Welcome to Class 11 Biology!

Biology is the study of life in its entirety. The growth of biology as a natural science during the last 1000 years is interesting from many points of view. One feature of this growth is an emphasis on the underlying principles that are common to all living entities, plants, animals, and microbes alike.

This digital textbook spans the entire CBSE Class 11 Biology curriculum. It has been specifically designed to not only meet the academic standards required for the board exams but also to foster a deep, conceptual understanding of the living world.

How to Use This Book

This book is organized into five core units, comprising 19 individual chapters.

Each chapter features:

• Comprehensive Theory: Detailed, easy-to-understand explanations of complex biological processes.
• High-Quality Illustrations: Custom-designed, scientifically accurate diagrams to visualize anatomical structures and cellular pathways.
• Competency-Based Questions: At the end of every chapter, you will find three rigorously designed competency-based questions with mathematically and biologically justified step-by-step solutions hidden in expandable blocks. These are invaluable for exam preparation.

Core Units Covered:

1. Diversity in the Living World: Chapters 1-4
2. Structural Organisation in Plants and Animals: Chapters 5-7
3. Cell: Structure and Functions: Chapters 8-10
4. Plant Physiology: Chapters 11-12
5. Human Physiology: Chapters 13-19

Prepare to embark on an incredible journey exploring the sheer diversity, structural organization, and intricate physiological mechanics of the living world!

This educational resource is tailored for the Central Board of Secondary Education (CBSE) Biology curriculum.

Chapter 1: The Living World

Biology is the story of life on earth. The living world is rich in variety. Millions of plants and animals have been identified and described, but a large number still remains unknown. The very range of organisms in terms of size, colour, habitat, physiological and morphological features makes us seek the defining characteristics of living organisms.

What is Living?

When we try to define ‘living’, we conventionally look for distinctive characteristics exhibited by living organisms. Growth, reproduction, ability to sense environment and mount a suitable response come to our mind immediately as unique features of living organisms. One can add a few more features like metabolism, ability to self-replicate, self-organise, interact and emergence to this list.

Biodiversity

Biodiversity refers to the number and types of organisms present on earth. The number of species that are known and described range between 1.7-1.8 million.

Need for Classification

It is nearly impossible to study all the living organisms. Hence, there is a need to devise some means to make this possible. This process is called classification. Classification is the process by which anything is grouped into convenient categories based on some easily observable characters.

Taxonomy and Systematics

Based on characteristics, all living organisms can be classified into different taxa. This process of classification is taxonomy.

The word systematics is derived from the Latin word ‘systema’ which means systematic arrangement of organisms. Linnaeus used Systema Naturae as the title of his publication. Systematics takes into account evolutionary relationships between organisms.

Three Domains of Life

The three-domain system is a biological classification introduced by Carl Woese in 1990. It divides cellular life forms into archaea, bacteria, and eukaryote domains.

Binomial Nomenclature

The system of providing a name with two components is called Binomial Nomenclature. This naming system given by Carolus Linnaeus is being practised by biologists all over the world. Each name has two components – the Generic name and the specific epithet. Example: The scientific name of mango is written as Mangifera indica. Here Mangifera represents the genus while indica, is a particular species, or a specific epithet.

Rules of Nomenclature:

1. Biological names are generally in Latin and written in italics.
2. The first word represents the genus while the second component denotes the specific epithet.
3. Both the words, when handwritten, are separately underlined, or printed in italics to indicate their Latin origin.
4. The first word denoting the genus starts with a capital letter while the specific epithet starts with a small letter.

Concept of Species and Taxonomical Hierarchy

Classification is not a single step process but involves a hierarchy of steps in which each step represents a rank or category. Since the category is a part of overall taxonomic arrangement, it is called the taxonomic category and all categories together constitute the taxonomic hierarchy.

Each category, referred to as a unit of classification, in fact, represents a rank and is commonly termed as taxon (pl.: taxa).

The taxonomic hierarchy:

• Kingdom
• Phylum (or Division for plants)
• Class
• Order
• Family
• Genus
• Species

Figure 1.1: Taxonomic Hierarchy

Competency Based Questions (Previous Years & Sample Papers)

Q1. A student found a new organism in a tropical rainforest. The organism has a cell wall but lacks a true nucleus. Based on the three domains of life proposed by Carl Woese, under which domain should this organism be primarily investigated, and why?

Q2. Evaluate the following mathematical expression that biologists might use when calculating a biodiversity index (like Simpson’s Diversity Index). Simplify the LaTeX equation:

$$ D = 1 - \sum \left( \frac{n_i}{N} \right)^2 $$

Given a population where type A has \(n_1 = 3\), type B has \(n_2 = 2\), and type C has \(n_3 = 5\). Total population \(N = 10\). Calculate the diversity index \(D\).

Q3. If the number of species in genus A and its related genus B are represented by \(x\) and \(y\) respectively, and their taxonomic relationship is given by the function \(f(x, y) = \frac{\sqrt{x^2 + y^2}}{x \cdot y}\), what happens as the number of species in both genera approaches infinity?

Chapter 2: Biological Classification

Since the dawn of civilisation, there have been many attempts to classify living organisms. It was done instinctively not using criteria that were scientific but borne out of a need to use organisms for our own use – for food, shelter and clothing. Aristotle was the earliest to attempt a more scientific basis for classification. He used simple morphological characters to classify plants into trees, shrubs and herbs. He also divided animals into two groups, those which had red blood and those that did not.

Five Kingdom Classification

In Linnaeus’ time a Two Kingdom system of classification with Plantae and Animalia kingdoms was developed that included all plants and animals respectively. This system did not distinguish between the eukaryotes and prokaryotes, unicellular and multicellular organisms and photosynthetic (green algae) and non-photosynthetic (fungi) organisms.

R.H. Whittaker (1969) proposed a Five Kingdom Classification. The kingdoms defined by him were named Monera, Protista, Fungi, Plantae and Animalia. The main criteria for classification used by him include cell structure, body organisation, mode of nutrition, reproduction and phylogenetic relationships.

Figure 2.1: R.H. Whittaker's Five Kingdom Classification

Kingdom Monera

Bacteria are the sole members of the Kingdom Monera. They are the most abundant micro-organisms. Bacteria occur almost everywhere. Hundreds of bacteria are present in a handful of soil.

Bacteria are grouped under four categories based on their shape:

• the spherical Coccus (pl.: cocci)
• the rod-shaped Bacillus (pl.: bacilli)
• the comma-shaped Vibrium (pl.: vibrio)
• the spiral Spirillum (pl.: spirilla)

Archaebacteria

These bacteria are special since they live in some of the most harsh habitats such as extreme salty areas (halophiles), hot springs (thermoacidophiles) and marshy areas (methanogens).

Eubacteria

There are thousands of different eubacteria or ‘true bacteria’. They are characterised by the presence of a rigid cell wall, and if motile, a flagellum. The cyanobacteria (also referred to as blue-green algae) have chlorophyll a similar to green plants and are photosynthetic autotrophs.

Kingdom Protista

All single-celled eukaryotes are placed under Protista, but the boundaries of this kingdom are not well defined. What may be ‘a photosynthetic protistan’ to one biologist may be ‘a plant’ to another.

In this group we include:

• Chrysophytes: Includes diatoms and golden algae (desmids).
• Dinoflagellates: These organisms are mostly marine and photosynthetic.
• Euglenoids: Majority of them are fresh water organisms found in stagnant water.
• Slime Moulds: Saprophytic protists.
• Protozoans: All protozoans are heterotrophs and live as predators or parasites.

Kingdom Fungi

The fungi constitute a unique kingdom of heterotrophic organisms. They show a great diversity in morphology and habitat. When your bread develops a mould or your orange rots it is because of fungi.

Features:

• Most fungi are heterotrophic and absorb soluble organic matter from dead substrates and hence are called saprophytes.
• Those that depend on living plants and animals are called parasites.
• They can also live as symbionts – in association with algae as lichens and with roots of higher plants as mycorrhiza.

Viruses, Viroids, Prions and Lichens

In the five-kingdom classification of Whittaker there is no mention of lichens and some acellular organisms like viruses, viroids and prions.

• Viruses: The viruses are non-cellular organisms that are characterised by having an inert crystalline structure outside the living cell. Once they infect a cell they take over the machinery of the host cell to replicate themselves, killing the host.
• Viroids: In 1971, T.O. Diener discovered a new infectious agent that was smaller than viruses and caused potato spindle tuber disease. It was found to be a free RNA; it lacked the protein coat that is found in viruses.
• Prions: In modern medicine certain infectious neurological diseases were found to be transmitted by an agent consisting of abnormally folded protein. These agents are called prions.
• Lichens: Lichens are symbiotic associations i.e. mutually useful associations, between algae and fungi. The algal component is known as phycobiont and fungal component as mycobiont.

Competency Based Questions (Previous Years & Sample Papers)

Q1. Consider the growth of a bacterial population in a conducive environment. The growth can be modeled according to the exponential equation $N\sb{t} = N\sb{0} \cdot 2^n$, where $N\sb{t}$ is the final population, $N\sb{0}$ is the initial population, and $n$ is the number of generations. If a population of E. coli starts with 5 cells and divides every 20 minutes, what will be the population after 3 hours? Calculate the exact value.

Q2. During a laboratory experiment, a student isolates an organism that has a well-defined nucleus, is unicellular, and possesses cilia for locomotion. It also shows a contractile vacuole for osmoregulation. Based on R.H. Whittaker’s five-kingdom classification, to which kingdom does this organism belong, and why?

Q3. Viroids differ from viruses in a fundamental biochemical structural aspect. If the molecular weight of a viroid’s genetic material is $M\sb{v}$ and the molecular weight of a comparable virus is $M\sb{vir}$, the relationship is generally $M\sb{v} < M\sb{vir}$. Explain the biological basis for this inequality based on the composition of viroids.

Chapter 3: Plant Kingdom

In the previous chapter, we looked at the broad classification of living organisms under the system proposed by Whittaker (1969) wherein he suggested the Five Kingdom classification viz. Monera, Protista, Fungi, Animalia and Plantae. In this chapter, we will deal in detail with further classification within Kingdom Plantae popularly known as the ‘plant kingdom’.

We must stress here that our understanding of the plant kingdom has changed over time. Fungi, and members of the Monera and Protista having cell walls have now been excluded from Plantae though earlier classifications placed them in the same kingdom. The cyanobacteria that are also referred to as blue-green algae are not ‘algae’ any more. In this chapter, we will describe Algae, Bryophytes, Pteridophytes and Gymnosperms under Plantae.

Figure 3.1: Evolutionary grouping of plants

Algae

Algae are chlorophyll-bearing, simple, thalloid, autotrophic and largely aquatic (both fresh water and marine) organisms. They occur in a variety of other habitats: moist stones, soils and wood. Some of them also occur in association with fungi (lichen) and animals (e.g., on sloth bear).

Classes of Algae

1. Chlorophyceae (Green algae): The plant body may be unicellular, colonial or filamentous. They are usually grass green due to the dominance of pigments chlorophyll a and b.
2. Phaeophyceae (Brown algae): Found primarily in marine habitats. They possess chlorophyll a, c, carotenoids and xanthophylls. They show great variation in size and form.
3. Rhodophyceae (Red algae): The members of Rhodophyceae are commonly called red algae because of the predominance of the red pigment, r-phycoerythrin in their body.

