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These lecture notes cover fundamental principles of biology, including the scientific method, properties of life, and major themes in biology. The document also introduces biomimicry and its applications. The document may contain exercises, quizzes, or questions related to the subject.

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BIO F 111: General Biology Shrikant Charde Burrs to Velcro Kingfisher Bird to Self Healing Concrete Shinkanshen Shark Skin Inspired Fish Inspired Robot Cactus Inspired Water Design Harvestin...

BIO F 111: General Biology Shrikant Charde Burrs to Velcro Kingfisher Bird to Self Healing Concrete Shinkanshen Shark Skin Inspired Fish Inspired Robot Cactus Inspired Water Design Harvesting Biology and Engineering Biomimicry and Innovation Sustainable Design Human Factor and Ergonomics Biotechnology and Healthcare Interdisciplinary Collaboration Scope and Objective Broad introduction to the major principles and topics in biology. The relationship of the living organism with its environment at the molecular level Gain an overall understanding of the core biological principles and wide- ranging applications of biology in industry, medicine, and human health. Books 1. Text book [TB]: Simon, E.J. et. al. Campbell Essential Biology with Physiology (5th edition). Noida: Pearson India Education Services Pvt. Ltd., 2016 2. Reference book(s) [RB]: Enger, E.D., Ross, F.C. and David B. Bailey. Concepts in Biology (14th edition, BITS-Pilani Custom Edition 2012). New Delhi: Tata McGraw-Hill Publishing Company Ltd., 2012. Raven, P.H., et. al. Biology (9th ed.). Singapore: McGraw-Hill Publishing Company Ltd., 2012. Starr, Cecie. Biology: Concepts and Applications (6th ed.). India: Thomson Brooks/Cole, 2007. Introduction to Biology and its scope Chapter 1 and 4 Biology –Scientific study of life Scientific means of studying life Science – an approach to understand the natural world based on Inquiry, Analysis & Survey Search for information, explanation and answers to specific questions Main Scientific Approaches: Discovery Science & Hypothesis Driven Science Discovery Science Relies on verifiable observations and measurements of structures and processes: defining nature Collection of DATA – e.g. Charles Darwin’s work in South America Hypothesis Driven Science Observations give rise to questions and efforts to seek answers – experimental investigations using the scientific method Mostly explaining nature - search for explanations Done by formulating a hypothesis to explain the natural world, that is tested. Hypothesis is a tentative answer to a question, proposed explanation for a set of observations A tentative insight into the natural world; a concept that is not yet verified but that if true would explain certain facts or phenomena. Investigations make use of scientific method Scientific Method A series of steps, process used for investigations Suggests a broad outline/steps for how investigation might proceed. A tentative insight into the natural world; a concept that is not yet verified but if proven true, it would explain the phenomena observed Scientists test a hypothesis many times and in different ways. A hypothesis may be revised or even rejected. What would you do if the TV remote is not working Applying Scientific Method to a Common Problem Observation- Maple trees lose their leaves in the fall. A possible explanation for this observation: - “cold weather causes maple trees to lose their leaves in the fall.” Is this statement testable. Grow maple trees in a warm enclosed environment such as a greenhouse and see if their leaves still dropped in the fall. Is this statement falsifiable. If the leaves still dropped in the warm environment, then clearly temperature was not the main factor in causing maple leaves to drop in autumn. Fresh water pond freezes more quickly in winter than ocean does Determine whether each following statement is a scientific hypothesis. Air pollution from automobile exhaust can trigger symptoms in people with asthma. 1.No. This statement is not testable or falsifiable. 2.No. This statement is not testable. 3.No. This statement is not falsifiable. 4.Yes. This statement is testable and falsifiable Natural disasters, such as tornadoes, are punishments for bad thoughts and behaviours. Hypothesis & Theory Facts in the form of verifiable observations and repeatable experimental results, are the prerequisites of science A scientific theory - comprehensive explanation supported by abundant evidences A theory is a well-tested explanation for a great variety of scientific observations. Enough to spin off many new testable hypotheses. Compared to a hypothesis, it is much broader in scope. Theory: "Adaptations such as mimicry evolve by natural selection.“ Hypothesis: "Mimicking poisonous snakes is an adaptation that protects nonpoisonous snakes from predators. unusual bone structure -Unique wing adaptation of White fur of polar bears-arctic habitat –camouflage humming birds-evolutionary adaption –advantage - Two seemingly unrelated hypothesis: Fur color/unusual bone structure Single Theory Adaptation to the local environment - evolved by NATURAL SELECTION Theories become widely accepted only if they are validated by significant number and variety of observations and evidences without any contradiction from existing scientific data The Nature of Life- 7 Properties of Life ▪ ORDER – Life is complex but ordered. E.g., cellular organization. ▪ REGULATION – Living things can regulate its internal environment irrespective of drastic changes in the external environment. E.g., Homeostasis, thermoregulation and osmoregulation. ▪ GROWTH and DEVELOPMENT – Information in the DNA controls the pattern of growth and development ▪ ENERGY PROCESSING – Living things are thermodynamically open systems. They can absorb energy/matter from the environment, process it, use it and release it back into the environment. ▪ RESPONSE to the ENVIRONMENT – Living things respond to Stimulus ▪ REPRODUCTION – Living things reproduce their own kind. ▪ EVOLUTION – The capacity to reproduce also endows living things with the ability to evolve. PROPERTIES OF LIFE -ORDER Living things are complex but highly organized into levels Coordinated structures consisting of one or more cells Cells are fundamental units of life Pinecone (Bacteria) - Unicellular organisms but complex Inside each cell, atoms make up molecules, which make up cell organelles and structures. Multicellular Organisms Cells Tissue Organs Organ System Organism Information flows in an ordered manner at all levels of organization Regulation ▪ Outside environment may change drastically but internal environment is always adjusted and kept constant ▪ Homeostasis- maintenance of a stable internal environment, even in the face of a changing external environment ▪ Osmoregulation- ▪ Thermal Regulation ▪ Hot- sweat - dilation of blood vessels-loose heat ▪ Cold –vasoconstriction-muscle movement generate heat – Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to stimuli, and cope with environmental stresses. Growth and Development ▪ Information encoded in the DNA controls the pattern of growth and development. ▪ Living organisms undergo regulated growth. ▪ Individual cells become larger in size –GROWTH (unicellular organisms) ▪ multicellular organisms accumulate many cells through cell division & GROW ▪ Body Growth depends on anabolic pathways - building large, complex molecules (proteins and DNA, the genetic material) ▪ Start out as a single cell and have tens of trillions of cells Energy Processing All organisms use a source of energy for their metabolic activities Some organisms capture energy from the sun and convert it into chemical energy in food (photosynthesis) Others use chemical energy in molecules they take in as food (cellular respiration). Transformation of energy from one form to another. Example - Food Chain METABOLISM - Vast network of interconnected chemical reactions –( within living cells) Energy from food –broken down, processed and is harnessed as Chemical bond energy - usable form ATP and some is emitted has heat The California condor (Gymnogyps californianus) uses Atoms– recycled –build new muscle tissues chemical energy derived from food to power flight Energy & matter transformation is important Disrupted- problems …metabolic pathways are inhibited Response to the Environment ▪ All organisms respond or react to environmental stimuli ▪ For example Response to infection Carnivorous -Venus fly trap Response to touch –Mimosa pudica Tropism – growth or movement of an organism in response to an external stimulus ▪ An example of a common tropism in plants is phototropism (or light response) ▪ Even tiny bacteria can move toward or away from certain chemicals (a process called chemotaxis) Reproduction Reproduction – Propagation of their own kind Ensures survival and growth of the population Single-celled organisms - reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form two new cells Splitting into two – BINARY FISSION Multi-cellular organisms – different methods, such as vegetative propagation, fusion of gametes etc. Evolution Populations of living organisms can undergo evolution - genetic makeup of a population may change over time Evolution