BioSci107 Notes

Six Levels of Organisation Chemical, Cellular, Tissue, Organ, Organ System, Organism/Individual Chemical involves the atoms and molecules that are bound together, creating the basic units that develop onwards to life. Molecules including glucose, DNA, proteins etc. Building blocks of life Cellular level is formed from chemicals, various cells are present within the body each carrying out specific functions. It is the basic structural and functional unit of a body Groups of cells go on to form tissues, where the cells will work together to cause the tissue to function properly. Four different types of tissue, connective, nervous, muscle and epithelial. Tissues go on to form organs, which again have a specific function within the body, with each tissue containing a different role for that organ. Two or tissue types. Organ system is made from a group of organs, with their own role in the body , whether it be protection or communication etc. One organ can be found in more than one system. Organism level is the final form of organisation, where all the parts of the body work together and function accordingly so that the individual functions properly. Eleven Systems of the Body, Functions and Components Integumentary System - Function is to protect the body, regulate temp, aid in production of vitamin D, eliminate wastes, detect pain, warmth, cold etc. Components include, hair, nails, skin, sweat and oil glands, mammary gland is a modified sweat gland Skeletal System - To provide support for body, a framework, areas for muscles to attach, to protect various organs in the body, allows movement to occur, production in blood cells in marrow and storage of minerals and lipids. Components include bones and joints, cartilage. Bones such as skull, femur etc, axial and appendicular skeletons. Muscular System - allows movement, generates heat, maintains posture Components include skeletal muscle tissues Nervous System - generates AP, to cause muscular contractions, secretions of glands and to regulate bodes activities. Components include neurones, brain, spinal cord, sensory, intermediate and motor pathways. Sensory organs also to pick up stimuli Cardiovascular System - function is to transport oxygen to cells along with various nutrients, and carry away CO2 and other wastes away from cells. Also carries white blood cells, platelets, proteins, helps regulate pH, temp and water content

Components include blood, heart, and associated blood vessels Respiratory System - function is to transfer oxygen to cells, and CO2 away and out of body, also regulates pH of body fluids plus as air flows out of lungs through larynx, sound is produced. Components include mouth/nose, pharynx, larynx, trachea, lungs, bronchial tubes, alveoli Endocrine System - function is produce and secrete hormones into blood for regulation of body activities Components include organs that produce and secrete hormones such as pancreas, thyroid gland, pituitary gland, hypothalamus, pineal gland, thymus, adrenal gland, ovaries, testes, parathyroid glands Pineal - wake/sleep pattern Pituitary - anterior - FSH and LH with ovulation, posterior is ADH for kidney and water volume maintenance Hypothalamus - aids in posterior pituitary Thyroid - produces thyroid hormones to control sensitivity of body to other hormones Parathyroid - controls amount of Ca in blood and bone Adrenal - adrenaline Pancreas - insulin and glucagon Gonads - testerone, progesterone, oestrogen Lymphatic and Immune System - carries lipids from gastrointestinal tract through the thoracic duct back to blood, brings back fluid and proteins to blood and contains sites of maturation and growth/development of B and T cells. The name of the lymph that is obtained from the small intestine/gastrointestinal tract is known as chyle. The specific lymphatic vessels that pick up the lipids from the small intestine are known as lacteals. Components include B and T cells, thymus, spleen, lymph nodes, lymphatic vessels and fluid and tonsils Digestive System - physical + chemical break down of food, eliminates solid waste and absorbs nutrients. Components include the digestive tract from mouth, pharynx, esophagus, stomach, small and large intestine, anus, salivary glands, liver, gallbladder and pancreas Urinary System - Produces, stores and eliminates urine, gets rid of wastes, regulates pH of fluid and water content and mineral balance in body plus helps regulate red blood cell production Components include urethra, bladder, ureters, kidney Reproductive System -gonads produce gametes so that they combine to form a zygote, hormone production to regulate reproduction, transportation and storing of gametes and mammary glands produce milk Components in females include ovaries, mammary glands, fallopian tubes, uterus and vagina. In males includes penis, prostate, seminal vesicles, ductus deferens, epididymides, testes. Tissue Types

Epithelial - covers the surface of the body while lining hollow organs, cavities and ducts and forming glands. It is there for protection, filtration, absorption, secretion, excretion Connective - connects, supports and protects body organs while distributing blood vessels to other organs. Involved with storing energy as fat also. Provides major transport system for body. Cells in matrix of fibres and ground substance. Nervous - Carries info from one place to another through nerve impulses, detects stimuli within or outside the body, and responds through generation of an action potential. Nerve cells + supportive neuroglia, which is the supportive cells of the nervous system found predominately in the brain and spinal cord. Muscle - generates heat and contracts to produce movement/generates physical force to move body structures. Contractile cells Germ Layers Germ layers will develop into the 4 different tissue types Endoderm - Goes on to develop into epithelial tissue. And this tissue goes on to form lining of whole GI tract except oral cavity and anal canal, + epithelium of associated glands, and also forms stomach, colon, liver and pancreas. Mesoderm - Develops into epithelial, connective and mostly muscle. There are various types of mesoderms present, each developing into different tissues, forming different components of the body, such as kidneys and gonads, cartilage, skeletal muscles. Bone and blood. Ectoderm - Develops into epithelial and nervous. Again, different types of ectoderm to different tissues. They will go on to form hair, nails, epidermis, brain, spinal cord, peripheral nervous system. Epithelium of skin Origin of Germ Layers Fertilised egg undergoes cleavage or cell division to form a solid ball of cells, known as morula. A fluid filled cavity known as the blastocoel, develops with cell division, to form a hollow ball of cells, known as blastula. Germ layers form when hollow blastula transforms into a three layered gastrula and this process is known as gastrulation. Cells from surface of blastula + deeper marginal zone move inwards through the blastopore, forming in the embryo. As involution occurs, the blastocoel gets closed up and another cavity, known as the archenteron is formed. The opening of this is closed by a yolk plug. Cells that move in are replaced by cells moving out, and this process of sheets of cells moving is known as epiboly. Blastopore closes, surrounding the yolk, marking location for anus. Blastopore forms opposite the entry point of the sperm in the endoderm Marginal Zone goes on to form future mesoderm

3 layered structure around a cavity, endoderm which lines the cavity, mesoderm derived from marginal zones and ectoderm, outermost layer which does not involute. Pancreas is found both in digestive and endocrine, similarly mammary gland is both integumentary and reproductive system. Pancreas secretes inuslin and glucagon for endocrine and secretes pancreatic juices that contain digestive enzymes, for aid in absorption of nutrients by small intestine. Erythropoiesis is the name of the process for the production of RBC's. Erythropoietin is the glycoprotein hormone that controls this process, produced by the interstitial fibroblasts in the kidney and perisinusoidal cells in the liver. Related to the urinary system. Ground substance in the connective tissue is the non cellular components of ECM which are fibres. It consists of all proteinaceous components including glycoproteins, proteoglycans, matrix proteins and water. Not including collagen. Skeletal muscles contain muscle fibres/cells and within these are myofibrils, and within them are sacromeres. Sacromere contains two bands, actin and myosin. Actin is lighter, thinner and myosin is darker, thicker. A band is where actin and myosin overlap, and where both are obviously present. I band is where actin is only present. H zone is where mysoin is only present. Z line is in the centre of each I band and marks the start of every new sacromere. Actin molecules are bound to the Z line. M line is inside the H zone. Cell Junctions Cells epithelium are held together by junctions. Epithelial cells also contain different surfaces which carry out different functions, ie apical surface, lateral surface and basal surface. Apical is the top, basal is the bottom and lateral is on the side of the cell. TIGHT - Tight junctions are found near the apical surface of the epithelial cell, it contains a transmembrane, occludin, that tightly binds two adjacent cells, preventing movement of any liquid or small molecules between the cells, and prevent leakage of any fluid from various organs such as stomach, intensities and urinary bladder into the blood. The cells line these organs. ADHERENS - found below tight junctions, on the lateral surface. It consists of a layer of protein known as plaque and this is attached to the microfilament, which consists of actin, which produces an adhesion belt that circulates the whole cell at that level. What joins the two cells together is the transmembrane glycoprotein, cadherin that attaches to the plaque on each cell and then to each other to cause the connection. Main function of this junction is to resist separation during contractile activities. DESMOSOMES - They contain plaque and cadherins also, however the attachment to the cytoskeleton is through the intermediate filament, which consists of keratin. Again, joining of cells is through cadherin attachment. The intermediate filaments range from one desmosome to the other that is on the other side of the cell and this contributes towards the stability of the cells and consequently the tissue. These junctions prevent epidermal cells (cells that make up outermost layer