Bryophytes

Bryophytes include the various mosses and liverworts that are found commonly growing in moist shaded areas in the hills. Bryophytes are also called amphibians of the plant kingdom because these plants can live in soil but are dependent on water for sexual reproduction. They usually occur in damp, humid and shaded localities.

• Liverworts: Grow usually in moist, shady habitats such as banks of streams, marshy ground, damp soil, bark of trees and deep in the woods.
• Mosses: The predominant stage of the life cycle of a moss is the gametophyte which consists of two stages: protonema and leafy stage. They play an important role in plant succession on bare rocks/soil.

Pteridophytes

The Pteridophytes include horsetails and ferns. Pteridophytes are used for medicinal purposes and as soil-binders. They are also frequently grown as ornamentals. Evolutionarily, they are the first terrestrial plants to possess vascular tissues — xylem and phloem.

The pteridophytes are found in cool, damp, shady places though some may flourish well in sandy-soil conditions. The main plant body is a sporophyte which is differentiated into true root, stem and leaves. The leaves in pteridophyta are small (microphylls) as in Selaginella or large (macrophylls) as in ferns.

Gymnosperms

The gymnosperms (gymnos : naked, sperma : seeds) are plants in which the ovules are not enclosed by any ovary wall and remain exposed, both before and after fertilisation. The seeds that develop post-fertilisation, are not covered, i.e., are naked. Gymnosperms include medium-sized trees or tall trees and shrubs.

One of the gymnosperms, the giant redwood tree Sequoia is one of the tallest tree species. The roots are generally tap roots. Roots in some genera have fungal association in the form of mycorrhiza (Pinus), while in some others (Cycas) small specialised roots called coralloid roots are associated with \text{N}_2- fixing cyanobacteria.

Competency Based Questions (Previous Years & Sample Papers)

Q1. A botanist discovers a new plant species in a damp, shaded forest. The plant is small and lacks true roots, stems, and leaves, but has root-like structures called rhizoids. It also requires a film of water for its sperm to swim to the egg for fertilization. Based on these characteristics, which major plant division does this species most likely belong to, and why? Estimate the ploidy level ($n$ or $2n$) of its main free-living plant body.

Q2. During a field trip, a student observes two different vascular plants. Plant A has large leaves (fronds) that uncoil as they grow, and produces spores on the undersides of its leaves. Plant B is a large tree with needle-like leaves and bears its seeds in cones, not enclosed in any fruit. Identify the broad groups to which Plant A and Plant B belong. If the number of chromosomes in the endosperm of Plant B is $3x = 36$, what would be the expected mathematical relationship for the ploidy of its endosperm compared to an angiosperm? (Note: Angiosperm endosperm is typically 3n)

Q3. Calculate the surface area to volume ratio ($SA/V$) for a spherical unicellular green alga with a radius $r = 10 \mu m$ and a filamentous green alga modeled as a cylinder of the same radius $r = 10 \mu m$ but length $h = 100 \mu m$. The formulas are: $SA_{sphere} = 4\pi r^2$, $V_{sphere} = \frac{4}{3}\pi r^3$, $SA_{cylinder} = 2\pi r^2 + 2\pi rh$, $V_{cylinder} = \pi r^2 h$. Which shape is more efficient for nutrient absorption from the surrounding water?

Chapter 4: Animal Kingdom

When you look around, you will observe different animals with different structures and forms. As over a million species of animals have been described till now, the need for classification becomes all the more important. The classification also helps in assigning a systematic position to newly described species.

Basis of Classification

Inspite of differences in structure and form of different animals, there are fundamental features common to various individuals in relation to the arrangement of cells, body symmetry, nature of coelom, patterns of digestive, circulatory or reproductive systems. These features are used as the basis of animal classification.

• Levels of Organisation: Cellular (Porifera), Tissue (Coelenterata, Ctenophora), Organ, and Organ system.
• Symmetry: Asymmetrical, Radial, and Bilateral symmetry.
• Diploblastic and Triploblastic Organisation: Animals with two embryonic layers (ectoderm and endoderm) are diploblastic. Those with three (including mesoderm) are triploblastic.
• Coelom: The presence or absence of a cavity between the body wall and the gut wall is very important in classification.

Figure 4.1: Broad classification of Kingdom Animalia based on common fundamental features

Classification of Animals

The broad classification of Animalia based on common fundamental features:

Non-Chordates

• Phylum Porifera: Sponges; cellular level of organisation; asymmetrical. Have a water transport or canal system.
• Phylum Coelenterata (Cnidaria): Aquatic, mostly marine; have cnidoblasts for defense and prey capture; radial symmetry. Examples: Hydra, Aurelia.
• Phylum Ctenophora: Commonly known as sea walnuts or comb jellies; exclusively marine; have 8 external rows of ciliated comb plates. Bioluminescence is well-marked.
• Phylum Platyhelminthes: Flatworms; dorso-ventrally flattened body; bilateral symmetry, triploblastic, acoelomate animals with organ level of organisation. Many are endoparasites.
• Phylum Aschelminthes: Roundworms; the body is circular in cross-section; pseudocoelomate animals.
• Phylum Annelida: Aquatic or terrestrial; their body surface is distinctly marked out into segments or metameres (e.g., Earthworm).
• Phylum Arthropoda: The largest phylum of Animalia which includes insects. They have jointed appendages. The body is covered by a chitinous exoskeleton.
• Phylum Mollusca: The second largest phylum. They have a soft body usually covered by a calcareous shell and an unsegmented body with a distinct head, muscular foot and visceral hump.
• Phylum Echinodermata: Animals with an endoskeleton of calcareous ossicles; adults have radial symmetry but larvae are bilaterally symmetrical. Have a unique water vascular system. Example: Starfish.
• Phylum Hemichordata: Small group of worm-like marine animals. They have a rudimentary structure in the collar region called stomochord, a structure similar to notochord.

Phylum Chordata

Animals belonging to phylum Chordata are fundamentally characterised by the presence of a notochord, a dorsal hollow nerve cord and paired pharyngeal gill slits.

Phylum Chordata is divided into three subphyla: Urochordata or Tunicata, Cephalochordata and Vertebrata.

Subphylum Vertebrata is further divided as follows:

1. Agnatha (lacks jaw):
   • Class Cyclostomata: Ectoparasites on some fishes; circular mouth without jaws.
2. Gnathostomata (bears jaw):
   • Super Class Pisces (bear fins):
     • Class Chondrichthyes: Cartilaginous fishes (e.g., Sharks).
     • Class Osteichthyes: Bony fishes (e.g., Rohu, Seahorse).
   • Super Class Tetrapoda (bear limbs):
     • Class Amphibia: Can live in aquatic as well as terrestrial habitats.
     • Class Reptilia: Creeping or crawling mode of locomotion; dry and cornified skin.
     • Class Aves: Birds; presence of feathers and most of them can fly except flightless birds. Forelimbs modified into wings.
     • Class Mammalia: Have mammary glands (milk producing glands) to nourish young ones. They have hair on the skin.

Competency Based Questions (Previous Years & Sample Papers)

Q1. An entomologist collects an unknown animal from the soil. Upon dissection, she finds that it has a bilateral symmetry, a true coelom lined by mesoderm, an open circulatory system, and its body is divided into a head, thorax, and abdomen with jointed appendages. Using the classification system, to which Phylum does this organism belong? Name the specific carbohydrate polymer that likely coats the exterior forming its exoskeleton.

Q2. The transition from an aquatic to a terrestrial lifestyle required several major adaptations in vertebrates. A key adaptation seen in Class Reptilia, Aves, and Mammalia but absent in Class Amphibia is the development of the amniotic egg. If a wildlife biologist observes an unknown vertebrate laying eggs in a dry, sandy environment, and the eggs have a leathery, calcium-based shell, list two Classes to which this animal most likely belongs. Why would an amphibian fail to reproduce in this exact spot?

Q3. Consider the allometric scaling of metabolic rate in mammals, which frequently follows Kleiber’s Law: $B \propto M^{3/4}$, where $B$ is the basal metabolic rate and $M$ is the body mass. A biologist compares two mammals: a mouse (mass $m$) and a human (mass $M = 10000m$). Calculate the ratio of the human’s metabolic rate to the mouse’s metabolic rate ($B_{human}/B_{mouse}$). Despite the human being 10,000 times heavier, explain why the ratio is not exactly 10,000.

Chapter 5: Morphology of Flowering Plants

Morphology is the study of the external structure of an organism. The wide range in the structure of higher plants will never fail to fascinate us. Even though the angiosperms show such a large diversity in external structure or morphology, they are all characterised by presence of roots, stems, leaves, flowers and fruits.

In this chapter, we will learn about the possible variations in different parts, found as adaptations of the plants to their environment, e.g., adaptations to various habitats, for protection, climbing, storage, etc.

The Root

In majority of the dicotyledonous plants, the direct elongation of the radicle leads to the formation of primary root which grows inside the soil. It bears lateral roots of several orders that are referred to as secondary, tertiary, etc., roots.

• Tap root system: The primary root and its branches constitute the tap root system, as seen in the mustard plant.
• Fibrous root system: In monocotyledonous plants, the primary root is short-lived and is replaced by a large number of roots originating from the base of the stem. Example: Wheat.
• Adventitious roots: Roots arising from parts of the plant other than the radicle are called adventitious roots (e.g., grass, Monstera and banyan tree).

Regions of the root include the root cap, region of meristematic activity, region of elongation, and region of maturation (with root hairs). Modifications of roots include storage roots (carrot, turnip, sweet potato), prop roots (banyan), stilt roots (maize, sugarcane), and pneumatophores (Rhizophora) for respiration.

The Stem

The stem is the ascending part of the axis bearing branches, leaves, flowers and fruits. It develops from the plumule of the embryo of a germinating seed. The stem bears nodes and internodes.

Stems can be modified to perform different functions:

• Storage: Underground stems of potato, ginger, turmeric.
• Tendrils: Developed from axillary buds, they are slender and spirally coiled to help plants climb (e.g., gourds, grapevines).
• Thorns: Woody, straight and pointed structures protecting plants from browsing animals (e.g., Citrus, Bougainvillea).

The Leaf

The leaf is a lateral, generally flattened structure borne on the stem. It develops at the node and bears a bud in its axil. Leaves originate from shoot apical meristems and are arranged in an acropetal order. They are the most important vegetative organs for photosynthesis.

• Venation: The arrangement of veins and the veinlets in the lamina of leaf is termed as venation (Reticulate in dicots, Parallel in monocots).
• Phyllotaxy: The pattern of arrangement of leaves on the stem or branch (Alternate, Opposite, Whorled).

The Inflorescence

A flower is a modified shoot wherein the shoot apical meristem changes to floral meristem. The arrangement of flowers on the floral axis is termed as inflorescence.

• Racemose: The main axis continues to grow, the flowers are borne laterally in an acropetal succession.
• Cymose: The main axis terminates in a flower, hence is limited in growth. The flowers are borne in a basipetal order.

The Flower

The flower is the reproductive unit in the angiosperms. It is meant for sexual reproduction. A typical flower has four different kinds of whorls arranged successively on the swollen end of the stalk or pedicel, called thalamus or receptacle. These are calyx, corolla, androecium and gynoecium.

