bioenergetics

Question 1

Bioenergetics

Answer 1

Bioenergetics is the quantitative study of energy relationships and energy conversions in biological systems. Biological energy transformations obey the laws of thermodynamics.

Question 2

ATP a Chemical Link

Answer 2

With the emergence of photosynthesis on earth, molecular oxygen began to accumulate slowly in the atmosphere. The presence of free oxygen made possible the evolution of respiration. Respiration releases great deal of energy, and couples some of this energy to the formation of adenosine triphosphate (ATP) molecules. ATP is a kind of chemical link between catabolism and anabolism.

Question 3

Photosynthesis

Answer 3

The process of photosynthesis helps understand some of the principles of energy transformation (Bioenergetics) in living systems. Photosynthetic organisms (higher land plants for instance) use solar energy to synthesize organic compounds (such as carbohydrates) that can not be formed without the input of energy.

Question 4

glycolysis and respiration are the processes where

Answer 4

by the energy stores in carbohydrate is released in a controlled manner. So the photosynthesis acts as an energy-capturing while respiration as an energy releasing process.

Question 5

Photosynthesis

Answer 5

Photosynthesis can be defined as the process in which energy-poor inorganic oxidized compounds of carbon (i.e. CO2) and hydrogen (i.e. mainly water) are reduced to energy-rich carbohydrate (i.e. sugar-glucose) using the light energy that is absorbed and converted into chemical energy by chlorophyll and some other photosynthetic pigments. The process of photosynthesis in green plants can be summarized as:
6CO2 + 12H2O + Light Chlorophyll⎯⎯⎯⎯⎯→ C6 H12 O6 + 6O2 + 6H2O

This is almost exactly opposite to the overall equation of aerobic respiration
C6 H12 O6 + 6O2 ⎯→ 6CO2 + 6H2O + energy

Photosynthesis uses the products of respiration and respiration uses the products of photosynthesis. There is another important difference between the two processes: Photosynthesis occurs only during day time, whereas respiration goes on day and night.

Question 6

During darkness in photosynthesis

Answer 6

During darkness leaves (and other actively metabolizing cells) respire and utilize oxygen and release carbon dioxide

Question 7

At dawn and dusk in photosynthesis

Answer 7

At dawn and dusk, when light intensity is low, the rate of photosynthesis and respiration may, for a short time, equal one another. Thus the oxygen released from photosynthesis is just the amount required for cellular respiration. Also, the carbon dioxide released by respiration just equals the quantity required by photosynthesizing cells. At this moment there is no net gas exchange between the leaves and the atmosphere. This is termed as compensation point.

Question 8

During day time in photosynthesis

Answer 8

As the light intensity increases, so does the rate of photosynthesis and hence the requirement for more carbon dioxide increases which respiration alone cannot supply. Similarly, the oxygen produced during photosynthesis is more than the need of the respiring cells, so the result is the net release of oxygen coupled with the uptake of carbon dioxide.

Question 9

Neil’s Hypothesis
(Water and Photosynthesis)

Answer 9

Oxygen released during photosynthesis comes from water, and is an important source of atmospheric oxygen which most organisms need for aerobic respiration and thus for obtaining energy to live.

Question 10

Neil’s Hypothesis
(Van Neil’s Hypothesis)

Answer 10

In 1930s, Van Neil’s hypothesized that plants split water as a source of hydrogen, releasing oxygen as a by-product. Neil’s hypothesis was based on his investigations on photosynthesis in bacteria that make carbohydrate from carbon dioxide, but do not release oxygen.

Question 11

Neil’s Hypothesis
(Experimental verification)

Answer 11

Neil’s hypothesis that source of oxygen released during photosynthesis is water and not carbon dioxide, was later confirmed by scientists during 1940s when first use of an isotopic tracer (O18) in biological research was made. Water and carbon dioxide containing heavy-oxygen isotope O18 were prepared in the laboratory. Experimental green plants in one group were supplied with H2O containing O18and with CO2 containing common oxygen O16. Plants in the second group were supplied with H2O containing common oxygen O16but with CO2 containing O18.
It was found that plants of first group produced O18 but the plants of second group did not.

Group-1 Plants: CO2 + 2H2O18 ⎯→ CH2O + H2O + O182
Group-2 Plants: CO182 + 2H2O ⎯→ CH2O18 +H2O18 + O2

Question 12

Neil’s Hypothesis
(Confirmation of Neil’s hypothesis)

Answer 12

Water is thus one of the raw materials of photosynthesis, other being carbon dioxide. Hydrogen produced by splitting of water reduces NADP to NADPH2 (NADPH + H+).
NADPH2 is the “reducing power” which, along with ATP also formed during ‘light reaction’, is used to reduce CO2 to form sugar during ‘dark reaction’.