of skin) and cardiac muclse cells from separating under tension and from pulling apart during contraction respectively. HEMIDESMOSOMES- Half a desmosome, contains only one layer of plaque on one cell, attached to intermediate filament also, however transmembrane glycoprotein is integrin and this goes out to the extracellular space, as hemidesmosomes attach cell to basement membrane. GAP JUNCTIONS - Involved in communication between cells through the fact that it allows small molecules and ions to pass from one cell to another. It keeps the cytoplasm between adjacent cells continuous, similar to plasmodesmata in plant cells, however this junction consists of connexins, which go on to make connexon between two connexins. (the tunnel is the connexon). Also allows nerve and muscle impulses to spread rapidly from one cell to another, essential in cardiac cells, uterus cells and grastrointestinal tract. BASEMENT MEMBRANE - Epithelial tissues separated from other tissues by a basement membrane that consists of basal lamina and reticular lamina, found between epithelium and connective tissue. Functions - supports overlying epithelium - provides a surface which epithelian cells may move along during growth and wound healing - acts as a physical barrier - participate in filtration of blood in kidneys Epithelia contain nerves but are avascular, connective tissue are vascularised, therefore nutrients and oxygen is taken by epithelial cells from connective tissue through means of diffusion and similarly for the transport of wastes and carbon dioxide away from the cells. Epthelial tissues have - selective barriers that limit or aid transfer of substacnes into and out of body - protective surfaces that resist abrasion - secretory surfaces that release products produced by cells onto their free surfaces. Basal - attached to basement membrane, keeps anchored Lateral - contains junctions Apical - faces surface, body cavity, lumen or tubular duct to secrete or absorb products. May contain cilia or microvilli Basal Lamina - contains proteins such as collagen, laminin, glycoproteins and proteoglycans. Laminin is what is connected to the integrin from hemidesmosomes. Reticular lamina - contains collagen produced by fibroblasts Two types of epithlial cells are present, the covering and lining cells and glandular cells. COVERING AND LINING - Form outer covering of skin and some internal organs, lining of blood vessels, ducts, body cavities, and interior of repiratory, digestive, urinary and reproductive systems. Simple - single layer, filtration, absorption, secretion Stratified - two or more layers, protection

Pseudostratified - appears to have many layers, however only one layer is present and all cells are in contact with the basement membane. Not all cells reach apical surface. Secretion Squamous - flat and thin, diffusion Cuboidal - shape of a cube, secretion and absorption Columnar - long and tall, secretion and absorption Transitional - varies from cuboidal to squamous, found in areas prone to stretching. Simple Squamous - Single layer, flat cells. - Lines cardiovascular and lymphatic system, known as endothelium, epithelial layer of serous membrane, known as mesothelium - Filtration, diffusion, secretion Simple Cuboidal - single layer, cube form - covers surface of ovary, lines anterior surface of capsule of lens, kidney tubules and smaller ducts of many glands, makes up secreting portions of some glands, thyroid and ducts of some glands such as pancreas. - secretion and absorption Non ciliated simple columnar - contains microvilli, single layer, tall and long. Microvilli will increase SA of cell, increasing rate of absorption - lines gastrointestinal tract, ducts of glands, gallbladder - secretion and absorption Ciliated Simple columnar - single layer, contains cilia, long and tall. Oval nucleus near base - lining of bronchioles, fallopian tubes, uterus, ventricles of brain - cilia move mucus towards various areas, beat in unison, Cilia also help move oocytes towards uterus in the tubes. Pseudostratified Columnar Epithelium - appears to have many layers, long and tall, all cells attached to basement membrane, Cilia - goblet cells to secrete mucus, non ciliated - lacks goblet cells - Ciliated, majority in upper respiratory tract, non ciliated - male urethra, epididymis and lines larger ducts of glands. - Ciliated - secretion Non ciliated - protection and absorption Stratified Squamous Epithelium - two or more layers, varies from cuboidal at bottom to squamous, flat at top. Describes shape at apical surface. Can be keratinised, causing it to be hard, tough layer in apical layer, ie soles of feet, for protection. The further away the cells become from the basement membrane, more keratin is present on the layer. Organelles in cell will die Non keratinised is constantly moistened by mucus from salivary and mucous glands. - Keratinised found in superficial layer of skin Non keratinised found in moist places such as lining of mouth, vagina, esophagus and covers tongue. - Protection against abrasion, water loss, IV and foreign invason Keratinised contains dead surface cells

Transition Epithelium - changes from cuboidal or columnar to squamous and flat. Ideal for lining hollow structures that are prone to expansion. More rounded on apical surface - found in lining of urinary bladder and portions of ureter and urethra - Stretch without rupturing GLANDULAR EPITHELIUM - Gland may consist of a single cell or a group of cells, secreting substances into ducts and then onto surfaces or straight into interstitial fluid and then diffuse directly into bloodstream. Endocrine - secretion of hormones into interstitial fluid and then diffusion into bloodstream, no ducts - pancreas, pituitary gland, thyroid and parathyroid, ovaries and testes, adrenal - hormone production and secretion to regulate body processes. Exocrine - secretes products into ducts that empty onto covering or lining of epithlium - sweat, oil, pancreas, ear wax glands - temp reg, digestive enzymes, salivary glands, CONNECTIVE TISSUES Connective tissues made of primarily ECM. It is composed of cells including fibroblasts and adipocytes and matrix between them. Connective tissues binds, supports and strengthens other body tissues. Major transport system (blood), major site of stored energy reserves, lipids, adipose tissue Matrix is composed of ground substance plus 3 different fibres in different proportions Ground substance is composed of mixture of substances, water, proteins and sugars including GAGs, glycosaminoglycans, which include chondriotin sulphate, dermatan sulphate andkeratin sulphate, which attach to proteins to form proteoglycans. GAGs collectively trap water to make ground substance more jelly like. Hyaluronic acid does not covalently bond to a core protein, not sulphated , attaches through glycoprotein link. 3 fibres are collagen fibre, reticular fibres and elastic fibres. Fibroblasts - widely distributed in connective tissue and are migratory. They secrete components of basement membrane, matrix, fibres(collagen) and ground substance. Adipocytes - under skin and around organs, present in red bone marrow and yellow bone marrow also. They store lipids as energy reserves. FIBRES Collagen Fibres - strong, provide high tensile strength, and provides flexibility. Often occurs in parallel bundles. Consist of protein collagen. Found in bone, cartilage, ligaments and tendons.

Elastic fibres - Branch and join together to form network in connective tissue. Contains elastic surrounded by fibrillin, adding strength and stability. Provides elasticity, found in skin, blood vessels, lung tissue. Reticular - consists of collagen arranged in fine bundles with glycoprotein coated, to support walls of blood vessels, form network around some tissues such as areolar, adipose, nerve fibres and smooth muscle. Produced by fibroblasts, provide support and strength, plentiful in reticular connective tissue, forming stroma of many organs. Fibres also help form basement membrane. Found around adipocytes, skeletal and smooth muscle and nerve fibres. MARFAN SYNDROME - hereditary defect in elastic fibres, dominant mutation in chromosome 15, coding for fibrillin - Fibrill is a large glycoprotein that provides a structural scaffold for elastin, essential for formation of elastic fibres. - Tissues rich in elastic fibres are weakened - Blurred vision. - secreted by fibroblasts - symptoms are usually tall, chest deformity ie protruding or collapsed sternum -weakened heart valves and arterial walls, weakening of aorta. CONNECTIVE TISSUE TYPES Mesenchyme or embryonic - gives rise to all connective tissues, consists of mesenchymal cells in a semi fluid ground substance containing reticular fibres. Found under skin, developing bones of embryo. Blood vessels. Loose Connective Tissue - many cells, fewer fibres Areolar - widely distributed, contains fibres and cells in ground substance - in and around every body structure, around blood vessels, nerves and body organs. in subcutaneous layer - strength, elasticity and support. Adipose - Cells derived from fibroblast, adipocytes. Each cell contains a large drop of triglyceride. With weight gain, amount of adipose tissue increases, increasing number of blood vessels, thus greater risk for high blood pressure. This is white adipose tissue. BAT, brown, widespread in fetus and infant, small in adults, contains rich blood supply and mitochondria. - is present wherever areolar connective tissue is present, yellow bone marrow, - reduces heat loss through skin, energy source, supports and protects organs. In infants, BAT generates heat to maintain proper body temp Dense Tissue, more fibres, less cells Regular - collagen fibres arranged in bundles with fibroblasts in rows between bundles. As collagen is not living, time is required to heal - forms tendons, most ligaments, and aponeroses - provides strong attachment, withstands tension along long axis of fibres. Collagen, high tensile strength.

Cartilage - dense network of collagen and elastic fibres Hyaline - collagen fibres present but not visible, thus glassy appearance, resilient gel as ground substance, contains chrondocytes surrounded by perichondrium. - most abundant, ends of long bones, parts of larynx, trachea, bronchi. Synovial joints - provides smooth surface for movement at joints, flexibility and support. Weakest cartilage. LIQUID CONNECTIVE TISSUE - Blood is a connective tissue and lymph also. Blood has liquid ECM, which is blood plasma, consisting mostly of water with dissolved substances in it, nutrients, waste, RBC, WBC, platelets, or erthroyctes, leukocytes, thrombocytes. Eosinophils, effective against parasitic worms, Lymphocytes, involved in immune response, basophils which release substances that intensify inflammatory reaction, neutrophils and macrophages, which are phagocytic. B cell goes on to form B plasma cell. Monocyte goes on to form macrophage. Eosinophil, basophil and neutrophil are all granular, whereas macrophage T and B cells are agranular. Platelets are formed form shedding of megakaryocyte. BONE TISSUE Bones are organs composed of several connective tissue types, including bone tissue, compact or spongy Four cells found in bone - Osteogenic cells - these are the mesenchymal stem cells from which osteoblasts develop from. These are the embryonic cells. - Osteoblasts - these are the bone forming cells that forms bone matrix -Osteocyte - developed from osteoblast, they are trapped osteoblasts, maintains daily activties of bone tissue such as exchange of nutrients and waste -Osteoclasts - Large, multinuclear cell that reabsorbs bone matrix, breaks down bone, formed from blood monocytes. They break down bone by secreting enzymes. The more ruffled the border, the greater the activity. Osteons - basic unit of compact bone, known as osteon system or haversian system. - Lamellae - concentric ring of ECM consisting of mineral salts for hardness and compressive strength and collagen fibres which provides tensile strength. Lamellae is responsible for compact nature of this type of bone tissue. Minerals include Ca and P, calcium phosphate, calcium hydroxide which form hydroxyapatite. - Lacuane - small spaces between lamellae which contain osteocytes. Canaliculi - projections from the lacunae. These provide the route for osteocytes to blood vessels in terms of nutrient and waste exchange. Central canal or haversian canal - the canal that contains blood vessels and nerves. Spongy bone lacks osteons, contains trabeculae which contains lamellae, osteocytes, lacunae and canaliculi, and spaces between trabeculae are filled with red bone marrow.

