The document contains the schedule and topics for a course on the Science of Living Systems. Key topics include nucleic acids, transcription and translation, protein structure, enzymes, photosynthesis, respiration, cellular architecture, cell division, and disease biology. The course will include two class tests and a mid-semester exam. Additional documents provide details on photosynthesis, including that it takes place in chloroplasts and converts carbon dioxide and water into glucose and oxygen through light-dependent and light-independent reactions.

1. Science of
Living System
Soumya De
School of Bioscience
Email: somde@iitkgp.ac.in
Tel: 03222-260514
BS20001

2. Lecture Date Topic
1 20/7/16 Nucleic acids
2 27/7/16 Transcription and Translation
3 3/8/16 Protein structure
4 10/8/16 Enzymes
5 17/8/16 Photosynthesis
6 24/8/16 Respiration
** 31/8/16 CLASS TEST-1
** 7/9/16 DISCUSSION AND REVISION
** 14/9 to 21/9 MID-SEM EXAM
7 28/9/16 Cellular architecture
8 5/10/16 Cell division and apoptosis
** 12/10/16 Autumn Break
9 19/10/16 Host defense/Disease biology/vaccines/antibiotics
10 26/10/16 Responses of living systems/scaling factors
12 2/11/16 Recombinant DNA Technology & its impact
** 9/11/16 CLASS TEST-2
** 16/11/16 DISCUSSION AND REVISION

3. Vital metabolism for survival of
life in the earth

4. The SUN: main source of energy for Life of Earth
Solar power can provide a
sustainable energy source
for some areas in the world
Agricultural crops are the primary means
for converting solar energy into chemical
energy for life on earth

6. Question
• Where does photosynthesis take place?
• Plants
Plants are autotrophs
(Self-producer)
Animals are
heterotrophs
(depend on
autotrophs)
Cyanobacteria can also
perform photosynthesis

7. • Almost all plants are photosynthetic autotrophs, as
are some bacteria and protists
– Autotrophs generate their own organic matter through
photosynthesis
– Sunlight energy is transformed to energy stored in the
form of chemical bonds
(a) Mosses, ferns, and
flowering plants
(b) Kelp
(c) Euglena (d) Cyanobacteria
THE BASICS OF PHOTOSYNTHESIS

8. • The energy from sunlight is used to initiate photooxidation reactions in
light-absorbing pigments that convert light energy into chemical energy.
• The light reactions of photosynthesis require a proton impermeable
membrane and a series of linked redox reactions to generate proton
motive force used for ATP synthesis.
• Photooxidation uses the oxidation of H2O to produce O2 in a process
that provides electrons for photophosphorylation and the reduction of
NADP+ to produce NADPH.
• Chemical energy in the form of ATP and NADPH is used to convert
CO2 to glyceraldehyde-3-Phosphate using enzymes in the Calvin
Cycle pathway. Plants use sunlight for photosynthesis during the day
and undergo aerobic respiration at night.
Key Concepts in Photosynthesis

9. Light Energy Harvested by Plants &
Other Photosynthetic Autotrophs

10. Overall Equation of Photosynthesis
• This is a Redox reaction (The transfer of one or
more electrons from one reactant to another).
• Two parts:
1. Oxidation
2. Reduction

11. Oxidation Reaction
• The loss of electrons from a substance.
• Or the gain of oxygen.
glucose
6CO2 + 6H2O  C6H12O6 + 6O2
Oxidation

12. Reduction Reaction
• The gain of electrons to a substance.
• Or the loss of oxygen.
glucose
6CO2 + 6H2O  C6H12O6 + 6O2
Reduction

13. Overview of Photosynthesis
Oxidation:
H2O  H+ + O2
Reduction:
CO2 + H+ 
C6H12O6

14. Light Reaction
glucose
6CO2 + 6H2O  C6H12O6 + 6O2
Oxidation

15. Dark Reaction
glucose
6CO2 + 6H2O  C6H12O6 + 6O2
Reduction

16. Location: Chloroplast in plant cell

17. Chloroplast Structure
• Inner membrane
called the
thylakoid
membrane.
• Thickened
regions called
thylakoids. A
stack of
thylakoids is
called a granum.
(Plural – grana)
• Stroma is a liquid
surrounding the
thylakoids.

18. WHY ARE PLANTS GREEN?
Plant Cells
have Green
Chloroplasts
The thylakoid
membrane of the
chloroplast is
impregnated with
photosynthetic
pigments (i.e.,
chlorophylls,
carotenoids).

20. • Chloroplasts
absorb light
energy and
convert it to
chemical energy
Light
Reflected
light
Absorbed
light
Transmitted
light
Chloroplast
THE COLOR OF LIGHT SEEN IS THE
COLOR NOT ABSORBED

21. Chlorophylls are light gathering pigments
Chlorophylls and other pigments have highly conjugated structure, which typically
have strong absorption in visible light.
Leaves
Carrots

22. Light Harvesting Complex LHCII

23. Chlorophylls funnel the absorbed energy to
Reaction Centers by Exciton transfer
Exciton is a
quantum of energy
passed from an
excited molecule to
another molecule in
a process called
exciton transfer.

