UNIT TWO

THE ANIMAL CELL A cell is the basic unit of a living organism. They are normally observed using a microscope. There are 2 types of microscopes i.e light microscope and electron microscope. The differences include:No. LIGHT MICROSCOPE 1. They are cheap 2. Magnification power relatively low x600 3. Poor resolution 4. Can be able to see living plants or animals directly e.g sperms 5. Use light ELECTRON MICROSCOPE - Expensive - Very high x M - Good resolution - Specimen observed under a vacuum, hence materials must be dead. - A beam of electrons

ULTRASTRUCTURE OF AN ANIMAL CELL Ultrastructure of a cell refers to its appearance when observed under an electron microscope. However, when observed under light microscope, it would appear as shown below:-

Cell membrane Nucleus Cytoplasm

The ultra-structure is as shown below:Photocopy F.A pg 17 pg NB: An organelle is a structure within the cell that has a particular function e.g:-

(i) Nucleus: It is usually the largest organelle 10-20pm. It is surrounded by a double nuclear membrane containing holes or pores, which controls substances leaving or entering the nucleus and in turn nucleus controls events in the cytoplasm. In the nucleus there are:(a) Nucleic acids i.e DNA and RNA (b) Proteins NB: The DNA is bonded to proteins forming chromatin which appear as tiny granules. (c) Nucleolus an extra-dense area consisting of DNA and protein. It is involved in the formation of ribosomes, controls cell growth and division.

(ii) Ribosomes: It is a non-membraneous organelle. It consists of two spherical joined structures that are not equal in size i.e Smaller sub-unit 20nm

Large sub-unit

Ribosome is the site for protein synthesis. They are found in all cells They occur freely within the cytoplasm or may be associated with E.R.

(c) Mitochondria: Their shape and size vary, but generally they are sausage shaped with a diameter of 1um and a length of 2.5 to 5 um. They are found embedded in the matrix of cytoplasm. The wall of a mitochondrion consists of two thin membranes separated by a narrow fluid filled space. The inner membrane is highly folded forming irregular partitions called cristae projecting to the interior. They increase the surface area for chemical reactions. In the interior is an organic matrix containing proteins, lipids and traces of DNA.

Most chemical reactions of respiration take place here i.e energy in the form of ATP is generated for chemical reactions. Cells whose functions require spending large amounts of energy usually contain large numbers of mitochondria. Mitochondria are packed together in the cell where energy is required e.g in sperms they are packed at the base of the tail. They are also found in muscles e.g flight muscles of birds, insects etc and cells that carry out active transport. Diagrams

(d) Centrioles / centrosome: Are non-membraneous. They usually occur in a pair in a cell and are at right angles to each other, They are hollow cylindrical organelles. The wall of each centriole is made up of nine triplets of microtubules arranged at an angle. They occur near the golgi bodies / apparatus. Diagram pg 138 3.1.5b (student book) They produce spindle fibres involved in the movement of chromosomes during cell division.

(e) Lysosomes: They are dark spherical bodies in cytoplasm of most cells. They contain digestive enzymes. They fuse with a membrane abound vacuole containing either food or worn out organelle. Their enzymes then breakdown the contents into molecules that can be reused. (autophage) FA pg 21 Lysosomes can also self-destruct i.e if an entire cell is damaged or wearing out, its lysosomes may rupture, releasing their enzymes to destroy the entire contents of the cell (apoptosis) or autolysis. Lysosomes are sometimes referred to as suicide bags

(f) (E.R): The membrane of E.R is continuous with nuclear membrane. It forms a system of flattened membrane bounded sacs called cisternae. In some E.R, granules called ribosomes are attached thus forming rough endoplasmic reticulum.

The ribosomes make proteins while R.E.R isolates and transport these proteins e.g digestive enzymes and hormones that are used out of the cell and hence move out be exocytosis. It provides a large S./A for synthesis of proteins. It also stores the synthesized proteins. It maintains cellular shape. NB: Cells that secrete materials e.g digestive enzymes in the lining of gut have a large amount of R.E.R (FA pg 17) E.R without ribosomes is called S.E.R. It synthesizes and transports (i) steroids e.g testosterone, oestrogen hence it is found in the testis. (ii) Lipids (g) Golgi apparatus: It is made up of stacks of parallel flattened membranes pockets called cisternae. Formed by vesicles from E.R fusing together hence is like E.R. The proteins enter the stacks. As they move, they are modified in various ways e.g carbohydrate is added to some proteins forming glycoproteins e.g mucus. It also produces materials for plant cell walls and insect cuticles. Some proteins are digestive enzymes and are enclosed in vesicles to form an organelle called lysosome, or are transported through golgi body then in vesicles to the C.S.M where they fuse with membrane to release extracellular digestive enzymes. Diagram pg 141 S.B fig 3.1.8 (h) Prokaryotes (bacteria): Pg 61 M/C pg

(i) Slime layer: It forms a loose soluble covering that is easily washed off, whereas capsules (firm) which may be composed of polysaccharides, polypeptides or mixture of both are bound more tightly to the C.W and have more gummy consistent. It is a protective layer against chemicals, dessication and stores waste products. In pathogenic bacteria, it prevents antibodies and phagocytic cells (W.B.C) forms binding to C.W hence are not destroyed.

(j) Cell wall:

It is composed of mixed polymer of hexose, sugar and amino acids called peptidoglycans, mucopeptides or murein. It provides a strong but flexible framework supporting cell contents. It protects bacterial cell from lysis. NB: Effectiveness of some drugs depends on their ability to destroy or prevent formation of peptidoglycans.

(k) C.S.M: It is composed of a lipid bi-layer with protein molecules embedded in it. (similar to cell membrane of eukaryotic cells). However, they have a higher ration of proteins to phospholipids molecules than in eukaryotic cells.

(l) Mesosomes: In some bacteria the C.S.M is extensively infolded forming mesosomes. This increases the surface area for metabolic activities generating A.T.P e.g respiration. It is involved in cell wall synthesis and also during cell division. In photosynthetic bacteria, C.S.M is infolded to form thylakoids on which are found pigment molecules and associated enzymes.

(m) Granules: They mainly consist of glycogen, lipid droplets etc. and they are energy rich storage compounds.

(n) Bacterial chromosome (circular DNA) / nuclear material: This is the bacterial DNA which is in form of a ring. It is very long and tightly coiled around basic protein molecules. No nuclear membrane surrounding it and the genes present on these bacterial chromosomes are those necessary for growth and maintenance.

(o) Plasmids:

Many bacteria contain circular pieces of extra chromosomes DNA called plasmids. They may be free in the cytoplasm or attached to bacterial chromosomes. They are independent and self-replicating. Genes on the plasmids may be concerned with resistance to drugs, or production of toxins and enzymes. Modern techniques in gene technology enable such plasmids to be manipulated in the lab and provides a means of introducing additional genetic information into bacterial cells.

(p) Flagella: They are made up of identical spherical sub units of the protein called flagellin. Is used in the locomotion of many motile bacteria. It is a rigid hollow cylinder of protein, the base of which rotates propelling the cell along e.g rhizobium.

DIFFERENCES BETWEEN PROKARYOTES AND EUKARYOTES

Prokaryotes (Bacteria) - Are small in size 1-10um - Rigid cell wall containing murein - No true nucleus - No nucleolus - No endoplasmic reticulum - Smaller ribosomes (705) - No membrane bound organelle e.g mitochondria etc - Flagella, when present lack microtubules ORGANIZATION OF CELLS

Eukaryotes (Animal cells) - Big in size 10-150um or even more - If present it contains cellulose (green plants) or chitin (fungi) - True nucleus present surrounded by a nuclear envelope. - Nucleolus present - Endoplasmic reticulum present with associated G. apparatus, lysosomes etc - Larger (805) ribosomes - Many membrane-bound organelles e.g mitochondria, chloroplast etc - Flagella have 9 + 2 arrangement of microtubules.

Multicellular organisms are made up of specialized cells, they o not operate on their own, but in groups of cells known as tissues. Thus a tissue is a group of cells, similar in structure, performing a particular function. The main type of tissues include:(i) Epithelial tissues e.g (a) Simple squamous

(b) Cuboidal (c) Columnar (d) Ciliated (e) Glandular (f) Compound stratified Pg 144 S/B NB: They line surfaces from both inside and outside. (a) Found on lining of blood vessels, capillary walls and lining of alveoli. (b) Lines many tubes in the body. (c) Ciliated epithelial often contain goblet that produce mucus found in lungs tubes oviduct. (d) Found where the surface is continually scratched and abraded e.g:(1) skin palm / soles (2) muscle tissues (3) nervous tissues (4) elastine tissues (5) glandular tissues (6) connective tissues e.g bone tissues, cartilage tissues ORGANS An organ is made up of a group of tissues that are grouped into a structure with a particular function e.g brain, lungs, liver, heart etc. S/B pg 145 Plants cells are grouped into tissues which in turn make an organ e.g the leaf is na organ with the following tissues:(1) (2) (3) (4) (5) Epidermis Palisade mesophyll Spongy mesophyll Phloem Xylem S/B pg 146 SYSTEMS In many cases as in animals a number of organs work together as a system e.g (1) Digestive system includes the following organs stomach, pancreas, small and large intestines. (2) Nervous system includes - brain, spinal cord and pheripheral nerves.

THE CELL CYCLE Cells divide on a regular basis to bring about growth and asexual reproduction. They divide in a sequence of events known as the cell cycle which consists of the following phases:- (a) Interphase (b) Mitosis (c) Cytocinesis Some small proteins called cyclins controls the cell cycle from one phase to the next. These cyclins attach onto enzymes called cyclin dependent kinases (CDKs) The CDK / cyclin complex formed adds phosphate groups to other proteins changing their shape and bring about the next stage in the cell cycle. Pg 147 fig 3.1.17 pg S/B Interphase (resting stage): It is further divided into the following stages:-

NB:

(a) G1- Stage Cells undergo rapid growth. New organelles are being synthesized thus structural proteins and enzymes required resulting to massive protein synthesis. (b) S-stage The DNA replicates Histones, proteins to which DNA is linked are built up. Chromosomes become divided into chromatids. (c) G2 - stage More cell growth takes place Some organelles replicate e.g centrioles There is accumulation of energy stores Diagram interphase pg 149 S/B Mitosis (nuclear division) It is divided into 4 main stages:-

(a) Prophase Chromosomes have replicated and are joined at the centomere. Nucleolus disappears.