MUSCLE TISSUE Skeletal Muscles -cylindrical cells, found all over the body, attached to bones by tendons it is voluntarily contracted, biceps brachii, triceps brachii, quadraceps, deltoids, trapezius etc. One muscle fibre is one muscle cell or myocyte. They are multinucleated and many peripheral nuclei, contains striations. Myofibrils go on to make a myocyte, sarcomeres go on to make myofibrils. Thin filaments and thick filaments, thin being mostly actin and thick being mysoin contribute to myofibril. These are known as myofilaments. Sarcomere, various bands are present, - Z line, which is a plate of dense material seperates two sarcomeres - I band, where thin filaments are only present - H zone - where thick filaments are only present - M line - middle of sarcomere, holds thick filaments together, found in H zone - A band - contains thick filaments overlapping thin to produce an extremely dark area Myofilaments do not extend length of myocyte. Sarcomere is basic function unit of a myofibril. Myofibril is the contractile units of the fibre. Myofibril fills sarcoplasm. CONNECTIVE TISSUES ASSOCIATED WITH SKELETAL MUSCLES - Tendon, dense regular CT - Epimysium - dense irregular CT, surrounds anatomical tissue - Perimysium - dense irregular CT, surrounds muscle bundles or fascicles - endmysium - areolar CT, surrounds each myocyte. FUNCTION OF SKELETAL MUSCLE is - motion - posture - protection - heat production CARDIAC MUSCLE TISSUE - centrally located nucleus, striated, contains junctions between cells, gap and desmosomes, known as intercalated discs. Desmosomes for adhesion during contraction and gap to allow rapid conduction of excitation waves during contraction. Branching occurs. Involuntary muscle. Found in wall of heart. SMOOTH MUSCLE TISSUE - Located in walls of hollow internal structures - Intestines, peristalsis - Blood vessels, constriction and dilation - connected by gap junctions - found in stomach, intestine, urinary bladder Small, spindle shape cells, thick in the middle, centrally located nucleus, no striations, thus smooth.

Non striated but bundles of thick and thin filaments are present, where thin and intermediate filaments attach to dense bodies, which contain similar function to Z discs. During contraction tension is transmitted from to IF, causing cell to twist, IF are not contractile. When contracted becomes significantly smaller in length. NERVOUS TISSUE Essential for nervous system, CNS and PNS CNS is brain and spinal cord, PNS is all nervous tissues outside CNS. Nervous system is involved in homeostasis, initiates voluntary contraction, perception, behaviour and memory.

Activities grouped into 3 functions. Sensory - detection of internal and external stimuli to CNS Integrative - analysis and storing of info Motor - stimulation of effectors through PNS, including muscles and glands Two types of cells, neurones and neuroglia. Neurones - cell bodies with nucleus, contains projections where action potentials are received and transmitted from one neurone to another until it reaches destination of tissue. Receiving end is dendron, transmitting end is axon. Multipolar - several dendrites, one long axon - Most CNS neurones Bipolar - one main dendrite and one main axon, cell body found between the two. Retina Unipolar - dendron and axon fused together, contains cell body that is connected to this structure. Many dendrites and one axon emerge as a single structure from cell body. Sensory receptors. Sensory - convey AP from receptor to CNS, unipolar Motor - convey AP from CNS to effector, Multipolar Interneurons - located within CNS, found between sensory and motor, mostly multipolar. Neuroglia - found in CNS and PNS, supportive cells, they can divide within mature nervous system, no generation of AP CNS - Astrocytes - star shaped, largest and most numerous, repair and supportive, contributes to blood barrier which is the barrier that prevents any leakage of blood into tissue fluid in such places as the brain. Also communicates with neurones through gliotransmitters. - Oligodendrocytes - forms myelin sheath around CNS axons for increase speed of AP conduction - Microglia - phagocytic, protection ( resident macrophages)

- Eppendymal cells - produce cerebrospinal fluid, CSF. Line CSF filled ventricles in brain and central canal of spinal cord PNS - Schwann cells - forming myelin sheaths around axons - Satellite cells, surround cell bodies for support and fluid exchange. HUMAN DEVELOPMENT Fertilisation - Fusion of sperm and oocyte, zona pellucida is present around the oocyte which contains glycoprotein ZP3, which acts as a sperm receptor. The sperm attaches to this and it triggers the acrosomal reaction, releasing contexts of acrosome, allowing sperm to penetrate the zona pellucida. - Both are haploids, fusing together to form a diploid - Corona radiata is covering the zona pellucida, which sperm wriggles around to reach - Fusion of sperm cell with oocyte causes actions to occur to prevent polyspermy, ie fertilisation by more than one sperm cell. Cell membrane of oocyte depolarises acting as a fast block to polyspermy, as depolarised oocyte cannot fuse with a sperm, and also depolarisation causes slow block to polyspermy, through release of Ca2+ ions, which secretes vesicles with molecules in them that inactivate ZP3 and harden entire zona pellucida. - Male pronucleus and female pronucleus forms and fuse together to form a single diploid nucleus, process known as syngamy and a zygote is formed - Dizygotic twins where two different oocytes have been fertilised by two different sperms. - Monozygotic - develop from single fertilised ovum, through separation of developing cells into two embryos. Cleavage - Rapid mitotic cell division, cleavage, occurs to zygote. Cells formed from this process are known as blastomeres. The fertilised ovum remains the same size while this process is occurring due to the fact that there is no uptake of nutrients after fertilisation, thus no production of materials to produce large cells after mitotic division, so cells get progressively smaller and smaller, while fertilised ovum remains same size and mass. - At one point, the blastomeres will undergo a process known as compaction, forming a solid ball of cells and this is known as a morula. Blastocyst Formation - As cleavage continues, it goes into a process known as blastocyst formation, where two different tissues will arise from the ball. The outer layer of cells will be known as the trophoblast and the inner cell mass is known as the embryoblast. During blastocyst formation, a cavity is formed through

cavitation. This is from a liquid, uterine milk, is produced by the uterine glands passes into uterine cavity into morula and through zona pellucida. This fluid provides nourishments for developing morula and also collects between the blastomeres, pushing the embryoblasts to one side of the embryo, forming a cavity, known as the blastocoel. When this cavity has formed, the morula has changed to a blastocyst. The trophoblast acts as the surrounding cells for the cavity. - Blastocyst will hatch from the zona pellucida around day 6 or 7 and implantation will occur. Role of zona pellucida was to ensure that the blastocyst, morula, zygote did not attach to any point within the ovary, fallopian tube or abdominal cavity as ectopic pregnancies can occur, which is pregnancies in areas other than the uterus. Tubal pregnancy, abdominal pregnancy and ovarian pregnancy. Implantation - Blastocyst loosely attches to endomerium, with embryoblasts being orientated towards the endometrium as blastocyst attaches. Trophoblast secretes enzymes which dissolves the endometrium allowing the blastocyst to burrow itself into the uterine lining. - Endometrium becomes largely vascularised before this occurs - As blastocyst burrows itself in, the endometrium becomes known as the decidua. 3 components present in decidua. The decidua capsularis, which is what separates the blastocyst from the uterine cavity. The decidua basalis, which is what surrounds the blastocyst/embryo. Separating it from rest of endometrium. Decidua perietalis is the remainder of the endometrium. Development of Trophoblast - Trophoblast develops into two tissues, syncytial trophoblast and cytotrophoblast, both of which are in contact with the endometrium. Syncytial TP is what secretes the enzymes, causing digestion and liquefying endometrial cells. - Blastocyst becomes burrowed in endometrium and one third myometrium - Trophoblast also secretes hCG, maintaining viability of corpus luteum, preventing menstruation from occurring. - hCG is what is detected by home pregnancy tests, if present in blood and urine - CT undergo normal mitotic division, ST undergo nuclear division however no cytokinesis occurs thus many nuclei are present within the same continuous cytoplasm Bilaminar Embryonic Disc - Embryoblasts differentiate into hypoblasts and epiblasts. These two form the bilaminar embryonic disc - Soon after this production, a cavity forms within the epiblast and this is known as the amniotic cavity. As it enlarges, simple squamous cells from the epiblast, begin to form the roof of the amniotic cavity, known as amnion, and the floor is the epiblast.

