Lecture 7

1. What is photoelectric effect?

Energy from light ejects electron from a metal surface.

2. What is the wavelength and energy range of sunlight?

380-750nm, energy range from 1.75 to 3.5 eV

3. Explain the bacteriorhodopsin (BR) molecule?

It consists of 7 hydrophobic transmembrane alpha-helices that span the lipid bilayer membrane. It is a
trimeric membrane protein. 3 BR molecules arrange as a donut with a central hole. Basic and acidic
amino acids form the cytoplasmic and extracellular surfaces while the transmembrane region is
hydrophobic.

4. How does BR pump proton? How BR creates bio battery?

BR can pump out 1 H+ for every photon absorbed. Gradient of H+ across the membrane is coupled to
the production of ATP. BR contains retinal which is chromophore attached to Lys 216 of BR. It lies in the
center of the transmembrane helices of BR. When light hits BR, photon absorbed by the retinal energy
from a photon induces a structural change in retinal and it acts like a switch. BR drives H+ from the cell
to create a bio battery by forming an electrochemical gradient. High H+ outside / low H+ inside
generates gradients. The H+ gradient forms an electrochemical potential energy across the membrane.

5. What is cis-trans conformation?

Trans: 180o torsion (opposite sides) angle, cis 0o (same sides)

6. How BR and ATP synthase are associated?

In BR, there is an ATP synthesis machinery, containing an extracellular part and a cytoplasm inside the
cell. Electrochemical gradient of protons (or protons + other ions) provides intermediate energy storage
and drive ATP synthesis machinery to produce ATP. The ATP will counteract excessive loss of water from
the cells.

7. What is ATP synthesis machinery - structural and functional aspects?

ATP synthesis machinery, containing an extracellular part and a cytoplasm inside the cell. The core ATP
systhase consists of alpha, beta, gamma subunits. Alpha and beta arrange alternatively, forming
hexamer, gamma docks inside hexamer. (need more info)

8. What is photosynthesis?

CO2 + water through chlorophyll which is hit by UV in sunlight, produce glucose and O2

9. What are the two major steps or process in photosynthesis?

The light dependent reactions convert the light energy into chemical energy (ATP, NADPH).
The light independent reactions use the chemical energy to synthesis organic compounds (e.g.
glucose).
10. What is chloroplast and what is its role?

It is a organelle and it captures light.

11. What is electron transport chain?

Chlorophyll is a complex photoreceptor molecule which absorbs energy from light. Chlorophyll is a
derivative of tetra pyrrole molecule.
The observed energy from light excites the electron from its ground level to higher level
These electrons are transferred from one molecule to other-called electron transport chain (ETC)

12. Why cell lose water for salty environment? And what is the consequence?

Since salty environment has high conc of salts, it tends to diffuse to the environment with lower conc.
But cell membrane blocks salt molecules, so only water can pass through, thus diffuse. Consequence is
dehydration.

13. What is a proton motive force?

The proton gradient across the thylakoid membrane creates a proton-motive force, used by ATP
synthase (machinery) to generate ATP

14. What are the similarities and differences between photoelectric effect and photosynthesis?

Both take advantage of light energy (photon) to convert to other forms of energy. Photoelectric
converts to electrical, photosynthesis convert to chemical

15. What is the common concept in producing photocurrent by a metal, proton pump in a bacterium
and glucose by plants?

Photoelectric effect

Lecture -8 Questions
What are the three major storage forms of cellular fuel?

Starch, glycogen, fat droplet

How is glucose obtained from starch?

In the body, starch is broken down by random cleavage of the branched and linear chains by a salivary
amylase enzyme. The oligosaccharides are shortened by a pancreatic amylase enzyme. Glucose is
produced by glucosidase enzymes.

Explain what is amylose and amylopectin?

A starch molecule consists of hundreds of glucose molecules as - branched (amylopectin) - unbranched

(amylose)

What is the difference between -D-glucose and -D-glucose?

Structures are almost identical, except in the form, the OH group on the far right is down, and, in the
form, the OH group on the far right is up.
 What is glycogen, how is it produced and where it is stored?

Glycogen, a glucose polysaccharide, consists of linear amylose chains with 1-4 linkages and branched
amylopectin 1-6 linkages as starch, also known as animal starch. In liver, glucose is converted into
glycogen for storage.

How is starch different from glycogen? List the differences.