Based on the position of calyx, corolla and androecium in respect of the ovary on thalamus, the flowers are described as:

1. Hypogynous: Ovary is superior (e.g., mustard).
2. Perigynous: Ovary is half inferior (e.g., plum, rose).
3. Epigynous: Ovary is inferior (e.g., guava, cucumber).

Figure 5.1: Position of floral parts on thalamus

Fruit and Seed

The fruit is a characteristic feature of the flowering plants. It is a mature or ripened ovary, developed after fertilisation. If a fruit is formed without fertilisation of the ovary, it is called a parthenocarpic fruit.

After fertilisation, ovules develop into seeds. A seed is made up of a seed coat and an embryo. The embryo is made up of a radicle, an embryonal axis and one (as in wheat, maize) or two cotyledons (as in gram and pea).

Competency Based Questions (Previous Years & Sample Papers)

Q1. Suppose the initial number of dividing cells in the meristematic region of a growing root is $N_0$. These cells undergo arithmetic growth, where only one daughter cell continues to divide while the other differentiates. If the rate of cell division adds $r$ new differentiating cells per day, express the total number of cells $N_t$ after $t$ days as a mathematical equation. If $N_0 = 100$ and $r = 50$ cells/day, what is the total number of cells after 10 days? Does this equation represent linear or exponential growth?

Q2. During a biology examination, a student is given a flower with a superior ovary and five petals. The petals show vexillary aestivation. Furthermore, the androecium is diadelphous (i.e., stamens are united into two bundles, usually $9+1$). Based on the syllabic structural constraints, identify the family to which this flower belongs. Is the fruit likely to be a berry or a legume?

Q3. Calculate the percentage change in the surface area of a strictly spherical grape (a type of berry) if its radius $R$ expands due to water absorption by $20%$. (Use the formula for the surface area of a sphere: $SA = 4\pi R^2$). Explain the physical significance of this relative increase for the fruit’s epidermis.

Chapter 6: Anatomy of Flowering Plants

You can very easily see the structural similarities and variations in the external morphology of the larger living organism, both plants and animals. Similarly, if we were to study the internal structure, one also finds several similarities as well as differences. This chapter introduces you to the internal structure and functional organisation of higher plants. Study of internal structure of plants is called anatomy.

The Tissues

A tissue is a group of cells having a common origin and usually performing a common function. A plant is made up of different kinds of tissues. Tissues are classified into two main groups, namely, meristematic and permanent tissues based on whether the cells being formed are capable of dividing or not.

Meristematic Tissues

Growth in plants is largely restricted to specialised regions of active cell division called meristems.

• Apical Meristems: Occur at the tips of roots and shoots and produce primary tissues.
• Intercalary Meristems: Occur between mature tissues (e.g., in grasses).
• Lateral Meristems: Cylindrical meristems that occur in the mature regions of roots and shoots. They are responsible for secondary growth (e.g., fascicular vascular cambium, cork cambium).

Permanent Tissues

The cells of the permanent tissues do not generally divide further. Permanent tissues having all cells similar in structure and function are called simple tissues. Permanent tissues having many different types of cells are called complex tissues.

• Simple Tissues: Parenchyma, Collenchyma, Sclerenchyma.
• Complex Tissues:
  • Xylem: Functions as a conducting tissue for water and minerals from roots to the stem and leaves. Composed of tracheids, vessels, xylem fibres and xylem parenchyma.
  • Phloem: Transports food materials, usually from leaves to other parts of the plant. Composed of sieve tube elements, companion cells, phloem parenchyma and phloem fibres.

The Tissue System

We can classify the tissue systems into three types on the basis of their structure and location:

1. Epidermal Tissue System: Includes the epidermis, stomata, and epidermal appendages (trichomes and hairs).
2. Ground Tissue System: All tissues except epidermis and vascular bundles constitute the ground tissue. It consists of simple tissues such as parenchyma, collenchyma and sclerenchyma.
3. Vascular Tissue System: Consists of complex tissues, the phloem and the xylem. The xylem and phloem forms together constitute vascular bundles.

Figure 6.1: Different types of vascular bundles

Anatomy of Dicotyledonous and Monocotyledonous Plants

For a better understanding of tissue organisation of roots, stems and leaves, it is convenient to study the transverse sections of the mature zones of these organs.

• Dicot Root vs Monocot Root: Dicot roots have fewer xylem bundles (usually 2-6) and a very small or inconspicuous pith. Monocot roots usually have polyarch xylem (>6 bundles) and a large, well-developed pith.
• Dicot Stem vs Monocot Stem: Dicot stems have vascular bundles arranged in a ring, which are ‘open’ (cambium present). Monocot stems have scattered vascular bundles, which are ‘closed’ (cambium absent) and surrounded by a sclerenchymatous bundle sheath.
• Dorsiventral (Dicot) Leaf vs Isobilateral (Monocot) Leaf: Dicot leaves have differentiated mesophyll (palisade and spongy) and stomata primarily on the lower epidermis. Monocot leaves have undifferentiated mesophyll and stomata on both surfaces. Monocots also have large, empty bulliform cells on the upper epidermis.

Competency Based Questions (Previous Years & Sample Papers)

Q1. The flow of water through the xylem vessels is described by the Hagen-Poiseuille equation for fluid dynamics in a pipe: $J_v = \frac{\pi r^4}{8\eta \Delta x} \Delta P$, where $J_v$ is the volumetric flow rate, $r$ is the radius of the vessel, $\eta$ is fluid viscosity, $\Delta P$ is the pressure difference, and $\Delta x$ is the distance. If a genetic mutation causes a plant’s xylem vessels to develop with a radius that is exactly half ($1/2$) of the normal radius $r$, by what factor will the volumetric flow rate $J_v$ decrease, assuming all other variables remain constant? Justify your mathematical output biologically.

Q2. During a microscopy lab, an anatomy student observes a transverse section (T.S.) of a young dicot stem. She counts 8 vascular bundles arranged in a regular ring. An hour later, she observes a T.S. of a monocot stem of similar age and notes 45 randomly scattered vascular bundles. Based on your knowledge of plant tissue systems, explain why the arrangement of vascular tissues inherently prevents secondary growth in the monocot stem, regardless of the number of bundles present.

Q3. Bulliform cells are modified epidermal cells in grasses that control leaf rolling during water stress. Suppose a grass leaf maintains a turgor pressure $P_t = 0.8 MPa$ well above its threshold $P_{thresh} = 0.3 MPa$, keeping the leaf completely unrolled. When the soil moisture drastically drops, the bulliform cells lose water and their pressure drops according to $P_t = 0.8 - 0.05h$ (where $h$ is hours without water). Calculate the threshold time in hours ($h$) before the leaf begins to roll inwards to conserve water.

Chapter 7: Structural Organisation in Animals

In the preceding chapters you came across a large variety of organisms, both unicellular and multicellular, of the animal kingdom. In unicellular organisms, all functions like digestion, respiration and reproduction are performed by a single cell. In the complex body of multicellular animals the same basic functions are carried out by different groups of cells in a well organised manner.

A group of similar cells along with intercellular substances perform a specific function. Such an organisation is called tissue. You may be surprised to know that all complex animals consist of only four basic types of tissues.

Animal Tissues

The structure of the cells vary according to their function. Therefore, the tissues are different and are broadly classified into four types:

1. Epithelial Tissue
2. Connective Tissue
3. Muscular Tissue
4. Neural Tissue

Figure 7.1: The four basic types of animal tissues

Epithelial Tissue

We commonly refer to an epithelial tissue as epithelium (pl.: epithelia). This tissue has a free surface, which faces either a body fluid or the outside environment and thus provides a covering or a lining for some part of the body.

• Simple epithelium is composed of a single layer of cells and functions as a lining for body cavities, ducts, and tubes.
• Compound epithelium consists of two or more cell layers and has protective function as it does in our skin.

Connective Tissue

Connective tissues are most abundant and widely distributed in the body of complex animals. They are named connective tissues because of their special function of linking and supporting other tissues/organs of the body. They range from soft connective tissues to specialised types, which include cartilage, bone, adipose, and blood. In all connective tissues except blood, the cells secrete fibres of structural proteins called collagen or elastin.

Muscular Tissue

Each muscle is made of many long, cylindrical fibres arranged in parallel arrays. These fibres are composed of numerous fine fibrils, called myofibrils. Muscle fibres contract (shorten) in response to stimulation, then relax (lengthen) and return to their uncontracted state in a coordinated fashion. Muscular tissue is of three types: skeletal, smooth, and cardiac.

Neural Tissue

Neural tissue exerts the greatest control over the body’s responsiveness to changing conditions. Neurons, the unit of neural system are excitable cells. The neuroglial cell which constitute the rest of the neural system protect and support neurons.

Morphology and Anatomy of Frog

Frogs are amphibians; they can live both on land and in freshwater. The most common species of frog found in India is Rana tigrina. They do not have constant body temperature; their body temperature varies with the temperature of the environment (poikilotherms or cold-blooded).

• Morphology: The frog body is divisible into head and trunk. A neck and tail are absent. The skin is smooth and slippery due to the presence of mucus.
• Digestive System: Consists of alimentary canal and digestive glands. The alimentary canal is short because frogs are carnivores and hence the length of intestine is reduced.
• Respiratory System: Frogs respire on land and in the water by two different methods. In water, skin acts as aquatic respiratory organ (cutaneous respiration). On land, the buccal cavity, skin and lungs act as the respiratory organs.
• Circulatory System: Frogs have a closed type circulatory system. They have a lymphatic system also. The heart is a muscular structure situated in the upper part of the body cavity. It has three chambers, two atria and one ventricle.

Competency Based Questions (Previous Years & Sample Papers)

Q1. An athlete sprains their ankle running on uneven terrain. The doctor diagnoses a tear in a specific dense regular connective tissue that connects muscle to bone. What is the name of this specific tissue? If the tensile strength $T$ of this tissue scales with its cross-sectional area $A$ such that $T = kA$, and the healing process initially deposits unorganized scar tissue with half the strength constant ($k_{scar} = k/2$), what must the relative area of the scar tissue ($A_{scar}/A$) be to temporarily restore the original tensile strength?

Q2. During a dissection of a frog (Rana tigrina), a biology student notices that the ventricle of the heart does not have a complete physical septum dividing the left and right sides. Consequently, oxygenated blood from the left atrium and deoxygenated blood from the right atrium mix before being pumped to the body. Given a scenario where the oxygen saturation of blood entering the left atrium is $96%$ and the entering the right atrium is $40%$, calculate the theoretical average oxygen saturation of the mixed blood entering the systemic circulation if the stroke volume contributions from both atria are mathematically equal ($1:1$).

Q3. Epithelial tissues are classified based on the number of cell layers and the shape of the cells. Compare simple squamous epithelium with stratified squamous epithelium. Why would the inner lining of the human cheek be composed of stratified squamous epithelium instead of simple squamous epithelium?

Chapter 8: Cell: The Unit of Life

When you look around, you see both living and non-living things. You must have wondered and asked yourself – ‘what is it that makes an organism living, or what is it that an inanimate thing does not have which a living thing has’ ? The answer to this is the presence of the basic unit of life – the cell in all living organisms.

All organisms are composed of cells. Some are composed of a single cell and are called unicellular organisms while others, like us, composed of many cells, are called multicellular organisms.