- The hypoblast at this point has formed the roof the blastocoel and is beginning to go round the cavity and cover it the whole way, so that at the bottom of the blastocyst, what was one cell layer thick will become two cell layers thick, the hypoblast and the CT - Inside amniotic cavity is the amniotic fluid, most of which is derived from maternal blood and later fetus adds to it through excreting urine. It acts as a shock absorber for the fetus, helps regulate temp, helps prevent fetus drying, prevents adhesions between skin of fetus and surrounding tissues - Amniocentisis - process of withdrawing some of the amniotic fluid that bathes developing fetus - ST will continue to grow and form large openings in the uterine tissue known as lacunae, which mother's blood leaks into, allowing exchange of gases, nutrients and waste between mother and embryo and the blood is drained by veins of mother. This is the first stage at which embryo obtains support from mother, as before this, embryo used yolk sac for development. - Yolk sac, developed from blastocoel, supplies embryo with nutrients, blood cells, contains primordial germ cells that will develop into gonads, differentiates into primitive germ cells and forms gametes, forms part of gut, functions as shock absorber, prevents drying of embryo. - Lacunae will form inerconnecting networks known as lacunar networks - The migrating hypoblast cells will differentiate into extraembryonic mesoderm, which is mesenchymal, form a connective tissue layer around amniotic and yolk sac. Large cavities form in EEM, and these cavities join up to form the EEM coelum. The EEM is the stalk and goes on to form the umbillical cord. - Mother's blood is separated from embryo by 3 embryonic layers, ST, CT and extraembryonic mesoderm, which these 3 go on to form the chorion. This with the decidua, go on to form the placenta. The chorion goes on to surround the embryo. Placenta - structure for exchange of materials between mother and fetus and also produces hormones that are needed to sustain pregnancy. - Chorion protects embryo and fetus from immune responses of mother by secreting proteins which block antibody production and by promoting production of T cells that suppress normal immune response in uterus. - Inner layer of chorion fuses with amnion, and development of chorion, causing EEC to be referred to as chorionic cavity. Gastrulation - Primitive streak is the first sign of grastulation, which defines both the midline and caudal end. Forms on the dorsal surface of the epiblast, elongating from posterior to anterior part of the embryo, clearly establishing the head and tail/ - Small group of epiblastic cells form a primitive node at the end of the primitive streak - Cells in epiblast start migrating towards midline on caudal end and downwards towards the hypoblast. As more cells migrate, primitive streak increases in length and as less, vice versa. The

process of cells moving down towards hypoblast and detaching themselves from the epiblast is known as invagination, and once this has occurred, the first wave of cells will displace hypoblast to the sides of the embryo, causing the first wave to replace hypoblast as roof of yolk sac. This first wave is the endoderm - The second wave to migrate places itself between the endoderm and the epiblast cells above it and this is mesoderm. These are loosely packed, mesenchyme. - The epiblast cells that did not involute form the ectoderm - Embryonic trilaminar disc has formed with the endoderm, mesoderm and ectoderm all present - During grastulation, embryonic disc elongates and forms an oblong shape to the initial circular shape - At the rostral end of the trilaminar disc, there is an area that is devoid of mesoderm, known as the oropharyngeal membrane and similarly at the caudal end, the cloacal membrane. These two structures will go on to form the opening of the mouth and anus respectively. Mouth forms first and then anus. - Gastrulation will occur faster at head than at tail Differentiation of Ectoderm - Ectoderm closer to midline will develop into nervous system whereas rest will give rise to epidermis of skin, hair, nails etc - Cells of ectoderm near midline become tall and columnar forming a neural plate, which is wider at the rostra end giving rise to brain and narrower at caudal end giving rise to spinal cord. This is what will give rise to CNS - Central bit of plate goes downwards while the edges of the plate, neural folds, will curl upwards and inwards, until neural folds meet and fuse together at the midline, forming a hollow tube known as the neural tube. This process of forming a tube from plate is known as primary neurulation - Neural tube completion occurs at various times at various points, not all the same time - Closure of neural tube starts around midline, then ends up zipping up caudally and rostrally. Does not fully close initially, leaving the anterior or rostral neuropore, and the posterior or caudal neuropore. - Failure to close RN can cause anencephaly, which is the absence of a large part of the brain and skull. Failure of CN can cause spina bifida, which is where back bond and spinal cord do not close before birth. - Neural tube will develop into 3 large regions, forebrain, midbrain and hindbrain, and also the spinal cord. NEURAL CREST

- Neural crests are a small group of cells from the ectodermal cells from the tube, which have migrated to form these cells. They become tip of neural folds and become mesenchymal, migrating out of lateral edges, forming different tissues at different parts of the embryo - At the spinal cord level, PNS is formed by neural crests, producing neurones that will carry sensory info to CNS and carry motor info to effectors or glands. Also produce hormone secreting cells of adrenal glands and melanocytes, the pigmented cells of skin - Cranial region neural crests can form cartilage, bone and muscles of the face and neck NON Neural Ectoderm - Found above neural tube, gives rise to epidermis of skin, hair follicles, nails, tooth enamel, epithelium of sweat glands and mammary glands. MESODERM - Mesoderm will give rise to well defined structures - Chordamesoderm or notochord - forms a rod like structure along midline of embryo - Paraxial mesoderm - will form at both sides of midline, somitic mesoderm - Intermediate mesoderm - forms as paired cylindrical structures, lateral to somitic mesoderm - Lateral mesoderm - flattened sheets lateral to intermediate NOTOCHORD - Notochord forms after grastulation and before primary neurulation, non paired mesodermal structure, plays important role in development of nervous system and in induction, process by which one tissue stimulates the development of an adjacent unspecialised tissue. Notochord induces certain mesodermal cells to develop into vertebral bodies as well as inducing ectodermal cells that are above it, in forming the neural plate. Gives rise to vertebral column PARAXIAL MESODERM - Paired segmented structures known as somites, found on both sides of the embryo midline - Start off as loosely packed cells known as somitomeres, but soon become compact and form somites - Form cartilage of vertebrae and ribs - Muscles of trunk and limbs - Tendons - Dermis of dorsal skin - Structure of circulatory system - Each somite will give rise to specific structures, so though identical looking, something different is present with each pair. - In cranial region, somite remains loose, and this with the notochord is known as head mesoderm, giving rise to connective tissue and muscles of head and neck that are not derived from neural crest

- Four different regions are present in somites - Sclerotome - part of somite closest to notochord and neural tube. Cells become mesenchymal, become cartilage cells of vertebrae and a large part of ribs. Cartilage cells eventually become bone - Syndetome - give rise to tendons - Myotome - migrate and give rise to skeletal muscles - Dermatome - region lying underneath ectoderm, contributing to connective tissues of dorsal skin INTERMEDIATE MESODERM - gives rise to urogenital system ie kidneys, gonads and associated ducts LATERAL PLATE MESODERM - Heart, blood vessels and blood cells, lining of body cavities and bones of limbs. Visceral gives rise to heart and smooth muscle and connective tissue of gut Parietal gives rise parietal peritoneium, smooth layer of tissue that lines inside of body wall, and at limbs, they proliferate and migrate to form skeletal structures of limbs Dermis of skin from somites and parietal lateral plate mesoderm Muscle from myotomes of somites Bone from parietal lateral plate mesoderm Tendons from syndetome of somites ENDODERM - Endoderm forms GI tract, associated glands that bud off digestive tube including liver, gallbladder and pancreas. Respiratory tube forms as an outgrowth of digestive tube - Ends of tubes are closed by oropharyngeal membrane and cloacal membrane, but these go on to form mouth and anus openings. SUPPORT SYSTEMS AND GROWTH Egg shell allows movement of O2 and CO2 however no removal of wastes such as urea - All 3 cavities surrounded by EE Tissue, all were initially developed for avian and reptilian embryos however in embryos with placental development, the amniotic cavity, the blastocoel and the EEC have all adapted - Amniotic cavity, formed from a cavity being produced between epiblastic cells. The roof of the cavity is known as the amnion, squamous cells derived from the epiblast and floor is epiblast cells which will later become known as the ectoderm. It's function is to prevent the drying out of the embryo, specifically for avian and reptilian since they are born as eggs on dry land. The fluid within the cavity is formed from mother's blood and urine of fetus, which the embryo will drink and it helps with the removal of wastes through foetal circulation. As transverse and longitudinal folding occurs, the AC begins to surround the whole embryo, providing a function in protection as a shock absorber.