Glycogen is more branched than starch. Heavier in mass. Starch branches in every 20-30 -4 linkages
whereas glycogen branches every 10-12 1-4 linkages. Starch has semi-crystalline granule when glycogen
has non-crystalline granule. Starch is stored in seeds, tubers, roots, when glycogen is stored in liver and
muscle.

How are the insoluble lipids being transported in our body?

Large fat droplets form emulsions of micelles with bile salts from the gall bladder
Lipase enzymes from the pancreas convert triglycerides into fatty acids and glycerol
Fatty acids and glycerol pass across the intestine membrane and reassemble into triglycerides and are
packaged into chylomicrons

What is chylomicron?

Chylomicrons are lipoprotein particles comprised of triglycerides (~85%), phospholipids (~10%),

cholesterol (~2%), and proteins (~1-3%). They transport dietary lipids from the intestines to other
locations in the body.

The non-polar lipids from food form the core of a vesicle with an
outer layer of phospholipid and lipoproteins.

Chylomicrons travel through the bloodstream to deliver the dietary lipids to the liver, adipose tissue,
and muscle.

How is the energy extracted from fatty acid? What are the three stages in fatty acid oxidation?

Lipases degrade triglycerides to glycerol and fatty acids. Glycerol is converted to pyruvate and then
glucose. Fatty acids are oxidized to Acetyl CoA and to CO2 and H2O. Electron transfer chain - proton
motive force - produce ATP

3 stages:

Stage 1: A long-chain fatty acid is oxidized to yield acetyl residues in the form of acetyl-CoA.
Stage 2: The acetyl residues are oxidized to CO2 via the Citric Acid Cycle.
Stage 3: Electrons derived from the oxidations of stages 1 and 2 are passed to O2 via the mitochondrial
respiratory chain, providing the energy for ATP synthesis by oxidative phosphorylation.

What is meant by renewable energy?

Renewable energy is generally defined as energy that comes from resources which are
naturally replenished on a human timescale, such as sunlight, wind, rain, tides, waves, and
geothermal heat.
 What are biofuels? (Hints: sugar -> Ethanol and fat/lipid -> biodiesel) How is ethanol obtained from
glucose? How is lipid converted into biodiesel? (Note: above 2-Qs are same).

A biofuel is a fuel that is produced through contemporary biological processes, such as

agriculture and anaerobic digestion. Ethanol is obtained from glucose through fermentation or
through catalytic cellulosic ethanol.

Why algae are a good source of biofuel?

Algae can grow in any kind of water body. Reduce greenhouse gas emissions. High oil content in algae
body. Productivity per unit area is much higher compared to others such as palm, jatropha.

What is greenhouse effect?

Greenhouse gases such as carbon dioxide, methane, water vapor, and nitrous oxide trap the heat and
keep the earth warm

What do we know about Jatropha biodiesel?

Jatropha produces inedible fruits, reduces wastage and food crisis, larger area available to grow.

List the advantages and disadvantages of bio and fossil fuels.

Fossil: lower cost of production, suitable for all kinds of engine

Bio: reduce greenhouse gas emissions, less air pollutant emissions (except NO2), biodegradable, suitable
for most modern engine, non-toxic, safer to handle, can be produced anywhere (no need to depend on
oil export countries)

