All the lecture notes for the course Biology 101 PDF

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All the lecture notes for the course Biology 101...

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Chapt er1 Humansi nt hewor l dofBi ol ogy  Sc i ence o Der i v edf r om Lat i nv er bs ci ent i ameani ng“ t oknow”  Knowl edgeder i v edf r om obs er v at i on,st udy ,andexper i ment at i onobj ect i v eanal ys i s ofanyoccur r ence  Sc i enceMUSTbeunbi ased-t her esear chercannotbel ooki ngf orapar t i c ul ar r esul t( cannothav eanagenda) o Cansc i encebeunbi ased?Oneoft hemaj orf undi ngs our ce i nCanada ar et obaccocompani esanddr ugcompani es… cant hesebi as r esear cher s ?  Howdoewemak esc i enceunbi ased? o Hy pot hesi sTest i ng  Hy pot hesi s

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o statement about observation that can be tested experimentally for acceptance or rejection o proposed explanation for a phenomenon o possible causes o reflect past experience with similar questions o makes predictions that are falsifiable o can be eliminated, but not confirmed with absolute certainty Experimentation o to test hypothesis designed to eliminate other explanations o well designed o experimental/control groups o experimental o group in which one factor or treatment is varied o control o group in which the independent variable is removed o necessary for comparison o allows conclusions to be made about effect of experimental manipulation o A note on controls: o - ALL groups must be treated EXACTLY the same except for the ONE CHANGE (called the independent variable) Theory: broad generalization o supported by many hypotheses which cannot be disproved by years of experimentation o comprehensive conceptual framework well supported by evidence and widely accepted by scientific community Modern biology is based on several great ideas, or theories o The Cell Theory o The Theory of Evolution by Natural Selection o Gene Theory o Homeostasis

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Biology o “the science dealing with living organisms” o knowledge derived from the observation, study and experimentation on the workings of the living world Biology – the science of life o Biology - the decathlon of the sciences  levels of organization (many)  diversity (great)  advances in knowledge (ever increasing)  specialization yet strong unifying themes o more unifying themes  many chemical pathways similar  same genetic code  evolutionary relatedness Making Sense of the World o Biologists have a particular way of interpreting the world. o There are alternative explanations from nonscience sources. o The key is to keep an open mind as you study. o There are Patterns in Biology A Pattern in Biological Organization o A general pattern of organization in nature begins with atoms and molecules. o The cell, composed of "biological molecules," is the smallest unit of life. o Multicelled organisms have increasingly complex levels of organization that result in tissues >> organs >> organ systems >> organisms >> populations >> communities >> ecosystems >> biosphere. What does it mean to be ‘living” o All living things share basic characteristics The theory of chemical evolution o H2, CH4 , CO2, CO, N2,UV radiation, Lightning, Water o Earth is thought to be 4.5 billion years old – based on isotope studies. Fossil evidence suggests that life has been on Earth for 3.8 billion years o How could life have evolved under such extreme conditions as were found on earth during this time? Could Chemical evolution have occurred over 300 million years with primitive earth conditions? o Oparin and Haldane ( chemists - 1920s)  suggested that these conditions actually favored the synthesis of small organic molecules from inorganic molecules

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o Miller and Urey – recreated the conditions in a laboratory supported the hypothesis o Then -once small organic molecules were produced it is relatively easy to produce larger molecules ( amino acids to proteins) o Miller's (and subsequent) experiments have not proven life originated in this way, only that conditions thought to have existed over 3 billion years ago were such that the spontaneous (inorganic) formation of organic macromolecules could have taken place. The simple inorganic molecules that Miller placed into his apparatus, produced a variety of complex molecules: Characteristics of ALL life o 1. Made up of organic molecules  Organic molecules have carbon and hydrogen covalent bonds along with other atoms. There are four types of biological macromolecules  Carbohydrates  Proteins  Nucleic Acids  lipids o 2. Composed of cells  Cell Theory: o All living things are composed of at least one cell o The cell is the fundamental unit of function in all living organisms o The chemical composition is fundamentally alike in all cells o All cells arise from pre-existing cells  Unicellular organisms  Prokaryotes and Eukaryotes  Multicellular organisms  A living Cell must have o -Plasma membrane o Selective permeability o Cytoplasm o Metabolic activities o Genetic Material of both DNA and RNA o 3. Reproduce  Sexual reproduction (sperm and egg)  Usually multicellular organisms  Asexual reproduction (splitting of the cell)  Usually unicellular organisms