Centrioles begins to move towards the poles and begins to produce spindle fibres forming aster. Nuclear membrane breaks down at the end of prophase. Diagram pg 149

(b) Metaphase The chromosomes line up at the equator. Spindle fibres from centrioles are attached to the centromere. Diag. Pg 149 (c) Anaphase The spindle fibres begins to contract The centromere breaks open. Chromatids are pulled towards the poles. Diag. pg 149 (d) Telophase The chromatids reach the poles and mature to form chromosomes. The nuclear membrane reappears. The nucleolus reappears. Chromosomes begin to condense. Disg. Pg 149 (e) Cytokinesis Is the process by which the cytoplasm divides into 2 and hence 2 daughter cells are formed. A graph to show quantity of DNA in arbitrary units during the cell cycle. m/c pg 70 ASEXUAL REPRODUCTION Mitosis is the basis of asexual reproduction, and results in genetically identical individuals or clones. Advantages of asexual reproduction: Only one parent is required. It gives to large numbers of offsprings. Good qualities are maintained. Disadvantages:

No variation (i.e are genetically similar) hence can easily be wiped out by a disease etc Bad qualities are inherited

There are varieties of asexual reproduction e.g (a) Binary fission: It involves mitosis followed by splitting of an individual. It is found in micro organisms such as bacteria, protoctists like amoeba etc. Can go binary fission every 20 minutes. NB: Similar method is used in cell reproduction for growth and repair in all living things. (b) Producing spores: Production of asexual spores involves mitosis. The spores are capable of growing into new individuals e.g in fungi, masses and ferns.

(c) Regeneration: It occurs when organisms replace parts of the body which have been lost e.g many lizards shed their tails when attacked and then grow another. Other organisms e.g certain starfish, fungi, flat worms, algae can reproduce themselves asexually from fragments of their original body.

(d) Producing buds: In this case, there is an outgrowth from the parent organism which produces a smaller but identical individual by mitotic cell division. The bud eventually becomes detached from the parent and has an independent existence e.g yeast cells.

NB: In budding the parent cell is larger than the bud. (e) Vegetative propagation:

It is like a more sophisticated version of reproductive budding but occurs in plants. The structure formed by plants develops and differentiates into a new plant identical to the parent. The new plant may be propagated from the stem, leaf bud or root of the parent. However, all these involves mitotic division. Vegetative propagation often involves perennating organs which normally contains stored food from photosynthesis e.g bulbs, corms, runners, suckers, rhizomes, stem tubers and root tubers. At times, farmers induce fragmentation artificially by taking a small piece of plant e.g shoot and planting it to grow on and develop by mitosis into another entire (identical) plant.

GROWTH Growth is a permanent increase in the number of cells, or in mass or size of an organism. Hence, there are 3 aspects of growth:(a) Cell division or mitosis is the basis for growth. (b) Assimilation It refers to when materials are incorporated into cell to produce new cell material. (c) Cell expansion this takes place when assimilation takes place.

MEASURING GROWTH Growth is affected by a number of factors e.g food availability, temperature, light intensity, genetic make up in the body. Linear dimensions are deceptive at times e.g when a camel takes a lot of water, no growth has taken place though stomach increases in size. Measuring mass also deceptive e.g water content of the cells varies as in plants while in animals faecal material and urine held in their bodies vary. Hence, dry mass is a more accurate way i.e the mass of the body of an organism with all the water removed from it. However, removing all the water from an organism kills it and hence further growth can not be measured. This method is useful to plants but for animals not easy or ethical to maintain and then kill and dry animals. This therefore means that less reliable indicators e.g height, wet mass to measure growth.

GROWTH PATTERNS There are different types of growth patterns:1.

Continuous growth height

Time This is shown by many animals after an initial slow start, then a rapid period of growth, and then slows down or may stop. Plants grow continually, as the marine animals. This pattern even if it stops at maturity is known as continuous growth. Discontinuous growth measured as dry mass

2. Discontinuous growth Measured as height

Height / length

mass

Time

Time

Insects shows a series of moults i.e sheds the outer exoskeleton and while the new exoskeleton is soft, they expand by taking in air or water and grow once the skeleton hardens, there is room for the tissue to increase in size and mass. Thus, if length is taken then insects appear to grow in a series of steps. NB: Different parts of the organism can grow at different rates e.g in human embryo, nervous system and head grow much faster, while at puberty stage, stops growing while long bones and rest of the body continue. At the beginning of life, mitosis is rapid. It does not stop if growth slows down or stops. This is because cells are continually being worn out and being replaced by mitotic division. This continues until onset of senescence or old age when cells dying out number those being formed, and results to death at certain point of life.

head

SEXUAL REPRODUCTION AND CELL SPECIALIZATION

(a) Gametes: It is the term used to refer to (eggs and the sperms). They normally have the number of chromosomes compared to other cells of the same organism, and are said to be haploid (n). Other cells are said to be diploid (2n) as they have 2 sets of chromosomes. They join by a process called fertilization to form a zygote. Gametes are formed in special organs called gonads (testis / ovaries)

(b) Meiosis: Meiosis takes place in the sex organs i.e the testis in seminiferous tubules and in the ovaries. There are 2 phases of division i.e meiosis I and meiosis II which follow one another. Meiosis I has the following stages:Interphase just like in mitosis. Prophase I: Chromosomes are thin threadlike and referred to as chromatin. They shorten and thicken becoming visible. The homologous chromosomes come together by a process known as synapsis forming a bivalent. Each of the chromosomes splits into 2 except at the centromere. The chromatids formed ovelap at places referred to as chiasmata where crossing over takes place (exchange of genetic material). Nucleolus and nuclear membrane disappear by the end of prophase. Centrioles move to the poles and begin to produce spindle fibres. Pg 140 fig 8.4 a, b, c Metaphase I: The homogolus chromosomes line up at the equator. Spindle fibres are attached onto the centromere of the chromosome. Fig 8.4 d Anaphase I: The spindle fibre contract, pulling the chromosomes towards the poles (homologus chromosomes part company)

Fig 8.4 e Telophase I: The chromosomes reach the poles and are surrounded by the nuclear membrane. The molecules reappear. Fig 8.4 f Cytokinesis takes place and 2 daughter cells are formed. Meiosis II Prophase II: The centrioles replicate and move towards the poles. The nuclear membrane and nucleolus disappear. The centrioles begin to produce spindle fibres. Fig 8.4g Metaphase II: The chromosomes line up at the equator. The spindle fibres attach onto the centromere. Fig 8.4 h Anaphase II: The spindle fibres contract, splitting the centromere and the chromatids are pulled towards poles. Fig 8.4 i Telophase II: The chromatids reach the poles and with time mature to form chromosomes. The nucleolus and nuclear membrane reappear. Fig 8.4 j Cytokinesis takes place and 4 daughter cells are formed. Sketch a graph to show how the quantity of DNA changes during the cell cycle.

IMPORTANCE OF MEIOSIS (1) It reduces the chromosome number in gametes from diploid to haploid. (2) It brings about variation in 2 main ways:(a) Independent or random assortment: The chromosomes obtained from the individuals two parents are distributed the gametes at random i.e each gamete produced receives 23 chromosomes any number from none to all23 could come from either material or paternal chromosomes. This guarantees variety in the gametes. UB pg 143 fig 8.5 (b) Crossing over or recombination: This takes place when maternal and paternal chromatids breaks at a point called chiasmata. The exchange of these portions which contain genetic material leads to added genetic variation. EB pg 159 fig 3.2.5 (c) Mutations: These are sudden changes that take place in the genetic material and can be inherited. DIFFERENCES BETWEEN MITOSIS AND MEIOSIS UB pg 142 table 8.2

into and

GAMETOGENESIS: This is the process by which gametes are formed. It is divided into 2 i.e (a) spermatogenesis process by which sperms are formed (b) oogenesis process by which eggs are formed. (a) Spermatogenesis: It stats during puberty stage. It takes place in the seminiferous tubules. The lining of the tubule contain cells referred to as primordial germ cells all of which can give rise to sperms. Each of the primordial germ cell undergoes mitosis several times forming spermatogonia. Each one of them (spermatogonia) increases in the size to form primary spermatocte.

The primary spermatocyte undergoes meiosis I forming secondary spermatocyte. The secondary spermatocyte undergoes meiosis II forming spermatids. Each spermatid undergoes differentiation / spermiogenesis to form spermatozoa. The spermatozoa attach onto sertoli cells from where they derive their nourishment. Spermatogenesis takes about 74 75 days.

EB pg 160 fig 3.2.6 Spermatozoa (many, mini, motile) they are specialized for their functions as explained in the following diagram. EB pg 161

(b) Oogenesis: The cells lining the ovary are referred to as primordial germ cells and they give rise to the ovum. Oogenesis begins at the foetus stage. Each primordial germ cell undergoes mitosis to give rise to ooginia. Each of this increases in size to form primary oocyte. The primary oocyte undergoes first meiotic division to form secondary oocyte and the 1st polar body. NB: Secondary oocyte is the one which leaves the ovary and goes to the oviduct (ovulation). The secondary oocyte undergoes second meiotic division just before fertilization takes place, to form an ovum and the 2 nd polar body. The 1st polar body may or may not undergo second meiotic division. If it undergoes, 2 more bodies are obtained. FORMATION OF POLLEN GRAINS / MICROGAMETES The anther contains four pollen sacs, where pollen grins develop. The pollen mother cell / microspore mother cell (2n) diploid undergo meiosis to give a tetrad of 4 haploid pollen grains. Within each pollen grain the haploid nucleus divides mitotically into nuclei, but cytokinesis does not take place. 2 nuclei are formed, generative nucleus (big) and the tube nucleus (smaller) The above events are accompanied by thickening of the walls of the pollen grains and become sculptured. FA pg 395

The tube nucleus has the function of producing a pollen tube, which grows down the ovary into the ovule. The generative nucleus fuses with nucleus of the ovule to form a new organism (seed).

FORMATION OF EGG CELLS (MEGAGAMETES) Each carpel (pistil) consists of an ovary, style and stigma. Ovary is hollow, its cavity containing one or more ovules. It starts as a small protuberance projecting into the cavity. It grows and then bends, its stalk or funicle is attached to the ovary wall by placenta. Initially, the ovule consists of uniform mass of cells called nucellus. As it develops, the wall of ovule differentiates into protective layer called integument, enclosing softer nucellus. Integuments leave 2 small opening chalaza and micropyle. At the centre of the ovule, a structure called embryo sac develops, which contains the female gamete (egg cell) which is haploid. The embryo sac arises from a single cell, the embryo sac mother cell, which undergoes meiosis to form 4 daughter cells (haploid). Three of these degenerates, the one remaining enlarges and then undergoes 3 successive mitotic divisions forming 8 daughter nuclei, four at each end. On nucleus from each end moves to the middle forming polar nuclei. The remainder 3 nuclei at each and become surrounded by cell wall. One of the cells at the micropyle end becomes the functional egg; the remaining 2 are called synergids (non-functional eggs). The other three at the other end are called antipodal cells.