Question 13

Chloroplasts − The Sites of Photosynthesis in Plants

Answer 13

All green parts of a plant have chloroplasts, but the leaves are the major sites of photosynthesis in most plants.
Number of Chloroplast
Chloroplasts are present in very large number, about half a million per square
millimeter of leaf surface. Chloroplasts are present mainly in the cells of mesophyll
tissue inside the leaf. Each mesophyll cell has about 20-100 chloroplasts.
Structure of chloroplast
Chloroplast has a double membrane envelope that encloses dense fluid-filled
region, the stroma which contains most of the enzymes required to produce
carbohydrate molecules. Another system of membranes is suspended in the stroma.
Thylakoid and Grana
These membranes form an elaborate interconnected set of flat, disc like sacs
called thylakoids. The thylakoid membrane encloses a fluid-filled ‘thylakoid interior-
space’ or lumen, which is separated from the stroma by thylakoid membrane. In some
places, thylakoid sacs are stacked in columns called grana (sing granum).
Role of Thylakoid
Chlorophyll (and other photosynthetic pigments) are found embedded in the
thylakoid membranes and impart green colour to the plant. Electron acceptors of
photosynthetic ‘Electron Transport Chain’ are also parts of these membranes. Thylakoid
membranes are thus involved in ATP synthesis by chemiosmosis.
Chlorophyll (and other pigments) absorb light energy, which is converted into chemical energy of ATP and NADPH, the products which are used to synthesize sugar in the stroma of chloroplast.

Question 14

Imp points 1

Answer 14

1. Photosynthetic prokaryotes lack
   chloroplasts but they do have unstacked photosynthetic membranes which work like thylakoids.
   2.

Question 15

Photosynthetic Pigments

Answer 15

Pigments
Light can work in chloroplasts only if it is absorbed. Pigments are the substances that absorb visible light (380-750) nm in wave length). Different pigments absorb light of different wave lengths (colours), and the wave lengths that are absorbed disappear.
Spectrophotometer
An instrument called Spectrophotometer is used to measure relative abilities of different pigments to absorb different wavelengths of light.
Absorption spectrum:
A graph plotting absorption of light of different wave lengths by a pigment is called absorption spectrum of the pigment.

Question 16

Kinds of Photosynthetic Pigments

Answer 16

 Thylakoid membranes contain several kinds of pigments, but chlorophylls are the main photosynthetic pigments.
 Other, accessory photosynthetic pigments present in the chloroplasts include yellow and red to orange carotenoids; carotenes are mostly red to orange and xanthophylls are yellow to orange. These broaden the absorption and utilization of light energy.

Question 17

Chlorophylls

Answer 17

There are known many different kinds of chlorophylls. Chlorophyll a, b, c and d
are found in eukaryotic photosynthetic plants are algae, while the other are found in photosynthetic bacteria and are known as bacteriochlorophylls.
Absorption range
Chlorophylls absorb mainly violet-blue and orange-red wave lengths. Green,
yellow and indigo wave lengths are least absorbed by chlorophylls and are transmitted or reflected, although the yellows are often masked by darker green colour. Hence plants appear green, unless masked by other pigments
Structure of chlorophyll
A chlorophyll molecule has two
main parts.
Porphyrin head
One flat, square, light absorbing
hydrophilic head and the other long,
anchoring, hydrophobic hydrocarbon tail.
The head is complex porphyrin ring which is made up of 4 joined smaller pyrrole rings composed of carbon and nitrogen atoms.
An atom of magnesium is present in the center of porphyrin ring and is coordinated with the nitrogen of each pyrrole ring That is why magnesium deficiency
causes yellowing in plants.
Haem portion of haemoglobin is
also a porphyrin ring but containing an iron atom instead of magnesium atom in the center.
Phytol tail:
Long hydrocarbon tail which attached to one of the pyrrole rings is
phytol (C20 H39). The chlorophyll molecule is embedded in the hydrophobic core of thylakoid membrane by this tail

Question 18

Difference between chlorophyll a and b

Answer 18

Chlorophyll a and chlorophyll b differ from each other in only one of the
functional groups bonded to the porphyrin; the methyl group (-CH3) in chlorophyll a is replaced by a terminal carbonyl group (-CHO) in chlorophyll b.
The molecular formulae for chlorophyll a and b are:
 Chlorophyll a : C55 H72 O5 N4 Mg
 Chlorophyll b : C55 H70 O6 N4 Mg
Due to this slight difference in their structure, the two chlorophylls show slightly different absorption spectra and hence different colours. Some wave lengths not absorbed by chlorophyll a are very effectively absorbed by chlorophyll b and vice-versa.
Most abundant and important
Of all the chlorophylls, chlorophyll a is the most abundant and the most
important photosynthetic pigment as it takes part directly in the light-dependent reactions which convert solar energy into chemical energy. It is found in all
photosynthetic organisms except photosynthetic bacteria. Chlorophyll a itself exists in several forms differing slightly in their red absorbing peaks e.g. at 670, 680, 690, 700 nm.
Chlorophyll b is found along with chlorophyll a in all green plants (embryophytes) and green algae.
Chlorophylls are insoluble in water but soluble in organic solvents, such as carbon tetrachloride, alcohol etc.