Cell Theory

In 1838, Matthias Schleiden, a German botanist, examined a large number of plants and observed that all plants are composed of different kinds of cells which form the tissues of the plant. At about the same time, Theodore Schwann (1839), a British Zoologist, studied different types of animal cells and reported that cells had a thin outer layer which is today known as the ‘plasma membrane’.

Schleiden and Schwann together formulated the cell theory. This theory however, did not explain as to how new cells were formed. Rudolf Virchow (1855) first explained that cells divided and new cells are formed from pre-existing cells (Omnis cellula-e cellula).

The cell theory as understood today is:

1. All living organisms are composed of cells and products of cells.
2. All cells arise from pre-existing cells.

Figure 8.1: Structural comparison of Plant and Animal Cells

Prokaryotic Cells

The prokaryotic cells are represented by bacteria, blue-green algae, mycoplasma and PPLO. They are generally smaller and multiply more rapidly than the eukaryotic cells. They may vary greatly in shape and size. The four basic shapes of bacteria are bacillus (rod like), coccus (spherical), vibrio (comma shaped) and spirillum (spiral).

The organisation of the prokaryotic cell is fundamentally similar even though prokaryotes exhibit a wide variety of shapes and functions. All prokaryotes have a cell wall surrounding the cell membrane except in mycoplasma. The fluid matrix filling the cell is the cytoplasm. There is no well-defined nucleus. The genetic material is basically naked.

Eukaryotic Cells

The eukaryotes include all the protists, plants, fungi and animals. In eukaryotic cells there is an extensive compartmentalisation of cytoplasm through the presence of membrane-bound organelles. Eukaryotic cells possess an organised nucleus with a nuclear envelope.

Cell Organelles

• Cell Membrane: The detailed structure of the membrane was studied only after the advent of the electron microscope. The currently accepted model is the Fluid Mosaic Model proposed by Singer and Nicolson (1972). The quasifluid nature of lipid enables lateral movement of proteins within the overall bilayer.
• Cell Wall: A non-living rigid structure which forms an outer covering for the plasma membrane of fungi and plants. Gives shape to the cell and protects the cell from mechanical damage and infection.
• Endomembrane System: Included are endoplasmic reticulum (ER), golgi complex, lysosomes and vacuoles, because their functions are coordinated.
  • ER: Rough ER has ribosomes on its surface (protein synthesis). Smooth ER lacks ribosomes (lipid synthesis).
  • Golgi apparatus: Discovered by Camillo Golgi. Functions primarily in packaging materials.
  • Lysosomes: Membrane bound vesicular structures rich in hydrolytic enzymes.
• Mitochondria: the ‘power houses’ of the cell, produce cellular energy in the form of ATP.
• Plastids: Found in all plant cells and in euglenoides. Chloroplasts contain chlorophyll.
• Ribosomes: Granular structures composed of RNA and proteins; they are the protein factories. Eukaryotes have 80S ribosomes, while prokaryotes have 70S.
• Nucleus: Contains the genetic material (DNA).

Competency Based Questions (Previous Years & Sample Papers)

Q1. The resolving power of an optical microscope is theoretically limited by the diffraction of light, given by Abbe’s limit equation: $d = \frac{\lambda}{2 \cdot NA}$, where $d$ is the minimum resolvable distance, $\lambda$ is the wavelength of light, and $NA$ is the numerical aperture of the objective lens. If an electron microscope uses an electron beam with a wavelength ($\lambda$) that is exactly $100,000$ times shorter than visible green light ($\lambda \approx 500 nm$), calculate the theoretical minimum resolvable distance $d_{electron}$ (in picometers) for the electron microscope, assuming the $NA$ is effectively $0.05$ (note: electron lenses have inherently small NAs). Explain why this difference was historically required to discover the Endoplasmic Reticulum.

Q2. During facilitated diffusion via biological membranes, the rate of transport ($V$) exhibits saturation kinetics as the concentration of the solute $[S]$ increases, modeled by the Michaelis-Menten-like equation: $V = \frac{V_{max} \cdot [S]}{K_m + [S]}$, where $V_{max}$ is the maximum transport rate and $K_m$ is the solute concentration at which the transport rate is exactly half of $V_{max}$. If a specific carrier protein in the cell membrane has a $V_{max} = 200 \text{ molecules/s}$ and $K_m = 5 mM$, what will be the transport rate when the external solute concentration $[S]$ is $5 mM$? Why does simple diffusion not exhibit an asymptote ($V_{max}$) in this manner?

Q3. Plant cells differ from animal cells in possessing a large central vacuole, a rigid cell wall, and plastids. A student observes an unknown eukaryotic cell under a microscope. The cell is placed in a hypertonic solution. After 10 minutes, the plasma membrane has shrunk away from a rigid outer boundary, collapsing inward, but the overall shape of the outer boundary has barely changed. What is this phenomenon called? Based on this observation, is the cell likely a plant cell or an animal cell?

Chapter 9: Biomolecules

There is a wide diversity in living organisms in our biosphere. Now a question that arises in our minds is: Are all living organisms made of the same chemicals, i.e., elements and compounds? You have learnt in chemistry how elemental analysis is performed. If we perform such an analysis on a plant tissue, animal tissue or a microbial paste, we obtain a list of elements like carbon, hydrogen, oxygen and several others and their respective content per unit mass of a living tissue.

If the same analysis is performed on a piece of earth’s crust as an example of non-living matter, we obtain a similar list. What are the differences between the two lists? In absolute terms, no such differences could be made out. However, a closer examination reveals that the relative abundance of carbon and hydrogen with respect to other elements is higher in any living organism than in earth’s crust.

Primary and Secondary Metabolites

• Primary Metabolites: Biomolecules like amino acids, sugars, etc., which have identifiable functions and play known roles in normal physiologial processes.
• Secondary Metabolites: Compounds like rubber, drugs, spices, scents and pigments whose exact physiological role in the host organism might not be completely understood but many of them are useful to human welfare (e.g., alkaloids, flavonoids).

Biomacromolecules

There is one feature common to all those compounds found in the acid insoluble pool. They have molecular weights ranging from ten thousand daltons and above. For this reason, biomolecules are broadly of two types: micromolecules (molecular weight < 1000 Da) and macromolecules.

1. Proteins: Polypeptides. They are linear chains of amino acids linked by peptide bonds. They function as enzymes, structural framework, antibodies, receptors, etc. Proteins have four levels of structure: primary, secondary, tertiary, and quaternary.
2. Polysaccharides: Long chains of sugars (e.g., cellulose, starch, glycogen). They are linked by glycosidic bonds. They act as structural components or energy stores.
3. Nucleic Acids: Polynucleotides (DNA and RNA). They consist of nucleotides linked by phosphodiester bonds. They store and transmit genetic information.
4. Lipids: Technically not strictly macromolecules as their molecular weight does not exceed 800 Da, but they form the insoluble cellular membranes. Unlike the polymeric macromolecules, lipids are not polymers.

Enzymes

Almost all enzymes are proteins. There are some nucleic acids that behave like enzymes (ribozymes). An enzyme like any protein has a primary structure, and a tertiary structure where the backbone folds upon itself to form ‘crevices’ or ‘pockets’. One such pocket is the ‘active site’. An active site of an enzyme is a crevice or pocket into which the substrate fits. Thus enzymes, through their active site, catalyse reactions at a high rate.

Figure 9.1: Concept of activation energy with and without enzyme

• Nature of Enzyme Action: The catalytic cycle involves the substrate binding to the active site, inducing a conformational change (induced fit model), formation of the Enzyme-Substrate (ES) complex, breaking/making of bonds to form the Enzyme-Product (EP) complex, and the release of the products.
• Factors Affecting Enzyme Activity: Temperature, pH, change in substrate concentration, and presence of specific chemicals that regulate its activity (Inhibition).

Competency Based Questions (Previous Years & Sample Papers)

Q1. The Michaelis-Menten kinetics of an enzyme-catalyzed reaction can be linearized using the Lineweaver-Burk plot equation: $\frac{1}{V} = \frac{K_m}{V_{max}} \frac{1}{[S]} + \frac{1}{V_{max}}$. A researcher plots $\frac{1}{V}$ on the y-axis against $\frac{1}{[S]}$ on the x-axis for an enzyme. She finds that the y-intercept is $0.02$ sec/$\mu$mol and the x-intercept is $-0.1$ mM$^{-1}$. Calculate the maximum velocity ($V_{max}$) and the Michaelis constant ($K_m$) for this enzyme. What does the value of $K_m$ biologically indicate about the enzyme’s affinity for its substrate?

Q2. DNA is a long polymer of deoxyribonucleotides. According to Chargaff’s rule for double-stranded DNA, the ratios between Adenine (A) and Thymine (T), and Guanine (G) and Cytosine (C) are constant and equals one. If a segment of double-stranded DNA from a newly discovered extremophile bacterium contains 1000 base pairs, and biochemical analysis reveals that there are 350 Adenine bases in this segment, calculate the total number of Cytosine bases and the total number of hydrogen bonds in this DNA segment.

Q3. Proteins exhibit structural hierarchy. A mutation causes a single amino acid substitution (e.g., glutamic acid to valine in sickle cell anemia) in a polypeptide chain. Identify the level of protein structure (primary, secondary, tertiary, or quaternary) that is directly and immediately changed by this substitution. Does this single change guarantee a change in the tertiary structure? Explain based on the properties of amino acid R-groups.

Chapter 10: Cell Cycle and Cell Division

Are you aware that all organisms, even the largest, start their life from a single cell? You may wonder how a single cell then goes on to form such large organisms. Growth and reproduction are characteristics of cells, indeed of all living organisms. All cells reproduce by dividing into two, with each parental cell giving rise to two daughter cells each time they divide. These newly formed daughter cells can themselves grow and divide, giving rise to a new cell population that is formed by the growth and division of a single parental cell and its progeny.

Cell Cycle

Cell division is a very important process in all living organisms. During the division of a cell, DNA replication and cell growth also take place. The sequence of events by which a cell duplicates its genome, synthesises the other constituents of the cell and eventually divides into two daughter cells is termed cell cycle.

Although cell growth (in terms of cytoplasmic increase) is a continuous process, DNA synthesis occurs only during one specific stage in the cell cycle.

Phases of Cell Cycle

The cell cycle is divided into two basic phases:

• Interphase: The phase between two successive M phases. It lasts for more than 95% of the duration of cell cycle. It is subdivided into:
  • $G_1$ phase (Gap 1): Cell is metabolically active and continuously grows but does not replicate its DNA.
  • $S$ phase (Synthesis): DNA replication takes place. The amount of DNA per cell doubles. If the initial amount of DNA is denoted as $2C$ then it increases to $4C$. However, there is no increase in the chromosome number.
  • $G_2$ phase (Gap 2): Proteins are synthesised in preparation for mitosis while cell growth continues.
• M Phase (Mitosis phase): Represents the phase when the actual cell division or mitosis occurs. It starts with nuclear division (karyokinesis) and usually ends with division of cytoplasm (cytokinesis).