is a long-term process wherein changes occur at the Giant leaf insect (Phyllium giganteum) genetic level for a better functioning and survival as a race Giant leaf insect - evolved to provide camouflage in its environment Evolutionary change is a central, unifying phenomenon of all life Evolution The polar bear has evolved over time from the common brown bear by changing its fur colour to white, the ideal colour to blend in with its ice-covered surroundings. Researchers believe that the brown bear migrated to the north during a warmer climate period and when a cold period subsequently set in, a group of brown bears may have become isolated and therefore forced to quickly adapt to the new colder conditions. www.cell.com/cell/abstract/S0092-8674(14)00488-7 Major Themes in Biology 1. Evolution-by natural selection is core theme - can be seen at every level in hierarchy of life 2. Structure/Function relationship-correlation seen at every level of biological organization(structure of lungs-exchange of oxygen brought in –diffuses into blood cells- concave indentations provide large surface area ) 3. Information flow-every cell contain information in the form of genes, hereditary units of information 4. Energy transformations -from one form to another makes life possible 5. Interconnections within systems- study of life extends from microscopic level of molecules, all biologic systems from molecules –ecosystem depend on interaction between components Atoms – molecules –organelle –membrane bound cells-tissue-organ-organ system-organism- population- community – ecosystem – biosphere. Communities interact with their environment -Ecosystem (all living organisms in a particular place and all non living components of environment) Sum of all ecosystem and communities on EARTH – BIOSPHERE (all places where life exist) Theme 1: Evolution Natural selection - does not promote changes - edits the changes that have already occurred – product of natural selection is ADAPTATION Examples - Fur color in bears –polar bears and brown grizzly –brown (similar species -share common ancestor) Resulted from Natural selection operating in their respective environment Finches (bird)- of Galapagos Island.Measured changes in beak size in a population of ground finches -dry and wet years Dry years- preferred small seeds are in short supply – birds have large seeds to eat- Advantage – great reproductive success Wet years- small seeds are abundant – smaller beaks more efficient in eating smaller seeds Average beak depth decreased over generations Changes in structure are measurable evidence of natural selection Development of antibiotic resistance bacteria Artificial selection – selecting breeding stocks with certain traits Plants we grow today have little resemblance to their wild relatives.customized crop breeding by many years of artificial selection ADAPTATION → NATURAL SELECTION → EVOLUTION Evolution of Polar Bears Evolution of Beak shape in Darwin’s finches Application of Natural Selection → Artificial Selection Abuse of Natural Selection Antibiotic resistance in cattle Plant and animal breeding Theme 2: The Relationship of Structure to Function Ribonuclease A (an enzyme/protein) – Structure: A pocket to fit RNA substrate Human Lungs – Structure: Human Lungs – Function: 600sqft in surface area Holds 6L of O2 (only 24cm in height!!!) Ribonuclease A – Function: Cleaves RNA Theme 3: Information Flow Life’s functions proceed in an ordered manner.Information flows in an ordered manner at all levels of organization Theme 4: Pathways that Transform Energy and Matter Theme 5: Interconnections within biological system Diversity of life There are zillions of organisms in the biosphere that fulfil that definition of life. In order to study them using scientific process we need to group them. All of us have a general sense of grouping. Can you apply that on the following: Taxonomy gives us a scientific basis for grouping Do you recognise these two organisms? Would you classify them in the same group – same species? Why or why not? TAXONOMY Branch of biology that names and classifies species by grouping them into logical categories and is an arrangement of species into hierarchy of broader and broader groups A classification of organisms into groups based on similarities of structure or origin etc. Taxonomists use morphological, behavioral, genetic and biochemical observations Species: Taxonomic group whose members live in the same place and time and have potential to interbreed to produce healthy offspring Classification of living forms On broadest level -Biologists divide the diversity of life into three Domains Eubacteria Archaea Eukaryotes Eubacteria and Archaea are together also called as Prokaryotes Every organism on earth belong to one of three domains DOMAIN EUBACTERIA Eubacteria- “eu”=true Small, prokaryotic, single celled organisms ranging in size from 1 to 10 um Lack nucleus & cell membrane bound organelles Cell wall contains a complex organic molecule called Peptidoglycan DOMAIN ARCHAEA Archaea- “archaios”=ancient Prokaryotic cell structure DNA of Archaea have large proportions of genes that are different from Eubacteria Cell membranes have unique chemical structures. Cell membrane does contain fatty acids but instead branched molecules called ISOPRENES Also known as extremophiles- they are found in extreme environments DOMAIN EUKARYA most members are multicellular Domain Eukarya includes three main Kingdoms- Kingdoms are distinguished partly by how the organism obtain food Plantae: produce their own sugar and food- Photosynthesis-autotrophic Fungi: decomposers, obtain their food by digesting dead organism and organic waste - heterotrophic Animalia: obtain food by ingesting and digesting other organisms-heterotrophic Eukaryotes not belonging to either of the three kingdoms fall in to a catch all group: Protists Protists are mostly single celled microscopic organisms such as amoeba or multicellular such as seaweeds. Other examples protozoa, unicellular algae, and slime molds The Microscopic World of Cells Cell theory states that all living things are composed of cells and that all cells come from earlier cells. every cell in our body (and in every other living organism on Earth) was formed by division of a previously living cell. © 2016 Pearson Education, Inc. The Two Major Categories of Cells All cells have several basic features. They are all bounded by a thin cell The countless cells on Earth fall into two basic categories. membrane. Inside all cells is a thick, jelly-like fluid Prokaryotic cells include called the cytosol - cellular components Bacteria and Archaea. are suspended. All cells have one or more chromosomes Eukaryotic cells include carrying genes made of DNA. 1. protists, All cells have ribosomes, tiny structures 2. plants, 3. fungi, and that build proteins according to the 4. animals. instructions from the genes. The Two Major Categories of Cells A prokaryotic cell lacks a nucleus. Prokaryotic cells are older than eukaryotic cells. DNA is coiled into a nucleus-like region Prokaryotes appeared about 3.5 called the nucleoid, billion years ago. No nuclear membranes. Eukaryotes appeared about 2.1 billion years ago. Eukaryotic cells Prokaryotic cells are Only eukaryotic cells have organelles, usually smaller than eukaryotic membrane-enclosed structures that perform cells and specific functions. simpler in structure. The most important organelle is the nucleus, houses most of a eukaryotic cell’s DNA and surrounded by a double membrane. Table 4.1 Cell wall-rigid covering outside the cell membrane protects the cell and helps maintain its shape. cell membrane (encloses cytoplasm) Cell wall (provides rigidity) Capsule (sticky coating) Flagella (for propulsion) Ribosomes (synthesize proteins) Colorized TEM Nucleoid (contains single circular bacterial chromosome) Figure 4.2 Pili (attachment structures) Prokaryotes can have Pili - short projections for attachment or adhesion to surfaces Flagella- long projections to propel them through their liquid environment capsules make bacterial surface components more slippery, helping the bacterium to escape engulfment by phagocytic cells An Overview of Eukaryotic Cells Eukaryotic cells - fundamentally similar. Cytoplasm - Region between the nucleus and cell membrane The cytoplasm of a eukaryotic cell consists of various organelles suspended in the liquid cytosol. Most organelles are found in both animal and plant cells. But there are some important differences. Only plant cells have chloroplasts (where photosynthesis occurs). Only animal cells have lysosomes (bubbles of digestive enzymes surrounded by membranes) Plant cells have cell wall which provides stiffness to plant structures END Nucleic Acids Lipids Proteins Carbohydrates 2. Introduction to important molecules of life : structure and function Of the 92 naturally occurring elements, 16 are known to be important constituents of living systems: C, H, O, N, P, S, K, Ca, Na, Cl, Mg, Fe, Cu, I, Mo, Zn Organic compounds - a large class of Carbon-containing chemical compounds in which one or more atoms of carbon are covalently linked to atoms of other elements, most commonly H, N, or O. Why is carbon the backbone of life? Why is it special? Simple organic compound Found natural Digestive tracts of Grazing animals It is possible to construct an endless diversity of C skeletons varying in size and branching pattern Variation in carbon skeletons contributes to the diversity of organic molecules. Carbon chains form the skeletons of most organic molecules. The skeletons vary in length & may be straight, branched, or arranged in closed rings.... Atoms of other elements can be bonded to the atoms of the carbon skeleton. 