- Yolk sac, contains egg yolk and albumen, contains vitelline arterties and veins and the veins transport nutrients to growing embryo. Formed from blastocoel, when hypoblast cells migrate over lining of blastocoel during formation of bilaminar disc. Though embryos with placental development contain all their nutrients from placenta after it has been formed, yolk sac provides nutrients prior to this plus it all contains precursors for blood cells and it produces cells for the embryos primordial germ line which migrate to the developing reproductive system and undergo spermatogenesis or oogenesis depending on the sex of the embryo. - Allantois was initially a waste storage compartment in ancient reptilians however now it has evolved to be quite large, highly vascularised and still functions as a waste storage with ability to contribute to gas exchange. It is formed when the cloacal membrane has been formed and a small sac evaginates from the yolk sac, forming the allantois. Allantoic sac in placetal developed embryos are vesitgial due to removal of nitrogenous wastes through placenta. However the allantois becomes surrounded by EEM stalk and this forms the umbillical cord. Due to high vascularisation of allantois, these blood vessels go on to form the umbillical arteries and veins, transporting between placenta and foetus. Two arteries going to placenta, one vein coming back to heart, bringing oxygenated blood. - Chorion is formed by CT, ST and EEM. This and the decidua basalis go on to form the placenta. The chorion has functions in gas exchange, and in placental mammals, it has also evolved nutritional, immune and endocrine functions. - Chorionic Villus - As embryo burrows itself into endometrium and ST secretes enzymes to do so, these enzymes erode connective tissue and blood vessels in uterine wall, forming lacunae, large spaces that are filled with the mother's blood. - End of 2nd week, ST and CT form finger like projections known as chorionic villi, that come into contact with the lacunae. They increase surface area of what is exposed to blood allowing maximal exchange between maternal and foetal blood. - Primary chorionic villus, only contains ST and CT. Cores of villi become filled with EEM, forming Secondary chorionic villus. By end of 3rd week, within the EEM has begun developing blood vessels, capillaries and blood cells, which the blood vessels will become connected to emrbyonic heart through vein and 2 arteries in the umbillical cord. Blood vessels develop due to increase in distance of villi, thus diffusion to obtain nutrients becomes less efficient so blood vessels produced reduce distance for diffusion. - Placenta is formed from chorion and decidua basalis. It is the structure that allows exchange of nutrients and waste material between mother and embryo. - Embryo is connected to placenta through the umbillical cord, which is formed from stalk of EEM surrounding the allantois TWINS - Fraternal twins, two different eggs were ovulated and both fertilised by two different sperm. - Maternal twins, one egg is fertilised and ovum produced, where this then divides into 2 to give rise to two embryos, identical as formed from as cell, same genetic makeup. Depending on point of split, the two embryos can go on to form their own chorion and amnion or end up sharing them

- Conjoined twins is possible if splitting is not complete - Parasite twin, where does not fully develop and the other is Morphogenesis of Embryo Morphogenesis is the shaping of the organism through embryological processes. In human embryo, morphogenesis occurs with longitudinal bending as well as transverse folding. In the end we obtain an organism with all the features of an adult vertebrae, ie ectoderm surrounding the outside, endoderm lining the gut and mesoderm between these two developing. The coelomic cavity, which is formed from the fusion of two lateral plate mesoderms, forming a cavity between them, go onto form 2 pleural coelomic cavities, peritoneal cavity and pericardium coelomic cavity, which all will contain serous fluid which helps keep a frictionless environment. Serous fluid secreted by serous membrane, a smooth consisting of a thin layer of cells and a thin membrane. - At about the fourth week of development, organs are beginning to form and morphogenesis occurs. At this point in time, the heart is anterior to the oropharyngeal membrane. - Longitudinal Bending - The trilaminar disc at anterior and posterior end, rostral and caudal end, begin to bend to form a C shape. - Transverse Folding - Lateral edges of trilaminar disc move downwards and inwards, where they meet at the midline, forming a "tube" and they begin to fuse, in the direction towards the mid trunk. The ectoderm will move towards the middle while longitudinal bending occurs, forming tubes with the blind ends, that will eventually become the gut. - Overall, amniotic fluid surrounds embryo, yolk sac becomes more long and narrow and only opening is found between yolk sac and gut and foetal position is now taken place, taking up less space, yet greater volume. - Closed membranes of oropharyngeal and cloacal to ensure no other tissues or substances get into embryo while development occurs. - Folding helps to form the coelomic cavity. - Occludes majority of yolk sac, small outpouch with gut, connection with gut. ORGAN DEVELOPMENT - At about one month post fertilisation, organs are in rudimentary stages, thus still continuation in development. - At week 4 neural tube will go onto form 3 brain vesicles, forebrain, midbrain and hindbrain, which will all develop into the brain that is present in adults today, and the end of the neural tube will go onto form the spinal cord

- Forebrain separated into 2 aspects, the forebrain and the diencephalon, then midbrain, then hindbrain containing pons and cerebellum and medulla oblongata. - Trunk Neural crests go on to form PNS, through neurones, glia and melanocytes. Also produces secreting cells of adrenal gland and cranial neural crests will go onto form muscles, cartilage and bone of head and neck, plus all the muscles not produced by cranial neural crests are produced by head mesoderm, consisting of notochord and unpacked mesoderm in paraxial mesoderm. CNC also produce neurones, glia and melanocytes. Development of Face and Neck Occurs through pharyngeal arches which are produced during folding of embryo. 5 arches, seen as paired segments, the cranial neural crests will migrate to the respective pharyngeal arch and go on to form the respective muscles, bone, cartilage, nerves etc of the face and neck. - Each pharyngeal arch consists of ectoderm surrounding the outside, endoderm surrounding the inside and mesoderm in between, where blood vessels will be along with where the CNC will migrate to. CNC will also migrate to frontal nasal process/prominence to go on to form the forehead. - CNC will contribute to formation of skeletal structures, sensory ganglia and connective tissue. - Ectoderm will form epithelium of mouth and face and also produce sensory ganglia - Mesoderm will form head and neck muscles as well as blood vessels - Endoderm will form lining and glands of pharynx - On the outside of arches, there are clefts and inside of arches, pouches are present. 1st PA cleft will form external auditory canal. - First pharyngeal arch forms 2 subunits, maxillary arch and mandibular arch, which will form jaw bone, part of inner ear bone, and CNC form trigeminal nerve, different from facial nerve, and innervates teeth and jaw. - Bones produced are maxilla, mandible, malleus and incus, squamous part of temporal, zygomatic and alisphenoid - Nerves produced are maxillary nerve and mandibular nerve -Muscles formed are muscles of mastication, which are masseter muscles and temporalis muscle. - Entering month 2, facial prominences will be present, which will go on to form the face. 1st PA provides all but lateral nasal prominence. -Frontal nasal prominence which goes on to develop into the forehead - Two nasal placodes, where centres have sunken in, forming future nostrils. Around these pits are medial nasal prominence and lateral nasal prominences. Philtrum formed from medial pit fusing. - Maxillary prominence increases in size, pushing medial nasal prominences towards midline and causing fusion of these and both lateral nasal prominences to form the upper lip. Lower lip is formed by mandibular prominence, along with jaw. - Cleft lip, when maxillary prominence and medial nasal prominence do not fuse properly, causing a gap to be present.

Development of Heart - Heart and circulatory system derives from visceral lateral plate mesoderm, plus neural crests. Heart, blood vessels and blood cells. - Heart is first functional organ to develop - Heart fields, have the ability to generate the heart - Cells that give rise to heart are found as two patches near rostral end of primitive streak - 2 tubes formed from cells and fuse together at midline, forming a single tube from two primordial tubes, occurring at about 3 weeks of gestation, carrying of embryo in mother, thus 4-5 week old embryo, has 2 chambers, primitive atrium and primitive ventricle. The sinus venosus is where blood enters from caudally, and blood leaves rostrally, at the bulbis cordis, - Morphogenic events, heart looping, causes heart to change shape and form four chambers, from the two. - Blood pumped out from bulbis cordis goes to aortic arches - The sinus venosus and primitive atrium migrate dorsally and rostrally or anteriorly, causing both inlet and outlet to be found in the cranial position - Ventricles occupy caudal end and formation of two from one occurs from formation of internal interventricular septum and similarly for atria also, separating pV into right and left ventricles. EMBRYONIC CIRCULATORY SYSTEMS - 3 circuits are present, the intraembryonic circuit, the vitelline circuit and the allantoic circuit. - Intraembryonic circuit - serves tissues of embryo - Vitelline circuit - gathers nutrients from yolk sac - Anntoic circuit or umbilical circuit - gets rid of nitrogenous wastes - Blood leaving dorsal aorta, goes to aortic arches, circulating embryo, where some of this blood goes into vitelline artery and to yolk sac where it absorbs nutrients and oxygen, returning through vitelline vein, entering at sinus venosus. Nutrients and oxygen umbilical ciruculation, connecting embryo to placenta and umbilical artery carries away waste. Intraembryonic Circuit - Blood leaving heart ascends to neck region, branching into aortic arches, where each pharyngeal arch is associated with an artery and as PA disappears, each aortic arch will form an artery and supply blood to the region that the PA was associated with and formed. - Blood in aortic arches discharge blood into dorsal aortas, to rest of embryo and blood comes back to heart through posterior and anterior cardinal vein, which forms one vein and enters through sinus venosus. Vitelline Circuit