Figure 10.1: A diagrammatic view of the cell cycle

M Phase (Mitosis)

Mitosis, or equational division, is divided into four stages of nuclear division (karyokinesis):

1. Prophase: Chromosomal material condenses to form compact mitotic chromosomes. Centrosomes move to opposite poles of the cell. Nuclear envelope breaks down.
2. Metaphase: Chromosomes align at the equator of the cell to form the metaphase plate. Spindle fibres attach to kinetochores of chromosomes.
3. Anaphase: Centromeres split and chromatids separate. Chromatids move to opposite poles.
4. Telophase: Chromosomes cluster at opposite spindle poles and their identity is lost as discrete elements. Nuclear envelope assembles around the chromosome clusters.

Meiosis

The production of offspring by sexual reproduction includes the fusion of two gametes, each with a complete haploid set of chromosomes. Gametes are formed from specialised diploid cells. This specialised kind of cell division that reduces the chromosome number by half results in the production of haploid daughter cells. This kind of division is called meiosis.

Key features of meiosis:

• Involves two sequential cycles of nuclear and cell division called Meiosis I and Meiosis II but only a single cycle of DNA replication.
• It involves pairing of homologous chromosomes and recombination (crossing over) between non-sister chromatids of homologous chromosomes during Prophase I (specifically Pachytene stage).
• Four haploid cells are formed at the end of Meiosis II.

Competency Based Questions (Previous Years & Sample Papers)

Q1. A eukaryotic cell with a diploid chromosome number of $2n = 16$ undergoes the cell cycle. Let the DNA content of a single haploid genome be representing as $C$. Trace the theoretical mathematical number of chromosomes and the DNA content of the cell at the following specific stages: a) End of $G_1$ phase, b) End of $S$ phase, c) Metaphase of Mitosis, d) Anaphase of Mitosis (per entirely dividing cell), and e) Each daughter cell after Cytokinesis is complete.

Q2. During Prophase I of meiosis, the phenomenon of crossing over occurs between non-sister chromatids of homologous chromosomes. Biologically, what is the primary evolutionary advantage of this process? Mathematically, if a cell possesses $n$ pairs of homologous chromosomes, how does the combination of random assortment at metaphase I and crossing over impact the geometric number of possible unique gametes from a single individual, compared to the baseline $2^n$ combinations without crossing over?

Q3. Anticancer drugs often work by disrupting specific phases of the cell cycle in rapidly dividing cancer cells. Drug A is a structural analog of thymidine. Drug B binds tightly to tubulin dimers, preventing microtubule assembly. Identify the exact phase of the cell cycle that each drug will specifically arrest, and explain the mechanistic reason why.

Chapter 11: Photosynthesis in Higher Plants

All animals including human beings depend on plants for their food. Have you ever wondered from where plants get their food? Green plants, in fact, have to make or rather synthesise the food they need and all other organisms depend on them for their needs. The green plants make or rather synthesise the food they need through photosynthesis and are therefore called autotrophs.

Photosynthesis is a physico-chemical process by which they use light energy to drive the synthesis of organic compounds. Ultimately, all living forms on earth depend on sunlight for energy.

Where does Photosynthesis take place?

You would of course answer: in ‘the green leaf’ or ‘in the chloroplasts’. Photosynthesis does take place in the green leaves of plants but it does so also in other green parts of the plants. The mesophyll cells in the leaves, have a large number of chloroplasts. Usually the chloroplasts align themselves along the walls of the mesophyll cells, such that they get the optimum quantity of the incident light.

Within the chloroplast there is a membranous system consisting of grana, the stroma lamellae, and the matrix stroma.

• Membrane system: Responsible for trapping the light energy and also for the synthesis of ATP and NADPH (Light Reactions).
• Stroma: Enzymatic reactions synthesise sugar, which in turn forms starch (Dark Reactions).

Figure 11.1: Z scheme of light reaction showing Electron Transport

Light Reaction

Light reactions or the ‘Photochemical’ phase include light absorption, water splitting, oxygen release, and the formation of high-energy chemical intermediates, ATP and NADPH.

• Electron Transport (Z-Scheme): In Photosystem II (PS II) the reaction centre chlorophyll a absorbs 680 nm wavelength of red light causing electrons to become excited and jump into an orbit farther from the atomic nucleus. These are picked up by an electron acceptor which passes them to an electrons transport system consisting of cytochromes. The electrons are passed onto PS I. Simultaneously, electrons in the reaction centre of PS I are also excited when they receive red light of wavelength 700 nm.
• Splitting of Water: The electrons that were moved from PS II must be replaced. This is achieved by electrons available due to splitting of water: $2H\sb{2}O \rightarrow 4H^+ + O\sb{2} + 4e^-$.

Dark Reaction (Biosynthetic Phase)

This process does not directly depend on the presence of light but is dependent on the products of the light reaction, i.e., ATP and NADPH.

• $C\sb{3}$ Pathway (Calvin Cycle): Occurs in three stages: Carboxylation of RuBP by RuBisCO, Reduction of 3-PGA to triose phosphate, and Regeneration of RuBP.
• $C\sb{4}$ Pathway: Plants growing in dry tropical regions use this pathway. It involves two cell types: Mesophyll and Bundle Sheath cells. Primary $CO\sb{2}$ acceptor is PEP (Phosphoenolpyruvate) catalyzed by PEPcase, forming a 4-carbon compound (OAA). It avoids photorespiration.

Competency Based Questions (Previous Years & Sample Papers)

Q1. The energy required to excite an electron in a chlorophyll molecule is given by the Planck-Einstein relation: $E = \frac{hc}{\lambda}$, where $h$ is Planck’s constant, $c$ is the speed of light, and $\lambda$ is the wavelength of the photon. Photosystem I (PS I) has a distinct absorption peak at $700 \text{ nm}$, while Photosystem II (PS II) peaks at $680 \text{ nm}$. Compare equations for $E\sb{PSI}$ and $E\sb{PSII}$. Which photosystem requires higher energy photons to excite its reaction center? Explain structurally why this slight energy difference is crucial for the unidirectional Z-scheme of non-cyclic photophosphorylation.

Q2. During the Calvin cycle ($C\sb{3}$ pathway), the fixation of $6$ molecules of $CO\sb{2}$ to generate one molecule of glucose requires an input of both ATP and NADPH. Let the stoichiometric ratio of $ATP:NADPH$ required per $CO\sb{2}$ fixed be denoted as $R\sb{C3}$. For a $C\sb{4}$ plant (like Sugarcane), the spatial separation of initial fixation and the Calvin cycle imposes an additional energetic cost of 2 ATP per $CO\sb{2}$ to regenerate PEP in the mesophyll cells. Calculate the ratio $R\sb{C3}$ for the $C\sb{3}$ pathway, and then calculate the total ATP required to synthesize one molecule of glucose in a $C\sb{3}$ plant versus a $C\sb{4}$ plant.

Q3. According to the Chemiosmotic Hypothesis, ATP synthesis in chloroplasts is driven by a proton ($H^+$) gradient established across the thylakoid membrane. If the internal thylakoid lumen has a pH of $4.0$ under active illumination, and the surrounding stroma has a pH of $8.0$, calculate the concentration gradient of protons $[H^+]\sb{lumen} / [H^+]\sb{stroma}$. Based on the $\Delta pH$, explain how the ATP synthase enzyme utilizes this specific gradient.

Chapter 12: Respiration in Plants

All of us breathe to live, but why is breathing so essential to life? What happens when we breathe? Also, do all living organisms, including plants and microbes, breathe? If so, how? All living organisms need energy for carrying out daily life activities, be it absorption, transport, movement, reproduction or even breathing. Where does all this energy come from? We know we eat food for energy – but how is this energy taken from food?

This chapter deals with cellular respiration or the mechanism of breakdown of food materials within the cell to release energy, and the trapping of this energy for synthesis of ATP.

Do Plants Breathe?

Well, the answer to this question is not quite so direct. Yes, plants require $O_2$ for respiration to occur and they also give out $CO_2$. Hence, plants have systems in place that ensure the availability of $O_2$. Plants, unlike animals, have no specialised organs for gaseous exchange but they have stomata and lenticels for this purpose.

Glycolysis

The term glycolysis has originated from the Greek words, glycos for sugar, and lysis for splitting. The scheme of glycolysis was given by Gustav Embden, Otto Meyerhof, and J. Parnas, and is often referred to as the EMP pathway. In anaerobic organisms, it is the only process in respiration.

Glycolysis occurs in the cytoplasm of the cell and is present in all living organisms. In this process, glucose undergoes partial oxidation to form two molecules of pyruvic acid. Substrate level phosphorylation occurs, yielding a net of 2 ATP per glucose molecule.

Fermentation

In fermentation, say by yeast, the incomplete oxidation of glucose is achieved under anaerobic conditions by sets of reactions where pyruvic acid is converted to $CO_2$ and ethanol. The enzymes, pyruvic acid decarboxylase and alcohol dehydrogenase catalyse these reactions. Other organisms like some bacteria produce lactic acid from pyruvic acid. In both types, not much energy is released; less than seven per cent of the energy in glucose is released and not all of it is trapped as high energy bonds of ATP.

Aerobic Respiration

For aerobic respiration to take place within the mitochondria, the final product of glycolysis, pyruvate is transported from the cytoplasm into the mitochondria. The crucial events in aerobic respiration are:

1. The complete oxidation of pyruvate by the stepwise removal of all the hydrogen atoms, leaving three molecules of $CO_2$.
2. The passing on of the electrons removed as part of the hydrogen atoms to molecular $O_2$ with simultaneous synthesis of ATP.

Tricarboxylic Acid Cycle (TCA Cycle / Krebs Cycle)

The TCA cycle starts with the condensation of acetyl group with oxaloacetic acid (OAA) and water to yield citric acid. The reaction is catalysed by the enzyme citrate synthase and a molecule of CoA is released. Citrate is then isomerised to isocitrate. It is followed by two successive steps of decarboxylation.

Figure 12.1: Outline of Aerobic Respiration

Electron Transport System (ETS) and Oxidative Phosphorylation

The metabolic pathway through which the electron passes from one carrier to another, is called the electron transport system (ETS) and it is present in the inner mitochondrial membrane. When electrons pass from one carrier to another via complex I to IV in the electron transport chain, they are coupled to ATP synthase (complex V) for the production of ATP from ADP and inorganic phosphate. The number of ATP molecules synthesised depends on the nature of the electron donor. Oxidation of one molecule of NADH gives rise to 3 molecules of ATP, while that of one molecule of $FADH_2$ produces 2 molecules of ATP. Oxygen acts as the final hydrogen acceptor.

Amphibolic Pathway

Glucose is the favoured substrate for respiration. All carbohydrates are usually first converted into glucose before they are used for respiration. Other substrates can also be respired, but they do not enter the respiratory pathway at the very first step. Because the respiratory pathway is involved in both breakdown (catabolism) and synthesis (anabolism) of molecules, it is better considered an amphibolic pathway.

Respiratory Quotient

The ratio of the volume of $CO_2$ evolved to the volume of $O_2$ consumed in respiration is called the respiratory quotient (RQ) or respiratory ratio. $$ RQ = \frac{\text{volume of } CO_2 \text{ evolved}}{\text{volume of } O_2 \text{ consumed}} $$ The respiratory quotient depends upon the type of respiratory substrate used during respiration. For carbohydrates, RQ is 1. For fats, it is less than 1.