2. Branched Chain 3. Ring 1. Straight Chain Carbon skeleton may vary in length C skeletons may have double bond in different locations Animation: Carbon Skeletons Carbon skeleton may be Carbon skeleton may be unbranched / branched arranged in rings Each biomacromolecule has one or more characteristic functional group(s) which give the molecule its specific properties and functions - they are often the centers of chemical reactivity. DNA – Phosphate; Proteins – Amino and carboxyl; Carbs – hydroxyl; Lipids – all of the above? Characteristics of Biological Molecules to Consider Subunits that serve as building blocks Connected by Dehydration Synthesis Process (condensation) Break down by Hydrolysis Process Covalent bonding Solubility in Water Monomer Polymers Dehydration Synthesis Process Monomers H HO H HO Polymer H2O H from one monomer (Glucose) & OH from another monomer (Fructose) are taken out. They form H2O. If dehydration synthesis continues for a long time, a long & complex carbohydrate chain a polysaccharide is formed. The bond between two carbohydrates is called a Glyosidic Linkage. Hydrolysis Giant Molecules from Smaller Building Blocks Monomers H2O Hydrogen hydroxide cation anion H HO C12H22O11 + H2O C6H12O6 + C6H12O6 A chemical reaction in which water reacts with a compound to produce other compounds; involves the splitting of a bond and the addition of the hydrogen cation & the hydroxide anion from the water. breaks bonds between monomers, adds a molecule of water, and reverses the dehydration reaction. Animation: Polymers Dehydration Synthesis- Bonds are formed through the removal of water. It is the chemical reaction in which two molecules are joined covalently by the removal of -OH from one molecule and -H atom from the other molecule. It is also known as condensation. Examples include reactions joining monomers to form polymers. Carbs - Monosaccharide + Monosaccharide -> Disaccharide + H20 Lipid - 1Glycerol + 3 Fatty Acids -> Lipid + 3 H2O Protein - 2 Amino Acids -> Dipeptide + H2O Nucleic Acid- Nucleotides -> Nucleic Acid + H2O Hydrolysis - Bonds are broken through the addition of water. It is the chemical reaction in which a molecule is split into smaller units by the reaction with water's addition. Examples include reactions which split polymers into monomers. It is how we break down food into smaller units that can be used for our cells. Carbs - Disaccharide + H2O -> Monosaccharide + Monosaccharide Lipid- Lipid + 3 H2O -> 1 Glycerol + 3 fatty Acids Protein- Dipeptide + H2O -> 2 Amino Acids Nucleic Acid - Nucleic Acid + H2O -> Nucleotides 1) CARBOHYDRATES © 2016 Pearson Education, Inc. Characteristics of Carbohydrates Carbohydrates = sugars (Saccharide means simple sugar) Sugars, Starches & Others Suffix used = -ose. Principle Elements: C, H, & O Characteristic formula Cn H2n On (1:2:1) From Photosynthesis Monomers: Monosaccharaides Polymers: Polysaccharides Water Soluble (Hydrophilic) Functions of Carbohydrates Energy Metabolism Structural Components Cell-to-Cell Contacts & Recognition Elimination of wastes (fiber) Trioses - 3 carbon atoms C3 H6 O3 glyceraldehyde Tetroses - 4 carbon atoms C4 H8 O4 erythrose Pentoses - 5 carbon atoms C5 H10 O5 ribose Hexoses - 6 carbon atoms C6 H12 O6 glucose, fructose, galactose What is Dextrose? Glucose dissolved in water; (mono) Dextrose is the name of a simple sugar made from corn or wheat that's chemically identical to glucose, or blood sugar Monosaccharides Disaccharides C5H10O5 C5H10O5 C6H12O6 C6H12O6 Glucose Fructose glucose + galactose = Lactose Milk sugar glucose + glucose = Maltose Malt sugar Isomers? Different forms of a compound having different arrangements of atoms but the same molecular weight glucose + fructose = Sucrose Table sugar Animation: Disaccharides Common sweetener - High-fructose Corn Syrup (HFCS) made by chemically treating sugars extracted from corn Glucose in the form of starch in sweet corn - processed by the enzyme glucose isomerase to convert it into fructose, which is much sweeter The average 20 oz. soda contains 15 teaspoons of sugar, all of it as HFCS Dangers of High Fructose Corn Syrup: Tooth decay Weight Gain Cancer Increased Cholesterol Levels Diabetes High Blood Pressure Heart Disease Empty calories? Calories derived from food containing NO nutrients. Seems like a bit of a contradiction, doesn’t it? Calories are supposed to give us energy, so how can they be empty? Well, an empty calorie does supply energy but is not nutritionally balanced. Most sweeteners contain only negligible amount of nutrients other than carbohydrates. If you’re trying to maintain / lose weight. It’s better to keep these at a minimum level. Polysaccharides - “complex carbohydrates” Cellulose Glycogen granules in muscle tissue Amylose Commonly known as “starch” is the way many plants store sugars – found commonly in rice, potatoes, corn, wheat, beans and so forth - Storage carb. There are no starches in meat, fish, eggs and none in your own body. So, what happens if you eat starch? Starch gets digested & broken down into individual glucose molecules and that’s what you absorb. Cellulose is made up of glucose monomer, just like starch. We as humans cannot digest or break apart these sugar molecules. Hence, it is referred to as “indigestible fibre,” “roughage,” or “insoluble fibre” - Structural carb. When you eat grains, celery, carrots, or any plant material, the outer plant cell walls are crushed by our teeth and only the contents of the cells are digested. The cellulose however, will remain unchanged and exit along with stools. Our digestive tract needs a certain amount of this indigestible fibre to keep it healthy. When we don’t have enough of this, it makes our digestive tract thin & weak. Easy bowl movements prevents constipation. Remember that cellulose (just like starch) exists only in plants. Glycogen = “animal starch”; The same way plants store sugar by creating starch, animals store sugar using glycogen. A long chain of glucose molecules - Storage carb! This is primarily stored in our liver and muscles. Athletes such as long-distance runners / cyclists, require endurance, and hence often indulge in ’carb-loading’. Eating lots & lots of carbs before an event, helps in absorbing these simple sugars & store it as glycogen in our liver & muscles for energy reserves. These stored sugars can then be broken down easily during the event. If you keep carb-loading, however, and don’t expend the energy within the Another important next couple days, whatstru will happen? a polymer of -glucose It will be turned into fat!! functional group. Chitin = A polymer of beta-glucose molecules having a nitrogen containing functional group – an important structural polysaccharide!! It is also indigestible like cellulose Used to build cell walls in fungi and exoskeletons in arthropods Classified as a carbohydrate even though it does not strictly follow the structural formula - Cn H2n On 2) Lipids © 2016 Pearson Education, Inc. Characteristics of Lipids Oils, fats, waxes, phospholipids, steroids Principle Elements: C, H, & O Some With P & N Water Insoluble (Hydrophobic) Functions of Lipids Energy Storage Protection & Cushioning of Body Organs Structural Components of Membranes Chemical Messengers (hormones) MAJOR TYPES OF LIPIDS Major types include Fats and Oils, Waxes, Phospholipids, and Steroids Phospholipids (Any of various compounds composed of fatty acids & phosphoric acid and a nitrogenous base; an important constituent of membranes) Triglycerides (neutral fats) Sterols (also known as steroid alcohols. They occur naturally in plants, animals, and fungi, with the most familiar type of animal sterol being cholesterol. Cholesterol is vital to cellular function, and a precursor to fat-soluble vitamins and steroid hormones). TRIGLYCERIDES Phospholipid Bilayer Waxes FATTY ACIDS GLYCEROLES Hydrophilic head Hydrophobic tails Phospholipids Saturated Fats Glycerol Saturated with H+ Fatty Acids Most animal fats are saturated, eg. butter Tend to be Solid at room temp (37oC) Unsaturated Fats Has one or more double bonds between carbons Most vegetable fats Tend to be Liquid at room temp DEHYDROGENATION is a chemical reaction that involves the removal of hydrogen from a molecule. It is the reverse process of hydrogenation. Dehydrogenation reactions are conducted both on industrial and laboratory scales. Dehydrogenation converts saturated fats to unsaturated fats. HYDROGENATION complete or partial, is a chemical process in which hydrogen is added to liquid oils to turn them into a solid form. Partially hydrogenated fat molecules have trans fats, and they may be the worst type of fat you can consume. Figure 3.12 TYPES OF FATS Saturated Fats Unsaturated Fats Margarine Plant oils Trans fats Omega-3 fats Cholesterol Steroids is an organic compound with four rings arranged in a specific molecular configuration. Eg. i) Dietary lipid cholesterol, ii) Sex hormones Estradiol (estrogen) &Testosterone. (Anatomical & physiological differences are brought in by these hormones) How do steroids affect the body? Some athletes take a form of steroids — known as Anabolic-Androgen Steroids / just anabolic steroids — to increase their muscle mass & strength. The main anabolic steroid hormone produced by our body is Testosterone. Testosterone has two main effects on our body Anabolic effects promote muscle building. Synthetic anabolic steroids are variants / alternatives of testosterone, mimic some of its effects, may be prescribed to treat diseases such as cancer and AIDS, are abused by athletes to build up their muscles quickly, and can cause serious physical and mental problems. Side effects of oral corticosteroids 1. Fluid retention, causing swelling in your lower legs. 2. High blood pressure. 