FERTILIZATION IN PLANTS Fertilization is the process by which the nucleus of the male gamete fuses with that of the female gamete to form a zygote. The pollen grains are taken into stigma by pollinating agents i.e wind, insects, water etc. They start germinating forming the pollen tubes. They grow down the style and round the ovary wall. It enters the ovule through the micropyle. P.t then touches the embryo sac and then t. nu disappears. Meanwhile the generative n. undergoes mitosis to form 2 male nuclei. The 1st fuses with the functional egg forming a zygote (2n) which then differentiate to to form a plumule and a radicle. The 2nd fuses with the polar nuclei to form primary endosperm (3n) that is triploid. Thus double fertilization.

(a) External fertilization:

It occurs outside the body where gametes are shed into the environment. It is common to aquatic animals e.g fish, amphibians as spermatozoa and ova are vulnerable to drying. Rapidly and large numbers are produced to increase the chances of fertilization. It is a wasteful process as many gametes do not meet.

(b) Internal fertilization: It involves transfer of male gametes directly to the female. This increases chances of fertilization. There are different forms of internal fertilization e.g in many species, males produces packages of sperms for the female to pick up and transfer to her body. In complex animals e.g vertebrates / insects, the male gametes are released directly into the body of the female during mating.

FERTILIZATION IN HUMANS Semen is ejaculated at the cervix, and with the help of flagella and energy from the mitochondria, they swim towards the egg by chance. During this time, the acrosome matures. The ovum released during ovulation is called secondary oocyte (meiosis incomplete). It is surrounded by a jelly like layer called zona pellucida, together with follicle cells. Many sperms surround the secondary oocyte, and on touching it, acrosome reaction begins. Enzymes released digest follicle cells and z. pellucida. (large no. of sperms produces large quantity of enzymes) When the sperm touches the membrane of oocyte, the oocyte undergoes its second meiotic division so that a haploid egg nucleus is formed. Cortical granules are released from the oocyte which combines with zona pellucida to form a tough fertilization membrane which prevents polyspermy. When the head of the sperm moves in, the tail gets cut off and remains outside. Sperm head absorbs water and swells, releasing its chromosomes to fuse with those of the ovum forming a diploid zygote. Fertilization is said to have taken place / or conception as in human beings. NB: The zygote is an organism, and therefore has its rights. It is not ethical to interfere with it. Pg 165 AS fig 3.2.11

AFTER FERTILIZATION The zygote undergoes cleavage I.e mitosis without the normal interphase for growth between divisions. A mass of small, identical and undifferentiated cells forming a hollow sphere known as blasocyst. The tiny cells of the human embryo are known as stem cells, they are undifferentiated cells, but have the potential to develop into many different types of specialized cells. The stem can be of 2 types:(i) Totipotent i.e a cell with the potential to form all known cell types within an organism. (j) Pluripotent i.e cells with the potential to form most of the cell types needed in an organism.

POTENTIAL SOURCES OF STEM CELLS They include:(a) Embryonic stem cells: The earliest embryonic cells are totipotent, however, by the time they reach blasocyst stage, inner cells are pluripotent. Pluripotent stem cells become more specialized as the embryo develops e.g (i) Blood stem cells give rise to blood cells (ii) Skin stem cells give rise to skin cells.

(b) Umbilical cord stem cells: Blood that drains from the placenta and umbilical cord after birth is a rich source of pluripotent stem cells. If such blood is frozen and stored, such stem cells will be available for use by the child or their family, when needed for treatment later in their lives. However, a lot of storage space is required if this is to be done for every one.

(c) Adult stem cells / somatic stem cells: Adults have different highly specialized cells. Adult stem cells exist in the form of undifferentiated cells found among the normal differentiated cells in a tissue or organ. Such cells can differentiate when needed to produce any of the cell types found in that organ or tissue e.g white bone marrow contains stem cells that can form WBC. Adult stem cells are small in number, difficult to extract, culture them in the lab and most of them form a very limited range of differentiated cells and hence they are said to be multipotent.

STEM CELL CLONING / THERAPEUTIC CLONING

Is a method used to produce healthy tissues, and treat someone with a disease caused by faulty cells e.g type 1 diabetes or Alzheimers. Cells are cloned from the patient by removing the nucleus from one of the normal body cells, and transferring it to a human ovum which has had its original nucleus removed. After electric shock, pre-embryo cells start to develop, producing genetically similar embryonic cells. Stem cells will be harvested from embryo, which is destroyed, then cultured in a suitable environment to differentiate into required tissue. The tissued organs are not rejected by the immune system.

PITFALLS FOR CELL THERAPY It is not known how genes in cells are switched on or off to form a particular type of a tissue. Stem cells could cause development of cancers in the body e. g bone marrow transplants to overcome leukemia, are likely to develop other cancers.

Advantages: Embryonic stem cell therapy avoids the rejection of a tissue or organ by the immune system. The immune system does not attack and destroy a developing embryo even if it has different markers (genes) on its cell from those of its mother.

Stem cell therapy could be used in a variety of diseases e.g

(a) Parkinsons disease: Is a brain disorder for old people 65 years. Nerve cells which produce dipamine stop working and are lost, thus dopamine level drops causing uncontrollable trmors in their hands and body. The body then becomes rigid, and finally cannot move normally at all. Stem cells transplant allow them to replce the lost brain cells and restore dopamine production. This has been proven in rats.

(b) Diabetes: Type 1 diabetes mellitus is usually for young. The B-cells may be destroyed or stop making insulin. Although insulin injection works, stem cell therapy could give them working pancrease cells again, restoring insulin production. NB: Insulin-producing islet of langehans cells have been successfully transplanted from one person to another.

(c) Damaged nerves: Damaged or destroyed nerve tissue in the brain and spine has no cure. They also dont re-grow. This can lead to permanent paralysis. Embryonic stem cells have been transplanted into mice and rats with damaged spines and the animals regained a certain amount of control and movement of limbs that had been paralyzed.

(d) Organs for transplant as mentioned earlier:

CAUSES FOR CELL DIFFERENTIATION It takes place as cells switch different genes on and off as required. Switching could be due to stimulus from the cell (internal stimulus0 or outside the cell (external stimulus) Different positions of cells in the embryo seem to result in different chemical gradients in their cytoplasm. This chemical differences appear to trigger the start of differentiation, but at later stages as shown below

Once differentiation starts and particular proteins are made, then chemical differences in the cells increases.

2. The human genome project confirmed that the human genome consists of less than 30,000 individual genes. In a differentiated cell between 10,000 and 20,000 of those genes are actively expressed. A different combination will be expressed in different cells, creating a variety of structure and functions seen in cells of different tissues. The genes which do not express themselves is due to super coiling of chromosomes and hence preventing transcription of the coiled parts thus particular proteins cannot be synthesized in such cells, as their respective MRNA cannot be formed. (in support of this gene probe is used as evidence) Use of gene probes allows scientists to identify particular pieces of DNA in a cell. Gene probe is done as follows:(i) DNA from some cells is isolated and heated gently this breaks the weak hydrogen bonds holding the 2 strands of DNA. (ii) Radioactively labeled MRNA for the required gene is added (this is the probe). (iii) Any DNA-RNA hybridization (attraction) that takes place shows that the required gene is present. (iv) This hybridization is pinpointed using the radioactive label on the MRNA which shows up on X-ray film.

Using gene probes, it has been shown that RBC and the neurons have the gene for haemoglobin as part of their DNA. However, if you use the probe on MRNA from the cells rather than DNA from the nuclei haemoglobin gene shows up in only the RBC. That is gene for production of haemoglobin is present in both types of cells but it is only expressed in RBC.

EXTERNAL STIMULI Moulting of exoskeleton in insects is controlled by 2 hormones. (a) Ecdysone controls the events of moult itself. (b) Juvenile hormone controls the kind of moult that occurs and as its level decreases, more adult characteristics occur. When there is no juvenile hormone, the pupa becomes adult. When ecdysone is injected artificially into an insect, puffs appear on the chromosomes, which are pieces of genetic material from the super coiled areas which have been opened up and made available for transcription. It is thought that they carry information about the new proteins needed in adult stage of life cycle.

EXPRESSING THE GENOME Interactions between gene and the environment: A gene is a section of a DNA that codes for a particular polypeptide chain and occupies a specific site on the chromosome known as locus. An allele is the alternative form in which a gene expresses itself e.g (i) the gene for skin colour can express itself as brown or dark which are the alleles. (ii) Gene for height in plants can express itself as tall or short (dwarf) these are the alleles. Genotype refers to the genetic (alleles) constitution of an organism, and symbols are used to represent them. Phenotype refers to the appearance of an organism due to the gene present in its body, and words are normally used to express it e.g tall, short, brown, green etc.

The interaction between genotype and the environment may influence the phenotype or appearance of an organism e.g (i) Animal hair colour: In Siamese cats and certain rabbit breeds have dark points on the ears, the muzzle and the paws due to environmental impact.

The genotype of these animals suggests that they should have dark fur all over the body due to melanin produced in a process involving the enzyme tyrosinase. However, mutation in Siamese cats results to tyrosinase that is inactive at normal body temperature, but works in low temperatures. Hence the extremities i.e ears, paws, nose where temperature is lower enzyme is not denatured, and as a result, the fur is dark

(ii) Human height: The impact of the environment on human height can be shown using:(a) Identical twins (clones) as they have same genetic material. (b) Non-identical twins as they dont have same genetic material but are closely related. (c) Ordinary normal siblings are used on a control group. The twins are separated at birth to be adopted by different families and are compared with non-separated identical, non-identical and ordinary siblings. If twins who have been reared apart show strong similarities in a trait e.g height or weight, then the influence of the genotype on the characteristic is very strong. If twins If twins reared apart show a greater difference, it suggests the environment has a strong influence on that characteristic.