o 4. Metabolize & take up molecules from their surroundings  Metabolism: the sum of all chemical reactions in an organism  The cells “metabolic machinery = enzymes  At any given moment, all the work being done by a cell is being done by enzymes  Even a “simple cell” like a bacteria cell - has about 1000 different types of enzymes floating in the cytoplasm at any given time  Enzymes are little “chemical reaction machines”- very specific proteins  The purpose of the enzyme is to allow the cell to carry on chemical reactions very fast – they allow the cell to build things and take things apart as needed – this is how the cell grows and reproduces  Anabolism: assembly of simple molecules into more complex molecules  Catabolism: breaking down of complex molecules into more simple ones o 5. Respond o All living things must be able to sense their environment and respond accordingly  Example: Touch a hot stove, pull hand away  Some bacteria can orient themselves with Earth’s magnetic field  Animals were the first to flee hours before the tsunami hit Asia in 2006 o 6. Maintain Homeostasis  A condition of dynamic equilibrium within any biological system  Our body temperature stays a pretty steady 37oC – how?  Homeostasis must be maintained for everything in the body – concentration of nutrients, temperature, size etc  Many different organs, organelles and tissues cooperate to maintain homeostasis o 7. Products of evolution  Evolution:  “the development of new types of organisms from pre-existing types by the accumulation of genetic differences over long periods of time”  Survival in nature:

Best “adapted” organisms survive = Natural Selection  Surviving organism pass along “adaptations” to next generation  Adaptive traits:  structural, functional or behavioral changes in a species that are particularly suited for a specific environment Basic Biological Chemistry  all living things are composed of the same basic building blocks – atoms molecules and compounds o What makes them different from non-living things and each other is the specific types of molecules and the high level of organization of the large molecular groups we refer to as “biological molecules”  Compounds and Chemical bonds o Two or more elements may combine to form a compound  A compounds characteristics are different from those of the elements o The number of electrons that are gained or lost is characteristic for each element, and ultimately determines the number and types of chemical bonds atoms of that element can form.  Chemical Bonds o Ionic bonds are formed when atoms become ions by gaining or losing electrons.  Oppositely charged atoms will be attracted to each other  An electron is stripped from one atom and added to another o Covalent bonds form when atoms share electrons. Since electrons move very fast they can be shared, effectively filling or emptying the outer shells of the atoms involved in the bond. Such bonds are referred to as electron-sharing bonds. o Polar and Non-Polar Covalent bonds  The electrons in a covalent bond will sometimes spend more  time with one atom than with the other  Molecules that contain oxygen ( a very electronegative atom) are often “polar” (water)  The unequal sharing gives one side of the molecule a slight negative charge and the other side of the molecule a slight positive charge 

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o Water molecules will spontaneously form hydrogen bonds because of the electrical attractions between polar areas on the molecule o Non-Polar molecules have electrons that are shared equally withing their covalent bonds.  The overall charge of the molecule is then neutral o Hydrogen bonds result from the weak electrical attraction between the positive end of one molecule and the negative end of another.  Individually these bonds are very weak, although taken in a large enough quantity, the result is strong enough to hold molecules together or in a threedimensional shape  The presence of polar areas in amino acids that make up proteins allow for hydrogen bonds to form – giving the molecule its 3D shape which is often vital to the proteins function Water: the solvent of life o On earth – water is the most widespread solvent  - a substance that is capable of forming a homogeneous mixture with molecules of another substance  Substances that dissolve in water are called solutes – the individual molecules will disperse throughout the water and become surrounded by clusters of water o Water is a very polar solvent—it will surround ions – shielding them from one another  A compound does not need to be ionic in order to dissolve in water – any polar substance will dissolve if there are ionic and polar regions on the surface The pH scale measures the concentration of hydrogen ions in a solution. o The numbers on the scale refer to the exponent of the concentration of hydrogen ions  Fluids in living things must be kept within a narrow range of pH for proper functioning of the enzymes involved in biochemical reactions. Major Molecules of life Biological macromolecules o The giant molecules of life o They are long chains called polymers made of repeating units called monomers o Carbohydrates, lipids, protein, and nucleic acid Carbrohydrates