3. Problems with mood swings, memory, behavior, and other psychological effects, such as confusion or delirium. 4. Upset stomach. 5. Weight gain, with fat deposits in your abdomen, your face and the back of your neck. How long do steroids stay in your system? If taken orally, steroids can show up in a urine test for up to 14 days. If injected, steroids can show up for up to 1 month. Proteins are polypeptides - polymers of amino acids. Characteristics of Proteins Principle Elements: C, H, O, & N Amino Acid Structure Monomers: Amino Acids Polymers: Polypeptides or Proteins Generally Water Soluble Functional Groups of Amino Acids [hydroxyl (Alcoholic), Carbonyl, Amino, Sulfhydryl, Phosphate, Methyl ] Carboxylic Acid (-COOH) Amine (-NH2) R-Groups (variable - 20 different kinds) Formation of Peptide Bonds Dehydration synthesis process Carboxyl group of one aa + Amino group of another aa Peptide bond Two Different Polypeptides The variation in R groups gives amino acids different properties Figure 3.15 Some of the varied roles played by proteins MAJOR TYPES OF PROTEINS Structural Proteins Storage Proteins Contractile Transport Proteins Enzymes (provide support) (provide amino Proteins (help transport (help chemical acids for growth) (help movement) substances) reactions) Functions of Proteins Enzymes Structural Proteins Chemical Messengers Hormones Antibodies The bond between two amino acids is called a Polypeptide / dipeptide bond The bond between fatty acids and glycerol is called an Ester linkage The bond between two carbohydrates (monosaccharides) is called a Glycosidic bond The diversity of protein function results from diversity of protein structure which is the result of variation in the sequence of amino acids Functional proteins can vary in length from about 50 amino acids to several thousand amino acids The diversity of amino acid sequence results in diversity of protein structure Protein structure can be classified at several different levels: primary, secondary, tertiary, and quaternary Levels of Protein Structure Primary structure: Linear sequence of amino acids NH3 Leu Cys Val Asp Phe COO Alpha helix Beta Pleated skirt Secondary structure: (likely to twist) (Hair) (Silk) H-Bonds Tertiary: highly coiled & Pleated – interact to form globular (153 amino acids) 3D configuration Weak bonds between side chains (Myoglobin & Cytochrome) Quaternary: Two or more polypeptides e.g. Hemoglobin (Hb) (immunoglobins / antibodies – involved in fighting infectious diseases like Flu, mumps, chicken pox etc.,) Primary structure Secondary structure Tertiary structure Quaternary structure The form and function of protein If a protein is to do its job effectively, it is vital to maintain a particular shape, sequence, 3D shape. e.g. Normal Hb found in RBC consist of 2 kinds of polypeptide chains– Alpha & Beta chains. The beta chain is 146 aa long, just one of these amino acids is replaced by different one cause drastic change CLASSIC EXAMPLES Sickle cell anemia – 6th aa in beta chain usually glutamic acid changes to valine BSE-Bovine Spongiform encephalitis (Mad Cow Disease) it is an infectious disease believed to be due to a misfolded protein, known as a PRION. An infectious protein particle similar to a virus but lacking nucleic acid Chronic Wasting Disease (CWD) is a contagious neurological disease affecting deer. CJD – Creutzfeldt Jacob Disease (caused by prions) brain cells damaged. CJD is a rare, degenerative, invariably fatal brain disorder. It affects about one person in every one million people/ year worldwide; in US there are about 300 cases / year. Characterized by progressive dementia & gradual loss of muscle control Denature of the egg white Medicines to be stored in brown bottle (light interactions) refrigerated (low temp) – otherwise loose the potency Characteristics of Nucleic Acids Nucleotide Structure Principle Elements: C, H, O, N, & P Monomers: Nucleotides Nitrogen Base Phosphate Polymers: Nucleic Acids Generally Water Soluble Sugar Nucleotide Components: Ribose (5-C) Sugar Phosphate Nitrogenous Base Functions of Nucleic Acids Genetic Instruction Set (DNA) Protein Synthesis (DNA & RNA) Energy Metabolism (ATP) Nucleotide Bases Nucleotide Sugars Nucleotide Bases Purines Pyrimidines Uracil Double-Stranded DNA Polynucleotides = Nucleic Acids DNA RNA Polymers made up of individual nucleotides The components of RNA are somewhat similar Nucleotides contain to DNA with 3 major differences. Phosphate group 1. The pyrimidine base uracil replaces thymine Five carbon sugar 2. ribose sugar replaces deoxyribose. Ring shaped nitrogen base 3. RNA mostly forms single stranded structure. DNA contains information for almost all cell activities There are 3 types of RNA directly involved in protein synthesis: Messenger RNA (mRNA) carries the instructions from the nucleus to the cytoplasm. The other two forms of RNA, ribosomal RNA (rRNA) and transfer RNA (tRNA), are involved in the process of ordering the amino acids to make the protein. ATP Role of ATP in Energy Metabolism Role of ATP in Energy Metabolism ATP → ADP + Pi + Energy 1) Passing the information to the next generation (Cell division - DNA replication) 2) Protein synthesis (Translation & Transcription. In a cell, this involves the synthesis of new molecules from food) MAJOR CLASSES Chapter 4 A Tour of the Cell © 2016 Pearson Education, Inc. 10 to 100 μm 0.1 to 5 μm The Microscopic World of Cells Cell theory states that all living things are composed of cells and that all cells come from earlier cells every cell in our body (and in every other living organism on Earth) was formed by division of a previously living cell © 2016 Pearson Education, Inc. What kind of organism do you think this is? And this one?? Valonia ventricosa, also known as bubble algae, sea grape, or sailor's eyeballs – one of the largest known UNICELLULAR organisms!! Caulerpa taxifolia, an algal species – green seaweed, often bred for use in aquariums – also consists of just a single cell with many nuclei!! In fact, it is the LARGEST KNOWN single- celled organism! PHOTOGRAPH BY UNIVERSAL HISTORY ARCHIVE/UNIVERSAL IMAGES GROUP VIA GETTY IMAGES - HTTPS://EDUCATION.NATIONALGEOGRAPHIC.ORG/RESOURCE/CELL-THEORY/ The Two Major Categories of Cells All cells have several basic features. They are all bounded by a thin plasma membrane. Inside all cells is a thick, jelly-like fluid called the cytosol, matrix of cytoplasm surrounding organelle -in which cellular components are suspended. All cells have one or more chromosomes carrying genes made of DNA. All cells have ribosomes, tiny structures that build proteins according to the instructions from the genes. Most organelles are found in both animal and plant cells. But there are some important differences. Only plant cells have chloroplasts (where photosynthesis occurs). Only animal cells have lysosomes (bubbles of digestive enzymes surrounded by membranes). © 2016 Pearson Education, Inc. Figure 4.3 IDEALIZED ANIMAL CELL Centriole Not in most Ribosomes Lysosome plant cells Cytoskeleton Plasma membrane Nucleus Cytoplasm Mitochondrion Rough endoplasmic Smooth reticulum (ER) endoplasmic IDEALIZED PLANT CELL Golgi reticulum (ER) Cytoplasm apparatus Cytoskeleton Mitochondrion Central vacuole Not in Cell wall animal cells Nucleus Chloroplast Rough endoplasmic reticulum (ER) Ribosomes Plasma membrane Smooth endoplasmic Channels between cells reticulum (ER) Golgi apparatus BioFlix Animation: Tour of an Animal Cell © 2016 Pearson Education, Inc. BioFlix Animation: Tour of a Plant Cell © 2016 Pearson Education, Inc. CHROMATIN ORGANIZATION NUCLEUS The Nucleus : Genetic Control of the Cell The nucleus is the control center of the cell. Contains DNA (contain genes) that stores the information Nuclear envelope necessary to produce a particular protein. Nuclear pore Chromatin fiber separated from the cytoplasm by a double membrane called the nuclear envelope. Nucleolus Pores - allow certain materials to pass between the nucleus and the surrounding cytoplasm long DNA molecules and associated proteins form fibers called chromatin. Each long chromatin fiber constitutes one chromosome. The nucleolus is a prominent structure within the nucleus and the site where the components of ribosomes are made. © 2016 Pearson Education, Inc. Ribosomes Ribosomes are responsible for protein synthesis In eukaryotic cells, the components of ribosomes are made in the nucleus and then transported