Question 19

Carotenoids-accessory pigments

Answer 19

Carotenoids are yellow and red to orange pigments that absorb strongly the
blue-violet range, different wave lengths than the chlorophyll absorbs. So they broaden
the spectrum of light that provides energy for photosynthesis.
Role of Accessory Pigments
These and chlorophyll b are called accessory pigments because they absorb light
and transfer the energy to chlorophyll a, which then initiates the light reactions. It is
generally believed that the order of transfer of energy is:
Carotenoids ⎯→ Chlorophyll b ⎯→ Chlorophyll a
Some carotenoids protect chlorophyll from intense light by absorbing and
dissipating excessive light energy, rather than transferring energy to chlorophyll. (Similar
carotenoids may be protecting humans eye).

Question 20

Light − The Driving Energy

Answer 20

Light is a form of energy called electromagnetic energy or radiations. Light
behaves as waves as well as sort of particles called photons. The radiations most
important to life are the visible light that ranges from about 380 to 750 nm in wave
length.
It is the sunlight energy that is absorbed by chlorophyll, converted into chemical energy, and drives the photosynthetic process. Not all the light falling on the leaves is absorbed. Only about one percent (1%) of the light falling on the leaf surface is absorbed, the rest is reflected or transmitted.Absorption spectrum
Absorption spectrum for chlorophylls (Fig. 11.4) indicates that absorption is
maximum in blue and red parts of the spectrum, two absorption peaks being at around
430 nm and 670 nm respectively. Absorption peaks of carotenoids are different from
those of chlorophylls.
Action spectrum
Different wavelengths are not only differently absorbed by photosynthetic
pigments but are also differently effective in photosynthesis.
Graph showing relative effectiveness
of different wavelengths (colours) of light in
driving photosynthesis is called action
spectrum of photosynthesis.
First action spectrum:
The first action spectrum was during photosynthesis.
a. Absorption spectrum of chlorophyll and carotenoids.
b. Action spectrum for photosynthesis.
obtained by German biologist, T.W.Engelmann in 1883. He worked on Spirogyra.
Action spectrum can be obtained by illuminating plant with light of different wavelengths (or colours) and then estimating relative CO2 consumption or oxygen release.
during photosynthesis.
a. Absorption spectrum of chlorophyll and carotenoids.
b. Action spectrum for photosynthesis.
As is evident from above figure 11.4, action spectrum of photosynthesis
corresponds to absorption spectrum of chlorophyll. The same two peaks and the valleyare obtained for absorption of light as well as for CO2 consumption. This also shows that
chlorophyll is the photosynthetic pigment.
Difference Between Absorption and Action Spectrum
However, the action spectrum of photosynthesis does not parallel the
absorption spectrum of chlorophyll exactly. Compared to the peaks in absorption
spectrum, the peaks in action spectrum are broader, and the valley is narrower and not
as deep.
(Photosynthesis in the most absorbed range is more than the absorption itself.
Likewise, photosynthesis in 500-600 nm (including green light) is more than the
absorption of green light by the chlorophyll).
Accessory Pigments
This difference occurs because the accessory pigments, the carotenoids, absorb
light in this zone and pass on some of the absorbed light to chlorophylls which then
convert light energy to chemical energy.
 When equal intensities of light are given there is more photosynthesis in red
than in blue part of spectrum.
Role of Carbon Dioxide:
A Photosynthetic Reactant:
Sugar is formed during light − independent reactions of photosynthesis by the
reduction of CO2, using ATP and NADPH, the products of light − dependent reactions.
Obviously photosynthesis does not occur in the absence of CO2.
CO2 from water or air
About 10 percent of total photosynthesis is carried out by terrestrial plants, the
rest occurs in oceans, lakes and ponds. Aquatic photosynthetic organisms use dissolved
CO2, bicarbonates and soluble carbonates that are present in water as carbon source.
Air contains about 0.03 − 0.04 percent CO2. Photosynthesis occurring on land utilizes
this atmospheric CO2.
Stomata
Carbon dioxide enters the leaves through stomata and gets dissolved in the
water absorbed by the cell walls of mesophyll cells. Stomata are found in a large number in a leaf; their number being proportional to the amount of gas diffusing into the leaf. Stomata cover only 1 − 2 percent of the leaf surface but they allow proportionality much more gas to diffuse.

Question 21

Role of Carbon Dioxide:

Answer 21

A Photosynthetic Reactant:
Sugar is formed during light − independent reactions of photosynthesis by the
reduction of CO2, using ATP and NADPH, the products of light − dependent reactions.
Obviously photosynthesis does not occur in the absence of CO2.
CO2 from water or air
About 10 percent of total photosynthesis is carried out by terrestrial plants, the
rest occurs in oceans, lakes and ponds. Aquatic photosynthetic organisms use dissolved
CO2, bicarbonates and soluble carbonates that are present in water as carbon source.
Air contains about 0.03 − 0.04 percent CO2. Photosynthesis occurring on land utilizes
this atmospheric CO2.
Stomata
Carbon dioxide enters the leaves through stomata and gets dissolved in the
water absorbed by the cell walls of mesophyll cells. Stomata are found in a large number in a leaf; their number being proportional to the amount of gas diffusing into the leaf. Stomata cover only 1 − 2 percent of the leaf surface but they allow proportionality much more gas to diffuse.

