Questions (Lecture 1- Lecture 5)

Lecture -1
1. How are biochemistry, bioengineering and biotechnology related?
All are related to living organism.
2. What are the major elemental compositions of human body?
Major components are O, C, H, N, Ca, P, containing 65.0, 18.5, 9.5, 3.2, 1.5, and 1.0 % of body
compositions respectively.
3. What is meant by organic chemistry?
Organic chemistry is the chemistry of compound containing C, except CO, CO2, CO3 24. What is a covalent bond?
Covalent bond is a chemical bond which involves the sharing of electron pairs between atoms.
5. What is the meaning of a cell in the biological system?
Cell is a machine in the body that carries out different function such as self-assembly, work,
evolution and development.
6. Give an example of a eukaryotic and a prokaryotic cell.
Human cell and E.coli
7. List any six components of a cell and their functions?
Plasma membrane: barrier, protection
Lysosome: garbage disposal
Mitochondria: produce energy
Ribosomes: protein synthesis
Nucleus: store genetic info
8. How are the larger structures assembled from the smaller components?
By noncovalent assembly (Van der Wall)
9. Explain the hierarchical organization of biological systems.
From macromolecules such as cytochrome, combining together to form supramolecular
molecular assembly such as inner mitochondrial membrane, then organelle such as
mitochondrion, then cell, tissue, organ and finally body.
10. What is meant by bioengineering, and biotechnology?
Bioeng is the application of engineering methods to scientific findings of biology.
Biotech is the tech app using biological systems, living organisms or derivatives thereof, to
make or modify products or processes for specific use
11. Give examples of biotechnological developments in Singapore.
Tuas Medical Park, oil refineries in Jurong Island
12. What is the science behind the fermentation of beer?
Using enzymes in yeast to convert carbohydrates into alcohol

Mass production biotech

13. What is meant by genetic modification organisms (GMO)? What are the major GM crops? List
four mega countries that use more GMOs.
GMO: certain part in the gene of known effect is modified to achieve a desired effect. Examples
of GM foods are pest-resistant rice plants, drought-resistant corns. Countries are US, China,
India and Argentina
14. List four applications of biotech in health care sector. Provide examples of drugs whose sales
cross over 1 billion dollars per year.
Diagnostics, therapeutics, regenerative medicines, vaccines
Eg: alpha-2-interferon treating cancer, hepatitis vaccine, insulin.
15. List two applications of biotech in the food and environment sector.
Renewable energy and biofuels, food safety testing
Lecture -2

1. What is oil? What are its major components?

Liquid fats, neutral, nonpolar, and immiscible with water.
Major components: triglycerides of fatty acids.
2. What is meant by van der Waals interactions?
Weak attraction between transient dipoles as electron distribution is not static
3. What is a fatty acid? What are the differences between saturated and unsaturated fatty acids?
Fatty acid is carboxylic acid of aliphatic hydrocarbon chains of 4-24 C. Saturated acid contain
only single bonds between 2 C atoms, unsaturated means double or even triple bonds.
4. How is a triglyceride formed? Give an example.
Glycerol + 3 fatty acids such as stearic acid, e.g. glyceryl tristearate C57H110O6)
5. What are the relationship between number of carbon atoms/chain length and the physical state
of the hydrocarbon?
The more, the more hydrophobic it becomes
6. Explain what a hydrogen bonding contact is.
Attraction formed by interactions between negative and positive sides of polar molecules, under
the form of electrostatic attraction.
7. What is meant by electronegativity? Give examples of high and low electronegative elements.
Electron attracting power of an atom. High is O, low is K
8. What is an emulsion?
Mixture of immiscible fluids
9. What is a surfactant?
Substance that reduces surface tension of water

10. How can you make soap? Briefly describe the action of soap.
Fat (triglyceride) undergoes base hydrolysis (saponification) with NaOH (aq), to form fatty acid
salt which is soap, and glycerin.
Soap (detergents) interact with the strain (e.g. oily stuff) and makes it soluble or soap
dissolves the strain - forms emulsion- washing with excess water the strain can be removed
11. What is meant by homogenization? Give an example.
The process of converting 2 immiscible fluids into an emulsion. E.g. Forcing milk at high
pressure thru a small hole onto impact surface, to make it easier for mixing.
12. What is micelle? What are the properties of lipid bilayers?
Micelles are lipid molecules arranging themselves in a spherical form in aqueous solutions.
Usually the hydrophobic tails face each other whereas hydrophilic heads in contact with
surrounding environment. Lipid bilayers are highly impermeable except with water and gas
molecules. Another property is fluidity, which allows protein structures inside the cell to move
freely, affecting membrane transport.
13. What are the major subunits of biological lipid bilayers?
Phospholipid, sphingolipid, cholesterol
14. How is cholesterol lipid different from other lipid bilayers?
Cholesterol disrupts the packing of tail groups in lipids.
15. How are liposomes used for targeted drug delivery?
They can contain both hydrophilic and hydrophobic inside them. Surface can also be modified to
alter bio-distribution and pharmacokinetics. Can be controlled of the release of drug by change
in temperature.
Lecture-3
1. What is rubber?
Rubber is a sticky, elastic solid produced from milky liquid called latex. It is a natural
biomaterial.
2. Why does rubber bounce?
Crosslinks between polyisopropene chains confer elasticity.
3. What is a vulcanized rubber?
It has the sulfur crosslinks which improve strength and elasticity.
4. What are the components of cellulose fiber? Give an example of natural cellulose.
It is made up of threads of macrofibril, which in turn are made up of microfibril which is a chain
of cellulose molecules. Cotton.
5. Explain how the cellulose polymer is being formed or what is a condensation reaction? Give
example.