Competency Based Questions (Previous Years & Sample Papers)

Q1. The complete combustion of Tripalmitin, a common triglyceride fat, is represented by the following chemical equation: $2(C_{51}H_{98}O_6) + 145O_2 \rightarrow 102CO_2 + 98H_2O + \text{Energy}$ Calculate the Respiratory Quotient (RQ) for the aerobic respiration of tripalmitin. If a plant’s measured RQ over a 24-hour period shifts from $1.0$ to $0.7$, what fundamental metabolic shift has likely occurred regarding its primary respiratory substrate?

Q2. During glycolysis, a 6-carbon glucose molecule is broken down into two 3-carbon pyruvate molecules. This sequence involves an initial “investment” phase and a “payoff” phase. Let $-I$ be the number of ATP molecules consumed per glucose, and $+P$ be the number of ATP molecules directly generated via substrate-level phosphorylation per glucose. Write the balanced equation for the net ATP yield ($Net_{ATP} = P - I$). If a metabolic toxin completely inhibits the enzyme Phosphofructokinase (an enzyme in the investment phase), mathematically what is the functional ATP yield of glycolysis?

Q3. Consider the theoretical ATP yield of aerobic respiration in classical eukaryotic models, where 1 NADH generates approximately 3 ATP, and 1 $FADH_2$ generates approximately 2 ATP. For a single glucose molecule undergoing complete oxidation, the net tallies are: - Glycolysis: 2 net ATP + 2 cytosolic NADH - Link Reaction: 2 NADH - Krebs Cycle: 2 ATP + 6 NADH + 2 $FADH_2$ If the cell uses the glycerol-3-phosphate shuttle (which transfers electrons from cytosolic NADH to mitochondrial FAD, dropping their energetic value to that of $FADH_2$), formulate an equation summing the total theoretical ATP. Conversely, what is the total if it uses the malate-aspartate shuttle (which retains the NADH value)?

Chapter 13: Plant - Growth and Development

You have already studied the organisation of a flowering plant in Chapter 5. Have you ever thought about where and how the structures like roots, stems, leaves, flowers, fruits and seeds arise and that too in an orderly sequence? Plant growth is virtually unlimited because they retain the capacity for unlimited growth throughout their life. This ability of the plants is due to the presence of meristems at certain locations in their body.

Growth and Development

Growth can be defined as an irreversible permanent increase in size of an organ or its parts or even of an individual cell. Generally, growth is accompanied by metabolic processes (both anabolic and catabolic), that occur at the expense of energy.

• Phases of Growth: The period of growth is generally divided into three phases, namely, meristematic, elongation and maturation.
• Arithmetic Growth: Following mitotic cell division, only one daughter cell continues to divide while the other differentiates and matures. (Mathematical expression: $L_t = L_0 + rt$).
• Geometric Growth: In most systems, the initial growth is slow (lag phase), and it increases rapidly thereafter – at an exponential rate (log or exponential phase). Both progeny cells following mitotic cell division retain the ability to divide. (Mathematical expression: $W_1 = W_0 e^{rt}$).

Figure 13.1: Graphical representation of Arithmetic vs Geometric Growth

Differentiation, Dedifferentiation and Redifferentiation

• Differentiation: The cells derived from root apical and shoot-apical meristems differentiate and mature to perform specific functions. During differentiation, cells undergo few to major structural changes both in their cell walls and protoplasm.
• Dedifferentiation: The living differentiated cells, that by now have lost the capacity to divide can regain the capacity of division under certain conditions. This phenomenon is termed as dedifferentiation.
• Redifferentiation: Plant products of dedifferentiation once again lose the capacity to divide and mature to perform specific functions.

Plant Growth Regulators (PGRs)

The plant growth regulators (PGRs) are small, simple molecules of diverse chemical composition.

1. Auxins: (e.g., IAA) Induce rooting, apical dominance, and prevent premature fruit drop.
2. Gibberellins: (e.g., $GA_3$) Cause elongation of intact stems, bolting in rosette plants, and delay senescence.
3. Cytokinins: (e.g., Zeatin) Induce cell division, overcome apical dominance, and promote lateral shoot growth.
4. Ethylene: A gaseous PGR. Highly effective in fruit ripening and inducing senescence and abscission of plant organs.
5. Abscisic acid (ABA): Acts as a general plant growth inhibitor and an inhibitor of plant metabolism. It stimulates the closure of stomata (stress hormone).

Competency Based Questions (Previous Years & Sample Papers)

Q1. Consider the geometric (exponential) growth of a bacterial colony, modeled by the equation $W_t = W_0 e^{rt}$, where $W_t$ is the final population size, $W_0$ is the initial population size, $e$ is the base of natural logarithms ($\approx 2.718$), $r$ is the relative growth rate, and $t$ is time. A culture starts with exactly $1,000$ cells ($W_0=1000$). After $10$ hours ($t=10$), the population has grown to exactly $1,000,000$ cells. Calculate the specific relative growth rate $r$ per hour for this colony. Provide the answer in terms of natural logarithm ($\ln$). Why does a plant’s overall growth eventually deviate from this exponential model?

Q2. During tissue culture experiments, a piece of mature, differentiated potato parenchyma (the explant) is placed on a sterile nutrient medium containing specific Plant Growth Regulators (PGRs). The cells lose their specific differentiation and begin to divide to form an unorganized mass of cells called a callus. A few weeks later, adjusting the ratio of Auxins to Cytokinins causes the callus cells to stop dividing and mature into functional vascular tissue and roots. Identify and sequentially name the three biological cellular processes taking place in this entire sequence.

Q3. Fruit growers often face the problem of synchronous fruit ripening. To quickly ripen an entire warehouse of green tomatoes uniformly, a specific volatile plant growth regulator is commonly pumped into the storage rooms. Name this specific PGR. Explain the biochemical mechanism by which this PGR accelerates ripening, and state one other commercially desirable physiological effect it has on crop plants when applied via aqueous solutions like ethephon.

Chapter 14: Breathing and Exchange of Gases

As you have read earlier, oxygen ($O_2$) is utilised by the organisms to indirectly break down simple molecules like glucose, amino acids, fatty acids, etc., to derive energy to perform various activities. Carbon dioxide ($CO_2$) which is harmful is also released during the above catabolic reactions. It is, therefore, evident that $O_2$ has to be continuously provided to the cells and $CO_2$ produced by the cells has to be released out. This process of exchange of $O_2$ from the atmosphere with $CO_2$ produced by the cells is called breathing, commonly known as respiration.

Respiratory Organs

Mechanisms of breathing vary among different groups of animals depending mainly on their habitats and levels of organisation.

• Lower invertebrates: Sponges, coelenterates, flatworms exchange $O_2$ with $CO_2$ by simple diffusion over their entire body surface.
• Insects: Have a network of tubes (tracheal tubes) to transport atmospheric air within the body.
• Aquatic animals: Special vascularised structures called gills (branchial respiration) are used by most fishes and aquatic arthropods/molluscs.
• Terrestrial animals: Vascularised bags called lungs (pulmonary respiration) are used by terrestrial forms for the exchange of gases.

Human Respiratory System

We have a pair of external nostrils opening out above the upper lips. It leads to a nasal chamber through the nasal passage. The nasal chamber opens into the pharynx, a portion of which is the common passage for food and air. The pharynx opens through the larynx region into the trachea. The larynx is a cartilaginous box which helps in sound production and hence called the sound box.

Trachea is a straight tube extending up to the mid-thoracic cavity, which divides at the level of 5th thoracic vertebra into a right and left primary bronchi. Each bronchus undergoes repeated divisions to form the secondary and tertiary bronchi and bronchioles ending up in very thin terminal bronchioles. The terminal bronchioles give rise to a number of very thin, irregular-walled and vascularised bag-like structures called alveoli.

Figure 14.1: Schematic of the Human Respiratory System

Mechanism of Breathing

Breathing involves two stages: inspiration during which atmospheric air is drawn in and expiration by which the alveolar air is released out. The movement of air into and out of the lungs is carried out by creating a pressure gradient between the lungs and the atmosphere.

• Inspiration occurs if the pressure within the lungs (intra-pulmonary pressure) is less than the atmospheric pressure, i.e., there is a negative pressure in the lungs with respect to atmospheric pressure.
• Expiration takes place when the intra-pulmonary pressure is higher than the atmospheric pressure. The diaphragm and a specialised set of muscles – external and internal intercostals between the ribs, help in generation of such gradients.

Respiratory Volumes and Capacities

• Tidal Volume (TV): Volume of air inspired or expired during a normal respiration (approx. 500 mL).
• Inspiratory Reserve Volume (IRV): Additional volume of air, a person can inspire by a forcible inspiration (2500 - 3000 mL).
• Expiratory Reserve Volume (ERV): Additional volume of air, a person can expire by a forcible expiration (1000 - 1100 mL).
• Residual Volume (RV): Volume of air remaining in the lungs even after a forcible expiration (1100 - 1200 mL). This prevents the alveoli from collapsing.

Competency Based Questions (Previous Years & Sample Papers)

Q1. According to Boyle’s Law, the absolute pressure $P$ and volume $V$ of a given mass of confined gas are inversely proportional at a constant temperature ($P_1V_1 = P_2V_2$). During human inspiration, the contraction of the diaphragm and the external intercostal muscles increases the overall volume of the thoracic cavity by approximately $2%$ over its resting Functional Residual Capacity ($FRC$ of $\sim 2500$ mL). If atmospheric pressure is $760$ mmHg, what is the theoretical new intra-pulmonary pressure immediately after this $2%$ volume expansion (before any air flows in)? Explain why air subsequently rushes into the lungs.

Q2. The specific rate of diffusion of gases across the alveolar-capillary membrane is mathematically governed by Fick’s Law of Diffusion: $V_{gas} \propto \frac{A}{T} \cdot D \cdot (P_1 - P_2)$, where $A$ is the surface area, $T$ is the membrane thickness, $D$ is the diffusion constant for the gas, and $(P_1 - P_2)$ is the partial pressure gradient. Emphysema is a chronic respiratory disorder associated with severe cigarette smoking. Structurally, emphysema results in the destruction of the alveolar walls, merging many tiny alveoli into fewer, vastly larger irregular air spaces. Based strictly on Fick’s Law, which specific variable is pathologically altered in emphysema, and mathematically how does this affect the net diffusion rate of oxygen?

Q3. Human Vital Capacity (VC) represents the maximum volume of air a person can breathe in after a forced expiration. Write the mathematical equation that defines Vital Capacity (VC) strictly in terms of the standard lung capacities (Tidal Volume (TV), Inspiratory Reserve Volume (IRV), and Expiratory Reserve Volume (ERV)). If a healthy athlete has a $TV = 500$ mL, $IRV = 3000$ mL, $ERV = 1200$ mL, and Residual Volume (RV) = $1200$ mL, calculate their Total Lung Capacity (TLC). Why can TLC never be explicitly measured using simply a spirometer?

Chapter 15: Body Fluids and Circulation

You have learnt that all living cells have to be provided with nutrients, $O_2$ and other essential substances. Also, the waste or harmful substances produced, have to be removed continuously for healthy functioning of tissues. It is therefore, essential to have efficient mechanisms for the movement of these substances to the cells and from the cells.

Blood is the most commonly used body fluid by most of the higher organisms including humans for this purpose. Another body fluid, lymph, also helps in the transport of certain substances.

Blood

Blood is a special connective tissue consisting of a fluid matrix, plasma, and formed elements.