Question 22

Reactions of Photosynthesis
Redox Process
Photosynthesis is a ‘redox proc

Answer 22

Redox Process
Photosynthesis is a ‘redox process’ that can be represented by the following
simplified summary equation:
Water Glucose
Oxidation
Carbon Oxygen
Dioxide
Reduction
+ + +
6 CO2 12 H O2 + light energy C H O 6 12 6 6O2 6H O2
Chlorophyll
However, it is not a simple, single step process, but is a complex one that is
completed by a series of simple steps or reactions. These reactions of photosynthesis
consist of two parts:
The light-dependent reactions (light reactions) which use light directly and
The light-independent reactions (dark reactions) which do not use light directly.Light reactions
Light dependent reactions constitute that phase of photosynthesis during which
light energy is absorbed by chlorophyll and other photosynthetic pigment molecules and
converted into chemical energy. As a result of this energy conversion, reducing and
assimilating power in the form of NADPH2 (NADPH + H+
) and ATP, are formed, both
temporarily storing energy to be carried alongwith H to the light independent reactions.
Dark reactions
NADPH2 provides energized
electron (and H+
), while ATP provides chemical energy for the synthesis of sugar by
reducing CO2, using reducing power and chemical energy of NADPH2 and ATP
respectively, produced by light reactions. The energy is thus stored in the molecules of
sugar. This phase of photosynthesis is also called dark reactions because these reactions
do not use light directly an can take place equally well both in light and dark provided
NADPH2 and ATP of light reactions are available.
An overview of photosynthesis: Light − Depend Reactions (Energy − conversion) and Light −
Independence Reactions (Energy − conservation)

Question 23

Light Dependent Reactions
(Energy-Conversion Phase; Formation of ATP and NADPH)

Answer 23

Photo System
As has been described previously, sunlight energy which is absorbed by
photosynthetic pigments drives the process of photosynthesis. Photosynthetic pigmentsare organized into clusters, called photosystems, for efficient absorption and utilization
of solar energy thylakoid membranes.
are organized into clusters, called photosystems, for efficient absorption and utilization
of solar energy thylakoid membranes.
Light harvesting photosystem. Energy of light (photon) absorbed by photosynthetic pigment molecules is
transferred from molecule to molecule, and finally reaches the reaction center where actual energy
conversion begins.

Each photosystem consists of a light-gathering ‘antenna complex’ and a ‘reaction
centre’.
Antenna Complex
The antenna complex has many molecules of chlorophyll a, chlorophyll b and
carotenoids, most of them channeling the energy to reaction center.
Reaction Center
Reaction center has one or more molecules of chlorophyll a along with a primary
electron acceptor, and associated electron carriers of ‘electron transport system’.
Chlorophyll a molecules of reaction center and associated proteins are closely linked to
the nearby electron transport system. Electron transport system plays role in generation of ATP by chemiosmosis. Light energy absorbed by the pigment molecules of antenna complex is transferred ultimately to the reaction center. There the light energy isconverted into chemical energy.

Question 24

Types of Photo System

Answer 24

There are two photosystems, photosystem I (PS I) and photosystem II (PS II).
These are named so in order of their discovery.
Photo system I
Photo-system I has chlorophyll a molecule which absorbs maximum light of 700
nm and is called P700, Photo-system II whereas reaction center of photo-system II has
P680, the form of chlorophyll a which absorbs best the light of 680 nm. A specialized
molecule called, primary electron acceptor is also associated nearby each reaction
centre. This acceptor traps the high-energy electrons from the reaction center and then
passes them on to the series of electron carriers. During this energy is used to generate
ATP by chemiosmosis.
Non-Cyclic Electron Flow
In predominant type of electron transport called non-cyclic electron flow, the
electrons pass through the two photo systems. In less common type of path called cyclic
electron flow only photo system I is involved. Formation of ATP during non-cyclic
electron flow is called non-cyclic phosphorylation while that during cyclic electron flow
is called cyclic phosphorylation.

Question 25

Non-cyclic Phosphorylation

Answer 25

1. Absorption of light by photo system II
   When photo system II absorbs light, an electron excited to a higher energy level
   in the reaction centre chlorophyll P680 is captured by the primary electron acceptor of PS
   II. The oxidized chlorophyll is now a very strong oxidizing agent; its electron “hole” must
   be filled.
2. Photolysis of water
   This hole is filled by the electrons which are extracted, by an enzyme, from
   water. This reaction splits a water molecules into two hydrogen ions and an oxygen
   atom, which immediately combines with another oxygen atom to form O2. This water
   splitting step of photosynthesis that releases oxygen is called photolysis. The oxygen
   produced during photolysis is the main source of replenishment of atmospheric oxygen.
3. 1st Electron transport chain
   Each photoexcited electron passes from the primary electron acceptor of photo
   system II to photo system I via an electron transport chain. This chain consists of an
   electron carrier called plastoquinone (Pq), a complex of two cytochromes and a copper
   containing protein called plastocyanin (Pc).
4. Photophosphorylation
   As electrons move down the chain, their energy goes on decreasing and is used
   by thylakoid membrane to produce ATP. This ATP synthesis is called
   photophosphorylation because it is driven by light energy. Specifically, ATP synthesis
   during non-cyclic electron flow is called non-cyclic photophosphorylation. This ATP
   generated by the light reactions will provide chemical energy for the synthesis of sugar
   during the Calvin cycle, the second major stage of photosynthesis.
5. Filling of electron hole of PSI
   The electron reaches the “bottom” of the electron transport chain and fills an
   electron “hole” in P700, the chlorophyll a molecules in the reaction center of
   photosystem I. This hole is created when light energy is absorbed by molecules of P700
   and drives an electron from P700 to the primary acceptor of photo system I.
6. 2nd electron transport chain
   The primary electron acceptor of photo system I passes the photoexcited
   electrons to a second electron transport chain, which transmits them to ferredoxin (Fd),
   an iron containing protein. An enzyme called NADP reductase then transfers theelectrons from Fd to NADP. This is the redox reaction that stores the high-energy
   electrons in NADPH. The NADPH molecule will provide reducing power for the synthesis
   of sugar in the Calvin cycle.
   The path of electrons through the two photosystems during non-cyclic
   photophosphorylation is known as Z-scheme from its shape.