- At level of abdomen, branching occurs at dorsal aortas to form vitelline arteries, which go to yolk sac to obtain nutrients and oxygen, where it enters vitelline vein and comes straight back to heart through SV. The VA will go on to form arteries that supply the dorsal mesentery of the gut. Allantoic/Umbilical Circuit - Brach off dorsal aorta, caudal to branch forming VA, is where umbilical artery is formed - Carries oxygen and nutrient poor blood to placenta where exchange of gas and materials occur, through villi, chorionic villi. Oxygen rich and nutrient rich blood comes back to heart through umbilical vein, discharging blood straight into heart, through SV, causing mixing of blood from rich and poor blood from cardinal vein and vitelline vein. - Left umbilical artery loses connection to heart and carries blood to developing liver, able to metabolise rich nutrients taken up in placenta. EXPERIMENTAL EMBRYOLOGY - Animal embryos used to understand the growth process of normal and perturbed development of humans - All cells derived from zygote - Differences between cells arrives from differences in gene activity through regulation, thus not all genes are transcribed and translated all the time in all cells. Anterio-Posterior axis, which is y axis, anterior going up, posterior down Proximo-Distal axis, which is x axis, proximo going left and distal going right Dorso-ventral axis, which is z axis, where dorso is back and ventral is belly. - Cells location can be described by these axis - Positions of cells causes activation of genome, to create appropriate structure - Chick has 3 digit in wing and four digits in leg, A-P axis, thus unequal number of phalanges in leg and wing -Limb develops from a region of cells in embryo known as limb field, which is first apparent when small limb buds develop - Each limb bud is composed of core mesenchyme surrounded by jacket of ectoderm - Ectodermal cells elongate distally to form AER, apical ectodermal ridge, the cells change from cuboidal to columnar - Limb buds extend in P-D axis and form 3D shape - Most of limb develops from mesechymal core however limb muslces, nerves and blood and lymph vessels migrate in - Morphogen, a chemical diffusible signal, is thought to be what causes the formation along the A-P axis - Cells in limb field respond to various concentrations of this chemical and will grow corresponding to that exposure of conc, and various conc arises in different areas due to position of cells in the limb bud - Morphogen provides positional info for development of cells - Small piece of mesodermal tissue at posterior edge, known as ZPA, zone of polarising activity, is

what gives rise to new digits, and it is hypothesised that the morphogen is produced by this structure - Morphogen will diffuse from posterior to anterior position - Cells closest to ZPA will have high conc of morphogen, thus will form a respective digit, in chicken, digit 4, and digit 2 is formed most furthest away from ZPA, and 3 in the middle, telling us that the threshold for differentiation for digit 4 is the greatest, lowest in 2 and middle for 3. - To experimentally prove this hypothesis, a 2nd ZPA was grated in the anterior position at various lengths away from the original ZPA. This caused a mirror image of digits to form, such as 432234, as going from one end to the other. If we vary the distance between ZPA we can varry the pattern of formation of digits, ie 2344334, if we moved 2nd ZPA closer to original and we are coming from anterior to posterior - Morphogen produces a concentration gradient, and thus when it passes a specific level of conc, the formation of a digit will change from one type to another - Carry out experiment and try to refute hypothesis, however if results do not refute it, then no reason to reject it or falsifiy it. Idea of falsifiability was Sir Karl Popper - Hypothesis suggests that cells in limb field respond to conc of morphogen by developing according to their position and in keeping with their genetic programme. - Effects of ZPA, which is pattern formation along the anterio-posterior axis, can be mimicked by applying retinoic acid, which is a vitamin A derivative. It is thought that the Sonic hedgehog protein is the morphogen produced by ZPA, it's production occurs in the same region. -The Sonic hedgehog protein is part of the hedgehog signalling pathway, which transmits info to embryonic cells for proper development - Polydactyly is the development of extra digits, which could result from changes in Sonic hedgehog expression. There is a mouse mutant known as extra toes mutant which expresses Sonic hedgehog both posteriorly and anteriorly and has extra digits. AER - necessary for proximo-distal limb development - area behind AER is known as progress zone, and posterior to progress zone is ZPA Progress Zone - Proximal to the AER, it is a layer of mesenchymal cells that are proliferating and undifferentiated. The AER in front produces a signal on position info, which is transmitted to the cells in the progress zone so they acquire these signals. The cells will interpret these signals according to their genome when they have emerged from the progress zone. - Progress zone is demarcated, meaning separated or distinguished from AER by chemical signals. The signals are thought to involve components of FGF fibroblast growth factor family. Genes with FGF influence proximo-distal patterning. Removing AER and replacing with FGF results in almost normal limb development.

- Positional vales for PD limb parts are specified by the length of time they spend in progress zone. Once emerged out of progress zone as limb elongates, the cells positional values become fixed. Thus the first cells to exit out of progress zone in developing chick would potentially be humerus, and then after, radius and ulna, then wrings and digits. The longer they spend in the progress zone the more distally elongated they become. When AER is removed, progress zone is ended and the only limb components which form are those that are present at the time of removal of AER - AER disappears when all limb components have formed. - Grafting AER or FGF to flank region causes ectopic limb formation THALIDOMIDE AND PHOCOMELIA - T, a mild sedative to combat nausea during pregnancy. Withdrawn as it was found to be a teratogen, an agent which causes anatomical deformities in foetus. Thalidomide resulted in congenital (condition existing at birth) limb malformations, observed at hands/feet, distal structures, causing resemblance of flippers of seal, phocomelia, the disorder - Lack of limb growth, meaning no cell division in progress zone, leads to cells being continously affected by AER and FGF, failing to differentiate as proximal structures. Dorso-Ventral Pattern Formation - When ectoderm of wing bud is recombined with mesoderm so that the axis is inverted, resulting limbs are inverted also, suggesting that ectoderm is responsible for providing primary cues for DV patterning. - en-1 is expressed in ventral ectoderm and represses wnt-7a, allowing its expression in dorsal ectoderm. - wnt-7a signals to underlying mesoderm to produce lmx-1, necessary for forming dorsal limb elements. - Ventral development may be specified by absence of lmx-1 - Mutations in protein en-1 allow wnt-7a, to be expressed ventrally as well as dorsally, leading to double dorsal limbs - In mice, wnt-7a gene mutants have double dorsal limbs

Cell Structure and Function

- Cell Theory - organisms made up of cells forming collaborative, functional networks - Cell is a fundamental unit of structure and function - Undertakes all functions necessary for life including - Survival Needs - Nutrients, Oxygen, Water, Normal Body Temperature, Appropriate Atmospheric Pressure - Functions Necessary to Maintain Life - Maintenance of Boundaries - Movement

-Growth - Responsiveness - Reproduction - Excretion -Digestion - Metabolism - Total function of all cells in the body reflect total function of the body Proteins in Plasma Membrane - Plasma membrane, selective permeability - Functions of proteins embedded into plasma membrane include - Transportation -Enzymatic -Cell to cell recognition - Signal transduction -Intercellular joining - Attachment to cytoskeleton and ECM - Transportation - Channel proteins and carrier proteins. Channel proteins will contain a hydrophilic channel that allows specific polar molecules and ions to pass through it to get either into or out of the cell, this action is passive and occurs by diffusion/facilitated diffusion. - Carrier proteins require ATP and their process is active transport, where substances are being moved against their concentration gradient, and the protein undergoes a conformational change in shape, thus ATP required. A phosphorylated intermediate is produced, causing change in shape of protein. Moves substances across plasma membrane - Enzymatic - Protein could be an enzyme with active site exposed to either ECM or cytosol. Several enzymes in membrane are organised in such a way that they will carry out sequential steps of a metabolic pathway - Signal Transduction - Protein that is known as a receptor, will have a binding site that is complementary to a specific molecule, ie chemical messengers, and the external messenger signalling molecule, could cause protein to change shape allowing it to relay the message to the inside of the cell usually by attaching itself to a cytoplasmic protein. - Cell recognition - Glycoproteins on the plasma membrane, proteins with chain of carbohydrate, will act as identification tags for cells, allowing other cells to recognise the cell through this molecule

- Intercellular joining/Junctions - Membrane proteins of adjacent cells may bind in such a way that they form junctions, such as tight junctions or gap junctions - Attachment to ECM and cytoskeleton - Fibres of cytoskeleton can non covalently bind to membrane proteins , maintaining cell shape and stabilising location of certain membrane proteins. Proteins that can bind to ECM molecules can coordinate extracellular and intracellular changes. Chromatin - Largest cell organelle is nucleus - Nuclear envelope is lined with lamina, which is a fibrillar network, consisting of intermediate filaments and membrane associated proteins. The intermediate filament, lamin, has many functions including anchoring nuclear pore complexes in envelope, closely associated with envelope and regulates DNA replication and cell division. - Nuclear pores are proteins surrounding a hole - Nucleolus, made from nucleic acid and proteins, produces ribosomes, non membrane bound structure - DNA found as chromatin in nucleus when during interphase, not condensed and unorganised form - DNA is associated with histones, and DNA will wrap around these histones to form a nucleosome, and these nucleosomes will attach together to form a 30nm chromatin fibre. Then looping will occur and form looped domains attached to a scaffold, changing from 30nm to 300nm fibre. After this, chromatid is formed and then chromosome, and these have significantly higher level foldings including lopped domains and helical compaction. - Nuclear envelope is continuous with ER, - ER is a network of cisternae -SER - produces lipids, Ca storage, detoxification, steroid production, also produces phospholipids and cholesterol for formation of plasma membrane -RER - production of proteins that are either found on plasma membrane or are secreted outside of cell by Golgi Complex - Golgi is stacksof separate cisternae, and this is where proteins from RER are modified, processed and secreted out - Protein arrives on cis side, and leaves trans side - Transport vesicles with proteins in them are secreted off trans side which will fuse with plasma membrane and either secrete proteins out or cause them to be embedded into plasma membrane. Exocytosis - Mitochondria - involved in aerobic respiration, production of ATP, can produce its own enzymes but gets most from cell itself - Cytoskeleton - contains microfilaments, microtubules and intermediate filaments. Function is to maintain cell shape, support transport within cell, movement of cell, contractibility, and tensile strength of cell.