From glucose monomers, condensation occurs to link them into glucose polymers. Cellulose, a
polymer formed by the condensation of -D-glucopyranose units.
Condensation reactions is which 2 molecules combine to form a large molecule with a loss of a
small molecule, most commonly water.
6. What is the difference between amorphous and crystalline regions of a cellulose fiber?
Amorphous region can absorb more water than crystalline region.
7. Explain the sulfur and hydrogen bond crosslinks.
Sulfur crosslinks are between polyisopropene chains, whereas H bond crosslinks are between
glucose polymer chains.
8. What is cellulose acetate?
Cellulose acetate is a semi-synthetic polymer - useful to cast, mold, and spin
Ester of cellulose and acetic acid.
9. Explain the steps involved in dry spinning.
Firstly, the polymer is dissolved into a volatile solvent and the solution is pumped thru a
spinneret with numerous holes. As fibers exit spinneret, air is used to dry the solvent so that the
fibers solidify.
10. Explain the properties of polycarbonates? Given an example of its application.
PC is another industrially important polymer - transparent, excellent toughness, thermal stability
- one of the most widely used thermoplastics. E.g. polycarbonate membrane
11. What are the major classifications in carbohydrates?
Simple and complex (polysaccharides). Simple has mono and disaccharides
12. List the name of four monosaccharaides.
Glucose, fructose, galactose, mannose
13. List the name two disaccharides and its monomers (single subunits).
Sucrose: glucose + fructose, lactose: galactose + glucose
14. What is agar? What are the properties of gel?
Agar, or agar agar, is a gelling agent extracted from red algae. Gel is mostly liquid, but behave
like solids; it has polymer network; it is elastic but brittle.
15. How the gel is obtained from agarose? Give an example for its application.
Agarose chain is formed from agarose thru covalent bonds, which then forms dimer helices by
H bonds, and finally forms gel thru crosslinks. An application is that DNA and protein
molecules are separated by agarose gel electrophoresis.

Lecture -4
1. What are the two major types of nucleic acids? List their differences.
DNA, RNA. Double and single strand, T and U. Long and short. Carry info and be functional

2. How the duplexes are formed?

Nucleic acids are formed from nucleotides thru phosphodiester bond, then H bond and
hydrophobic effect will make nucleic acids into duplex
3. What is a phosphodiester bond?
Bond between pentose sugar and phosphate group
4. List five different types of nucleobases? What is the difference between purine and
pyrimidine?
Adenine, thymine, uracil, guanine, cytosine. Pyrimidines (one ring structure) or purines (two
rings structure)
5. What are the nucleotides which make three hydrogen bonding contacts in the DNA duplex?
A-T and G-C
6. What is 5 and 3 in a polynucleotide?
Top of the strand is 5, bottom is 3. In antiparallel duplex, a 3 end is near a 5 end. Usually 5
contains phosphate group whereas 3 contains OH group.
7. How the DNA strands self-assemble to form duplex?
8. When the DNA structure was discovered?
1953
9. Explain minor groove and major groove in the DNA duplex.
Minor groove is smaller. Both are voids of double helix and provide space for binding with
proteins.
10. What are the four forces that govern the double helix formation?
H bond pairs for base pairing A with T (U), G with C. Hydrophobic effect and Van der Waal,
leading to base stacking. Negative charges oppose double helix.
11. What is meant by complementary base pairs in the duplex?
A with T (U), G with C
12. Explain stem loop secondary structure.
Only H bonds taken into account, ss DNA or RNA will form a simple hairpin shape.
13. Give an example of RNA nucleoprotein complex and what is its function?
mRNA: messenger
14. Give an example of DNA nucleoprotein complex and what is its function?
Chromatin, to pack DNA into smaller vol to fit the cell
15. Given an example of DNA technology.
GM food, modify DNA, give cell new function.