Question 26

Products of Z-scheme

Answer 26

Non-cyclic electron flow during photosynthesis generates ATP, NADPH and
oxygen. (Each photon of light excite single electron).Non-cyclic electron flow during photosynthesis ATP, NADPH and oxygen are generated. The arrows
trace the current of light-driven electrons from water to NADPH. Each photon of light excites single
electron, but the diagram tracts two electrons at a time, the number of electrons required to reduce
NADP+. The numbered steps are described in the text.
Cyclic Phosphorylation
Under certain conditions, photoexcited electrons take an alternative path called
cyclic electron flow. This path uses photosystem I but not photosystem II.

Question 27

Conditions for non-cyclic phosphorylation

Answer 27

Possibly it happens when
i. The chloroplast runs low on ATP for the Calvin cycle.
ii. The cycle slows down
iii. NADPH accumulate in chloroplast.
This rise in NADPH may stimulate a temporary shift from non-cyclic to cyclic
electron flow until ATP supply meets the demand.

Question 28

Short Circuit

Answer 28

The cyclic flow is short circuit: The electrons cycle back from primary electron
acceptor to ferredoxin (Fd) to the cytochrome complex and from there continue on to
the P700 chlorophyll. ATP is generated by the coupling of ETC by chemiosomosis.

Question 29

Products of non-cyclic flow

Answer 29

 There is no production of NADPH and no release of oxygen.
 Cyclic flow does, however, generate ATP. This is called cyclic
photosphosphorylation.

Question 30

Mechanism of Chemiosmosis

Answer 30

Chemiosmosis
In both cyclic and non-cyclic photosphosphorylation, the mechanism for ATP
synthesis is chemiosmosis, the process that uses membranes to couple redox reactions
to ATP production.
Pumping of protons (H+
)
Electron transport chain pumps protons (H+
) across the membrane of thylakoids
in case of photosynthesis into the thylakoids space.
Energy for Proton Pumping
The energy used for this pumping comes from the electrons moving through the
electron transport chain.
H
+
gradient establishment
This energy is transformed into potential energy stored in the form of H+
gradient across the membrane.
ATP synthase
Next the hydrogen ions move down their gradient through special complexes
called ATP synthase which are built in the thylakoid membrane. During this diffusion of
H+ the energy of electrons is used to make ATP.

Question 31

Light Independent (Or Dark) Reactions
Calvin cycle: carbon fixation and reduction phase, synthesis of sugar