Consider the following results:-

Trait

Height difference Mass difference IQ score difference

Identical twins reared apart 1.8cm 4.5kg 8.2

Identical twins reared together 1.7cm 1.9kg 5.9

Non-identical twins 4.4cm 4.6kg 9.9

Non-twin siblings 4.5cm 4.7kg 9.8

From the above, height appears to have a strong genetic component and is influenced relatively little by environmental factors. Body mass is influenced by environmental factors. IQ seems to be a combination of both, with environment playing a distinct role. For such experiments, a large number of individuals are required and for a long period of time e.g effect of smoking on birth weight or pre-mature births. Pg 189

(iii) Monoamine oxidase A (MAOA): It is an enzyme found in nervous system, liver and gut. It breaks down monoamines which include neurotransmitters e.g serotonin, noradrenaline, dopamine at the synapse. If there is too much of the enzyme present, then many of neurotransmitter substances are broken down and this can have profound effect on your mood; hence it is linked to depression and functioning of different areas of your brain. Levels of MAOA are determined genetically and different mutations can cause raised or lowered levels of the enzyme. Low levels o the enzyme is linked to:(a) Depression (b) Addictive behaviour e.g to alcohol (c) Criminal behaviour High levels are linked to:(a) Risk-taking (b) Aggressive behaviour

(iv) Cancer: Cancer cells divide rapidly to form a mass of abnormally growing cells (a tumour). These tumours may split (metastasis) releasing small clumps of cells into the blood or lymph where they are circulated, and lodge in different areas of the body, and continue their uncontrolled division forming secondary tumours. A tumour that invades surrounding tissues and metastasizes is referred to as a malignant tumour. Causes for cancer in (i) Environmental e.g due to viral infections e.g human papillomavirus that triggers uncontrolled cell growth in the cervix. (ii) Mutation of the DNA of normal body cells as they reproduce and divide, it usually takes several mutations for a cell to become cancerous. Some genes known as proto-oncogenes code for the proteins that stimulates the cell cycle. If one of these genes mutates, its forms oncogene which produces uncontrolled amount of proteins which stimulates the cell cycle constantly causing cancer. Oncogene allele is dominant. Tumour suppressor gene produce chemicals that suppress the cell cycle. If mutation occurs in these genes, no suppression takes place and the cell goes into uncontrolled growth (cancer). Mutagenic agents such as :(a) Chemical e.g cigarette smoke, alcoholic drinks, asbestos (b) Radiation e.g ionizing radiation brings about mutation in the DNA. (c) U.V light in the suns rays caused mutations in the skin cells, leading to malignant tumours.

(d) Melanoma, a cancer of the cells that produce the pigment melanin, metastasises rapidly. NB: - Brown or dark skinned people have plenty of melanin which is a natural sun screen and protects the skin from damage. - For white skinned people, they need to wear sun screens when they go out in the sun. - With thinning of the ozone layer, the risk from U.V is increasing. See pg 195 for graphs How lactose switches on the production of the enzyme that digests it. Pg 187 HOW GENES INTERACT Most genes have 2 alleles. Multiple alleles refers to when a gene has more than 2 alleles e.g:(a) Gene for blood group has 3 alleles i.e I A, IB and IO, whereby any 2 can combine to give the blood group of a person. (b) Gene for coat colour in rabbits has four alleles i.e agouti, chinchilla, Himalayan and albino. Polygeic traits (characters) are those which result due to interaction of a number of different genes. The term epistasis refers to when a gene alters or affects the expressions of another e.g wild mouse have a coat colour called agouti, where individual hairs are black with a yellow band. Agouti (a) is dominant to black coat colour (a) which is produced by black hair. In order for the coat colour pigment to be synthesized, at least one dominant allele of another independently inherited gene (C) is required. When the individuals are homozygous recessive (cc) for the second gene, no pigment is formed and the mice are albino. - A pure breeding black mouse (CCaa) was crossed with an albino (ccAA). Show how you would obtain F1 and F2. What is the phenotypil ratio of the F2? In cats, a number of genes affect coat colour. 2 of such genes affect the coat pattern i.e the agouti gene which is associated with tabby coat pattern gene. The Agouti alleles are A and a. AA or Aa gives an agouti coat i.e grey / black hairs with a yellow band, aa gives a pure black or grey coat. The tabby coat pattern gene has 3 alleles i.e T, T B and tb. TT or Ttb gives a mackerel tabby coat pattern with vertical carvings black stripes. tbtb is recessive and gives the classic blotched-tabby coat with swirls of black. TBT, TBTB or TBtb gives a ticked or freckled appearance.

However, without at least one dominant agouti allele, none of the tabby patterns will show up in the phenotype, as the cat will have a solid coat colour. Pg 185 In this case aa coat colour gene is epistatic to coat-marking (pattern) genes.

X-CHROMOSOMES INACTIVATION During the early development of embryonic cells of a female mammal, one of the x-chromosomes is inactivate by super coiling to form a mass known as the barr body. The inactivated x-chromosomes is by chance in each embryonic cell, but all the cells later descended from that cell will have the same inactivated xchromosome. Hence, in females, some cells have one x-chromosome inactivated and some with the other e.g tortoise shell cat is heterozygous for the coat colours black and orange i.e half of x-chromosomes carry an allele for black and half for orange. In humans mutation of x-chromosomes causes anhidrotic ectodermal dysplasia i.e patches on skin. If a man inherits the faulty x-chromosomes, he will have no teeth, body hair or sweat glands. If a woman inherits faulty x-chromosomes, she will have a random pattern of missing teeth, no sweat glands and patches on the body.

VARIATION This refers to the differences found among members of the same species. These differences are due to genotype of the organism as well as from the environment. Types of variations:(a) Discontinuous variations: These are features that are either present or not, they are generally determined by one or at most very few genes and the environment has no effect on them e.g Sex you are either a male or a female (ii) Blood group A, B, AB or O. (iii) Ability to roll the tongue Thus discontinuous variation is very clear cut. (b) Continuous variation: These are characters which vary very marginally from one organism to another. Such features include:- height, weight, number of leaves on a plant etc. These features are

determined by a number of genes (polygenic characters) and they are also affected by the environment. The following should be taken into account when studying continuous:(i)To take a large sample (ii)The large sample should be randomly collected (iii) Present the data to show the frequency distribution of the character.

If a character shows a continuous variation, then the frequency distribution will be a normal distribution curve i.e a bell shaped curve. The mean of the character under investigation e.g height is exactly at the centre of the normal distribution curve and all the heights are distributed equally about the mean. The amount of variation can be judged using standard deviation. It measures the amount of difference from the mean in the sample. It depends on sample size as well as distance of measurements from the mean e. g about 68% of the sample will be within 1 standard deviation 95% - within 2 standard deviation. See pg 191 and draw. If a standard d is small, then there is very little variation in your population i.e all the sampled individuals are very close to the mean. If a standard d is large, it indicates a lot of variation i.e there is a wide range of measurements away from the mean.

PLANT STRUCTURES There are two main polysaccharides associated with plant i.e 1. Starch 2. Cellulose

(1) Starch: There are two main types:(a) Amylose (b) Amylopectin (a) Amylose: It is made up of x-glucose monomers which are joined by 1, 4 glycosidic bonds which are formed by condensation reactions. They form long chains which may be coiled. Show how four monomers combine together

(b) Amylopectin: It is made up of x-glucose monomes joined by 1-4 glycosidic bonds which are formed by condensation reaction. They form long chains which are coiled and from these, branches formed from 1, 6 glycosidic bonds may arise. Formation of hydrogen bonds within the chain and branches makes it to be very compact occupying very small space. Hence, starch is used as for storage purposes (also insoluble and does not participate in chemical 2xn. 2. Cellulose: It is made up of B-glucose monomers joined 1, 4 glycosidic bonds formed by condensation reactions. One of the monomer units has to be turned round (inverted) so the bonding can take place. Hence, the hydroxyl (-OH) groups stickout on both sides of the molecule. Pg 201 fig. 4.1.3 This makes hydrogen bonds to be formed between partially +vely charged hydrogen atom of the hydroxyl groups and the partially vely charged oxygen atoms. This is known as cross-linking and holds adjacent chains firmly together. Cellulose molecules do not coil or spiral but remain as long straight chains. In the cell wall groups of 10-100,000 cellulose molecule form microfibrils pg 202 fig 4.1.4 Cellulose fibrils are laid down in layers held together by a matrix of hemicellulose and other short chain carbohydrates acting as glue. The sugars involved include mannose, gratonose, xylose etc. The combination of the cellulose microfibrils in the flexible matrix makes a composite material. This makes the cell firm (turgid) giving the strength to support the plant in a vertical position. When water is short supply plants wilts and the cells become flaccid. Cellulose molecules do not spiral but microfibrils do hence are arranged in spirals within the cell wall. The more vertical the spiral and closer together the turns, the stronger is the structure of the cell in the vertical section. Cell wall is permeable to water but can be impregnated by suberin or lignin to produce wood which makes it to be impermeable.

The plant cell wall consists of several layers:(a) Middle lamella: It is the first layer to form when a plant cell divides into 2 new cells.

It is made from pectin a polysaccharide which acts like glue, joining cell walls of neighbouring cells. Pectins has a lot of negatively charged carboxyl (-coo-) groups which combine with calcium ions to form calcium pectates.

(b) Cellulose microfibrils / and matrix: They build up on either side of middle lamella. Initially, these walls are very flexible with cellulose microfibrils, all oriented in a similar direction and are referred to as primary cell walls. As the plant ages, secondary thickening takes place. A secondary cell wall builds up with cellulose microfibrils laid densely at different angles to each other, making the composite material much more rigid, while hemi-cellulose hardens it further. NB: In some plants lignin is added to the cell walls to produce wood which makes the structure area more rigid. In structure of plants, there are many long cells with cellulose cell wall that are heavily lignified and are known as plant fibres which can be exploited by humans.

Plasmodesmata: These are structures which allow communication between cells. They consist of cytoplasmic threads, and allow substances to pass from one cell to the next (symplast).

Vacuole: Is a fluid filled space inside the cytoplasm surrounded by a membrane. Are permanent in plant cells, unlike in animal cells. Are surrounded by a membrane called tonoplast filled with cell sap - a solution of various substances, in water which cause water to move in by osmosis. This causes turgidity which keeps whole plant upright. Some vacuoles store pigments e.g betacyanin pigment of beetroots and they leak out when cut or the beetroot is heated. Other vacuoles store proteins in the cell of seeds and fruits. In some plants it may contain lytic enzyme. In plants like digitalis, it stores waste products. Chloroplast: Diag. pg 204 They have a biconcave shape. They are made up of 2 membranes i.e outer and inner. The stroma consists of a number of structures e.g starch grains, ribosomes, DNA and membranes.

The membrane increases the surface area on which enzyme-controlled reactions takes place. The membranes can be in groups (stack) where they form grana or in singles, and are referred to as thylakoid or lamella. Within the membranes are chlorophyll molecules which trap light energy for photosynthesis. Chloroplasts are formed from stem cells referred to as leucoplasts.

Amyloplasts: They are specialized plant organelles like chloroplast. They develop from Leucoplasts. They are colourless and are used to store amylopectin, which when required can be broken down to glucose that provides energy during respiration. They are found in large numbers in areas of a plant that stores starch e.g potato tubers.

