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Principles of Biology. Pre-Exam 1 Notes

by: KennyFry Notetaker

Principles of Biology. Pre-Exam 1 Notes BIOL 1020-001

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These are chapters 1-5 notes. This will be all the information on the 1st Exam in September.
Principle of Biology
James Zanzot
Class Notes
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This 15 page Class Notes was uploaded by KennyFry Notetaker on Friday September 2, 2016. The Class Notes belongs to BIOL 1020-001 at Auburn University taught by James Zanzot in Summer 2016. Since its upload, it has received 7 views. For similar materials see Principle of Biology in Biology at Auburn University.


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Date Created: 09/02/16
08/17/2016 Qualities shared by all living organisms  Ordered and Organized  Regulates Itself  Energy Processing  Growth and Develop  Reproduction  Response to the Environment  Evolutionary Adaptation Life as we know it also has physical properties  Requires water (Ch. 3)  Carbon-based (Ch. 4)  Made up of units called cells (Ch. 6)  DNA based transfer of hereditary information (Unit 3)  Integrated with other organisms (Unit 4) What is a Virus? Viruses are not alive. Yet they are made up of stuff living organisms are made up of. Theories in science  Evolutionary Theory  Atomic Theory  Plate Tectonic Theory  Big Bang Theory  Cell Theory  Germ Theory  Theory of Gravity  Theories of Relativity What is a Theory?  A scientific theory is a broad framework or model for explaining natural phenomena.  A theory generates more specific, testable hypotheses.  A theory must be supported by observational and experimental evidence.  A theory has practical application  NOT a wild guess -08/19/2016 Key Concepts  Matter consists of chemical elements in pure form and in combinations called compounds  An elements properties depend on the structure of its atoms  The formation and function of molecules depend on chemical bonding between atoms  Chemical reactions make and break chemical bonds. Matter consists of chemical elements in pure form and in combinations called compounds. Matter  Takes up space  Has mass  Can exists as solid, liquid, gas, (plasma) Element: a substance which cannot be broken down by chemical means  Eg oxygen, iron, gold Compound: Substance Chemical symbols- Elements have 1 or 2 letter symbols Eg- Au, B, U, Rn Elements and Compounds Sodium (Na) + Chlorine (Cl) = Sodium Chloride (NaCl) Humans are mainly- 96.3% Oxygen, Carbon, Hydrogen, and Nitrogen Subatomic particles- Has a Nucleus: with Protons and Neutrons. Electrons are on outside. Elemental Properties are determined by atomic structure  Atoms: the smallest unit of matter, indivisible by chemical means  Nucleus: the central part of the atom  Proton: a nuclear particle with positive charge  Neutron: nuclear particle with no charge  Mass p= Mass n= 1.7 X 10- 24g  Electron: atomic particle with negative charge, 1/2000 Mass p or n Atomic number and atomic mass  Atomic NUMBER determined by number of protons (bottom left number)  Atomic MASS determined by number of protons and neutrons (top left number)  Isotopes are when elements have a different number of neutrons than they do of protons. Which gives it a different mass.  When they become unstable they decay and become radioactive Atoms are mostly empty space- If they were the size of a football stadium. Than the nucleus would be the size of the pencil eraser on the 50yd line. Electrons would be flies wising around. Nuclei are not directly involved in most chemical reactions.  Chemical reactions make and break bonds  Bonds are interactions between electrons Energy  Energy is the capacity to do work or effect change, comes in many forms (Chemical, mechanical, heat, light)  Potential energy: reflects position or structure (Like a water tower with its pressure) Energy levels of electrons  Electrons live in their orbital layers. The first shell has lowest energy level. Further away means more energy. (Negative) Electrons = # of (Positive) Protons for a charge of 0 --08/22/16 Strong Chemical bonds form  Because atoms are more stable when their valence (outermost) shells are filled. Chemical Bonds  Are how molecules are formed  Strong bond (intramolecular) o Covalent o Ionic  Weaker Bonds (intermolecular) o Hydrogen bonds o Can der Waals interactions Covalent Bonds- Are formed when two electrons are shared by two atoms (Trying to fill the shell) Bonding Capacity  The number of bonds an atom can form  Is dependent on the number of valence electrons  How many unpaired electrons required to complete valence shell  H -1  C -4  O -2  N -3  ^ Needed to complete valence shell. Ionic Bonds- Are when atoms have one to a few extra electrons but instead of trying to gain far more electrons it requires less energy to lose the few or one electron it does have to complete both electrons valence shells. Creates Cation (Positively charged) and an Anion (Negatively charged) atom. Ions – Are charged atoms or molecules  # of protons does NOT = the # of electrons  + charged ion= Cation  - charged ion = Anion  Ionic compounds, generally, are SALTS  Environment affects ionic bond strength Weak Chemical Bonds  Hydrogen bonds  Van der Waals interactions Van der Waals attraction  Typically, in non-polar molecules  Asymmetry in charge distribution  Large molecules, packed together  Weaker than H- bonds  Strength in #’s Molecular shape and function  Molecules are 3-D  All of these types of bonds contribute to shape of Molecules  Shape is essential to function Chemical reactions make and break bonds Reactants + Reactants  Reaction = Products  Chemical reactions are dynamic processes  Reactions are reversible  Concentration of reactants affects the rate of reactions  Equilibrium: rates of forward and reverse rxns are the SAME Summary  Matter consists of chemical elements in pure form and in combinations called compounds  An elements properties depend on the structure of its atoms  The formation of function of molecules depend on chemical bonding between atoms  Chemical reactions make and break chemical bonds. End Chapter Video Commentary Notes- Cohesion- Ability to stick to itself (Hydrogen bonds) Adhesion- Ability to stick to other things Polar Molecule- H2o Chapter 3 08/24/16 Water- Key Concepts  Polar covalent bonds in water molecules results in hydrogen bonding  Four emergent properties of water contribute to Earths suitability for life  Acidic and basic condition affect living organisms. Four Properties of Water  Cohesion of water molecules  Moderation of temperature aby water  Ice Floats  Water is the solution (at least the solvent) Water 3moderates’ temperature  ENERGY: is the capacity to do work or effect change  Heat Vs Temperature  Heat -> the total kinetic energy  Temperature -> the average kinetic energy Temperature Vs Heat A larger mass of water usually has more heat (a pool with people in it) Vs. a hot cup of coffee which is temperature hotter but not heat hotter. Heat  Measured in calories  1 calorie -> amt of heat to 1g h2o by 1C  Food calories are actually kcal (1000 calories)  Heat is a form of energy so can also measure in joules 1 J = 0.239 cal Specific heat  Amount of heat required to change temperature  Water changes temperature less rapidly than other substances  What happens if you put an empty kettle on a hot stove? Phases of Matter  Density o Gas < Liquid < Solid Ice floats… Because it is less dense due to hydrogen bonds being stable in its crystal state. Chemical Solutions  Solution- a uniform mix of 3 or more substances  Solvent- The liquid dissolving reagent in a solution (The wet stuff) Water  Solute- The dissolved reagent in a solution (The dry stuff) Kool-Aid powder Salt dissolves completely because of Oxygens negative charge takes the sodium and hydrogen’s charge takes the chlorine. Therefore, completely dissolving NaCl (Salt) Hydrophilic and Hydrophobic substances  Substances which attract water are hydrophilic  Substances which repel water are hydrophobic (Oil)  Generally, ionic or polar substances are hydrophilic  Substances which are non-ionic are hydrophobic (Oil) Concentration and Molarity  Amounts of reagents are important  Molecular weight = sum of atomic weights  Sucrose: C12 H22 O11  MW= 12*C + 22*H + 11*O = 342 Da/Molecule  Avogadro’s Number -> 6.02 x 10 “23” -> 1 mole o Converts daltons to grams  342 grams of sucrose is 6.02 X 10 “23” molecules  Moles help us to fix ratios of molecules  1 mole sucrose is 1 L of water o 1 Molar solution o 1M sol’n  Molarity is # of moles solute per liter Acids and Bases  Water is not all H20  Can dissociate into Ions  H20 -> <- H+, OH-  1 molecule in 554 million typically  In pure water @ 25C, [H+] = 10^-7 M  Also [OH-] = 10^-7M  Ions are more reactive than H20  Other ionic compounds, added to water will dissociate, like: o HCL -> <- H+ CL- o NaOH-><- Na+ OH-  These will dramatically affect [H+] and [OH-]  Compounds which contribute H+ are ACIDS  Compounds which contribute OH- are BASES Acidic have more H+ then OH- Bases have more OH- then H+ The pH scale  pH = -log [H+]  [H+] can vary from 10^0 – 10 ^-14 M  [OH-] varies reciprocally 10^-14 – 10^0 M Imagine the number 1 with 7 [0]’s over it. The negative log of that number would be 7  10^0 = 1M --Acid  10^-1 = 1/10M-- Neutral  10^-4 = 1/10,000M –Base  pH + pOH = 14  pH 1 = pOH 13  pH 3 = pOH 11 POH is the reciprocal of pH and refers to the base  pH 4: [H+] = 1/10,000M Buffers minimize changes in pH  Buffers act as acids or bases or both  They are weakly ionizing  Many buffers are both acid and base at the same time, depending on pH of surrounding sol’n  Bicarbonate is an important buffer in vertebrate blood  Carbon dioxide (CO2) + Water(H20)  Carbonic acid (H2CO3)  (H+) + Bicarbonate ion (HCO-3) Ecological effects of pH  Acid precipitation results from burning  Natural and human made  I.e. Volcanic eruption decreases pH (makes it more acidic Chapter 4. 