Computational Biology Unit 1 (Part-1) PDF

UNIT I ▪ Introduction ▪ Cell theory, ▪ Whitaker’s kingdom classification ▪ Cell organelles, and their functions ▪ Homeostasis, ▪ Replication and cell Division ▪ Tissue differentiation ▪ Stem cells and their applications ▪ Genetic algorithms Introduction 2 ...

UNIT I ▪ Introduction ▪ Cell theory, ▪ Whitaker’s kingdom classification ▪ Cell organelles, and their functions ▪ Homeostasis, ▪ Replication and cell Division ▪ Tissue differentiation ▪ Stem cells and their applications ▪ Genetic algorithms Introduction 2  Concept of evolution The process by which different kinds of living organism are believed to have developed from earlier forms during the history of the earth. Jean Baptistae Lamarck (1801)- spontaneous generation of species according to needs and functionalities of the mutation Charles darwin (1859)- Based on survival of the fittest mutations 3  Living Organism A living organism may be defined as a complex unit of physicochemical materials that is capable of self-regulation, metabolism, and reproduction. Furthermore, a living organism demonstrates the ability to interact with its environment, grow, move, and adapt. 4  What Are the Main Characteristics of organisms? 1. Made of CELLS 2. Require ENERGY (food) 3. REPRODUCE (species) 4. Maintain HOMEOSTASIS 5. ORGANIZED 6. RESPOND to environment 7. GROW and DEVELOP 8. EXCHANGE materials with surroundings (water, wastes, gases) 5  Five Kingdoms and their chief characteristics Unicellular organisms that lack a nucleus and many of the specialized cell parts, called organelles. Such organisms are said to be prokaryotic (pro =‘‘before’’; karyotic =‘‘kernel,’’ ‘‘nucleus’’) and consist of bacteria. All of the other kingdoms consist of eukaryotic (eu = ‘‘true’’) organisms, which have cells that contain a nucleus and a fuller repertory of organelles. Whitaker’s Five Kingdom Classification ( 1969) 6  Cell-basic unit of life Smallest living form Inside the cell some structure transport Metabolize Respire Reproduce (Meiosis) Multiply (Mitosis) Energy producing Keep information 7  CELL THEORY All living things are made of cells Cells are the basic unit of structure and function in an organism (basic unit of life) Cells come from the reproduction of existing cells (cell division) 8  Prokaryotes Nucleoid region (center) contains the DNA Surrounded by cell membrane & cell wall (peptidoglycan) Contain ribosomes (no membrane) in their cytoplasm to make proteins 9  Eukaryotes Cells that HAVE a nucleus and membrane-bound organelles Includes protists, fungi, plants, and animals More complex type of cells 10 Cell Structure and Function 11  Organelles Very small (Microscopic) Perform various functions for a cell Found in the cytoplasm May or may not be membrane-bound Plant Cell 12  Cell or Plasma Membrane Composed of double layer of phospholipids and proteins Surrounds outside of ALL cells Controls what enters or leaves the cell Living layer Outside of cell Carbohydrate chains Proteins Cell membrane Inside of cell Protein 13 (cytoplasm) channel Lipid bilayer  Cytoplasm of a Cell cytoplasm Jelly-like substance enclosed by cell membrane Provides a medium for chemical reactions to take place Contains organelles to carry out specific jobs Found in ALL cells 14  The Control Organelle - Nucleus Controls the normal activities of the cell Contains the DNA in chromosomes Bounded by a nuclear envelope (membrane) with pores Usually the largest organelle Each cell has fixed number of chromosomes that carry genes Genes control cell characteristics 15  Nucleolus Inside nucleus Cell may have 1 to 3 nucleoli Disappears when cell divides Makes ribosomes that make proteins 16  Cytoskeleton Helps cell maintain cell shape Also help move organelles around Made of proteins Microfilaments are Cytoskeleton threadlike & made of ACTIN Microtubules are tube-like and made of TUBULIN Microtubules Microfilaments 17 Centrioles Found only in animal cells Paired structures near nucleus Made of bundle of microtubules Appear during cell division forming mitotic spindle Help to pull chromosome pairs apart to opposite ends of the cell 18  Mitochondrion (plural = mitochondria) “Powerhouse” of the cell Generate cellular energy (ATP) More active cells like muscle cells have MORE mitochondria Both plants & animal cells have mitochondria Site of CELLULAR RESPIRATION (burning glucose) 19 MITOCHONDRIA Surrounded by a DOUBLE membrane Has its own DNA – Mitochondria come from cytoplasm in the egg cell during fertilization – Therefore you inherit your mitochondria from your mother! Folded inner membrane called CRISTAE (increases surface area for more chemical reactions) Interior called MATRIX 20  Endoplasmic Reticulum - ER Network of hollow membrane tubules Connects to nuclear envelope & cell membrane Functions in Synthesis of cell products & Transport Two kinds of ER ---ROUGH & SMOOTH 21 Rough Endoplasmic Reticulum (Rough ER) Has ribosomes on its surface Makes membrane proteins and proteins for EXPORT out of cell Proteins are made by ribosomes on ER surface They are then threaded into the interior of the