STRUCTURE OF PLANT STEMS The stems of plants have the following functions: Holds the leave in bet position for obtaining sunlight for photosynthesis. Support flowers for pollination. Movement of materials i.e water and mineral salts towards leaves and manufacture food to storage organs etc. Some are green hence they carry out photosynthesis. Storage organs

(a) Epidermis: The epidermal cells secrete cutin, a waxy substance that prevents water loss and proteins against entry of pathogens. Hair: (i) Which trap moist air and thus reducing water loss. (ii) Some are hooked and therefore help climbing plants to grip their support. (iii) Others are protective, stiff, and bristly or may be loaded with irritant chemicals.

(b) Parenchyma and collenchyma: Parenchyma cells are also referred to as packing tissue and they are unspecialized and can be modified in many ways e.g:(i) The outer layers of the parenchyma may contain chloroplast hence can photosynthesis. (ii) Others could be modified into collenchyma and sclerenchyma.

Collenchyma: They have thick primary cell walls, which are even thickest at their corners. They are found around outside of the stem but inside the epidermis. They are living, hence they stretch as the plant grows and provide support. They have very little or no intercellular spaces. Pg 207 fig. 4.1.10 Sclerenchyma: It is a modified parenchyma. It provides support to the upper part of a plant, hence it develops as the plant gets bigger. It is found around the vascular bundles in older stems and in leaves. They have strong secondary walls made of cellulose micro-fibrils laid down at right angles. Some sclerenchyma form fibres in bundles. Lignin is deposited on the cell walls of these fibres in either spiral or a ring pattern, making them strong yet flexible. Once the fibre is lignified, the cell contents die because lignin is impermeable to water and so the fibres are hollow tubes which are dead. Hence, they can no longer grow and therefore growth has to take place higher up in the stem. When sclerenchyma becomes completely impregnated with lignin, they form sclereids. These cells (sclerenchyma) taper and are connected to one another by simple parts. Pg 207 fig. 4.1.11a TRANSPORT TISSUES IN PLANTS The vascular bundles consist of the transport tissues i.e:(a) Phloem which is a living tissue made of phloem cells which transport dissolved products of photosynthesis (sucrose) from leaves to growing points, storage organs etc. NB: Cambium is a layer of unspecialized cells which divide to give rise to specialized cells forming xylem or phloem (b) Xylem the tissues carry water and dissolved minerals from roots to the photosynthetic parts of the plant (movement always upwards). It consists of different types of cells e.g xylem vessels which are dead. Xylem starts off as a living tissue, and the first form is called protoxylem. It is able to stretch and grow as the walls are not fully lignified.

The cellulose microfibrils in the xylem are laid down vertically in the stem; this increases the strength of the tube, allowing it to withstand compression forces from the weight of the plant pressing downwards. With age, lignin is laid down on cell walls and cells stop growing. The cells become stronger and more supportive and the content of the cell dies. This lignified tissue is known as metaxylem. The end walls between the cells breaks down so the xylem forms hollow tubes running from root tips to shoot tips. Water and mineral salts are transported from one end to the other by transpiration stream. Water moves out of xylem through pits i.e holes in the walls of xylem. Diag. pg 208 fig. 4.1.12

TO SHOW THE LOCATION OF XYLEM IN STEM A dye such as easin is placed in a beaker. A shoot is cut under water to prevent entry of air / to maintain water column. It is then inserted into the beaker, and kept in a sunny, windy environment which promote transpiration (for a few hours). A cross-section is then made from the stem and observed under the microscope, only the xylem will be found to be with the dye. Pg 209 fig 4.1.18 THE UPTAKE OF WATER BY PLANTS The roots are responsible for the uptake of water and have the following structure:-

The root hair cell provides a large surface area for the absorption of water. The vacuole contains salt and sugar solutions which decreases the water potential (i.e water amount becomes less) Hence, water moves in by osmosis, and the cells become more dilute compared to the neighbouring cells. Hence, a concentration gradient exists across the root section from root hair cells to xylem. Thus, from one cell to the next, water moves by osmosis till it reaches the cut. The water seems to pass through different routes i.e (i) Vacuolar pathway: In this case, water passes from one cell to the next through their vacuoles. (ii) Symplast pathway: Here water moves from one cell to another through cytoplasm. (apoplast pathway). In this case water passes between the cell wall and the cell membrane from one cell to another. NB: In all the above pathways, water passes from one cell to the next through plasmodesmata.

In all pathways, water reaches the endodermis which contains casparian strip, that is impermeable to water. Some cells do not have capacian strip and are referred to as passage cells and this is where water passes. The endodermis transports mineral ions actively to the xylem, thus making water potential low.

MOVEMENT OF WATER IN THE STEM Several forces are involved:(a) Root pressure: When a plant is cut off from the root, root sap will continue to ooze from the root xylem. This is as a result of root pressure. The same root pressure is responsible for guttation i.e water drops are forced out of leaves when transpiration rates are low e.g night time. (b) The transpiration stream: This is the continuous flow of water from the soil into the root through root hairs, through the stem and out through the leaves to the atmosphere. It is aided by transpiration i.e the loss of water vapour from the surface of the plant mainly from the leaves.

When molecules of water leave the xylem to enter a cell by osmosis, tension is created in the column of water in xylem. This tension is transmitted up to the roots due to the cohesion of water molecules because of their dipolar nature and hydrogen bonds that form between them makes water molecules to stick together. This gives column of water a high tensile strength, hence cannot break easily. Adhesion is the attraction between unlike molecules in this case it is between water and xylem. This supports the entire column of water in the xylem. The combination of adhesion and cohesion brings about capillary attraction i.e upward movement of water. Diag. pg 211 fig. 4.1.16

NB: Translocation refers to the movement of substances around plants. How would you set up an experiment to show the rate of transpiration? IMPORTANCE OF WATER TO PLANTS 1. Transport media for mineral ions, manufactured food etc. 2. Required for all chemical reactions that take place in a cell as a media. 3. It brings about cooling effect during transpiration as it requires a high latent heat of vapourisation. 4. Due to its high specific heat capacity, temperatures in plants are maintained at narrow ranges. 5. Makes cells to be turgid and therefore provides support. 6. Photosynthesis uptake of minerals plants. The following ions are required by plants for healthy growth:(a) Nitrate ions: They provide the element nitrogen required to make amino acids, which in turn combine to form proteins e.g enzymes to catalyze various reactions, hormones etc It also helps in making DNA When plants lack nitrates, the older leaves turn yellow and die and grow this stunted.

(b) Calcium: It combines with pectines found in middle lamella forming calcium pectate which holds plant cells together. It plays a role in the permeability of membranes.

Lack of calcium causes growing points to die back, while young leaves are yellow and crinkly.

(c) Magnesium: Magnesium ions are needed during the formation of chlorophyll. It is required to activate some plant enzymes. Also required in synthesis of nucleic acids. Absence of magnesium causes yellowing of older leaves and growth slows down.

(d) Phosphate: Required for the phosphate groups in ATP, ADP involved in energy transfer in cells. Lack of phosphate makes the leaves to become very dark green, veins turn purple and growth is stunted.

The mineral ions in the soil are in very low concentrations compared to the concentration in the cytoplasm of root hair cells. Hence, They are taken up by active transport. They pass through apoplast or until they reach the endodermis. They can also pass through symplast pathway possibly by active transport. On reaching endordermis, they enter the cytoplasm of the cells either by diffusion or active transport. The minerals reach the xylem to be transported in the water that moves upward continuously in transpiration stream. Ions move from xylem into the cells either by diffusion or active transport. PLANTS AS NATURAL RESOURCE Plants provide materials to humans for:(a) Food (b) Drinks (c) Dyes (d) Fuel (e) Medicine (f) Building (g) Clothing etc (a) Food: Plants provide macronutrients (required in large quantities) as well as micronutrients (required in small quantities) Most plants contain amyloplasts, which is a starch storage used by:(i) Plants to survive difficult conditions e.g storage tubers of potato.

(ii) Developing embryo for rains such as wheat, rice etc. (iii) Used as food stuff for people by providing plenty of carbohydrates. Plants also contain fibre in the cellulose cell wall which cannot be digested but helps in peristalsis. They provide oils e.g sunflower, linseed, groundnuts, cashew-nut etc Pulses such as beans, peas, soya beans etc provide a lot of proteins especially to vegetarians. Fleshly and succulent fruits are also important sources of sugars and vitamins. Plants provide food to herbivores.

(b) Fibres: They are long sclerenchyma cells and xylem tissues, produced by plants like jute, manila flux, sisal etc for making ropes, paper cloth etc. Cellulose and lignified cellulose are not easily broken down by chemicals or enzymes. However, matrix of pectales + lignin around the fibres can be dissolved or removed. They have great tensile strength i.e cannot be easily broken by pulling and are very flexible. In most cases, they occur in bundles which are much stronger than individual cells.

PROCESSING OF FIBRES FOR VARIOUS PRODUCTS (a) Paper: It is made from fibres from wood. Wood fibres are not easy to extract as the matrix around cellulose fibres contain a lot of lignin. Thus wood is soaked in strong alkali e.g NaoH to produce a pulp consisting of cellulose and lignified cellulose fibres in water. Thin layers of pulp are pressed onto frames where they dry to form paper. NB: Traditionary fibres were produced by the natural action of decomposers on the materials surrounding the fibres, a process known as retting. However, in developed countries, chemicals and enzymes are used which are faster.

(b) Cotton: The widely used natural fibre is from cotton since it is produced as almost pure fibres packed around the seeds. Thus, no need for retting. Spinning pulls short single fibres and twist them altogether to form a continuous thread. The resulting threads are then woven together to make a fabric.

IMPORTANCE OF NATURAL FIBRES These fibres are obtained from plants which are sustainable i.e materials which can be replaced. The plants take up CO2 from atmosphere and lock it up in cell structures (carbon sink) Have a wide range of uses e.g clothing fabrics, ropes, insulating materials etc. Are more comfortable to wear because they absorb body fluids e.g sweat unlike synthetic fibres like nylon, polyester Biodegradable

(c) Wood: It is a composite material made of lignified cellulose fibres embedded in hemicellulose and lignin. The cellulose fibres make wood very resistant to compression (squeezing by weight) hence very good for weight bearing in buildings e.g supporting columns, beams etc Due to intermeshing cellulose, fibres do not tend to crack. Has a wide range of uses boats, furnitures, good insulators etc. It also locks up CO2 and is sustainable if managed carefully with replanting programmes. Wood is carbon-neutral as it releases CO2 during burning but uses it when growing.

(d) Bioplastics: Plastics are synthetic polymers of e.g ethane, propene etc. They vary from soft flexible with low melting points to brittle material with a high M.P and make a wide range of products. Plastics such as polythene and PVC are made from petrochemicals originating from oil which is non-renewable. Non-bioegradable leading to plastic pollutition. Bioplastics are based on biological polymers e.g starch or cellulose and are of importance compared to synthetic plastic since:(i) They are sustainable resource i.e plants such as wheat, maize and potatoes can be grown to supply the needs for bioplastic industry. (ii) Bioplastic are biodegradable i.e can be broken down by M/o.