- Microfilament, found in microvillus and surrounding the cell's edges. - Consists of mainly actin subunits in two intertwined strands -7nm - Maintenance of cell shape through tension bearing elements - Changes in cell shape - Muscle contraction - Cytoplasmic streaming - Cell motility in terms of psuedopodia - Cell division in cleavage furrow formation, leading to cytokinesis - Intermediate filament, found throughout the cell, consists of one subunit from several different proteins in keratin family, depending on cell. Fibrous proteins, supercoiled into thicker cables - 8-12nm - Maintenance of cell shape through tension bearing elements - Formation of nuclear lamina - Anchorage of nucleus and other specific organelles - Microtubules, found arising from centrioles - Hollow tubes, subunit is tubulin - 25nm with 15nm lumen - Maintenance of cell shape through compression resisting girders - Cell motility in terms of cilia and flagella, with dyenin for travel Dyenin is a motor protein - Chromosome movements in cell division - Organelle movements - Contains a positive and negative terminal, positive at ends of cell, negative in centre. - ECM - provides anchorage and support of cells, segregates tissues from one another and regulates intercellular communication. - ECM will vary from one cell/tissue to another, depending on needs of cell/tissue. - Interphase chromosome looped domains appear to be attached to nuclear lamina, which is the lining of the nuclear envelope, and also to fibres of nuclear matrix - Interphase chromosome, visibly as irregular clumps, condensed state, is known as heterochromatin - Then there is less compacted and more dispersed, euchromatin - Due to compaction of heterchromatin, it is largely inaccessible to transcription machinery, whereas euchromatin is, and these will be transcribed, - Motor proteins, travel on microtubule, ATP driven - Carries vesicles and certain particles for intracellular movement - Receptors on vesicles to bind on top of motor proteins - Dyenin and Kinesin, not directly Ca regulated - Dyenin - Travels towards negative pole, centre of cell - Much larger motor protein - Moves cilia and flagella - Multiple subunits

- Kinesin - Positive end of microtubule/tubule, towards end of cells - Similar to myosin heads and use of ATP similar to myosin - Cell organelles and other substances may be linked to kinesin to move them within the cell. Harvesting Chemical Energy - Signalling requires energy to occur - Reaction that is used to generate energy occurs through the ATP cycle - When going through anabolic reactions, ATP is used and hydrolysed to ADP and Pi, to form larger molecules from smaller ones - When these macromolecules undergo catabolic reactions, to form simple molecules, then energy is released and used to form ATP from ADP and Pi and cycle continues. - Cell extracts energy stored in food molecules through redox reactions - To maintain blood glucose levels, homeostatis occurs, with use of pancreas secreting hormones from either Beta cells or alpha cells, depending on the situation in which the blood glucose level is in. BGL must remain within certain limits for a properly functioning body - When BGL is low, alpha cells in Islet of Langerhans, in pancreas, secrete glucagon, which acts on liver cells to break down glycogen to glucose and skeletal muscles, to increase the rate of synthesis (gluconeogenesis) and release of glucose and to use fat as respiratory substrate, break down fat to fatty acids, in adipose tissues. - This will cause BGL to increase back to norm - If it goes over threshold, then beta cells in pancreas secrete insulin and this acts on liver and muscle cells. Increase rate of formation of glycogen from glucose, increase rate of uptake by cell, increase rate of glucose utilisation and ATP generation, increased amino acid absorption and protein synthesis and in adipose tissues, increase in triglyceride synthesis. - Inside cells, through various processes, glucose is oxidised to CO2 and oxygen is reduced to water -Electrons lose potential energy during transfer from organic compound to oxygen, and this energy is what is used to drive ATP synthesis - Electrons given to NAD+ to form NADH - These pass electrons to ETC - ETC carries electrons down chain and as electron moves from one carrier to another, energy is lost and this energy is used to actively transport protons into the intermembrane space from mitochondiral matrix. They then must undergo facilitated diffusion through protein that contain ATP sythase, down a proton gradient, and ATP is formed. - Four major parts in aerobic respiration, glycolysis, link reaction or conversion to acetyl coenzyme A, Krebs cycle and ETC. - Glycolysis occurs without presence of oxygen, occurs in cytoplasm of cell, all other steps require oxygen to be present

- Conversion to acetyl coenzyme A and Krebs cycle occur in mitochondrial matrix and oxidative phosphorylation or ETC occurs in cristae. - Glycolysis, 2ATP molecules required to phosphorylate glucose molecule to activate it and reduce Ea, so that it may lyse. It goes on to form 4 ATP molecules, 2 pyruvate molecules and 2 NADH molecules. Net amount of ATP produced then is only 2 ATP molecules. These ATP molecules are produced by substrate level phosphorylation. - Oxidising glucose to pyruvate - Conversion into acetyl coenzyme A, pyruvate enters mitochondria, where it is converted by first being decarboxylatd and dehydrogenated and then combining with coenzyme A to form acetyl conezyme A. CO2 and NADH is produced. Therefore per molecule of glucose,2CO2 is produced and 2NADH produced - Acetyl coenzyme A enters Krebs cycle, combing with 4C carbon to form citrate. 4C is oxaloacetate. From here, citrate is decarboxylated twice, dehydrogenated 4 times and ATP produced once, thus substrate level phosphorylation occurs again, per molecule of pyruvate, thus double for per molecule of glucose. - 3NADH and 1 FADH2 molecules produced for one molecule pyruvate in Krebs cycle. - ETC, Oxidative phosphorylation - Cristae, site of ETC, NADH and FADH2 molecules arrive here, release hydrogen molecule, splits into electron and proton and electrons are taken up by ETC. At the end of the chain, ETC is transferred to oxygen, reducing it to water with protons that are present, however before this occurs, during ET, it causes integral membrane protein complexes to pump protons form matrix into intermembrane space, setting up a proton gradient, and these protons will be facilatatively diffused out of membrane space through specialised protein complexes that produce ATP, through the phosphorylation of ADP. Per molecule of glucose, ETC produce 32 -34 ATP molecules, so altogether 36 - 38 molecules of ATP are produced from one glucose molecule. - Breakdown of lipids can go on to form glycerol which will enter glycolysis, or fatty acids, which will help in conversion to acetyl CoA. - proteins will break down to amino acids, where they will enter pyruvate molecules, or go on to combine with pyruvate molecules to form a specific substance, or help in formation of pyruvate. - Aerobic respiration, controlled and regulated by feedback mechanisms, targeting allosteric enzymes at key points in glycolysis and Krebs cycle. - Phosphofructokinase - ATP inhibits, citrate inhibits, AMP stimulates - Diabetes Mellitus - Lack of functional insulin either due to - Type 1 - none being produced by the pancreas, specifically the beta cells

-Type 2 - Or insulin is produced however it is not recognised by liver cells or not functioning correctly. - When diabetes is present, BGL has the potential to rise or to drop to significant levels, past homeostatic limit, and this can affect volume of osmolarity of blood, dehydration, hunger, coma can be induced, tired. - Also means little to no glucose present for ATP production CELL CYCLE, REGULATION AND CANCER - Cell division for growth, repair and development - Some are being continuously renewed whereas others do not undergo mitosis once they have reached their mature stages. Blood cells, epithelial cells and cells in skin and cornea against nerve and muscle cells. - Chromosome is separated into chromatids during anaphase, allowing each daughter cell to get full set of diploid genome - Cell Cycle consists of interphase, mitosis and cytokinesis, and within interphase there is G1, S and G2 - In prophase, spindle forms and chromatin begins to condense to chromosome (chromosome condensation) - Premetaphase, Nuclear envelope begins to break down forming fragments and chromosomes attach to microtubules at the site of centromeres - Metaphase, Chromosomes line up in the equator of the cell, of line up in metaphase plate - Anaphase - sister chromatids separate and move as new chromosomes to the each pole - Telophase - Cell nuclei forms, spindle disappears, nucleolus forms, chromatids begin to expand to form chromatin. - Cytokinesis, oustide of mitotic cycle, separates the cytoplasm between the two poles of the cells, forming two daughter cells - In interphase, G1 is lasts for 8-10 hours, and here the cell is metabolically active, duplicates organelles and cytosolic components - S is when DNA replication occurs and centrosome is also replicated. Centrosome are two centrioles. This lasts for 8 hours - G2 lasts for 4-6 hours and this is where cell growth continues and enzymes and other proteins are synthesised. - To control cell cycle, 2 points are present where maintenance over cell cycle occurs, the G1/2 transition and G2/M transition - G2/M transition is the most substantial in maintenance of control - Cyclical changes in regulatory proteins work as a mitotic clock - cdks or cyclin dependent kinases remain in cytoplasm during whole cycle and will complexes with cyclin only before mitosis occurs, as cyclin only accumulates before mitosis occurs. - The complex, MPF is formed, and contains activity during mitosis. - Once mitosis is complete, cyclin is degraded and MPF complex is no more. Degraded by proteases - MPF is an active regulator, phosphorylates other proteins, control cell cycle check points and cell cycle processes. - External signals, growth factors, control cell cycle check points through signalling transduction