Lecture 9
What is petroleum? How is it formed?
Viscous liquid of hydrocarbons, from decomposed organics in the earth, extracted and refined into fuels
What are the different types of hydrocarbons in petroleum?
alkanes, napthas and aromatics.
Alkanes are the major component and it consists of 11 to 32 carbon atoms with one or more 6-
membered rings. Napthas consist of 5 to 12 carbon atom containing hydrocarbons, whereas the
aromatics mainly consist of benzene ring with other structures.
How is crude oil converted into fuel products?
refining process. The first
step in this process is based on the boiling point (i.e. crude oil is separated by distillation). Lightest
components that have low boiling point that comes out first, and the heaviest one, which has the
highest boiling point, will condense at the bottom of the distillation column. After the distillation of
crude oil, various fractions are collected and taken for the next level of refining process to further
separate the independent components of each fraction. These processes include steam creaking,
catalytic cracking, isomerization and reforming. As a last step of refining, the separated products are
treated with chemicals (e.g. lead) and removed unwanted chemicals (e.g. sulfur) to alter the
combustion property.
What is isomerization in petroleum refining?
Isomerization - is the chemical process in which hydrocarbon molecules are rearranged into a more
useful molecule.
Differentiate heat of combustion and oxidation.
Combustion is the complete oxidation of organic compound into
CO2 and H2O in the presence of O2 gas
Combustion reactions are exothermic, that gives light and heat.
This light is normally called as burning.
Not all oxidizing reactions are combustions, but all combustion
reactions are oxidizing reactions. E.g. iron (Fe) becomes iron
oxide (Fe3O4) when it reacts with oxygen. It is an oxidization, not
combustion.
Not all oxidation reactions involve heat, whereas combustion
reactions involve heat
What is exothermic reaction? Explain the combustion of methane.
An exothermic reaction is a chemical reaction that releases energy by light or heat
How are the energy and enthalpy related?
Same unit
What is the implication of fossil fuel usage in greenhouse gas emission?
Fossil fuels emit greenhouse gas.
Define energy density and specific energy.
Energy density is the amount of energy stored in a given system per unit volume
Specific energy (Es) is the energy (E) per unit mass (m) of a fuel
What are the three major oil refineries in Singapore? What are their capacities?
ExxonMobil Refinery 605,000 bbl/d (96,200 m3/d)
Singapore Refining Corporation (SRC), 290,000 bbl/d (46,000 m3/d)
Shell Pulau Bukom Refinery (Royal Dutch Shell), 500,000 bbl/d (79,000 m3/d)
Why fat has similar specific energy as gasoline?
Fat is mostly lipid. Lipid has high hydrocarbon content and thus has similar specific energy as gasoline
How is the energy released from ATP?
Energy released from the hydrolysis of phosphoanhydride linkage
How is the energy extracted from glucose?
Respiration cellular reactions that extract energy from glucose into 30-38
ATPs (energy) and end products, CO2 and H2O
When the body is able to supply the cells with the oxygen and glucose that
they need, it carries our aerobic respiration
When the body cannot supply the cells with the oxygen needed to break
down glucose, then it has to carry out anaerobic respiration.
Energy is released without oxygen.
What is meant by respiration? What are its types and explain the differences.
Respiration cellular reactions that extract energy from glucose into 30-38
ATPs (energy) and end products, CO2 and H2O
When the body is able to supply the cells with the oxygen and glucose that
they need, it carries our aerobic respiration
When the body cannot supply the cells with the oxygen needed to break
down glucose, then it has to carry out anaerobic respiration.
Energy is released without oxygen.
What is chemiosmosis?
Chemiosmosis is the movement of ions across the membrane, more specifically, it relates
to the generation of ATP by the movement of hydrogen ions (H+) across a membrane.
Questions Lecture -10
What is a gene? How it is related to a genome?

Gene: DNA sequence that contains instructions to make a protein.

What is the approximate length of DNA in a single human cell and what is the total length of all DNA in
all cells of the human body? Genome: The complete set of genes or genetic material present in a cell or
organism.

A single cells DNA (in 23 pairs of Chromosomes) stretches approx. 2 meters

Adult humans have about 10 trillion cells
If you stretched the DNA in all the cells out, end to end - they should stretch over 744 million miles
The sun is 93,000,000 miles away your DNA would reach there and back about 4 times

What is a codon? How many codons code for the 20 unique amino acids?

A codon is a sequence of three DNA or RNA (triplets of) nucleotides that corresponds with a
specific amino acid or stop signal during protein synthesis. 61 codons for 20 amino acids.

What is the role of start and stop codons?

Start and stop the process???

Explain what is DNA coding strand and DNA template strand.

Coding strand: mRNA-like strand, contains codons, these codons are translated into protein.

Template strand refers to the sequence of DNA that is copied during the synthesis of mRNA.

What is transcription in protein biosynthesis?

Transcription: Copying the coded message of the DNA in RNA called messenger RNA (mRNA)

What is the role of ribosome in translation?

Amino acids that are encoded by nucleotides in the DNA coding strand (mRNA-like strand) are translated
into protein by the ribosome

What is bioinformatics? Why is it important?

BIOINFORMATICS is the collection, classification, storage (database), and analysis of biochemical and
biological information using computers and various programs.

The raw genome sequencing data have little interest as such

Biological knowledge is important and that should be extracted from the raw data
The principal role of bioinformatics is to help the biologists in this task, particularly by integrating data
from very diverse origins (raw sequencing data, results of in silico analysis, data from generic or specific
databases, data from large-scale experiments and etc.)
Overall bioinformatics analysis saves time and resources helps understanding the data and provides
clue for designing the experiments

Explain 2 applications of bioinformatics.

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