TYPES OF BIOPLASTICS 1. Cellulose based plastics from wood pulp used for making plastic wrapping for food.

2. Thermoplastic starch this is starch from potatoes, maize etc which is mixed with gelatine which capsules to contain drugs in pharmaceutical industry. 3. Polylactic acid (PLA) from maize or sugar cane used for making computer casings, mobile phones and dinking cups. 4. Poly-3-hydroxybutyrate (PHB) which is stiff, used in making ropes, bank notes, car parts etc. NB: When broken down by m/o, they produce methane, a greenhouse gas 25 times more potent than CO2. Energy released during burning can be used to generate electricity and make more plastics. Bioplastics 1. Do not have 2. Are more expensive 3. Sustainable resources Oil based plastics 1. Have extremely useful properties 2. Cheaper 3. Not sustainable

Ethical issues: The use of crops e.g maize, wheat, sugarcane, sugar beets etc for food for biofuel and bioplastics, when there is no enough food globally; it seems not to be ethical. PLANT PHARMACIES How to investigate the antimicrobial properties of plants Plant extracts are obtained by squeezing etc Discs of filter papers are then soaked in the plant extract. Culture plates are then prepared e.g Petri-dishes which contain agar that provide nutrients to the m/o. The discs are then placed on an agar plate (culture). If the plant extract kills bacteria or stops them from growing, a clear area of jelly can be seen around the disc. Agar & bacteria growing Clear sole with no bacteria

Filter paper disc

Before

After

NB: The lager the clear area, the better the plant extract in killing / stopping growth for m/o. There is need to extract, purify the beneficial drugs in plants, so that it is possible to give known, repeatable doses of active ingredient. However, the active ingredient in any part of a plant will vary:(i) With age of plant (ii) Season of the year (iii) Time of the day For industrial scale production, then enormous amounts of plant material are needed.

Impact of plant drugs: People dont become sick often, thus live longer. Closed parts of the world due to diseases have now opened up e.g malaria

DEVELOPING DRUGS FROM PLANTS William withering approach: William Withering a doctor had no drugs for his heart patient. Thus, was taken to a herbalist who gave him a recipe with about 20 different herbs. From these 20 herbs, William guessed that foxglove contained the active ingredient. Over the next 10years, he tested a variety of portions made from foxglove on 163 patients with dropsy (swelling-oedema). The side effect included nausea, vomiting but with the right dose they produced large quantities of urine, while their hearts beat more regularly and strongly. With time Withering discovered that the best treatment for dropsy and heart failure was to give a patient tea made from the dried and powdered leaves of the foxglove. From the above, William was extracting the chemical digitalin from the leaves of foxglove. Today, this approach is no longer used as new medicines have to go through many stages and safety checks before they are given to patients.

MODERN DRUGS DEVELOPMENT Nowadays medicines which come to the market have to undergo years of research and development (R & D). Any medicine must be:(a) Effective i.e cures or prevents the disease it is designed for or relieves the symptoms. (b) Safe non toxic and without bad side effect.

(c) Stable able to be stored for some time and used under normal conditions. (d) Easily taken into and removed from your body i.e gets to its target in the body and can be got rid off once it has done its job. (e) Capable of being made on a large scale and should be in pure form, large quantities and relatively cheap. New medicines are looked for by investigating chemicals that bind our protein receptors or the active sites of enzymes. A chemical that might make useful medicine is patented i.e it gives the inventor the right to be the only one to make and sell for the next 20 years though much of this time will be taken up by more testing. The new compound is tested on cell cultures, tissue cultures as well as organs in the lab. These tests are designed to see if the compound does what the scientist thought it would. After this the compound passes to research and development.

DRUGS DEVELOPMENT AND ANIMAL TESTING Having passed the requirement of a new medicine, as well as delivery, It is then tested on animals like mice and rats as they are similar to humans. Animals are then replaced by tissue culture. NB: some people have ethical objections to the use of animals in this way.

CLINICAL TRIALS These are done if animal testing has been successful. In some countries e.g UK one has to apply for clinical trial authorization with Medicines and Health care products Regulatory Agency (MHRA)

Phase 1 trial: The new drug is given to a small number of healthy volunteers. This is to check whether the drug works as expected in the human body and does not cause any unexpected results. If successful, it proceeds to phase 2 trials.

Phase 2 trials: The new drug is used with patients affected by the targeted disease. Between 100 500 patient volunteers are given the new drug. The volunteers are closely monitored to find out more about the ideal dose, effectiveness of the drug and any side effects. Before the new drug is fully approved, it must be used on thousands of patients with the target disease.

Phase 3 trials: Over 500 volunteer patients are used. Phase 2 and 3 trials are normally carried out as double-blind trials where neither the doctor nor the patient knows whether the patient is receiving the new medicine, a control medicine or a placebo (something that looks like drug but has no active ingredients). Patients often appear to respond to a treatment a they believe that it will do good to them i.e the mind affect the body. This response is known as placebo effect. Phase 3 trials (testing) are used to confirm the effectiveness and safety of the new drug as the number of patients is large and have a better chance of showing any side effect. Data is then collected and assessed to see if there are any statistically significant differences between the new medicine and the placebo or currently available dug.

SET BACKS OF THE CLINICAL TRIALS Patients stops taking the medicine for various reasons:(a) (b) (c) (d) Insufficient effect Protocol violation Consent withdrawn Adverse effects etc

ECOLOGY: It refers to interactions of organisms (species) with the physical world (environment) and other living organisms. TERMS USED IN ECOLOGY (a) Habitat a place where an organism normally lives e.g woodland, rocky shore etc. Microhabitats these are smaller areas within a habitat e.g sing tree. (b) Population is a group of organisms of the same species, living and breeding together in a particular habitat. (c) Community a group of organisms of different species living together in a given area. (d) Ecosystem refers to interaction of organisms (plants & animals) and the environment in which they live in.

ADAPTATION TO NICHES A successful species is well adapted to its surrounding and have characteristics that enable it to survive. These characteristics are passed on to the next generation. Adaptations are of different kinds:(i) Anatomical (ii) Physiological (iii) Behavioural

(i) Anatomical: They include thick layer of blubber in seals and whales to help in swimming. Sticky hairs on the sundew plant which enables it to capture insects ready to digest. Long loop of henle in camels allows absorption of water hence conserving it.

(ii) Physiological adaptations: It includes differences in metabolic pathways or enzymes hence the way the body works e.g diving mammals can stay under water for a longer period than non-diving mammals without drowning. This is because once under water, the heart rate drops dramatically hence less blood is pumped and less oxygen is used. The body muscles can respire anaerobically than those of land-living mammals. Hence, oxygen carrying blood is directed to the brain and heart where it is still needed. This is known as mammalian diving response. Pg 235 fig 4.3.7 (Draw)

(iii) Behavioural adaptations: Reptiles and insects orientate themselves to get the maximum sunlight on their bodies when the surrounding is cold. This allows them to warm up and move fast enough to feed and escape from predators. When hot, they change their orientation to minimize their exposure or shelter from it. Social behaviour e.g hunting as a team or huddling together for warmth thus increasing chances of survival. Migration e.g birds to avoid harsh conditions. Courtship rituals e.g in birds

The great cormorant can be found in normally where water temp. = 12 and green land 50c. They are not well insulated by fat and have poorly waterproofed feathers, hence are easily affected by cold. Feeding behaviour of the birds in the 2 regions differs e.g birds in Greenland spent 70% less in water than those in Normandy. They take less time swimming on surface of water dives and returns to the land more often. The total daily energy intake of cormorants was similar in both areas but prey capture rates in Greenland were 150% higher than in Normandy. This was due to behaviour adaptations that resulted to greater efficiency at finding food hence were more important than physiological. NB: A niche refers to entire way of life e.g what an organism does, feeding habits etc and its role in the community.

SPECIES AND EVOLUTION Biodiversity is a measure of the variety of living organisms (smaller to largest) and their genetic differences and the ecosystem in which they are part of. This includes diversity within species, between species and of ecosystem species. It also refers to every form of life from smallest to largest organisms, the genes that give them their specific characteristics and the ecosystem of which they are part of. It is a group of organisms that are capable of inter-breeding to produce fertile offsprings. Initially the scientists used the morphology i.e outer and inner appearance of an organism and the degree of similarity or difference was used to group them into species. However, a number of factors can affect appearance of an organism and hence a large amount of variation in related organisms. Currently, the chemicals of life i.e DNA, RNA and proteins are used as they show differences when they are broken down into constituents parts and hence are used for molecular phylogeny (analysis of different chemicals and genes in different organisms to identify relationships).

REPRODUCTIVE DEFINITION OF SPECIES If two individuals from different populations mate and give rise to fertile offsprings then they are regarded as same species as genes are combined or flow from parents to offsprings e.g a horse and a donkey give rise to a mule which is sterile hence are not in the same species. Also a Shire horse and Shetland pony fertile-lions and tigers give rise to fertile offsprings.

OTHER DEFINATIONS OF SPECIES (a) Ecological species these are species based on the ecological niche occupied by the organism. (b) Recognition species these are species based on the unique fertilization systems including behaviour patterns in animals. (c) Genetic species these are species which are based on DNA evidence. NB: Each of these definitions has its strengths and weaknesses and the vast majority of species we know were identified by morphology. MOLECULAR PHYLOGENY AND THE 3 DOMAINS For a long time, classification of organisms was based on observations of anatomy e.g counting of hairs, embryo similarities etc. Nowadays, biochemical relationships are used to back up or clarify relationship based on morphology. This analysis of different chemicals and genes to identify inter-relationships is known as molecular phylogeny. Quite often, biochemical analysis support or conflict with relationships based on morphology e.g (a) All green plants have similar pathways for photosynthesis; hence it can be assumed they evolved from a common ancestor. (b) American porcupines and African porcupines occupy similar niches and look similar but chemical analysis show they are very distantly related. (c) Blood pigment analysis has shown that all vertebrates and some invertebrates have haemoglobin. All polychaete worms have chlorocruorin while mollusis and crustaceans have haemocyanin. (d) Analysis of the sequence of amino-acids in particular proteins e.g fibrinogen reveals how closely different groups of mammals are related. (e) Comparative anatomy and embryology of vertebrates and echinoderms star fish, sea urchins etc appear to come from one line of ancestors (it seems not obvious e.g sheep and star fish)

For many years, biologists thought there were 2 domains i.e (the largest groups of living organisms i.e (a) Eukaryotes with a complex cell structure. (b) Prokaryotes such as bacteria whereby the theory was that eukaryotes had evolved from prokaryotes billions of years ago. HOW EUKARYOTES EVOLVED FROM PROKARYOTES Pg 231 fig 4.3.3

NB: Some scientists think that chloroplast became part of eukaryotic ancestor cell first while others think it is the mitochondria. Some scientists then used molecular phylogeny techniques to investigate the above theory. They observed ribosomes, enzymes, DNA, RNA from prokaryotes and Eukaryotes and developed a theory that there were 3 domains i.e 2 prokayote domains i.e Archaea and bacteria and the eukaryotes. Archaea and bacteria are very different from one another as they are from eukaryotes. Pg 232 table 4.3.1 Genetic study shows that all the 3 groups probably had a single common ancestor. Further evidence suggests that Archaea are more closely related to eukaryotes than bacteria. Pg 233 fig. 4.3.5 NATURAL SELECTION AT GENE LEVEL The niche an organism inhabits has an effect on the genetic make up of the population. Natural selection results in organisms adapted to fit a particular habitat (niche). In the real sense, natural selection act on the genes as they also control the morphology of organisms.