through the pores of the nuclear envelope into the cytoplasm Some ribosomes are suspended in the cytosol, making proteins that remain within the fluid of the cell. Ribosomes attached to endoplasmic Others are attached to the outside of the nucleus reticulum visible as & the endoplasmic reticulum, making proteins tiny dark blue dots that are incorporated into membranes or secreted by the cell. Both these types of ribosomes are structurally identical © 2016 Pearson Education, Inc. How DNA Directs Protein Production DNA DNA transfers its coded Synthesis of information to a molecule called mRNA in the nucleus messenger RNA (mRNA). mRNA mRNA exits the nucleus through pores in the nuclear envelope and travels to the cytoplasm, where it binds to a ribosome. Movement of mRNA into cytoplasm via A ribosome moves along the nuclear pore Ribosome mRNA, translating the genetic message into a protein with a specific Synthesis of protein in the Protein amino acid sequence. cytoplasm © 2016 Pearson Education, Inc. Actively transcribing DNA (viewed under a microscope) The Endomembrane system The Endomembrane System: Manufacturing and Distributing Cellular Products The endomembrane system-internal network of membranes in a cell consists of the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, and vacuoles. These membranous organelles are either physically connected or linked by vesicles, sacs made of membrane. © 2016 Pearson Education, Inc. The Endoplasmic Reticulum The endoplasmic reticulum (ER) - one of the main manufacturing facilities in a cell. connected to the nuclear envelope composed of interconnected rough and smooth ER that have different structures and functions. Cells specializing in the production of proteins - have a larger amount of rough ER (With ribosomes attached) Cells producing lipids (fats) and steroid hormones - have a greater amount of smooth ER. Some products manufactured by rough ER are chemically modified and then packaged into transport vesicles- Vesicles - sacs made of membrane that bud off from the rough ER. These transport vesicles may be dispatched to other locations in the cell. cells of the pancreas and digestive tract produce a high volume of protein that function as digestive enzymes. © 2016 Pearson Education, Inc. Figure 4.12 3 Secretory 4 Vesicles bud off proteins depart. from the ER. 2 Proteins are modified in the ER. Transport Ribosome vesicle 1 A ribosome links amino acids. Protein Rough ER Polypeptide Smooth ER The smooth ER lacks surface ribosomes - produces lipids, including steroids (hormones in the adrenal cortex and endocrine glands) Cells of ovaries and testis –enriched with SER- produce steroid sex hormones detoxifying a number of organic chemicals converting them to safer water-soluble products. Large amounts of smooth ER are found in liver cells – Enzymes of SER functions to detoxify products of natural metabolism (drugs /antibiotics) It contains enzymes that catalyze a number of reactions ; that can make lipid- soluble drugs and metabolic wastes into water-soluble, so that these (drugs and waste) can easily be expelled out of the body. To assist with this, smooth ER can double its surface area within a few days, returning to its normal size when the assault has subsided detoxify overloads of ethanol derived from excess alcoholic drinking and barbiturates from drug overdose. © 2016 Pearson Education, Inc. Figure 4.11 contains enzymes that catalyze a number of reactions ; that can make lipid- soluble drugs and metabolic wastes into water-soluble, so that these (drugs and waste) can easily be expelled out of the body. Nuclear envelope Ribosomes Rough ER Smooth ER The Golgi Apparatus Rough ER “Receiving” side of the “Receiving” side of Golgi apparatus the Golgi apparatus Golgi apparatus Transport vesicles carry enzymes and 1 other proteins from Transport the rough ER to the vesicle Golgi for processing. “Shipping” side of the Golgi apparatus 2 Lysosomes carrying 3 digestive enzymes Plasma Colorized SEM can fuse with other membrane vesicles. “Shipping” side of Glogi apparatus Secretory protein Figure 4.13 The Golgi apparatus works in partnership with the ER and receives, refines, stores, and distributes chemical products of the cell. The Golgi Apparatus The Golgi apparatus consists of a stack of membrane plates. Products made in the ER reach the Golgi apparatus in transport vesicles. Proteins within a vesicle are usually modified by enzymes during their transit from the receiving to the shipping side of the Golgi apparatus. The shipping side of a Golgi stack is a depot - finished products can be carried in transport vesicles to other organelles or to the plasma membrane. © 2016 Pearson Education, Inc. Lysosomes A lysosome is a membrane-enclosed sac of digestive enzymes found in animal cells. Most plant cells do not contain lysosomes, they contain lytic vacuoles Lysosomes originate from vesicles that bud off from the Golgi apparatus Enzymes in a lysosome can break down large molecules such as proteins, polysaccharides, fats, and nucleic acids Lysosomes provide a safe compartment for breakdown of these molecules, without putting the cell’s other organelles and important molecules in danger of being broken down by these enzymes! © 2016 Pearson Education, Inc. Digestive enzymes Lysosomes Lysosome have several types of digestive functions: Digestion 1) Many single-celled protists engulf nutrients in tiny cytoplasmic sacs called food vacuoles. Food vacuole Lysosomes fuse with the food vacuoles, exposing the food to digestive enzymes. A lysosome digesting food Small molecules that result from this digestion, such as amino acids, leave the lysosome and nourish the cell. Lysosomes can also 2. destroy harmful bacteria (e.g. WBCs - immunity), 3. engulf and digest parts of another organelle (recycling) and, 4. sculpt tissues during embryonic development, helping to form structures such as fingers. © 2016 Pearson Education, Inc. A lysosome digesting food Digestive Lysosome enzymes In lower eukaryotes like Protista (Paramecium) Digestion Food vacuole Lysosome Digestive enzymes Digestion Vesicle containing damaged organelle A lysosome breaking down the molecules of damaged organelles In higher eukaryotes Lysosomes Lysosomes are important to cell function and human health as suggested by a group of hereditary disorders called lysosomal storage diseases. A person with such a disease: is missing one or more of the digestive enzymes normally found within lysosomes, and has lysosomes that become engorged with indigestible substances, which eventually interferes with other cellular functions. Most of these diseases are fatal in early childhood For example, in Tay-Sachs disease, deficiency of a lipid-digesting enzyme results in accumulation of excess lipids in nerve cells, leading to their death. © 2016 Pearson Education, Inc. Vacuoles Vacuoles are large sacs made of membrane that buds off from the ER or Golgi apparatus. They have many types of functions in different cell types: 1) Certain freshwater protists like Paramecium, amoeba etc. have contractile vacuoles - pump out excess water that flows into the cell from the outside environment. The contractile vacuole acts to regulate the quantity of water inside the cell. In freshwater environments - the concentration of solutes inside the cell is high concentration than outside the cell (i.e., the environment is hypotonic). water flows from the environment into the cell by osmosis. The contractile vacuole acts as part of a protective mechanism that prevents the cell from absorbing too much water and possibly lysing (rupturing) through excessive internal pressure. © 2016 Pearson Education, Inc. Figure 4.15-1 A vacuole filling with water LM A vacuole contracting LM (a) Contractile vacuole in Paramecium Vacuoles 2) A central vacuole can account for more than half the volume of a mature plant cell. The central vacuole of a plant cell is a versatile compartment that may: store organic nutrients like proteins, absorb water causing cells to expand, thus contributing to plant growth, and contain pigments (e.g., in cells of flower petals) that attract pollinating insects contain poisonous chemicals that protect against plant-eating animals/bugs (e.g., nicotine, caffeine etc.) 3) A food vacuole which buds into the cell from plasma membrane as a vehicle for ingesting food particles from outside © 2016 Pearson Education, Inc. Rough ER “Receiving” side of the Golgi apparatus Golgi apparatus Transport vesicles carry enzymes and other proteins from the rough ER to the Transport Golgi for processing. vesicle “Shipping” side of the Golgi apparatus Lysosomes carrying digestive enzymes Plasma can fuse with other membrane vesicles. Secretory protein Energy Transformations: Chloroplasts and Mitochondria A cell converts energy obtained from the environment to forms that can be used directly by it Two organelles act as cellular power stations: 1. Chloroplasts, and 2. Mitochondria © 2016 Pearson Education, Inc. MITOCHONDRIA TEM Outer membrane Inner membrane Cristae Matrix Space between membranes Figure 4.18 MITOCHONDRIA Mitochodrial DNA (mtDNA) is circular unlike the linear nuclear DNA. It codes for proteins that are involved in cellular respiration. MITOCHONDRIA Are found in almost all eukaryotic cells, Are the organelles