pathways - MPF, mitosis promoting factor or maturation promoting factor, it phosphorylates proteins required in mitosis during G2 phase, so that cell can enter mitosis. MPF must be activated by an enzyme before functioning as it is inhibited by phosphate group that was added before - Cancer cells escape from normal cell cycle regulation and divide out of control - Mutations of cytoplasmic signalling molecules gives rise to these cancerous cells - Proto-oncogenes function normally in that they promote the correct progression through the cell cycle of a cell, however if this is mutated, then it can cause proto oncogenes, to become oncogenes, constitutively active, causing cell to divide in the absence of growth factors -Ras mutations - Tumour suppressor proteins inhibit cell division, but when mutated, lose control ability such as p53 signalling - Control of cell cycle is a balance between proto oncogenes and tumour suppressor proteins, so development of cancer is a loss in a combination of many types of both proteins - If cell is over stimulated to undergo cell division or go through cell cycle, or if cell cycle is not inhibited, then both these effects can go on to cause increased cell division and form cancerous cells/tumour. -Proto - oncogenes to oncogenes - Mutations - Increased amount of protein through increased expression or stability of mRNA molecules or gene duplication - Chromosomal translocation causing PO to be moved to area where it can be expressed more or moved PO to a site where it will fuse with another gene forming a protein that has increased oncogenic activity FROM GENE TO PROTEIN - Transcription - process of transcribing a template strand of DNA to mRNA, which will be used for protein synthesis - Occurs in nucleus for eukaryotes and cytoplasm for prokaryotes - Transcription catalysed by RNA polymerase, with the aid of various transcription factors, activator proteins to form transcription initiation complex, TIC - Promoter is a sequence of bases found before start of gene, area where complex will attach to prior to transcription. In eukaryotes, contains a TATA box, TATA box is sequence of TATAAAA on one strand, complementary on other - Regulation through activators and enhancers, and specific transcription factors, which are the activators - Transcription occurs until termination sequence reached, either termination sequence in pro or polyadenylation signal on eu, where signal sequence is transcribed, then proteins that aid in RNA growth will cut mRNA free from RNA polymerase 2, where RNA processing must occur before translation RNA Processing

- pre mRNA contain introns and exons, firstly it is modified by adding a 5 prime cap to the 5 prime end and a poly-A-tail to the 3 prime end and this is to ensure RNA is not degraded, protects from degradation once it leaves nucleus and also aids in translation, with 5 prime end attaching to small subunit - Introns are removed through splicing - Splicing occurs with spliceosomes, which are made up of snurps and proteins. Snurps are made up of snRNA and other proteins - Spliceosomes then remove introns and splice exons together, introns are degraded immediately - Mature mRNA is formed and this is what leaves the nucleus through the nuclear pores -Used as template for translation -Contains areas of UTR on 5 prime end and 3 prime end Translation - Ribosomes catalyse synthesis of protein - Initiation, Elongation, Termination - mRNA already attached to tRNA, mRNA attaches to small ribsomal subunit at mRNA binding site with the 5 prime cap, and small ribosomal subunit arrives at start codon - Large subunit attaches to form the translation initiation complex - P site, where first tRNA is present, A site where next aminoacyl - tRNA will attach to - Formation of translation initiation complex requires GTP to by hydrolysed to GDP, releasing energy - Attachment to A site of next aminoacyl tRNA requires energy, GTP to GDP - Formation of peptide bond between amino acids - Polypeptide chain attached to tRNA in A site, rather than P site at this point - Ribosome moves down one codon, P site tRNA becomes E site, A site to P site, GTP to GDP for energy to move - tRNA in E site exits and then next amino acid arrives at A site - tRNA in P site is hydrolysed from amino acid before it moves to E and exits - Ribosome reaches stop codon, where release factor is present - Release factor deassembles ribosome, hydrolyses tRNA and polypeptide chain, 2 GTP required to break complex - Protein that is shaped into specific secondary and tertiary and potentially quaternary structure with help of chaperones or occurs as it emerges from ribosome 3 codons code for 1 amino acid - wobble effect for last base sequence between tRNA and mRNA for certain codons - complementary base pairing mRNA molecule degraded PROTEIN FOLDING, PROCESSING AND SORTING - Nascent meaning growing - Folding of protein - To form 3D shape to carry out function, globular or fibrous - Primary structure - chain of amino acids in the sequence it is found for that polypeptide, linear,

held by covalent peptide bonds. This is the backbone of protein - Secondary structure includes alpha helix or beta pleated sheets - Both are formed through hydrogen bonding between amide groups of polypeptide back bone. - Alpha helix, coiled, beta pleated sheets, molecule zig zags back and forth forming strands, which are held together by hydrogen bonds - Tertiary structure, overall 3D shape of protein, formed through various interactions occurring between the R groups of amino acids. Such include hydrogen bonds, ionic bonds, hydrophilic interactions, ie van der Waals forces, and disulfide bridges, specifically between cysteine amino acids, SH and SH to form S-S, reduction - These interactions are weak compared to intramolecular force of peptide bonds - These tertiary structures can oligomerise with others to form larger macromolecular complexes to achieve full functionality, ie Hb, keratin Protein processing and Sorting - Proteins found in cytoplasm are produced by ribosomes that are free in the cytosol - Membrane bound proteins and secretory proteins are formed fully in lumen of ER, however initially, these proteins will be translated by ribosomes free in cytosol. Once they form, a small sequence of amino acids, known as signal peptide will also be produced - Once this emerges, signal recognition particle or SRP, will target these ribosomes to specific receptors in ER membrane - signal sequence located normally at N terminus, inserts into ER membrane and growing polypeptide chain is translated across membrane, into the lumen, thus translation is occurring with ribosome attached to ER membrane, thus known as RER - Once translation is complete, all detach and protein is now in the lumen of ER - For secretory protein, chain is completely translocated and signal sequence cleaved off by signal peptidase - This causes protein to be solubilised into lumen of ER - Membrane proteins, one or more hydrophobic segments of polypeptide chain anchor it in bulayer -Before this occurs however, they must be transported, through vesicles and also modified and processed for use, which occurs in the Golgi complex - Arrives at cis side, leaves at trans, leaves in the vesicle, made of components of plasma membrane - Glycoproteins formed here, addition of carbohydrate - Some vesicles are targeted to lysosomes where they serve degradation of nutrients or facilitate renewal of cell's own macromolecules. - Medial cisternae found between cis cisternae and trans cisternae. HOW CELLS COMMUNICATE WITH EACH OTHER - Communication between cells occurs with use of small molecules or chemicals - These can be direct contact, such as diffusion of signalling molecules through gap junctions or can be through secretion of signalling molecules that are recognised by receptors present on plasma membrane - Cell signalling involves 3 steps, reception, transduction, response - Transduction involves a relay molecules, phosphorylation cascades, a specific pathway - Received signal converted to a response in a series of steps known as signal transduction pathway

Different receptors are present - G Protein coupled receptors - Ligand, such as a hormone, attaches to the receptor and causes a conformational change in the receptor protein - This causes activation of a specific cytoplasmic G protein by causing it to exchange a GDP with GTP - This activated protein will then go on to active an enzyme known as adenylyl cyclase, by binding to it - The activation of this produces a second messenger known as cAMP - cAMP goes on to activate cAMP dependent protein kinase, PKA, which will activate further downstream kinases and effectors - Activated G protein will hydrolyse GTP to GDP and Pi and become inactive, until re-activation occurs by receptor/reception - Receptor Tyrosine Kinases RTK - Example, RAS phosphorylation cascade receptor, cell division control, proto oncogene, stimulates synthesis of protein which will stimulate cell division to occur - Signal molecule or ligand, growth factor, will attach to receptor and causes the RTK to dimerise, forming one complex out of the two that were present - Auto phosphorylation of cytoplasmic tyrosines occurs - Dimerisation activates tyrosine kinase region of each monomer and each tyrosine kinase adds a phosphate from ATP molecule to a tyrosine on the tail of the other monomer - Receptor is now fully activated - 6 ATP molecules needed as 6 tyrosine molecules present, 3 on each receptor - Relay proteins recognise activation of tyrosine, they become activated by binding to the tyrosine that is phosphorylated, to a specific one, and phosphorylate further downstream relay protein usually kinases - Starting a cytoplasmic signal transduction cascade - Kinase is an enzyme that catalyses the transfer of phosphate groups - Ligand gated channels - Can be found at post synaptic neurones - Signalling molecules, such as neurotransmitters, cause ligand gated ion channels to open in PSM resulting in an influx of sodium ions, allowing local depolarisation to occur so that an AP can be generated allowing transmission to next neurone or muscle fibre - Conformational change in shape of receptor protein, acts as a gate once signal molecule attaches - Voltage gated ion channels, dependent on electrical signals -Intracellular Receptor - Receptors can be present within cytoplasm or nucleus of cytoplasm, depending on ability of cell signalling molecule to be able to cross membrane - Thyroid and testosterone act as intracellular signal molecules

- Transduction - Activation of proteins through addition or removal of a phosphate group or release of other small molecules or ions that act as messengers, ie second messengers, cAMP and Ca ions - Amplification of response, many steps, many activation of proteins during transduction if it contains many steps, plus coordination and regulation, much more opportunity. - Protein Phosphorylation and Dephosphorylation - Kinases, will phosphorylate proteins downstream which will go on to phosphorylate others and so on until the very last protein kinase will phosphorylate the protein that will bring about the response. Phosphorylation occurs by adding a phosphate group from ATP - Protein phosphatses dephosphorylate all these kinases/proteins for reuse - This pathway is known as phosphorylation cascade, just the phosphorylating part, no de - Second messengers, first considered to be extracellular signalling molecule, ligand - cAMP and calcium ions, polar, diffusable, quick - cAMP in G proteins - Ca ions, low cytoplasmic conc, high ER, mitochondria and extracellular conc - Increase in cytosolic conc of Ca ions to produce cellular responses, muscle contractions, secretion of certain substance (neurotransmitters) and cell division - Output will be activity or function of cell that meets the requirement that initiated the signal in the first place