• Plasma: A straw coloured, viscous fluid constituting nearly $55%$ of the blood. $90-92%$ of plasma is water and proteins contribute $6-8%$ of it. Fibrinogen, globulins and albumins are the major proteins.
• Formed Elements: Erythrocytes, leucocytes and platelets collectively are called formed elements and they constitute nearly $45%$ of the blood.
  • Erythrocytes (RBCs): The most abundant of all the cells in blood. A healthy adult man has, on an average, 5 million to 5.5 million of RBCs $mm^{-3}$ of blood.
  • Leucocytes (WBCs): Colourless due to the lack of haemoglobin. They are nucleated and are relatively lesser in number which averages $6000-8000$ $mm^{-3}$ of blood.
  • Platelets: Also called thrombocytes, are cell fragments produced from megakaryocytes (special cells in the bone marrow).

Human Circulatory System

Human circulatory system, also called the blood vascular system consists of a muscular chambered heart, a network of closed branching blood vessels and blood, the fluid which is circulated.

Heart, the mesodermally derived organ, is situated in the thoracic cavity, in between the two lungs, slightly tilted to the left. It has the size of a clenched fist. It is protected by a double walled membranous bag, pericardium, enclosing the pericardial fluid. Our heart has four chambers, two relatively small upper chambers called atria and two larger lower chambers called ventricles.

Figure 15.1: Sectional view of the human heart

Cardiac Cycle and Output

To begin with, all the four chambers of heart are in a relaxed state, i.e., they are in joint diastole. Blood flows into atria, leading to atrial systole, which pumps blood into ventricles. The ventricular systole follows, heavily pumping blood out into the pulmonary artery and the aorta.

The volume of blood pumped out by each ventricle per minute is called the cardiac output and it is equal to the product of stroke volume (approx. $70$ mL) and heart rate (approx. $72$ beats/min), which averages out to $5000$ mL or $5$ litres in a healthy individual.

Electrocardiograph (ECG)

An ECG is a graphical representation of the electrical activity of the heart during a cardiac cycle. The standard ECG consists of:

• P-wave: Represents the electrical excitation (or depolarisation) of the atria, which leads to the contraction of both the atria.
• QRS complex: Represents the depolarisation of the ventricles, which initiates the ventricular contraction.
• T-wave: Represents the return of the ventricles from excited to normal state (repolarisation).

Competency Based Questions (Previous Years & Sample Papers)

Q1. Cardiac output ($CO$) is defined mathematically as the product of Heart Rate ($HR$, in beats/min) and Stroke Volume ($SV$, in mL/beat): $CO = HR \cdot SV$. During intense aerobic exercise, a highly trained athlete’s heart rate increases to $180$ beats/min, and their Stroke Volume increases to $140$ mL/beat. Calculate the athlete’s cardiac output during this exercise in Liters per minute. If a normal resting cardiac output is roughly $5.0$ L/min, by what factor has the athlete’s heart increased its pumping efficiency to meet the immense oxygen demands of the skeletal muscles?

Q2. The universal donor and universal recipient blood groups in the ABO system are traditionally taught as O negative (O-) and AB positive (AB+), respectively. Consider a patient with blood type B-. List all the possible blood types this patient can safely receive in a massive transfusion without triggering an acute hemolytic transfusion reaction. Genetically, what happens regarding antigens and antibodies if this patient mistakenly receives A+ blood?

Q3. On a standard clinical ECG tracing, the interval from the beginning of the P-wave to the beginning of the QRS complex is known as the PR interval (normal duration: $0.12 - 0.20$ seconds). Functionally, this interval represents the time taken for the electrical impulse generated by the SA node to travel through the atria and the AV node before reaching the ventricles. If a patient’s ECG consistently shows a massively prolonged PR interval of $0.35$ seconds, where specifically in the anatomical conduction system of the heart is the pathological delay likely occurring, and structurally why is a slight delay specifically designed into that exact node in a healthy heart?

Chapter 16: Excretory Products and their Elimination

Animals accumulate ammonia, urea, uric acid, carbon dioxide, water and ions like $Na^+$, $K^+$, $Cl^-$, phosphate, sulphate, etc., either by metabolic activities or by other means like excess ingestion. These substances have to be removed totally or partially. This chapter deals with the mechanisms of elimination of these substances with special emphasis on common nitrogenous wastes.

Ammonia, urea and uric acid are the major forms of nitrogenous wastes excreted by the animals. Ammonia is the most toxic form and requires large amount of water for its elimination, whereas uric acid, being the least toxic, can be removed with a minimum loss of water.

Human Excretory System

In humans, the excretory system consists of a pair of kidneys, one pair of ureters, a urinary bladder and a urethra. Kidneys are reddish brown, bean shaped structures situated between the levels of last thoracic and third lumbar vertebra close to the dorsal inner wall of the abdominal cavity.

Each kidney has nearly one million complex tubular structures called nephrons, which are the functional units. Each nephron has two parts – the glomerulus and the renal tubule.

The Nephron

Glomerulus is a tuft of capillaries formed by the afferent arteriole. Blood from the glomerulus is carried away by an efferent arteriole. The renal tubule begins with a double walled cup-like structure called Bowman’s capsule, which encloses the glomerulus. Glomerulus alongwith Bowman’s capsule, is called the Malpighian body or renal corpuscle. The tubule continues further to form a highly coiled network – Proximal Convoluted Tubule (PCT). A hairpin shaped Henle’s loop is the next part of the tubule which has a descending and an ascending limb. The ascending limb continues as another highly coiled tubular region called Distal Convoluted Tubule (DCT).

Figure 16.1: Structure of a typical Nephron

Urine Formation

Urine formation involves three main processes namely, glomerular filtration, reabsorption and secretion, that takes place in different parts of the nephron.

1. Glomerular Filtration: The first step in urine formation is the filtration of blood, which is carried out by the glomerulus and is called glomerular filtration. On average, $1100-1200$ mL of blood is filtered by the kidneys per minute.
2. Reabsorption: A comparison of the volume of the filtrate formed per day (180 litres per day) with that of the urine released (1.5 litres), suggest that nearly 99 per cent of the filtrate has to be reabsorbed by the renal tubules.
3. Secretion: During urine formation, the tubular cells secrete substances like $H^+$, $K^+$ and ammonia into the filtrate.

Regulation of Kidney Function

The functioning of the kidneys is efficiently monitored and regulated by hormonal feedback mechanisms involving the hypothalamus, JGA and to a certain extent, the heart.

• Antidiuretic Hormone (ADH): Released from the posterior pituitary, it facilitates water reabsorption from latter parts of the tubule, thereby preventing diuresis (excess urine loss).
• Renin-Angiotensin mechanism: The JGA plays a complex regulatory role. A fall in glomerular blood pressure activates JG cells to release renin which converts angiotensinogen to angiotensin I and further to angiotensin II (a powerful vasoconstrictor and stimulator of aldosterone).

Competency Based Questions (Previous Years & Sample Papers)

Q1. The glomerular filtration rate (GFR) in a healthy adult is roughly $125 \text{ mL/min}$. The total plasma volume of an average human is approximately $3000 \text{ mL}$ (3 Liters). Calculate the number of times the entire plasma volume is filtered by the kidneys in a standard 24-hour day. If a pharmaceutical drug is specifically designed to completely block the sodium-glucose transport proteins (SGLT2) in the Proximal Convoluted Tubule, dynamically how will this alter the final urine output volume and its glucose concentration?

Q2. Desert mammals, such as the Kangaroo Rat, survive the harsh arid environment without ever needing to drink free water. Their survival depends exclusively on metabolic water generation and drastic minimization of excretory water loss. Structurally, the Kangaroo Rat has incredibly long Loops of Henle that extend deep into the inner medulla. According to the counter-current multiplier mechanism, biologically and mathematically, how does the extreme length of the Loop of Henle correlate to the extreme concentration (high osmolarity) of their final urine compared to humans?

Q3. Uricotelism is the standard mode of excretion in terrestrial birds and reptiles. Uric acid is extremely insoluble in water, allowing these animals to excrete it as a semi-solid white paste with minimal water loss, which is highly advantageous for conserving water and minimizing body weight for flight. However, synthesizing uric acid from ammonia is an intensely energetically expensive multi-step biochemical pathway compared to producing urea or direct ammonia. Formulate an evolutionary argument explaining why natural selection favored this metabolically expensive pathway specifically for oviparous (egg-laying) terrestrial vertebrates.

Chapter 17: Locomotion and Movement

Movement is one of the significant features of living beings. Animals and plants exhibit a wide range of movements. Streaming of protoplasm in the unicellular organisms like Amoeba is a simple form of movement. Movement of cilia, flagella and tentacles are shown by many organisms. Human beings can move limbs, jaws, eyelids, tongue, etc. Some of the movements result in a change of place or location. Such voluntary movements are called locomotion.

Types of Movement

Cells of the human body exhibit three main types of movements, namely:

1. Amoeboid: Exhibited by macrophages and leucocytes in blood, caused by streaming of protoplasm to form pseudopodia.
2. Ciliary: Occurs in most of our internal tubular organs which are lined by ciliated epithelium (e.g., removing dust in the trachea, passage of ova through the female reproductive tract).
3. Muscular: Movement of our jaws, limbs, tongue, etc. requires muscular movement. The contractile property of muscles is effectively used for locomotion.

Muscle

Muscle is a specialised tissue of mesodermal origin. Based on their location, three types of muscles are identified: Skeletal, Visceral, and Cardiac. Skeletal muscles are closely associated with the skeletal components of the body. They have a striped appearance under the microscope and hence are called striated muscles. As their activities are under the voluntary control of the nervous system, they are known as voluntary muscles too.

Structure of Contractile Proteins

Each skeletal muscle consists of many muscle bundles (fascicles), which in turn contain muscle fibres. Each muscle fibre contains parallelly arranged myofibrils. Each myofibril has alternate dark and light bands on it. This striated appearance is due to the distribution pattern of two important proteins – Actin and Myosin.

• Actin: Forms the light bands (I-band or Isotropic band). The filaments are thinner.
• Myosin: Forms the dark band (A-band or Anisotropic band). The filaments are thicker.

The portion of the myofibril between two successive ‘Z’ lines is considered as the functional unit of contraction and is called a sarcomere.

Figure 17.1: Diagrammatic representation of a Sarcomere

Mechanism of Muscle Contraction

Mechanism of muscle contraction is best explained by the sliding filament theory which states that contraction of a muscle fibre takes place by the sliding of the thin filaments (actin) over the thick filaments (myosin).

• Muscle contraction is initiated by a signal sent by the central nervous system (CNS) via a motor neuron.
• This releases a neurotransmitter (Acetylcholine) at the neuromuscular junction, generating an action potential in the sarcolemma.
• This triggers the release of Calcium ions ($Ca^{++}$) from the sarcoplasmic reticulum into the sarcoplasm.
• Calcium binds to troponin on actin filaments, unmasking the active sites for myosin.
• Utilising the energy from ATP hydrolysis, the myosin head binds to the exposed active sites on actin to form a cross-bridge, pulling the attached actin filaments towards the centre of the ‘A’ band.

Skeletal System and Joints

Skeletal system consists of a framework of bones and a few cartilages (total 206 bones in humans). Joints are points of contact between bones, or between bones and cartilages.