in which cellular respiration takes place, and Produce ATP from the energy of food molecules Cells use molecules of ATP as the direct energy source for most of their work Different cells have different amounts of mitochondria depending on their energy requirements the muscle cells have a lot of mitochondria, the liver does too, the kidney as well, and to a certain extent, the brain, which lives off the energy those mitochondria produce. © 2016 Pearson Education, Inc. MITOCHONDRIA An envelope of two membranes encloses the mitochondrion, and the inner membrane encloses a thick fluid called the mitochondrial matrix The inner membrane of the envelope has numerous infoldings called cristae The folded surface of the membrane: includes many of the enzymes and other molecules that function in cellular respiration, and creates a greater surface area in which more of these enzymes can be embedded, maximizing ATP output © 2016 Pearson Education, Inc. MITOCHONDRIA Mitochondria and chloroplasts contain their own DNA that encodes some of their own proteins made by their own ribosomes. Each chloroplast and mitochondrion contains a single circular DNA chromosome that resembles a prokaryotic chromosome, and can grow and pinch in two, reproducing themselves. These observations suggest that these two organelles could have originated from prokaryotic cells which were engulfed by larger cells and over time developed a symbiotic relationship © 2016 Pearson Education, Inc. MITOCHONDRIA mitochondria and chloroplasts evolved from ancient free-living prokaryotes that established residence within other, larger host. This phenomenon, where one species lives inside a host species, is a special type of symbiosis. Over time, mitochondria and chloroplasts likely became increasingly interdependent with the host, eventually evolving into a single organism with inseparable parts. © 2016 Pearson Education, Inc. Inner and outer CHLOROPLASTS membranes Space between membranes Stroma (fluid in Granum chloroplast) TEM Figure 4.17 CHLOROPLASTS Most of the living world runs on the energy provided by photosynthesis. Photosynthesis is the conversion of light energy from the sun to the chemical energy of sugar and other organic molecules. Chloroplasts are The organelles that perform photosynthesis They are unique to the photosynthetic cells of plants and algae © 2016 Pearson Education, Inc. CHLOROPLASTS Chloroplasts are divided into compartments by two membranes, one inside the other. The stroma is a thick fluid found inside the innermost membrane. Suspended in that fluid, a network of membrane-enclosed disks and tubes forms another compartment. The disks occur in interconnected stacks called grana that resemble stacks of poker chips. The grana are a chloroplast’s solar power packs, the structures that trap light energy and convert it to chemical energy. © 2016 Pearson Education, Inc. Figure 4.3 IDEALIZED ANIMAL CELL Centriole Not in most Ribosomes Lysosome plant cells Cytoskeleton Plasma membrane Nucleus Cytoplasm Mitochondrion Rough endoplasmic Smooth reticulum (ER) endoplasmic IDEALIZED PLANT CELL Golgi reticulum (ER) Cytoplasm apparatus Cytoskeleton Mitochondrion Central vacuole Not in Cell wall animal cells Nucleus Chloroplast Rough endoplasmic reticulum (ER) Ribosomes Plasma membrane Smooth endoplasmic Channels between cells reticulum (ER) Golgi apparatus PLASMA MEMBRANE Structure/Function: The Plasma Membrane Composed mainly of phospholipids, which group together to form a two-layer sheet called a phospholipid bilayer Each phospholipid is composed of two distinct regions: 1. a “head” with a negatively charged phosphate group and 2. two nonpolar fatty acid “tails.” The hydrophobic tail - (i) Prevents unwanted polar ions and molecules to pass in the cell (ii) Restricts the movement of water-soluble molecules such as amino acids, glucose etc. out of the cell Certain proteins are suspended throughout the phospholipid bilayer of most biological membranes These help to regulate traffic across the membrane and perform many other functions © 2016 Pearson Education, Inc. Structure/Function: The Plasma Membrane – Fluid Mosaic Model The plasma membrane is not a static sheet of molecules fixed in their place but a fluid mosaic: fluid because molecules can move freely past one another, and a mosaic because of the diversity of proteins in the membrane Functions of membranes are analogous to our human skin in some aspects: detect stimuli, engage in gas exchange, and serve as sites of excretion and absorption. © 2016 Pearson Education, Inc. Cell surfaces Plant cells have a cell wall made from Animal cells lack cell walls and usually secrete a cellulose fibers, surrounding the plasma sticky coat called the extracellular matrix (ECM) membrane - A large network of proteins and other molecules that surround, support, and give Plant cell walls structure to cells and tissues in the body. protect the cells, ECM - Fibers made up of the protein collagen maintain cell shape, and which hold the cells together in tissues and can keep cells from absorbing too much also have protective and supportive functions. water to avoid bursting In addition, the surfaces of most animal cells Plant cells are connected via channels contain cell junctions, structures that connect passing through cell walls and joining their cells together into tissues, allowing the cells to cytoplasm with each other function in a coordinated way. These channels also allow water and other small molecules to move between cells – integrating them into a functional tissue © 2016 Pearson Education, Inc. Animation: Tight Junctions Collagen Cells embedded in an extracellular matrix of an animal cell © 2016 Pearson Education, Inc. Plant Cell: Plasmodesmata Various components of ECM Functions of membrane proteins (Chapter 5 of reference book) Functions of membrane proteins – Transport Passive Transport Active Transport Endocytosis (phagocytosis & pinocytosis) Exocytosis Biological membranes are selectively permeable!! Passive Transport No energy required Movement due to gradient differences in concentration, pressure, charge Movement in order to equalize gradient High moves toward low Can be of two types – diffusion or facilitated diffusion Types of Passive Transport - Diffusion A passive flow of substances down a concentration gradient Cell does not spend energy Only small molecules like gases, hydrophobic compounds, or even some polar molecules like ethanol can pass through Diffusion Gases and Liquids have random movement of molecules (due to their Kinetic Energy) and due to their constant motion they tend to mix together. Ex. A sugar cube dissolves in a glass of Water Ex: Oxygen and carbon dioxide. Oxygen is taken into the cells and carbon dioxide is given out as a waste product Molecules move to equalize concentration Application of passive diffusion - Dialysis To remove wastes from blood in patients with malfunctioning kidney Blood passed through series of tubes with semipermeable membrane Toxins diffuse into the surrounding fluid and the cleansed blood returns to the patients. Types of Passive Transport – Facilitated Diffusion 1. A passive process 2. Down the concentration gradient 3. Passage through proteins – carrier proteins (or transporters) and channel proteins 4. Cell does not spend energy 5. Facilitated diffusion therefore allows polar and charged molecules to cross the plasma membrane Transport sugars, amino acids and nucleosides. E.g., Transport small molecules like water (aquaporins) and ions (ion glucose transporter. Transport is facilitated by change in channels in nerves and muscles). Highly selective (size), very shape of the protein. fast (millions of ions per second) and gated. Facilitated Diffusion Differentially permeable membrane Channels help a specific molecule or ion to enter or leave the cell Channels usually are transport proteins (aquaporins facilitate the 1.Protein binds with molecule movement of water) 2.Shape of protein changes 3.Molecule moves across membrane No energy is used glucose molecules- too large to fit in membrane pores Solution Differences & Cells Solvent + solute = solution Hypotonic - Solutes present in higher concentration inside the cell Outside solvent will flow into cell Isotonic Solutes equal inside & out of the cell For example, sponges, jellyfishes etc. are isotonic in oceanic conditions Hypertonic - Solutes present in higher concentration outside the cell Fluid will flow out of cell Osmosis Net Movement of solvent (diffusion) across a selectively permeable membrane towards higher solute concentration. It can be defined as movement of water molecules from higher to lower concentration of water or from lower to higher concentration of solute Often involves movement of water Into the cell Out of the cell Examples of Osmosis Swelling of Brain cells in response to excess water. Plants also exhibit osmosis - Turgidity Lettuce cells—Crisp when they absorb water Salad dressing exhibit osmosis Osmoregulation – water balance is maintained –freshwater fish have kidneys and gills – prevent excess build up of water Humans can suffer consequences of disrupted osmoregulation: Drinking less water - Dehydration - fatigue Drinking too much water – water Intoxication –overdilution of necessary ions Both can be fatal Active Transport