08/29/2016 Carbon and the molecular diversity of life  Carbon- The backbone of life  Living organism consist mostly of carbon-based compounds  Carbon is unparalleled in its ability to form large, complex, and diverse molecules  Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds Organic Chemistry is the study of carbon compounds  Organic chemistry is the study of compounds that contain carbon  Organic compounds range from simple molecules to colossal ones  Most organic compounds contain hydrogen atoms in addition to carbon atoms Vitalism vs. Mechanism  Friedrich Wohler synthesized a Urea (living organism) from carbon  Vitalism- is the idea that living things can only be made of living things and found in living things.  Mechanism- Is the synthesizing of living organisms from nonliving sources Stanley Miller experiment created a synthetic “Atmosphere” Carbon atoms can form diverse molecules by bonding to four other atoms  Electron configuration is the key to an atoms characteristic  Electron configuration determines the kings and number of bonds an atom will form with other atoms  Can form four covalent bonds Hydrogen valence of 1 Oxygen valence of 2 Nitrogen valence of 3 Carbon valence of 4 Molecular Diversity arising from carbon skeleton variation  Carbon chains form the skeletons of most organic molecules Hydrocarbons  Hydrocarbons are organic molecules consisting only carbon and hydrogen  Many organic molecules such as fats, have hydrocarbon components  Hydrocarbons can undergo reactions that release a large amount of energy Octane- 8 carbon atoms the rest are hydrogen Isomers- are compounds with the same molecular formula but different structures and properties  Structural isomers have different covalent arrangements of their atoms  Cis-trans isomers have the same covalent bonds but differ in spatial arrangements  Cis are on same side, Trans are on opposite sides/diagonal  Enantiomers are isomers that are mirror images of each other A few chemical groups are key to the functioning of biological molecules  Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it  A number of characteristics groups can replace the hydrogens attached to the skeletons of organic molecules Functional group- Hydroxyl- -OH Alcohols,  Is polar as a result of the electrons spending more time near the electronegative oxygen atom  Can form hydrogen bonds with water molecules helping dissolve organic compounds such as sugar Carbonyl- C=O Ketones and Aldehydes Carboxyl- Carboxylic acids or organic acids  Acts as an acid, can donate an H+ because the covalent bond between oxygen and hydrogen is so polar  Found in cells in the ionized form with a charge of 1- and called a carboxylate ion. Amino- Amines  Acts as a base, can pick up an H+ from the surrounding solution  Found in cells in the ionized form with a charge of 1+  Somewhat polar Sulfhydryl- Thiols  Two sulfhydryl groups can react, forming a covalent bond. This Cross linking helps stabilize protein structure  Cross- Linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be permanently curled aby shaping it around curlers and then breaking and re-forming the cross linking bonds. Phosphate- Organic phosphates  Contributes negative charge to the molecule of which it is a part  Molecules containing phosphate groups have the potential to react with water, releasing energy. ATP- An important source of energy in cellular respiration Methyl- Methylated compounds  Addition of a methyl group to DNA or to molecules bound to DNA affects the expression of genes  Arrangement of methyl groups in male and female sex hormones affects their shape and function. WRITE DOWN WHA TTHE OBECTIVES ARE FROM POWERPOINTS Chapter 5 Notes 8/31/16 The structure and function of large biological Molecules Part 1- Introduction of carbohydrates and lipids The molecules of life  All living things are made up of four classes of large biological moles: o Carbohydrates o Lipids o Proteins o Nucleic acids  Macromolecules are large molecules and are complex  Large biological molecules have unique properties. Macromolecules are polymers built from monomers  A polymer is a long molecule consisting of many similar building blocks  The repeating units that serve as building blocks are called monomers  Three of the four classes of life’s organic molecules are polymers o Carbohydrates o Proteins o Nucleic acids The synthesis and breakdown of Polymers  Enzymes are specialized macromolecules that speed up chemical reactions  A dehydration reaction occurs when two monomers bond together through the loss of a mater molecule  Polymers are disassembled to monomers by hydrolysis a reaction that is essentially the reverse of the dehydration method. The diversity of polymers o Each cell has thousands of different macromolecules o Macromolecules vary among cells of an organism vary more within a species and vary even more between species o A huge variety of polymers can be built from a small set of monomers. Carbohydrates serve as fuel and building blocks o Carbohydrates include sugars and the polymers of sugars o The simplest carbohydrates are