Rough ER to be modified and transported 22  Smooth Endoplasmic Reticulum Smooth ER lacks ribosomes on its surface Is attached to the ends of rough ER Makes cell products that are USED INSIDE the cell Makes membrane lipids (steroids) Includes nuclear Regulates calcium (muscle membrane connected to cells) ER connected to cell membrane (transport) Destroys toxic substances (Liver) 23  Ribosomes Made of PROTEINS and rRNA “Protein factories” for cell Join amino acids to make proteins Process called protein synthesis Can be attached to Rough ER OR Be free (unattached) in the cytoplasm 24  Golgi Bodies Stacks of flattened sacs Have a shipping side (trans face) and CIS receiving side (cis face) Receive proteins made by ER Transport vesicles with modified TRANS proteins pinch off the Transport ends vesicle 25  Golgi Bodies Look like a stack of pancakes Modify, sort, & package molecules from ER for storage OR transport out of cell 26  Lysosomes Contain digestive enzymes Break down food, bacteria, and worn out cell parts for cells Programmed for cell death (AUTOLYSIS) Lyse (break open) & release enzymes to break down & recycle cell parts) 27  Lysosome Digestion Cells take in food by phagocytosis Lysosomes digest the food & get rid of wastes 28  Vacuoles Fluid filled sacks for storage Small or absent in animal cells Plant cells have a large Central Vacuole No vacuoles in bacterial cells In plants, they store Cell Sap Includes storage of sugars, proteins, minerals, lipids, wastes, salts, water, and enzymes 29  Chloroplasts Found only in producers (organisms containing chlorophyll) Use energy from sunlight to make own food (glucose) Energy from sun stored in the Chemical Bonds of Sugars ❖Surrounded by DOUBLE membrane ❖Outer membrane smooth ❖Inner membrane modified into sacs called Thylakoids ❖Thylakoids in stacks called Grana & interconnected ❖Stroma – gel like material 30 surrounding thylakoids  Chloroplasts Contains its own DNA Contains enzymes & pigments for Photosynthesis Never in animal or bacterial cells Photosynthesis – food making process 31 Homeostasis 32  Homeostasis Definition : Maintenance of the relative stability of the physical and chemical aspects of the internal environment within a range compatible with cellular function. Maintaining a constant internal environment with all that the cells need to survive (O2, glucose, minerals, ions, and waste removal) is necessary for individual cells. The processes by which the body regulates its internal environment are referred to as homeostasis. Components : 1) sensor 2) afferent pathway 3) integration center or comparator 4) efferent pathway 5) effector organ(s) Physiological control systems are the nervous system, endocrine system, and immune system through feedback mechanisms. 33 34  Extrinsic homeostatic systems Nervous System The nervous system maintains homeostasis by controlling and regulating the other parts of the body. – A deviation from a normal set point acts as a stimulus to a receptor, which sends nerve impulses to a regulating center in the brain. The brain directs an effector to act in such a way that an adaptive response takes place. The nervous system has two major portions: the central nervous system and the peripheral nervous system. Regulating centers are located in the central nervous system, consisting of the brain and spinal cord. – The hypothalamus is a portion of the brain particularly concerned with homeostasis; it influences the action of the medulla oblongata, a lower part of the brain, the autonomic nervous system, and the pituitary gland. The peripheral nervous system consists of the spinal nerves. The autonomic nervous system is a part of peripheral nervous system and contains motor neurons that control internal organs. It has two divisions, the sympathetic 35 and parasympathetic systems.  Endocrine System The endocrine system consists of glands which secrete special compounds called hormones into the bloodstream. Each hormone has an effect on one or more target tissues. In this way the endocrine system regulates the metabolism and development of most body cells and body systems. For e.g. the endocrine system has sex hormones that can activate sebaceous glands, development of mammary glands, alter dermal blood flow, and release lipids from adipocytes etc besides governing reproduction. In the muscular system, hormones adjust muscle metabolism, energy production, and growth. In the nervous system, hormones affect neural metabolism, regulate fluid/electrolyte balance and help with reproductive hormones that influence CNS (central nervous system), development and behaviours. In the cardiovascular system, hormones regulate heart rate and blood pressure. Hormones also have anti-inflammatory effects and 36 control the lymphatic system.  Negative feedback : a control system that causes the value of a physiological measurement to change in the direction opposite to the initial deviation from set point. Positive feedback : a control system that causes the value of a physiological measurement to change in the same direction as the initial deviation from set point. 37