1. Fibrous joints: Do not allow any movement (e.g., flat skull bones fusing via sutures).
2. Cartilaginous joints: The bones involved are joined together with the help of cartilages, permitting limited movement (e.g., between vertebrae).
3. Synovial joints: Characterised by the presence of a fluid-filled synovial cavity between the articulating surfaces. Allow considerable movement (e.g., Ball and socket joint, Hinge joint).

Competency Based Questions (Previous Years & Sample Papers)

Q1. According to the sliding filament theory, during maximum skeletal muscle contraction, the length of the A-band mathematically remains strictly constant, while the I-band shortens. If the resting length of a single sarcomere is $2.5 \mu m$, the A-band (thick filaments) is $1.6 \mu m$ long, and the specific Z-lines are assumed dimensionless, calculate the total length of the I-band region belonging to this sarcomere at rest. If the maximum contraction allows the thin filaments to meet exactly in the center of the H-zone (reducing the H-zone to $0 \mu m$), calculate the new mathematical length of the entire deformed sarcomere.

Q2. Rigor mortis is the profound muscular stiffening that occurs in mammals a few hours after clinical death. It is caused by the depletion of intracellular ATP. Based directly on the biochemical steps of the cross-bridge cycle in muscle contraction, structurally explain exactly why the absence of ATP locks the muscle into a state of rigid contraction, rather than relaxation. Furthermore, what physiological event occurs roughly $48-72$ hours later that finally resolves the rigor?

Q3. Elite endurance marathon runners typically possess skeletal muscles with a massively high proportion of “Type I” (Red) muscle fibers, whereas elite Olympic weightlifters have a high proportion of “Type IIb” (White) muscle fibers. List the primary mechanisms used by Type I fibers to generate ATP, and identify the specific oxygen-binding protein causing their red color. Why does the metabolic pathway utilized by White fibers mathematically result in rapid, paralyzing muscle fatigue during sustained exercise compared to Red fibers?

Chapter 18: Neural Control and Coordination

As you know, the functions of the organs/organ systems in our body must be coordinated to maintain homeostasis. Coordination is the process through which two or more organs interact and complement the functions of one another. For example, when we do physical exercises, the energy demand is increased for maintaining an increased muscular activity. The supply of oxygen is also increased. The increased supply of oxygen necessitates an increase in the rate of respiration, heart beat and increased blood flow via blood vessels.

In our body the neural system and the endocrine system jointly coordinate and integrate all the activities of the organs so that they function in a synchronised fashion.

Neural System

The neural system of all animals is composed of highly specialised cells called neurons which can detect, receive and transmit different kinds of stimuli. The human neural system is divided into two parts:

• Central neural system (CNS): Includes the brain and the spinal cord and is the site of information processing and control.
• Peripheral neural system (PNS): Comprises of all the nerves of the body associated with the CNS. It is divided into the Somatic neural system (relays impulses from CNS to skeletal muscles) and Autonomic neural system (relays impulses from CNS to involuntary organs and smooth muscles).

Neuron as Structural and Functional Unit

A neuron is a microscopic structure composed of three major parts, namely, cell body, dendrites and axon.

• Cell body: Contains cytoplasm with typical cell organelles and certain granular bodies called Nissl’s granules.
• Dendrites: Short fibres which branch repeatedly and project out of the cell body. They transmit impulses towards the cell body.
• Axon: A long fibre. Its distal end is branched. Each branch terminates as a bulb-like structure called synaptic knob which possesses synaptic vesicles containing chemicals called neurotransmitters. The axons transmit nerve impulses away from the cell body to a synapse or to a neuro-muscular junction.

Figure 18.1: Structure of a Neuron

Generation and Conduction of Nerve Impulse

Neurons are excitable cells because their membranes are in a polarised state. Different types of ion channels are present on the neural membrane. These ion channels are selectively permeable to different ions.

• Resting Potential: When a neuron is not conducting any impulse, i.e., resting, the axonal membrane is comparatively more permeable to potassium ions ($K^+$) and nearly impermeable to sodium ions ($Na^+$). This ionic gradient is maintained by the active transport of ions by the sodium-potassium pump which transports $3 Na^+$ outwards for $2 K^+$ into the cell. As a result, the outer surface carries a positive charge while its inner surface becomes negatively charged.
• Action Potential: When a stimulus is applied, the membrane becomes freely permeable to $Na^+$. This leads to a rapid influx of $Na^+$, reversing the polarity (depolarisation). The electrical potential difference across the plasma membrane at that site is called the action potential, which is in fact termed as a nerve impulse.

Synapse

A nerve impulse is transmitted from one neuron to another through junctions called synapses. A synapse is formed by the membranes of a pre-synaptic neuron and a post-synaptic neuron, which may or may not be separated by a gap called synaptic cleft.

At a chemical synapse, when an impulse arrives at the axon terminal, it stimulates the movement of the synaptic vesicles towards the membrane where they fuse with the plasma membrane and release their neurotransmitters in the synaptic cleft. The released neurotransmitters bind to their specific receptors, present on the post-synaptic membrane.

Competency Based Questions (Previous Years & Sample Papers)

Q1. The resting membrane potential of a typical mammalian neuron is mathematically recorded as $-70 \text{ mV}$ inside relative to the outside. This electrochemical gradient is largely maintained by the electrogenic $Na^+/K^+$ ATPase pump. If a powerful neurotoxin completely binds and inhibits all $Na^+/K^+$ ATPase pumps in a neuron, calculate mathematically how an immediate single action potential event (depolarization and repolarization) will be visibly affected on an oscilloscope tracing in the millisecond timeframe. Explain what will happen to the resting potential and subsequent action potentials if the pump remains inhibited over a long period (minutes).

Q2. Multiple Sclerosis is a severe demyelinating disease where the patient’s own immune system systematically destroys the myelin sheath surrounding the axons of the Central Nervous System. Based on the bio-physics of saltatory conduction, mathematically and structurally explain why the destruction of the myelin sheath drastically slows down or completely halts the conduction of action potentials along the axon, causing severe neurological deficits.

Q3. Organophosphate pesticides are lethal neurotoxins that irreversibly inhibit the enzyme Acetylcholinesterase centrally located in the synaptic cleft of neuromuscular junctions. If an unfortunate agricultural worker is heavily exposed to this pesticide, trace the specific biochemical sequence of events that occurs at their synapses. Physiologically, why does this exposure lead to violently sustained, paralyzing muscle spasms (tetanus) rather than muscle flaccidity?

Chapter 19: Chemical Coordination and Integration

You have already learnt that the neural system provides a point-to-point rapid coordination among organs. The neural coordination is fast but short-lived. As the nerve fibres do not innervate all cells of the body and the cellular functions need to be continuously regulated; a special kind of coordination and integration has to be provided. This function is carried out by hormones. The neural system and the endocrine system jointly coordinate and regulate the physiological functions in the body.

Endocrine Glands and Hormones

Endocrine glands lack ducts and are hence, called ductless glands. Their secretions are called hormones. The classical definition of hormone as a chemical produced by endocrine glands and released into the blood and transported to a distantly located target organ has current scientific definition as follows: Hormones are non-nutrient chemicals which act as intercellular messengers and are produced in trace amounts.

Human Endocrine System

The endocrine glands and hormone producing diffused tissues/cells located in different parts of our body constitute the endocrine system.

• Hypothalamus: The basal part of the diencephalon. It produces releasing hormones (e.g., GnRH) and inhibiting hormones (e.g., Somatostatin) that regulate the synthesis and secretion of pituitary hormones.
• Pituitary Gland: Located in a bony cavity called sella tursica. The anterior pituitary secretes Growth Hormone (GH), Prolactin, Thyroid Stimulating Hormone (TSH), ACTH, LH, and FSH. The posterior pituitary stores and releases Oxytocin and Vasopressin (ADH).
• Pineal Gland: Secretes melatonin, which regulates the 24-hour diurnal rhythm of our body (sleep-wake cycle, body temperature).
• Thyroid Gland: Secretes thyroxine ($T_4$) and triiodothyronine ($T_3$), which regulate the basal metabolic rate, and Thyrocalcitonin (TCT) which regulates blood calcium levels.
• Parathyroid Gland: Secretes Parathyroid hormone (PTH), which increases the $Ca^{2+}$ levels in the blood.
• Adrenal Gland: The adrenal medulla secretes epinephrine and norepinephrine (fight or flight hormones). The adrenal cortex secretes glucocorticoids (e.g., cortisol) and mineralocorticoids (e.g., aldosterone).
• Pancreas: A composite gland. The endocrine portion (Islets of Langerhans) secretes glucagon (from $\alpha$-cells) and insulin (from $\beta$-cells) to regulate blood glucose homeostasis.
• Gonads: Testes secrete androgens (testosterone). Ovaries secrete estrogens and progesterone.

Figure 19.1: Location of major endocrine glands in the human body

Hypo- and Hyperactivity Disorders

The delicate balance of hormones is crucial. Over-secretion or under-secretion leads to severe clinical disorders.

• Dwarfism: Hyposecretion of Growth Hormone (GH) during childhood causes stunted growth.
• Acromegaly: Hypersecretion of GH in adults causes severe disfigurement, especially of the face.
• Cretinism: Hypothyroidism during pregnancy causes defective development and maturation of the growing baby leading to stunted growth (cretinism) and mental retardation.
• Goitre: Enlargement of the thyroid gland due to iodine deficiency in the diet.
• Exopthalmic Goitre (Graves’ Disease): A form of hyperthyroidism characterized by enlarged thyroid gland, protrusion of the eyeballs, and increased basal metabolic rate.
• Diabetes Mellitus: Caused by prolonged hyperglycemia due to deficiency or cellular resistance to Insulin.
• Addison’s Disease: Underproduction of hormones by the adrenal cortex alters carbohydrate metabolism causing acute weakness and fatigue.

Competency Based Questions (Previous Years & Sample Papers)

Q1. The regulation of blood glucose is tightly controlled by a negative feedback loop primarily involving the hormones Insulin and Glucagon, secreted by the Islets of Langerhans in the pancreas. Mathematically, consider normal fasting blood glucose to be set at $90 \text{ mg/dL}$. If a patient consumes a massive carbohydrate meal and their blood glucose spikes to $180 \text{ mg/dL}$, which specific cell type physically detects this mathematical error ($\Delta = +90 \text{ mg/dL}$), what hormone is immediately secreted, and what are the primary biochemical pathways activated in the liver to bring the variable back to the set-point?

Q2. The mechanism of hormone action fundamentally differs based on the chemical nature of the hormone. Steroid hormones (like Cortisol or Estrogen) and Peptide hormones (like Insulin or Oxytocin) interact with their target cells through entirely different physical and mathematical models. Explain structurally why a steroid hormone can directly physically enter a target cell to alter gene expression, while a peptide hormone must absolutely bind to an extracellular membrane receptor, and describe the mathematical “amplification” consequence of the second messenger system used by peptide hormones.

Q3. The Hypothalamus is often referred to as the “Master Control Center” because it directly regulates the Pituitary Gland (the “Master Gland”). Interestingly, the hypothalamus controls the Anterior Pituitary and the Posterior Pituitary through two structurally distinct mechanisms. Describe these two separate mechanisms. For example, if a dehydrated individual needs Anti-Diuretic Hormone (ADH) to save water, exactly where is the hormone synthesized, and physically how does it reach the bloodstream?