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o Carbohydrates function in short-term energy storage (such as sugar); o as intermediate-term energy storage (starch for plants and glycogen for animals); o and as structural components in cells (cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods. Monosacharides o Simple sugars ( ribose, glucose and fructose)  May have the same chemical formula but different structures  Classification is done by the number of carbon atoms and the types of functional groups ( aldehydes and ketones)  In an aqueous solution ( cytoplasm of the cell) Linear sugars are usually found in a ring form Disacharides o Two monosacharides joined together by glycosidic linkage  This is the special name given to the covalent bond that holds two carbohydrate molecules together Polysacharides o Large molecules composed of individual monosaccharide units - the most important for cells are starch, glycogen, cellulose o Starch (plants)  long term storage form of glucose in plants o Glycogen (animals)  = storage form in animals the glucose is linked in a similar manner but the branches are different o Cellulose o Glucose molecule linked together but the glycosidic linkage is different  Animals have not evolved the enzyme required to digest (break down) cellulose. However there are bacteria cells that do have this ability ( in guts of termites and cattle) Lipids o - molecules that are defined by their solubility not their structure o They are insoluble in polar solvents ( water )  For long term energy storage  Structural components ( major component of the cell plasma membrane)

Protection ( internal organs) Lubricants Signalling molecules ( hormones) communicate within and between cells Triglycerides ( fats and oils) o Composed of fatty acid bonded to a glycerol molecule o fatty acid is a long chain of 12-24 carbon atoms with hydrogens attached to them o At one end is a carboxyl group ( acid group) o This will be used to join the FA to the glycerol molecule ( called an ester linkage) o Will require specific enzymes o The non-polar C-H bonds in the “tails” of the fatty acids are the reason fats are hydrophobic o Animals will convert excess sugars ( beyond glycogen storage). Into fat – fats can store 6 times more energy than glycogen Saturated and Unsaturated fats o Lipids will have different characteristics depending on their level of “ saturation” o Saturated fatty acids – contain “all the hydrogens they can hold”  There are no carbon- carbon double bonds  These fats are typical of animals and are thought to cause blockage of arteries leading to strokes and heart attacks o Unsaturated fatty acids – contain double bonds  Results in a kink in the molecule  These fats may be liquid at room temp depending on the structure o their tails (polyunsaturates) Cholesterol and steroids o Cholesterol has many biological uses  A strucral component of animal cell membranes  Has a role in forming the sheath surrounding neurons  Forms the ‘backbone’ of many steroid hormones (the only difference between testosterone and estrogen is round in the attached functional groups Phospholoipids o Formed by replacing one of the terminal fatty acids in a triglyceride wit ha phosphate group PO4  Because the oxygen are so electronegative – this part of the molecule now becomes very polar (hydrophilic)  The fatty acid part of the molecule however remains very non- polar (hydrophobic)   

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They are considered to be ambivalent or amphipathic when they are placed in a water environment  They will spontaneously form circular structures called micelles  In an environment where there is water on both sides (cell) they form bilayer structures Proteins (polypeptides) o Although there are many different structures and functions fro proteins they are all constructed form the same set of 20 amino acids o The amino acids have a ‘general stucture’ which contains a central Carbon atom with four different functional groups attached Four levels of Protein Structure o Primary structure  The unique sequence of amino acids joined together by pepetide bonds results in a ‘ribbon’ or string like structure. o Secondary structure  Occurs when coiled or folded patterns emerge- as result of hydrogen bonds between Hydrogen and oxygen’s / nitrogens in the repeating chain (backbone) sequences (electronegative atoms)  Individually the bonds are very weak but because they are repeated many times over a relatively long region Tertiary Structure o “side chain interaction” the R groups of the individual amino acids will come into contact with each other to produce a variety of interactions o Hydrophobic side chains will cluster together – out of contact with water o Hydrogen bonds can form between polar side chains o Disulphide bridges can form between cysteine amino acid side chains o Even ionic bonds can form betweencharged side chain components Quaternary Structure o Aggregation of polypeptide subunits  Collagen – helical subunits that are intertwined into a larger triple helix ( great strength)skin, bone, tendons, ligaments o Hemoglobin 