24. A. Cyclic Electron Flow
• Occurs in the thylakoid membrane
• Uses Photosystem I only
• P700 reaction center- chlorophyll a
• Uses Electron Transport Chain
(ETC)
• Generates ATP only
ADP + ATPP

25. P700
Primary
Electron
Acceptor
e-
e-
e-
e-
ATP
produced
by ETC
Photosystem I
Accessory
Pigments
SUN
Photons
ETC: Electron Transport Chain
A. Cyclic Electron Flow

26. • Occurs in the thylakoid membrane
• Uses PS II and PS I
• P680 rxn center (PSII) - chlorophyll a
• P700 rxn center (PS I) - chlorophyll a
• Uses Electron Transport Chain (ETC)
• Generates O2, ATP and NADPH
B. Noncyclic Electron Flow

27. P700
Photosystem I
(protein complex)
P680
Photosystem II
(protein complex)
Primary
Electron
Acceptor
Primary
Electron
Acceptor
ETC
Enzyme
Reaction
H2O
1/2O2 + 2H+
ATP
NADPH
Photon
2e-
2e-
2e-
2e-
2e-
SUN
Photon
B. Noncyclic Electron Flow: Z-scheme
ETC: Electron Transport Chain

28. • ADP +  ATP
• NADP+ + H  NADPH
• Oxygen comes from the splitting of
H2O, not CO2
H2O  1/2 O2 + 2H+
(Reduced)
P
(Oxidized)
B. Noncyclic Electron Flow

29. • Powers ATP synthesis.
• Occurs in the thylakoid membranes.
• Uses Electron Transport Chain and ATP
synthase (enzyme) to make ATP.
• Photophosphorylation: addition of phosphate to
ADP to make ATP.
Chemiosmosis

30. Chemiosmosis

31. • Two main parts (reactions)
1. Light Reaction or Light
Dependent Reaction
Produces energy from solar
power (photons) in the form of
ATP and NADPH.
2. Calvin Cycle or Light
Independent Reaction or
Carbon Fixation or C3 Fixation
Uses energy (ATP and
NADPH) from light reaction to
make sugar (glucose).
Light Chloroplast
Light
reactions
Calvin
cycle
NADP
ADP
+ P
Overview of Photosynthesis

32. Calvin Cycle
• Carbon Fixation (light independent rxn).
• C3 plants (80% of plants on earth).
• Occurs in the stroma.
• Uses ATP and NADPH from light rxn.
• Uses CO2.
• To produce glucose: it takes 6 turns and
uses 18 ATP and 12 NADPH.

33. Calvin Cycle Strategy
6CO2 Glucose
(Ideal)
(Real)
6CO2 + 6RuBP G6P + 6RuBP
6C 30C 6C 30C
(Mechanism)
6CO2 + 6RuBP 12 molecules of G3P
RuBP: ribulose 1,5 biphosphate
G3P: glyceraldehyde 3-phosphate

35. Synthesis of Sucrose and Starch
F6P  G6P  G1P
ADP-glucose
ATP
PPi
(glucose)n
ADP + (glucose)n+1
Starch
(amylose)
UDP-glucose
fructose-6-PO4
UDP + Sucrose-6-PO4
H2O
Pi
UTP
PPi
Stroma
Cytosol
Sucrose

36. CO2 + ATP + NADPH 
Glyceraldehyde-3-P + ADP + Pi + NADP+
Glyceraldehyde-3-P may be converted to other CHO:
• metabolites (e.g., fructose-6-P, glucose-1-P)
• energy stores (e.g., sucrose, starch)
• cell wall constituents (e.g., cellulose).
Glyceraldehyde-3-P can also be utilized by plant cells as
carbon source for synthesis of other compounds such as
fatty acids & amino acids.
glyceraldehyde-
3-phosphate
OH
H2C
CH
CHO
OPO3
2
OCO
carbon
dioxide
Summary of
Calvin Cycle

37. Ribulose-1,5-bisphosphate
carboxylase/oxygenase RuBisCO
• RuBisCO is the most abundant protein in leaves.
• It is the most abundant enzyme on earth.

38. When O2 reacts with ribulose-1,5-bisphosphate, the
products are 3-phosphoglycerate plus the 2-C
compound 2-phosphoglycolate.
This reaction is the basis for the name RuBP
Carboxylase/Oxygenase (RuBisCO).
OH
H2C
CH
C
OO
OPO3
2

H2C
C
OPO3
2
O
O
3-phospho- phosphoglycolate
glycerate
Photorespiration:
O2 can compete with
CO2 for binding to RuBisCO,
especially when [CO2] is low
& [O2] is high.
Photorespiration is a wasteful process, substantially
reducing efficiency of CO2 fixation, even at normal ambient
CO2

39. PHOTORESPIRATION
Definition 1:
An interference with carboxylation caused by
the deviant interaction of RUBISCO with oxygen
The aberrant use of oxygen by chloroplasts
A process that leads to only one 3PGA being
produced in the dark reaction in
chloroplasts
Definition 2:
O2
O2
O2 O2
O2
O2

40. • Carbon dioxide is broken and “fixed” into
glucose or fructose molecules in the CALVIN
CYCLE!!!!
• Glucose subunits can make cellulose or other
polysaccharides, such as fruit sugars.
• The carbon skeleton in glucose also helps to
synthesize other important biochemical
compounds such as, lipids, amino acids, and
nucleic acids.
Overview of the Dark Reactions