Lecture -5
1. Who and when the first synthetic fiber was invented?
1935, by DuPonts
2. Give an example of simple polyamide formation.
Nylon
3. What is polymerization? Explain with example.
Monomers -> dimers, trimers, all these combine to form small fragments; combination of
small fragments is called polymers. E.g. PVC
4. What is Crystallinity? What are its influences in the property of plastics?
It is the degree of structural order in a solid (or ordered structure). Higher crystallinity makes
plastics more brittle, less elastic.
5. What is an amino acid? Explain with example.
-COOH and NH2, glycine
6. Write the full name and their classification of the amino acids: R, D, K, F, W, N, Q, E and Y.
R: arginine, D: Aspartic acid, K: Lysine, F: phenylalanine, W: tryptophan, N: asparagine, Q:
glutamine, E: glutamic acid, Y: tyrosine
7. What is a peptide? Explain with example.
Chain of amino acids linked together by peptide bond (condensation between NH2 and
COOH groups). E.g. spider silk
8. What is a peptide bond? Draw and explain with example.
9. Explain -sheet and -strand.
-strand is a stretch of 3 or more linear aa and it should be a part of -sheet
-strands form a planar sheet with side chain lie above and below plane
H-bonds between adjacent (antiparallel) or alternate (parallel) subunits (-strands)
sheet can be all parallel, all antiparallel, or mixed -strands
10. What is a parallel and anti-parallel -sheet? Given an example of -sheet fiber.
Parallel: C to C, N to N; antiparallel: C to N and vice versa
11. What is an -helix? How the coiled-coil helices are formed? Give an example.
H bonds with 4th aa form helix. E.g. Keratin
12. Explain collagen triple helix. How is it stabilized?
Steric repulsion between proline a.a in the monomer drives helix formation. Interchain H bonds
stabilize triplex
13. List any 3 applications of collagen.
Gelatin, artificial skin, extra cellular matrix
14. List and briefly explain the key steps involved in gelatin formation.

Heat dissociates collagen triple helix to monomer strands, cooling re-associates strands into a
gel
15. How the amino acid Glycine and Proline are different from other amino acids?
Glycine has no side chain, thus is more flexible, whereas proline has side chain fused with main
chain of amino acids, making it very rigid.
Lecture-6
1. What are the major functions of proteins?
Structure, regulation, signaling, transport, movement, catalysis
2. What are the differences between peripheral and integral membrane protein?
Peripheral proteins are attached to the surface of the membrane while integral proteins are
embedded in the lipid bilayer.
3. What are the main functions of a membrane protein?
Transporter-facility the movement of molecules/ions across the membrane
Receptor-bind ligands and sense change-relay signals between cells internal and external
environment
Enzymes-catalyse chemical reactions at the extracellular or intracellular surfaces of the
membrane
Anchor/attachment/recognition-attachment point at the intracellular matrix(cytoskeleton)-Extra
cellular matrix component-cell:cell interaction-crosslink between one cell membrane to another
cell membrane
4. List different types of membrane proteins?
Integral: transmembrane a-helix and b-barrel
Peripheral: peripheral extracellular and peripheral cytosolic, lipidanchored and helixanchored.
5. General property of a transmembrane region of a protein?
Hydrophobic
6. List steps involved in protein folding process?
Unfolded random structure-local secondary structure-condense and packing into compact
globular shape-proteins function only after folding is complete.
7. Types of hydrogen bonds in proteins?
Backbone vs. backbone, backbone vs. side chain, side chain vs. side chain
8. Where the hydrophobic amino acids side chains are found in a well-folded globular
protein? Why?
Cluster together in the interior of protein molecules and form hydrophobic cluster to avoid water
molecules.
9. Explain disulfide bond in proteins and its importance.
Disulfide bond formed between side chains of two Cys amino acids, which may be distant in the
linear sequence but adjacent in the 3d space
Contribute to the formation of folded native 3d structure which is important for the function.
10. What are the difference between acid and enzyme cleavages of a protein?why?
Acid cleavage is random while enzyme cleavage is specific. Because acid cleavage attacks all
peptide bonds while enzyme only cleave specific position fits its active side.
11. What is meant by hydrolysis?

Hydrolysis is cleavage of chemical bonds by water molecules

12. Example of protease and their specificity.
Trypsin cleaves the bond after a Lys or Arg (basic amino acid)
Chmotripsin cleaves the bond after Tyr or Trp or Phe (hydrophobic aa)
13. Active side of serine protease?
Located at the suface of the structure: Serine, histidine, aspartate
14. Nucleophilic attack is bond formation between a nucleophile(electron donating) and
electron deficient substrate.
15. Ea is the minimum energy required for a reaction to proceed.