Answer 31

The dark reactions take place in the stroma of chloroplast. These reactions do not
require light directly and can occur in the presence or absence of light provided the
assimilatory power in the form of ATP and NADPH, produced during light reactions is
available. Energy of these compounds is used in the formation of carbohydrates from
CO2, and thus stored their in.
Equation of Calvin cycle
These reactions can be summarized as follows :
3CO2 + 6NADPH + 9ATP ⎯⎯→ (CH2O)3 + 6NADP + 9ADP + 9Pi + 3H2O
Carbohydrate
Discovery of Calvin Cycle
The details of path of carbon in these reactions were discovered by Melvin Calvin
and his colleagues at the University of California. Calvin was awarded Nobel Price in
1961.
The cyclic series of reactions, catalyzed by respective enzymes, by which the
carbon is fixed and reduced resulting in the synthesis of sugar during the dark reactions
of photosynthesis is called Calvin Cycle.
Phase of Calvin Cycle
The Calvin cycle can be divided into three phases:
 Carbon fixation  Reduction
 Regeneration of CO2 acceptor (RUBP) (Fig 11.10).
Phase 1: Carbon fixation
Carbon fixation refers to the initial incorporation of CO2 into organic material.
Keep in mind that we are following three molecules of CO2 through the reaction (because
3 molecules of CO2 are required to produce one molecule of carbohydrate, a triose). The
Calvin cycle beings when a molecule of CO2 reacts with a highly reactive phosphorylated
five – carbon sugar named ribulose bisphosphate (RUBP).
Rubisco
This reaction is catalyzed by the enzyme ribulose bisphosphate carboxylase, also
known as Rubisco (it is the most abundant protein in chloroplasts, and probably the
most abundant protein on Earth). The product of this reaction is an highly unstable, six –
carbon intermediate that immediately breaks into two molecules of three – carboncompound called 3 – phosphoglycerate (phosphoglyceric acid-PGA). The carbon that
was originally part of CO2 molecule is now a part of an organic molecule; the carbon has
been “fixed”. Because the product of initial carbon fixation is a three – carbon
compound, the Calvin cycle is also known as C3 pathway.
Phase 2: Reduction:
Each molecule of (PGA) receives an additional phosphate from ATP of light
reaction, forming 1,3 – bisphosphoglycerate as the product. 1,3 bisphosphoglycerate is
reduced to glyceraldehyde 3-phosphate (G3P) by receiving a pair of electrons donated
from NADPH of light reactions. G3P is the same three-carbon sugar which is formed in
glycolysis (first phase of cellular respiration) by the splitting of glucose. In this way fixed
carbon is reduced to energy rich G3P with the energy and reducing power of ATP and
NADPH (both the products of light-dependent reactions), having the energy stored in it.
Actually G3P, and not glucose, is the carbohydrate produced directly form the Calvin
cycle. For every three molecules of CO2 entering the cycle and combining with 3
molecules of five-carbon RuBP, six molecules of G3P can be counted as a net gain of
carbohydrate. Out of every six molecule of G3P formed, only one molecule leaves the
cycle to be used by the plant for making glucose, sucrose starch or other carbohydrates,
and other organic compounds; the other five molecules are recycled to regenerate the
three molecules of five-carbon RuBP, the CO2 acceptor.
Phase 3: Regeneration of CO2 acceptor, RuBP:
Through a complex series of reactions, the carbon skeletons of five molecules of
three-carbon G3P are rearranged into three molecules of five-carbon ribulose
phosphate (RuP). Each RuP is phosphorylated to ribulose bisphohate (RuBP), the very
five-carbon CO2 acceptor with which the cycle started. Again three more molecules of
ATP of light reactions are used for this phosphorylation to three RuP molecules. These
RuBP are now prepared to receive CO2 again, and the cycle continues.

Question 32

Respiration

Answer 32

Living organisms need energy to carry on their vital activities. This energy is
provided from within the cells by the phenomenon of respiration. Respiration is theuniversal process by which organisms’ breakdown complex compounds containing
carbon in a way that allows the cells to harvest a maximum of usable energy.
Two ways of Respiration
In biology the term respiration is used in two ways.
 External respiration
 Cellular respiration
External Respiration
More familiarly the term respiration means the exchange of respiratory gases
(CO2 and O2) between the organism and its environment. This exchange is called
external respiration.
Cellular Respiration
The cellular respiration is the process by which energy is made available to cells
in a step by step breakdown of C-chain molecules in the cells.
Aerobic and Anaerobic Respiration
The most common fuel used by the cell to provide energy by cellular respiration
is glucose

Question 33

Glycolysis

Answer 33

Glycolysis (1st step of cellular respiration)
The way glucose is metabolized depends on the availability of oxygen. Prior to
entering a mitochondrion, the glucose molecule is split to form two molecules of pyruvic
acid. This reaction is called glycolysis (glycolysis literally means splitting of sugar), and
occurs in the cytosol and is represented by the equation:
This reaction occurs in all the cells and biologists believe that an identical
reaction may have occurred in the first cell that was organized on earth.The next step in cellular respiration varies depending on the type of the cell and
the prevailing conditionsPyruvic Acid
Cell processes pyruvic acid in three major ways:
 Alcoholic fermentation
 Lactic acid fermentation
 Aerobic respiration.
The first two reactions occur in the absence of oxygen and are referred to as
anaerobic (without oxygen). The complete breakdown of glucose molecule occurs only
in the presence of oxygen, i.e. in aerobic respiration. During aerobic respiration glucose
is oxidized to CO2 and water and energy is released.
(i) Alcoholic Fermentation: In primitive cells and in some eukaryotic cells such
as yeast, pyruvic acid is further broken down by alcoholic fermentation into
alcohol (C2 H5 OH) and CO2.(ii) Lactic acid fermentation: In lactic acid fermentation, each pyruvic acid
molecule is converted into lactic acid C3 H6 O3 in the absence of oxygen gas:
This form of anaerobic respiration occurs in muscle cells of humans and other
animals during extreme physical activities, such as sprinting, when oxygen cannot be
transported to the cells as rapidly as it is needed.
Energy yield
Both alcoholic and lactic acid fermentations yield relatively small amounts of
energy from glucose molecule. Only about 2% of the energy present within the chemical
bonds of glucose is converted into adenosine triphosphate (ATP).
Aerobic respiration (Discussed in detail under cellular respiration)