Molecular movement against the concentration/electrochemical gradient Requires energy (against gradient) provided by coupling with ATP hydrolysis Example is sodium-potassium pump – vital for nervous system 3 Na+ are pumped out of the cells against the concentration gradient 2 K+ are pumped into the cells against the concentration gradient Na+-K+ pump maintains osmotic balance and cell volume Turgidity of guard cells controls the opening & closing of stomata, depending on water availability for the plant. This turgor is controlled by a combination of active & passive transport, with K+ ions being actively pumped into guard cell vacuoles to allow water inflow, making them turgid & inducing stomatal opening. Endocytosis Movement of large sized materials like: Particles Organisms Large molecules into the cells Types of endocytosis bulk-phase (nonspecific) receptor-mediated (specific) Process – 1.Plasma membrane surrounds material 2.Edges of membrane meet 3. Membranes fuse to form vesicle Forms of Endocytosis : 1) Phagocytosis- is the process of engulfing large particles, such as cells. Eg: protozoa engulf food and WBC engulf bacteria by wrapping them with membrane and taking them into the cell. Hence some WBCs are called phagocytes. When phagocytosis occurs, the material to be engulfed touches the surface of the cell and causes a portion of the plasma membrane to be indented. The indented plasma membrane is pinched off inside the cell to form a vacuole containing the engulfed material. Inside the cell the vacuole fuses with the lysosomes and the enzymes of the lysosomes degrade the contents on the vacuole. 2) Pinocytosis - is the process of engulfing liquids and the materials dissolved in the liquids, such as useful hormones. Energy is used – active process. Here the sacs formed are very small, compared with those formed during phagocytosis. Due to their small size, they are called vesicles 3) Receptor mediated endocytosis- is the process in which molecules from the cell’s surroundings bind to receptor molecules on the plasma membrane. The membrane then folds in and engulfs these molecules. Examples : transport of Insulin into animal cells Iron is carried through blood tightly bound to transferrin protein carrier – membrane has receptors proteins for transferrin Cholesterol uptake from blood by liver cells Exocytosis: occurs in the same manner as endocytosis, just reverse (inside to outside) Membranous sacs containing materials from the cell migrate to the plasma membrane and fuse with it. This results in the sac contents being released from the cell Many materials such as mucus, digestive enzymes and molecules produced by nerve cells, tears from tear glands etc. Exocytosis Exocytosis of neurotransmitters – brain Cell discharges material Vesicle moves to cell surface Membrane of vesicle fuses Materials expelled HUMAN SKELETON CYTOSKELETON The Cytoskeleton: Cell Shape and Movement The cytoskeleton-cell skeletal system is a network of protein fibers extending throughout the cytoplasm, and serves as both skeleton and “muscles” for the cell, functioning in support and movement. Just like bony skeleton in body help in fixing organs-cytoskeleton provide anchorage and reinforcement to many organelle in a cell Example- Nucleus is held in place by a cage of cytoskeletal filaments Lysosome –reach food vacuole by gliding along microtubule track Microtubules – guide movements of chromosomes when cell divides Give mechanical support to the cell © 2016 Pearson Education, Inc. Cytoskeleton - provides mechanical support to the cell and helps a cell maintain its shape. Filaments & fibers Made of 3 fiber types Microtubules -hollow tubes of protein Intermediate filaments Microfilaments - thinner and solid Microtubule, microfilaments and intermediate filaments are all interconnected within the cytoplasm of the cell. Maintaining Cell Shape A cell’s cytoskeleton is dynamic. It can be quickly dismantled in one part of the cell by removing protein subunits and re-formed in a new location by reattaching the subunits. Such rearrangement can provide rigidity in a new location, change the shape of the cell or even cause the whole cell or some of its parts to move. Amoeboid crawling ,WBC movement © 2016 Pearson Education, Inc. Cilia and Flagella In some eukaryotic cells, microtubules are arranged into structures called flagella and cilia Extensions from a cell that aid in movement. Eukaryotic flagella propel cells through an undulating, whip-like motion. They often occur singly, such as in human sperm cells © 2016 Pearson Education, Inc. Cilia and Flagella Cilia (singular, cilium) are generally shorter and more numerous than flagella and move in a coordinated back-and-forth motion, like the rhythmic oars of a crew team. Both cilia and flagella propel various protists through water. On cells lining the human trachea, cilia help sweep mucus with trapped debris out of the lungs. Tobacco smoking – can inhibit or destroy these cilia © 2016 Pearson Education, Inc. Cilia lining the respiratory tract Animation: Cilia and Flagella © 2016 Pearson Education, Inc. Cilia and Flagella human sperm rely on flagella for movement - problems with flagella can lead to male infertility. Some men with a type of hereditary sterility also suffer from respiratory problems because of a defect in the structure of their flagella and cilia. © 2016 Pearson Education, Inc. How cells Acquire energy Chapter 5 ,6 Topics to be covered ATP and cellular work Enzymes Cellular respiration Fermentation ATP and cellular work Carbohydrates, fats and other fuel molecules - obtained from food cannot be directly used as fuel by our cells Chemical energy released by the breakdown of these fuel molecules is stored in the form of ATP molecules ATP then powers cellular work Structure of ATP The transfer of chemical energy within living cells is managed by a nucleotide - adenosine triphosphate (ATP) Chemical energy is stored during ATP synthesis and is released when ATP molecules are broken. ATP has a tail of three phosphate groups attached at one end - is the key part that provides energy for cellular work. Each phosphate is negatively charged and these negative charges repel each other. The crowding of the negative charge in the tail contributes to the potential energy of ATP. The bonds holding the last 2 phosphates are the high-energy phosphate bonds, which are easily broken. When broken, the energy released is transferred to a lower energy molecule or released to the environment. ATP powers cellular processes ATP powers cellular processes by transferring a phosphate group to another molecule (a process called phosphorylation). This transfer is carried out by enzymes that couple the release of energy from ATP to cellular activities that require energy. Example - Moving a muscle fiber when a cyclist pedals uphill -transfer of phosphate group from ATP to motor proteins – change in protein shape – contraction of muscles Chemical energy = > mechanical energy The ATP Cycle Cells spend ATP continuously ATP is like a chargeable battery Enzymes are biochemical catalysts Enzymes & Activation Energy Enzymes work by lowering the activation energy How cells use Enzymes Living organisms need energy to do work. The energy is either received from the visible light or energy stored in the covalent bonds of certain compounds by means of a biochemical reaction. The set of processes including formation, breakdown and rearrangement of molecules to provide organisms with essential energy and building blocks are known as biochemical reactions The energy required to get these reactions started is called Activation energy. In living organisms, to sustain life these reactions should occur at an extremely rapid rate. But How? i. Raising the temperature routinely helps in supplying the activation energy in laboratory settings. However, this rise in temperature will results in denaturation of the proteins in cells. ii. Hence, the use of a catalyst helps in increasing the rate of the reaction, without affecting the cells proteins. An enzyme is a protein molecule that acts as a catalyst to speed up the rate of the reaction by lowering the activation energy required for its initiation! Enzymes can be used repeatedly until they are worn out or damaged Organisms make their own enzymes like any other protein through the set of instructions present in their DNA ENZYMES are BIOCATALYSTS responsible for supporting almost all of the chemical reactions that maintain ANIMAL HOMEOSTASIS In summary: Enzymes are usually globular proteins, produced within cell in small amounts They have complex structure and geometry specific to them (unique primary sequence of amino acid determines a unique 3D geometry) They act on a specific substrate They accelerate reaction rate without themselves being changed and They increase rate of reaction by lowering activation energy Enzyme Activity Enzymes Bind selectively to Substrates: The 3-Dimentional shape, size and charge of an enzyme are responsible for allowing it to combine with a reactant and lower the activation energy. The molecule to which the enzyme attaches (binds) itself is called the substrate and the temporary molecule formed is called the enzyme- substrate complex. Site where substrate binds is known as binding site and the site where the reaction happens is called as the Active site i.e. catalytic site. How Enzymes Speed Chemical Reaction Rates ✓ Some enzymes have different binding sites for small molecules which are often direct or indirect products of the reaction catalyzed. ✓ This binding can act to increase or decrease the enzyme activity - providing a means for feedback regulation ✓ When enzyme is bound to the substrate, its chemical bonds are less stable and more likely to be altered to form new bonds – this instability created in the substrate molecule is how enzymes lower the activation energy ✓ The enzyme is specific because it has a particular shape, which can combine with specific parts of certain substrate molecules. ENZYME SPECIFICITY : Enzymes are specific to the reaction they catalyze & substrate involved in the reaction Different models of enzyme specificity: 1) LOCK and KEY MODEL: lock is the enzyme and key is the substrate – unique key to every lock makes its specific! No change occurs in either the enzyme or the substrate. 