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Consists of 4 polypeptide subunits with a nonpolypeptide component called heme ( iron atom)Binds oxygen in red blood cells Nucleic Acids o Encode information o Base molecule is a 5 carbon sugar + nitrogenous base + at a1 phosphate group o DNA  Sugar = deoxyribose sugar  Bases = guanine, adenine, thymine or cytosine  Double stranded o RNA  Sugar = ribose sugar  Bases = guanine, adenine, uracil or cytosine  Single stranded o ATP  Energy containing molecule Cell Types o PROKARYOTIC  bacteria & archaebacteria no true nucleus DNA in nucleoid region, circular DNA no membrane-bound organelles small (1 - 10 mm) o EUKARYOTIC  protists, plants, fungi, animals  true nucleus; bounded by nuclear envelope  DNA within nucleus  membrane-bound organelles  large (10 - 100 mm) Classification of Organisms 3 Domains = bacteria, archea (prokaryotes) and eukaryotes Cell Fractionation o Take cells apart and separate the major organelles from each other o Centrifuge spins test tubes at various speeds o Resulting force separates cellular components by size and density o Has been used to assign various functions to the different organelles( for example: the fraction that was found to hold the enzymes in cellular respiration – was also found to contain mitochondria) Membrane Structure and Function Plasma membrane = 8nm  responsible for selective permeability 

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o Regulation of what enters and leaves the cell – the ability of a cell to discriminate its chemical exchanges with its environment is fundamental to life o general principles of “membrane traffic” also apply to the many varieties of internal membranes that partition a eukaryotic cell Plasma Membrane: Functions o 1. maintains structural integrity of cell o 2. regulates movement of ions & molecules into & out of cell o 3. cell-cell recognition o 4. communication between cells o 5. sticks cells together to form tissues & organs Membrane Proteins Two types of membrane proteins: o - peripheral o - transmembrane ( integral) Different cell types will have different sets of proteins embedded in their membranes ( at least 50 different types in red blood cells) In some cells a single protein can carry out many different functions ( large complex proteins) Transmembrane Proteins o “integral protein” with hydrophobic regions ( stretches of non-polar amino acids – usually coiled into helices) o and hydrophillic regions that are exposed to the water solutions on either side of the membrane o These areas of the proteins can act as binding sites for substances to be brought into the cell through “channels” and as “gates” that open and close to allow large molecules in or out Peripheral Proteins o These proteins are not embedded in the hydrophobic region of the membrane – but are like “appendages” loosely bound to the surface o They can be either on the cytoplasmic side ( maybe interacting with the cytoskeleton ) or on the outside of the cell ( perhaps anchoring the cell to the extracellular matrix) o They can also be attached to the exposed parts of integral proteins Membrane Carbohydrates o Cell-cell recognition – the ability to distinguish one cell type from another is crucial to the functioning of an organism o Sorting of cell into tissues o Rejection of foreign tissue by the immune system

o Recognition is via “surface molecules” = specific carbohydrates on the outer surface of the plasma membrane o Usually short – branched sugars that may be linked to lipids or proteins ( glycolipids or glycoproteins)  Movement across the membranes o Diffusion = the net movement of a substance ( liquid or gas) from an area of higher concentration to one of lower concentration  Since molecules of any substance are in constant motion – kinetic energy is what moves them  The overall ( net movement) will occur until the molecules reach a state of equilibrium where they are equally distributed throughout  Diffusion is the principle method of movement in /through cells Facilitative Diffusion and Transport all cells require molecules and ions from the surrounding environment ( Na+, Ca++, glucose, amino acids ) - There is also movement of molecules across the membranes of some organelles ( mitochondria, chloroplasts, nucleus) - these tend to be very large molecules ( mRNA, proteins, ATP) Therefore two problems must be overcome: - In order for diffusion to move the molecules – the relative concentrations must be orien...