Question 34

Role of Mitochondria In Respiration

Answer 34

Structure
Mitochondria are large granular or filamentous organelles that are distributed
throughout the cytoplasm of animals and plant cells. Each mitochondrion is constructed
of an outer enclosing membrane and an inner membrane with elaborate folds or cristae
that extend into the interior of the organelle.Function
Mitochondria play a part in cellular respiration by transferring the energy of the
organic molecules to the chemical bonds of ATP. A large “battery” of enzymes and
coenzymes slowly release energy from the glucose molecules. Thus mitochondria are
the “Power houses” that produce energy necessary for many cellular functions.
Adenosine triphosphate and its importance
Adenosine triphosphate, generally abbreviated ‘ATP’ is a compound found in
every living cell and is one of the essential chemicals of life. It plays the key role in most
biological energy transformations.Conventionally, ‘P’ stands for the entire phosphate group. The second and the third
phosphate represent the so called “high energy” bonds. If these are broken by
hydrolysis, far more free energy is released as compared to the other bond in the ATP
molecule.
Energy yield
The breaking of the terminal phosphate of ATP releases about 7.3 K cal. of
energy. The high energy ‘P’ bond enables the cell to accumulate a great quantity of
energy in a very small space and keeps it ready for use as soon as it is needed.Use of ATP
The ATP molecule is used by cells as a source of energy for various functions for
example:
 Synthesis of more complex compounds
 Active transport across the cell membrane
 Muscular contraction
 Nerve conduction, etc.

Question 35

Biological Oxidation

Answer 35

The maintenance of living system requires a continual supply of free energy which is
ultimately derived from various oxidation reduction reactions. Except for photosynthetic
and some bacterial chemosynthetic processes, which are themselves oxidation
reduction reactions, all other cells depend ultimately for their supply of free energy on
oxidation reactions in respiratory processes.
Dehydrogenase
In some cases biological oxidation involves the removal of hydrogen, a reaction
catalyzed by the dehydrogenases linked to specific coenzymes. Cellular respiration is
essentially an oxidation process.
Cellular Respiration
Cellular respiration may be sub-divided into 4 stages:
i. Glycolysis ii. Pyruvic acid oxidation
iii. Krebs cycle or citric acid cycle iv. Respiratory chain
Out of these stages the first occurs in the cytosol for which oxygen is not
essential, while the other three occur within the mitochondria where the presence of
oxygen is essential.

Question 36

Glycolysis

Answer 36

Glycolysis is the breakdown of glucose upto the formation of pyruvic acid.
Glycolysis can take place both in the absence of oxygen (anaerobic condition) or
in the presence of oxygen (aerobic condition). In both, the end product of
glucose breakdown is pyruvic acid. The breakdown of glucose takes place in a
series of step, each catalyzed by a specific enzyme. All these enzymes are founddissolved in the cytosol. In addition to the enzymes, ATP and coenzymes NAD
(nicotinamide adenine dinucleotide) are also essential.
Phases of glycolysis
Glycolysis can be divided into two phases.
 Preparatory phase
 Oxidative phase
In the preparatory phase breakdown of glucose occurs and energy is expended. In
the oxidative phase high energy phosphate bonds are formed and energy is stored.

Question 37

I. Preparatory Phase

Answer 37

1. Phosphorylation of glucose
   The first step in glycolysis is the transfer of a phosphate group from ATP to
   glucose. As a result a molecule of glucose-6-phoshapte is formed.
2. Rearrangement (Isomerization)
   An enzyme catalyzes the conversion of glucose-6-phosphate to its isomer,
   fructorse-6-phosphate.
3. Phosphorylation of fructose 6-bisphosphate
   At this stage another ATP molecule transfers a second phosphate group.
4. Spliting of fructose 1, 6-bisphosphate
   The product is fructose 1,6-bisphosphate into two fragments. Each of these
   molecules contains three carbon atoms. One is called 3-phospo-glyceraldehyde,
   3-PGAL or Glyceraldehyde 3-phosphate (G3P) while the other is
   dihydroxyacetone phosphate.
5. Interconvertion (isomerization)
   These two molecules (G3P and DAP) are isomers and in fact are readily
   interconverted by yet another enzyme of glycoslysis.

Question 38

II. Oxidative (Payoff) Phase

Answer 38

1. Oxidation and phosphorylation
   The next step in glycolysis is crucial to this process. Two electrons or two
   hydrogen atoms are removed form the molecule of 3-phosphoglyceraldehyde (PGAL)
   and transferred to a molecule of NAD. This is of course, an oxidation-reduction reaction,
   with the PGAL being oxidized and the NAD being reduced. During this reaction, a second
   phosphate group is donated to the molecule from inorganic phosphate present in the
   cell. The resulting molecule is called 1,3 Bisphosphoglycerate (BPG).
2. ATP formationThe oxidation of PGAL is an energy yielding process. Thus a “high energy”
   phosphate bond is created in this molecule. At the very next step in glycolysis this
   phosphate group is transferred to a molecule of adenosine diphosphate (ADP)
   converting it into ATP. The end product of this reaction is 3-phospho glycerate (3-PG).
3. Rearrangement (isomerization)
   In the next step 3-PG is converted to 2-Phosphoglycerate (2PG).
4. Dehydration and PEP formation
   From 2PG a molecule of water is removed and the product is phosphoenol.
   pyruvate (PEP).
5. Pyruvic acid formation
   PEP then gives up its ‘high energy’ phosphate to convert a second molecule of
   ADP to ATP. The product is pyruvate, pyruvic acid (C3 H4 O3).
    It is equivalent to half glucose molecule that has been oxidized to the extent of
   losing two electrons (as hydrogen atoms).