monosaccharides or simple sugars o Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks. Sugars (usually ends in “ose” e.g. Trioses, Pentoses, Hexoses) o Monosaccharides have molecular formulas that are usually multiples of CH20 o Glucose (C6H12O6) is the most common o Monosaccharides are classified by o The location of the carbonyl group (Aldoses “Carbon groups are on outside” AND Ketoses “Carbon group are on inside”) o The number of carbons in the carbon skeleton Though often drawn as linear skeletons, however, in aqueous solutions man sugars form rings Monosaccharides are fuel. Disaccharides o A disaccharide is formed when a dehydration reaction joins two monosaccharides o This covalent bond is called a glyosidic linkage Polysaccharides o Polysaccharides, the polymers of sugars, have storage and structural roles o The architecture and function of a polysaccharide are determined by its sugar monomers and the positions of its glyosidic linkages. Storage Polysaccharides o Starch, A storage polysaccharide of plants, consists entirely of glucose monomers o Plants store surplus starch as granules within chloroplasts and other plastids o The simplest form of starch is amylose. Glycogen Is the storage polysaccharide Structural Polysaccharide o The polysaccharide Cellulose is a major component of the tough wall of plant cells o Like starch cellulose is a polymer of glucose but the glyosidic linkages differ o The difference is based on two ring forms for glucose: alpha and beta Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze Beta linkages in cellulose o The cellulose in human food passes through the digestive tract as insoluble fiber o Some microbes use enzymes to digest cellulose Lipids are a diverse group of hydrophobic molecules o Lipids are the one class of large biological molecules that does not include true polymers o The unifying feature of lipids is that they mix poorly if at all with water o Lipids are hydrophobic because they are nonpolar o The most biological are fats Fats o Fats are constructed from two types of smaller molecules: glycerol and fatty acids o Glycerol is a three carbon alcohol with a hydroxyl group attached to each carbon o A fatty acid consists of a carboxyl group attached to each other Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds  Fats separate from water because water molecules hydrogen-bond to each other and exclude fats  In a fat three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol or triglyceride  The fatty acids in a fat can be all the same or of two or three different kinds  Fatty acids vary in length (number of carbons) and in the number and locations of double bonds  Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds  Unsaturated fatty acids have one or more double bonds  Fats made from saturated fatty acids are called saturated fats and are solid at room temperature  Most animal fats are saturated  Fats made from unsaturated fatty acids are called unsaturated fats or oils  Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen  Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds  These trans fats may contribute more than saturated fats to cardiovascular disease.  Trans fats are typically produced by artificial hydrogenation of fatty acids. Omega 3 fatty acids Refers to 3 carbon at tail end  Certain unsaturated fatty acids are not synthesized in the human body  These must be supplied in the diet  These essential fatty acids include the omega- 3 fatty acids, which are required for normal growth and are though to provide protection against cardiovascular disease. Functions of fats  The major function of fats is energy storage  Humans and other mammals store their long term food reserves in adipose cells  Adipose tissue also cushions vital organs and insulates the body. Phospholipids  In a phospholipid, two fatty acids and a phosphate group are attached to glycerol  When phospholipids are added to water they self-assemble into double layered structures called bilayers  At a surface of a cell, phospholipids also arranged in a bilayer with hydrophobic tails pointing toward the interior Steroids  Steroids are lipids characterized by a carbon skeleton consisting of four fused rings  Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized Chapter 5 Biological molecules Part 2 Proteins and nucleic acids 9/2/16  Proteins account for more than 50% of the dry mass of most cells  Protein functions include structural support, storage, transportation, defense, structure, etc. Amino acid monomers  Amino Acids are organic molecules with carboxyl and amino groups  Amino acids differ in their properties due to differing side chains, called R groups Amino acids polymers  Amino acids are linked by peptide bonds  A polypeptide is a polymer of amino acids  Polypeptides range in length from a few to more than thousand monomers  Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) [Like Christmas lights and extension cords, with male and female adapters]


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