNA replication, is an example of a DNAprotein complex.
DNA technology has many applications, of which genetic engineering is one of the most important. Genetic
engineering engineers the DNA of a cell to alter its function to produce new products; for example, the production
of human proteins in bacteria.

Brief Notes (Summary) - L5

Nylon is an artificial silk invented in 1935 as the first synthetic fiber by Wallace Carothers. Nylon
can be obtained by reacting an acid and a base. The reaction between a dicarboxylic acid and a
diamine will result in the formation of a polyamide (6, 6 Nylon) through formation of an amide
bond. A polymer may contain n number of polyamides. Polymers interact (self-assembly)
through cross-linking (hydrogen-bond) to form a fiber. Crystallinity (which gives an ordered
structure) drastically improves the mechanical property of the polymer, such as stiffness, melting
point and yield to stress.
Amino acids (a.a) have amino and carboxyl groups. There are 20 common amino acids in nature
that combine to form proteins. These amino acids can be grouped into different categories, such
as non-polar (no charge) a.a, aromatic a.a, positively charged (basic) a.a, and negatively charged
(acidic) a.a. Amino acids join to form amide bonds (otherwise called peptide bonds) through a
condensation reaction: i.e., the carboxyl group of one a.a reacts with the amino group of the other
a.a, releasing a water molecule (H2O).
A peptide is a chain of amino acids. The direction of a peptide is from the N-terminus (amino
group of the first a.a) to C-terminus (carboxyl group of the last a.a). The peptide bond is fixed;
all atoms associated with the peptide bond are in one plane.
Structures associated with peptides and proteins: The primary structure is the linear order of an
a.a sequence in a peptide or protein. The secondary structure is held together by hydrogen
bonding contacts (for example: -sheet and -helix). A -strand is a stretch of 3 or more linear
a.a; it should be part of a -sheet. Two or more -strands form one -sheet. -sheet assembly is
maintained by the hydrogen bond crosslink between the backbone atoms of adjacent -strands.
Strands in a -sheet can be all parallel, all anti-parallel, or both. In a parallel -sheet, all of the
-strands in that sheet will be running in the same direction (either N C or C N); in an antiparallel -sheet, the -strands will run in a combination of directions (N C and CN). One
example of a -sheet fiber is spider silk.

-helix resembles a spring and is a helical-like structure. The systematic hydrogen bonding
contacts between the main-chain atoms maintain this helical arrangement. In several proteins,
the -helices form a coiled-coil structure, like the thread of a rope. The coiled-coil arrangement
is mostly due to the systematic presence of some specific a.a in the helices. Keratin and collagen
are the best examples of coiled-coil helical bundle structures. Keratin is a fibrous protein that is
the main component of hair. Four keratin molecules (tetramer coiled-coil bundle) form
protofilaments and subsequently form keratin filaments. Or simply, the keratin molecules
copolymerize to form filaments. In collagen, the triple helical bundle assembles to form collagen
fibrils which combine to form collagen fibers. The repeating sequence often follows a pattern
Gly-Pro-X or Gly-X-Hyp (where X is any a.a). This pattern forms a systematic interaction that
allows for the triple helical bundle arrangement in collagen. Collagen triple helices are stabilized
by (1) repulsive forces between the proline a.a. within the monomer (keeps them away); and (2)
the inter-chain hydrogen bonds that form among the monomers (chains) that will create the
helical bundle arrangement and stabilize the collagen triple helix.
Gelatin is an ancient product of collagen biotechnology. Heating dissociates the collagen triple
helices into monomers, and cooling systematically reassociates the monomers and forms gelatin.
Collagen has several applications in medicine, biotechnology, and cosmetics.
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