Question 39

Pyruvic Acid Oxidation

Answer 39

Pyruvic acid (pyruvate), the end product of glycolysis, does not enter the Krebs
cycle directly.
 The pyruvate (3-carbon molecule) is first changed into 2-carbon acetic acid
molecule. One carbon is released as CO2 (decarboxylation).
 Acetic acid on entering the mitochondrion unites with coenzyme-A (CoA) to
form acetyl CoA (active acetate).
 In addition, more hydrogen atoms are transferred to NAD (Fig 11.13).
Krebs Cycle or Citric Acid Cycle:
Acetyl CoA now enters a cyclic series of chemical reactions during which
oxidation process is completed. This series of reactions is called the Krebs cycle (after
the name of the biochemist who discovered it), or the citric acid cycle.
Citrate formation
The first step in the cycle is the union of acetyl CoA with oxalocetate to form
citrate. In this process, a molecule of CoA is regenerated and one molecule of water is
used. Oxaloacetate is a 4-carbon acid. Citrate thus has 6 carbon atoms.
Isocitrate formation
After two steps that simply result in forming an isomer of citrate, isocitrate.
Oxidative decarboxylation (ketoglutrate formation)
It is conversion of isocitrate into ketoglutrate.
Here NAD-mediated oxidation takes place. This is accompanied by the removal
of a molecule of CO2. The result is ketoglutarate.
Succinate formation
ketoglutarate in turn, undergoes further oxidation (NAD + 2H → NADH2)
followed by decarboxylation (CO2) and addition of a molecule of water. The product
then has one carbon atom and one oxygen atom less. It is succinate. The conversion of
-ketoglutarate into succinate is accompanied by a free energy change which is utilised
in the synthesis of an ATP molecule.
Oxidation of succinate
The next step in the Krebs cycle is the oxidation of succinate to fumarate. Once
again, two hydrogen atoms are removed, but this time the oxidizing agent is a coenzyme
called flavin adenine dinucleotide (FAD), which is reduced to FADH2.
Outline of the Kerbs cycle. The brackets give the number of carbon atom in each intermediate of the
cycle.
Malate Formation
With the addition of another molecule of water, fumarate is converted to
malate.
Oxidation of Malate
Another NAD mediated oxidation of malate produces oxaloacetate, the original
4-carbon molecule. This complete the cycle. The oxaloacetate may now combine with
another molecule of acetyl CoA to enter the cycle and the whole process is repeated (Fig
11.13).
Respiratory Chain
In the Krebs cycle NADH and H+
are produced from NAD+
. NADH then transfers
the hydrogen atom to the respiratory chain (also called electron transport system)
where electrons are transported in a series of oxidation-reduction steps to react,
ultimately, with molecular oxygen. (Fig. 11.14).
Components of Respiration Chain
The oxidation reduction substances which take part in respiratory chain are:
i. A coenzyme called coenzyme Q
ii. A series of cytochrome enzymes (b,c,a,a3)
iii. Molecular oxygen (O2)
Cytochrome
Cytochromes are electron transport intermediates containing haem of related
prosthetic groups, that undergo valency changes of iron atom. Heam is the same iron
containing group that is oxygen carrying pigment in heamoglobin. The path of electrons
in the reparatory chain appears to be as follows.

Question 40

Steps in Electron Transport Chain

Answer 40

i. Oxidation of NADH
NADH is oxidized by coenzyme Q. This oxidation yields enough free energy to
permit the synthesis of a molecule of ATP from ADP and inorganic phosphate.
ii. Oxidation of Co-enzyme Q
Coenzyme Q is in turn oxidized by cytochrome b which is then oxidized by
cytochrome c. This step also yields enough energy to permit the synthesis of a molecule
of ATP.
iii. Reduction of cytochrome c
Cytochrome c then reduces a complex of two enzymes called cytochrome a and
a3 (for convenience the complex is referred as cytochrome a).
iv. Oxidation of cytochrome a
Cytochrome a is oxidized by an atom of oxygen and the electrons arrive at the
bottom end of respiratory chain. Oxygen is the most electronegative substance and the
final acceptor of the electrons. A molecule of water is produced. In addition, this final
oxidation provides enough energy for the synthesis of a third molecule of ATP.
v. Oxidative phosphorylation
Synthesis of ATP in the presence of oxygen is called oxidative phosphorylation.
Normally, oxidative phosphorylation is coupled with the respiratory chain. As already
described ATP is formed in three steps of the respiratory chain

Question 41

Equation of ETC

Answer 41

The equation for this process can be expressed as follows:
NADH + H+
+ 3 ADP + 3Pi + ½ O2 → NAD+ +H2O + 3ATP
Where Pi is inorganic phosphate.
Mechanism of Oxidative Phosphorylation
 The molecular mechanism of oxidative phosphorylation takes place in
conjunction with the reparatory chain in the inner membrane of the
mitochondrion.
 Her also, as in photosynthesis, the mechanism involved is chemiosmosis by
which electron transport chain is coupled with synthesis of ATP.
 In this case, however the pumping/movement of protons (H+
) is across the inner
membrane of mitochondrion folded into cristae, between matrix of
mitochondrion and mitochondrion’s intermembrane space.
 The coupling factors in respiration are also different from those in
photosynthesis.