MUTATIONS AND NATURAL SELECTION Mutations are sudden changes in genetic material and are inherited. They bring about variation on which natural selection acts. They also increase the gene pool. A mutation in a gene may result in a change in physical appearance of an organism (morphology), physiology or behavioural pattern. If the change is advantageous so that individuals will be more likely to survive and reproduce then the frequency of advantageous alleles increases (allele frequency). If a mutation is disadvantageous, natural selection results in its removal from the gene pool. Neutral mutations neither decrease / increase success of the individual, but will remain in the gene pool e.g war farin a chemical that prevents blood fro clotting is used as rat poison. When it was introduced, some rats already had a harmless mutation which gave them resistance to the poison.

This increased the frequency of the resistant allele and soon majority of rats were resistant to war farin and more powerful poison had to be developed.

EFFECTS OF SMALL POPULATIONS Large populations have large gene pools and hence the chance of loosing an allele is less e.g if an allele occurrence is 10% of the population, then if the population has 10 individuals, only 1 will have it and if such an individual is eliminated, so is the allele. If the population was 5000 then 500 individuals will have the allele. Hence, genetically diverse populations are required to maintain biodiversity. If a small number of individuals leave the main population to start a new one, genetic diversity is lost. The alleles they carry are part of the gene pool, but in different frequencies. Any unusual gene in the founder members of the new population may become amplified as population grows and this is known as founder effect. E.g by the Amish an American religious sect which developed Ellis-van Creveld syndrome (had dwarf limbs, extra digits etc) became much more after they separated themselves from the main population.

EVOLUTION IN ACTION Organisms that are not well adapted to the given environment may not survive to reproduce or may reproduce fewer offsprings than those well adapted and their characteristics will become less common in the population. This is what Darwin meant by survival of the fittest and is what we now call natural selection (process by which the organisms best suited to a particular environment are most likely to survive and pass on their advantageous genetic characteristics to their offsprings) If the niche changes due to changes in the environment, other characteristics may make an organism more successful. Natural selection will favour the survival of individuals with those different characteristics and we say selection pressure has changed. (S.P = changes in an environment that means that certain characteristics will give an organism an advantage) Changes in selection pressure result in changes (evolution) with the species. Depending on how different the individuals are, they may be considered a new species.

TYPES OF SELECTION PRESSURE (a) Directional selection: It occurs anywhere that environmental pressure is applied to a population. It leads to a change in the phenotype of a population in a particular direction, making them better suited to their environment e.g

(i) Fur length in certain mammals was 1.5mm which was in equilibrium with the environment 100c. Change of temperature to 50c ensured that those with longer fur 2.0mm survived better and reproduced and with time the whole population changed. (ii) Oyster yields from malpeque Bay 1915-1940 disease devastated the populations but as a result of increased selection of the disease-resistant allele within the population, large healthy oyster beds returned. (iii) Where insects and plants are regarded as pests and sprayed with insecticides or herbicides a few generations resistant individuals become more common within the population. (iv) Introduction of rabbit disease myxomotosis wiped out a large rabbit population, but those that had the allele that made them to be resistant are now in large numbers. Pg 239 fig 4.3.13

(b) Diversifying / disruptive selection: Unlike directional, the out come is an increase in the diversity of the population rather than a trend in one particular direction. It occurs when conditions are diverse and small sub-populations evolve different phenotypes suited to their very particular surroundings e.g when there is a wide range of temperature through out the year, there is continuous variation for length around mean of 1.5cm. Where summer temperature is static around 150c and winter static around 50c, individuals with 2 distinct fur length predominates i.e those with 1.0cm and 2.0cm. After many generations, 2 distinct sub-populations are formed.

(c) Balancing or stabilizing selection: It occurs in all populations and tends to eliminate the extremes within a group. This reduces the variability of a population, and hence reduces the opportunity for evolutionary change e.g when there is a wide range of temperatures, there will also be a wide range of fur length about the mean of 1.5cm. When the average environmental temperature is consistently around 100c, individuals with very short or very long hair are eliminated from the populations over a number of generations. Balancing selection takes place due to natural selection whereby variety is maintained by keeping an allele within the population even though it might be disadvantageous e.g thalassaemia allele affecting human haemoglobin whereby the homozygous form is usually lethal while the heterozygous form

gives protection against malaria, thus the allele remains at a relatively high frequency in the population and this is known as heterozygous advantage or hybrid vigour. NATURAL SELECTION IN ACTION ON GENE POOL Peppered moths (Biston betularia) exist in its natural form typical. Another form is carbonaria which is black in colour. Moths are active

(Thalassaemia genetic disease in which blood proteins are not manufactured properly leading to severe anaemia). INCREASING BIODIVERSITY (speciation) Sometimes one species can evolve into more than one other species e.g Darwins Finches. These are birds found on Galapagos Islands where there are number of feeding niches for birds such as seeds, large nut and insects living in rotten bark. The birds that first came had variations in alleles and characteristics and these were accommodated by the different niches on island e.g birds with slightly smaller, stronger beaks would get more food by eating seeds, hence enable them to survive, reproduce and pass on its beak characteristic to its offsprings. Over generations, natural selection resulted in birds with small, strong beaks for eating seeds. Those which had longer, thinner beaks were more successful in probing dead wood for insects and in successful generations gave rise to long thin beaks finches. By exploiting different niches, finches avoided competition for some scarce food resources. In all the above cases, food was the selection pressure and resulted to 14 different species of finches, over several millions of years. It was also important for the finches to mate according to similarities, in order to pass on the advantageous characteristics. Otherwise mating of different beak shaped finches, produce a variety of offsprings that are less well adapted. Thus, other phenotypic and behavioural changes that made choosing the right mate easier were selected for. However, DNA analyses show that finches are genetically similar, despite feeding on a variety of foods and being of different body sizes. Selection of four features that give reproductive success is known as sexual selection. Sexual selection in action pg 243 fig 4.3.17

ISOLATING MECHANISMS This refers to the various ways by which members of a population are isolated from one another, thus leading to formation of different species. When isolated, mating does not take place and hence flow of the genes e.g (a) Geographical isolation: In this case, a physical barrier such as a river, mountain range separates individuals from an original population.

(b) Ecological isolation: Two populations that inhabit the same region but develop preferences for different parts of the habitat.

(c) Seasonal isolation: The timing of flowering or sexual receptiveness in some parts of a population drifts away from the norm for the group this can lead to 2 groups reproducing several months apart.

(d) Behavioural isolation: These are changes which occur in the courtship ritual where some organisms display a mating pattern so that some animals do not recognize others as being potential mate. Mutation could cause changes in colour or patterns of markings.

(e) Mechanical isolation: A mutation may occur that changes the genitalia of animals, making it physically possible to mate successfully with only some members of the group or changes the relationship stigma and stamens making pollination impossible.

Allopatric speciation: It occurs as a result of a population becoming geographically isolated i.e any physical barrier which prevents 2 groups of the same species from meeting must prevent them from breeding e.g mountain ranges, deserts, oceans, rivers etc. Sympatric speciation: It occurs when organisms inhabiting in the same area become reproductively isolated into 2 groups for reasons other than geographical.

Endemism: This is a situation whereby a species of an organism is found only within a particular area. Such organisms are said to be endemic. This could be due to:(a) Availability of niches to species. (b) Different selection pressure of those niches. (c) Founder effect of a limited gene pool. (d) Migration limited by geographical barriers e.g mountains, rivers etc NB: Thus islands tend to have endemic species. EXAMPLES OF ENDEMISM (a) Madagascar species found in Madagascar are almost endemic to island e.g (i) Giant baobab trees (ii) Ring-tailed lemurs (iii) Elephants foot plant (iv) Yellow-streaked tenrec (b) Hawaii has the following:(i) Native flowers 1000 species (ii) Insects 10,000 species (iii) Land snail 1000 species (iv) Birds 100 species Analysis of the DNA of the native population shows that they are very closely related despite looking very different. The insect species evolved from around 400 original species while there were seven founder species of land birds. Endemism have a rich biodiversity in terms of species number but low genetic diversity hence, such areas are vulnerable to introduction of disease. (c) Australia it consist of:(i) Marsupials (mammals) which protect their young in pouches e.g kangaroo. (ii) Monotremes egg-laying mammals. ENDEMISM AND OTHER ISOLATING MECHANISMS Endemism can occur where there is plenty of food, restricting for moment e.g in rainforests and estuaries. Isolating mechanisms easily separates populations while complex interactions develop different species to produce new specialized niches e.g in rainforest many plant species are pollinated by one kind of insect. NB: Analysis of modern species under threat of extinction shows that island species are at more risk e.g in pacific island 110 species of birds face extinction.

This is because island ecosystems are small and very vulnerable to interference and damage by human beings. MEASURING BIODIVERSITY It is measured by specie richness i.e the number of species in a given area. Measuring include:(a) Indicator species or (bioindicators) these are species which are particularly susceptible to changes in the overall balance of the ecosystem e.g salmon are found in rivers that are relatively pollution free with high levels of O2 in the water hence are used as indicators of water quality. Also lizards which eat insects and are in turn eaten by mammals thus forming part of the food chain. Lizards are sensitive to many pesticides and hence are indicators of the effect of pesticide spraying. (b) Size of population of different species if they are few, they may find it difficult to get a mate and there wont be sustainable breeding population. (c) Gene pool if it is reduced, many individuals share the same alleles, faculty traits show up more and there is less variety hence changes in the environment e.g introduction of a disease can wipe out a small population. (d) The population sizes of keystone species a species which has a major effect on its environment. A large number of other species depend on keystone species for their survival.