2) INDUCED FIT THEORY : DANIEL KOSHLAND Since enzymes are partially flexible in structure, the active site can be reshaped slightly when it interacts with the incoming substrate The enzyme can bend or fold to fit the substrate or have subtle changes in the binding site pocket’s shape. This is called induced fit hypothesis. The fit is induced because the presence of the substrate causes the enzyme to mould or adjust itself to the substrate as the two come together. substrate plays a great role in determining the final shape of active site of enzyme. Models of Enzyme Specificity Control of Cellular Processes via Enzymes In an organism all the metabolic activities take place in proper sequence (co-ordination) and at the proper rate (regulation). The co-ordination of enzymatic activities in a cell results when the specific reactions occur in a given sequence. Eg: A B C D E Incase the cell is unable to coordinate its reactions, essential products will not be formed or will be formed at the wrong time or at random - leading to cell death. Hence the regulation of the biochemical reactions is a way to control the amount of chemical product formed. For instance, certain products when formed in excess are harmful to the cell – like lipids Body temporarily shut down biochemical pathways when a product is not required Enzyme inhibitors An inhibitor is a molecule that attaches itself to an enzyme and interferes with its ability to form an enzyme-substrate complex. Competitive inhibition: Some inhibitors have a shape that closely resembles the normal substrate (substrate imposters) of the enzyme and hence the enzyme cannot differentiate between the two. The inhibitor competes with the substrate for the active site of the enzyme. As long as the inhibitor is bound to the enzyme, the active site of the enzyme is not available for the substrate and hence the reaction the enzyme catalyzes does not occur – thus, the product is not formed. This is termed as Competitive inhibition. Non-Competitive inhibition: Other types of inhibitors bind to the enzyme at a different site remote from the active site, but this binding changes the enzyme’s shape, thereby not allowing the substrate to bind at the active site. Cellular Control Processes and Enzyme Inhibition Negative feedback inhibition – product as inhibitor Negative feedback inhibition is another method of controlling the synthesis of many molecules within the cell. This regulation occurs within an enzyme-controlled reaction sequence. As the number of the end product increases, some product molecules feed back to one of the previous reactions and have a negative effect on the enzyme controlling that reaction. i.e.: they inhibit or prevent that enzyme from performing at its best. A-ase B-ase C-ase D-ase A B C D E After inhibition when the end product molecules are lesser in number, they fail to have a negative effect and hence the enzyme resumes its original activity. Again, as the end product accumulates, its feedback inhibits the enzyme and the self-regulatory loop continues. Why do we need ENZYMES? Living organisms need ________________ to do work. The energy is either received from the visible light or energy stored in the _______________________by means of a biochemical reaction. The formation, breakdown and rearrangement of molecules to provide organisms with essential energy and building blocks are known as________________________________ The input of energy required to get these reactions started is called ___________________. In living organisms , to sustain life these reactions should occur at an extremely ____________________rate. In the laboratory, the rate of a reaction can be increased by supplying activation energy by ________________________________. But raising the temperature in living cells will __________________ the cell. The alternative option of increasing the reaction rate is by lowering the _____________________________ __________________helps in increasing the rate of the reaction by lowering the activation energy. What are enzymes? ENZYMES are __________________________________ An enzyme is a ________________________ that acts as a catalyst to speed the rate of biochemical reactions (metabolism). Enzymes can be ____________________ until they are worn out or damaged The production of enzymes (proteins) is directly under the control of an organism’s _______________________________. Organisms make their ______________________ enzymes. Enzymes catalyze almost all of the chemical reactions that maintain _____________________. All enzymes are globular proteins Every enzyme has a unique ____________________ sequence which gives rise to a unique 3D shape. Each enzyme has a uniquely shaped _______________ where only _____________________ substrates can bind. Cellular Respiration Cellular respiration is defined as a process of aerobic harvesting of chemical energy from organic fuel molecules A Road map for Cellular Respiration Net Reaction C6H12O6 + 6O2 6CO2 + 6H2O + energy (~32 ATP + heat) Aerobic Respiration Step 1: Glycolysis Pyruvate Pyruvate Takes place in the cytosol Involves 10 steps catalysed by 10 enzymes 1 Glucose gives 2 pyruvic acid + 4 ATP + 2NADH +2H+ Glucose Loses Electrons and gets Oxidised (LEO) NAD+ Gains Electrons and gets Reduced (GER) Energy Status!!! From Glycolysis No. of ATP No of ATP Net ATP No of No of H+ used produced produced NADH produced produced 2 4 2 2 2 Aerobic cellular respiration is a series of enzyme controlled chemical reactions in which oxygen is involved in the breakdown of glucose to carbon dioxide and water The chemical energy in glucose is made available to the cell in the form of ATP The net yield of the reaction between sugar and oxygen to form carbon dioxide and water: Glucose + Oxygen carbon dioxide + water + energy C6H12O6 + 6O2 6CO2 + 6H2O + energy (ATP + heat) When the chemical bonds in glucose molecules are broken, the energy of the electrons can be used to phosphorylate ADP molecules to produce high-energy ATP molecules, and Hydrogen ions (protons) are released in the process as well which play a very important role in energy harvesting later on Removal of electrons from glucose result in the glucose being oxidized These high energy electrons must be controlled. Electron transfer molecules like NADH and FADH2 temporarily hold the electrons and transfer them to other electron carriers. ATP is formed when these transfers take place. In aerobic cellular respiration oxygen serves as the terminal electron acceptor. When the electrons are added to oxygen it becomes a negatively charged ion (O--) and hence becomes reduced. LEO says GER The positively charged hydrogen ions that are released from glucose molecule combine with the negatively charged oxygen ions to form water. Once all the hydrogen atoms are removed from the glucose molecule, the remaining carbon and oxygen atoms are rearranged to form individual molecules of CO2. The redox reactions are complete. All the hydrogen removed from glucose combines with oxygen to form water. The energy released is used to generate ATP. The process can produce 32 ATP for each glucose molecule consumed. In eukaryotic cells, the process of releasing energy from food begins in the cytoplasm and is completed in the mitochondria. There are three distinct enzymatic pathways or stages involved: Glycolysis, Krebs cycle and Electron transport chain. Glycolysis: Glycolysis (glycos = sugar; lysis = split) takes place in the cytoplasm of the cells and results in the breakdown of glucose with the release of electrons and the formation of ATP. Glucose has energy added to it from 2 ATP molecules. This extra energy makes some of the bonds in glucose unstable and glucose is more readily broken down. After passing through four enzymatic reactions, 6-C is cleaved into 2, 3- C molecules. These undergo 5 more reactions to form Pyruvic acid or pyruvates. Electrons released from the bond splitting are picked by NAD+ to form NADH. In addition to NADH, glycolysis also makes 4 ATP molecules directly when enzymes transfer phosphate groups from fuel molecules to ADP. Since 2 ATP molecules are consumed in starting the reaction, the net gain of ATP is 2 ATP per molecule of glucose in glycolytic pathway. 2 N

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