MEASURING SPECIES RICHNESS Measuring species richness as well as the size of their populations involves:(a) Sampling several small areas of the area given: A quadrat (a sq frame of 1m2 is used). Other sizes can be used. It is useful for plants and animals that move much. The technique is known as quantative sampling. The number of different species is recorded in each quadrat. The average of different species is calculated considering the number of quadrats taken. (b) Capture recapture technique: Used to estimate population in a given area e.g night-flying insects where light traps are used to capture them. They are then marked in a way that does not affect their survival e.g too bright paint as can be seen by predators. They are then released.

After a period of time, they are captured again. The numbers marked in the second catch are recorded. Estimate population is:No. in 1st catch x No. in 2nd catch No. marked in 2nd catch (c) Animals in tree canopies are collected by beating branches and collecting what falls out: This method misses many populations that live at the top of trees e.g birds. Others are too small and are missed out e.g weevils. Currently, some researchers spray an entire tree with anaesthetic gas or smokes (fogging) then collect the organisms that fall out. However, bark dwellers still remain immune.

MEASURING GENETIC BIODIVERSITY Genetic diversity refers to variety of genes and alleles within a population. It is done by analyzing the DNA and comparing particular regions for similarities and differences. From this analysis, it has been discovered that cheetahs have little genetic diversity and their numbers are also low hence are in danger of being wiped by a single disease or small change in the environment. Thus modern populations are related to a few founder members. NB: From molecular phylogeny maps based on both number of species and DNA similarities e.g for bees fig 4.4.11 pg 253 Importance of such maps is that if one is trying to conserve biodiversity with limited funds, then areas with highest biodiversity are given priority. IMPORTANCE OF BIODIVERSITY It is based on the interdependence of all the organisms which affects the physical conditions around them e.g Air and water of the planet are purified by the action of a wide range of organisms. Waste is decomposed and made non-toxic by fungi, bacteria e.g toxic ammonia is converted to nitrates which are taken and used by plants. Plants:(i) Transpire and this may determine rainfall distribution. (ii) Roots hold soil together affecting the surface run off which in turn reduce risk of flooding. (iii) Pollination, seed dispersal, soil fertility, nutrients recycling like nitrogen cycle depends on thriving biodiversity.

(e) Biodiversity provides the genetic diversity to develop production of crops, livestock, fisheries and forests and enables breeding and genetic engineering. This will cope with problems due to disease climate change. (f) Production of medicine. NB: Keystone species are those which have important impact on the environment in which they live though they may not be the obvious species in the area . E.g 1 The sea otter have ensured the survival of giant kelp forests in the ocean. Kelp provides a wide range of species but provides food to purple and red sea urchins. Urchins free predators and roam the sea floor where they eat kelp as it starts to grow, hence keeping it short, thus reducing biodiversity. Sea otters are major predators of sea urchins and eat them in large numbers but some hide in rock crevices. This allows kelp to grow several centimeters in a day. As kelp forest forms, bits of kelp break off and fall to the bottom providing food for urchins in crevices. Thus, sea otters are key species. E.g 2 Scots pine It is the largest species and longest living organism in the forest a huge number of species are dependent on these trees. Pg 248 fig 4.4.3 (name the organisms which depend on Scots pine) Some areas such as wet tropics have the highest biodiversity e.g in less than 0.1 hectare in the Amazon forest there are about 150 280 tree species. Since each species of a tree is associated to other plants and animals, then species richness becomes very high, and such areas are referred to as biodiversity hot spot (area which is particularly rich in different species). Areas of greatest biodiversity (biodiversity hot spots) and not always the same as areas with endemic species hence it becomes difficult to prioritize areas for conservation. Biodiversity hot spots could be due to:1) A very stable ecosystem that allows many complex relationships to develop species. 2) High level of productivity, thus supporting more niches. 3) Organisms reproducing fast and more mutations are experienced which introduce more variety which needs to adapt to particular niches and evolve to form new species.

NATURE OF EXTINCTION Extinction refers to the permanent loss of all members of a species e.g dinosaurs, dodo saber-toothed tigers etc. They become extinct due to changes in their habitat e.g

(a) Temperature which may affect food supplies. (b) A rise in sea level causing floods. (c) Arrival of a new species. NB: The extinction rate is about 1-100 species every year but is now increasing to 27,000 species mainly due to human activities. Species which are about to become extinct both their population sizes and genetic diversity falls and the can be classified as follows:(a) Critically endangered - these are species facing an extremely high risk of extinction in the wild. (b) Endangered these are species facing a very high risk of extinction in the wild. (c) Vulnerable these are species facing a high risk of extinction in the wild. HUMAN CAUSES OF EXTINCTION Human activities are the major causes for extinction. This is because they:(a) Need land for building house, roads, industrial premises, growing food etc. (b) They pollute seas, rivers, lakes with sewage and with chemicals from industries and farms e.g fertilizers and pesticides. Thus, in great lakes 7/10 most valued fish species have almost vanished. (c) Eat plants and some animals driving them to extinction e.g dodo which lived in Mauritius. (d) Introduce other plants, animals or diseases which cause extinction e.g the prickly pear cactus opuntia was introduced in Australia and it increased in number to occupy 62,000km2 hence caterpillars (in cactus moth) were introduced as biological control and later the natural Australian flora returned. Currently, the cactus moth has been accidentally transferred to USA where it is destroying the natural cactus population of florida hence they are destructive rather than useful. (e) Bring about climatic changes that in turn cause extinction e.g some breeding populations of sea birds depend on sand eels to feed their chicks but due to temperature increase by 10c, eel population peak earlier and are no longer synchronized with arrival of chicks this may cause extinction / or the bird may breed earlier too as temperature increases. CONSERVING HABITATS Conservation refers to keeping and protecting a living and a changing environment. NB: For species to be conserved, it needs a long-term habitat hence the need for government to be involved in protecting large areas with such species e.g (a) In UK there are over 200 National Nature Reserves (NNRs)

(b) Sites of special scientific interests where endangered plants & animals thrive / or rich diversity. (c) National parks (14) where native species are protected and conserved. SUSTAINABILITY Habitats and ecosystems can be conserved by sustainable methods of land use e.g (a) Illegal logging of trees, slash and burn i.e cutting down all the trees and burning the remains etc then replanting should be carried out while harvesting should be done selectively, and in so doing biodiversity can be maintained in the rain forests and people continue to use the forest for income. (b) Sustainable agriculture i.e farming methods which minimize damage to the environment like monoculture should be avoided. It also involves using:- Little artificial fertilizers - Using biological pest control - A little chemical spraying - Maintaining hedgerows and leaving verges around fields. (c) Prioritizing of issues e.g need for sustainable agriculture and tourism to conserve biodiversity while still providing the food and income that people need. - From research, food and other resources can be produced in a way that minimizes loss of biodiversity or increasing it. - Tourism can be developed in a way that is sustainable with minimum damage to environment and jobs for local people created. SAVING ANIMAL SPECIES Animal species cannot be conserved in the wild as the conditions that have put them under threat of extinction continues. In captive breeding programmes, individuals of an endangered species are bred in zoos and wildlife parks in an attempt to save the species from extinction e.g white rhino and przewalskis horse in UK. The problems of captive breeding and re-introduction are:(a) No enough space / resource for zoos and parks for endangered species. (b) It is difficult to provide the right conditions for breeding e.g giant panda. (c) Unless the original reason for species being pushed to the edge of extinction is removed, re-introduction to the wild is unsuccessful. (d) Animals in captivity may have problems in adjusting to unsupported life in the wild. (e) When the population is small, the gene pool is reduced. (f) Re-introduction programmes can be very expensive, time consuming and they may fail.

For the most endangered species, captive breeding include cross-species cloning i.e cloning animals using closely related species as surrogate mothers e.g scientists cloned a guar an endangered species of ox. DNA from the cells of a male animal which had died 8 years earlier was fused with cows ova from which the nucleus had been removed. Of the 692 ova used, only one produced a healthy embryo that was implanted in an ordinary cow and a guar bull calf was born but died 48 hours from gut infections.

SAVING PLANT SPECIES About 25% of the worlds flowering plant species could disappear in the next 50 years i.e about 60,500 species. Cross-breeding back to original wild plants or using them to supply genes for genetic engineering are ways by which long term health of our crops plants can be maintained.

SAVING THE SEEDS Botanic gardens mainly consists of collections of plants (plants can also be conserved as seeds) e.g - The royal botanic gardens set up a seed bank which is a home of more than 4000 different wild flower seeds. - The millennium seed bank had 2 aims:(a) To collect and conserve seeds of entire UK native flora. (b) Conserve the seeds of 10% of the flora of the whole world by 2010 especially from dry lands, arid, sub-arid and sub-humid areas where there is rapid loss of habitat. Live seeds are collected from wild, removed from the fruits and cleaned. They are screened using x-rays to ensure they contain fully developed embryos. They are dried and put in jars and stored between -20 - - 400c where they can remain viable for 200 years (the life span of seeds doubles for every 5 0c drop in temperature or 2% fall in relative humidity). Seeds are usually small hence can be stored in large numbers in a small space. They contain all the genetic materials of the plant.

NB: Other countries have started this project and there are now over 1000 seed banks around the world. However, some seeds do not store well e.g mango, rubber, avocado, cacao, coconut etc. Hence, are conserved differently e.g may be grown where they are found naturally in field gene banks such as plantation, tissue cultures etc.

The species is grown on year after year and take a lot of room and work e.g International Potato Centre (IPC) in Peru with 4100 different clones of potatoes all of which have to be planted annually.

EDUCATION AND SCIENTIFIC RESEARCH Zoos and botanic gardens are centres of scientific research and general education. For this reason, university department work closely with Zoos in their research and therefore increases awareness of available conservation opportunities for issues. Media also has a role to play in highlighting the problems of falling biodiversity e.g T.V, radio, magazines, books, internet etc

NATURAL SELECTION IN ACTION ON GENE POOL Peppered moth (Bison betularia) exists in its natural light form (typical). Another form is carbonaria which is black in colour. Moths are active during the night, but they rest on the bark of trees during the day. In rural areas where there is no population, the bark of trees is lighter in colour and covered by lichens. In industrialized towns, soot is deposited on the barks and hence few lichens grow as sulphur dioxide prevents them to grow. The typical peppered moth is difficult to see against the bark of a tree in rural areas, but the black form is very conspicuous. However, when viewed against the back of a soot covered tree, the reverse is true. Moths are eaten by birds e.g thrushes, robin etc. It is supposed that the conspicuous forms are more likely to be predated and will therefore be selected against. Since these phenotypes are determined genetically, then this will reduce the gene pool as well as the frequency of the alleles that cause these colours.