LECTURE NOTES WEEK 2
LECTURE NOTES WEEK 2 BIOL 2460-001
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This 5 page Class Notes was uploaded by Mercy on Wednesday September 16, 2015. The Class Notes belongs to BIOL 2460-001 at University of Texas at Arlington taught by Dr. Michelle Badon in Summer 2015. Since its upload, it has received 90 views. For similar materials see Nursing Microbiology in Biology at University of Texas at Arlington.
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Date Created: 09/16/15
LECTURE NOTE WEEK 2 Friday September 11 2015 2002 Please take note of words in bold and italics The chemistry of biology Cell This is where chemicals come to life It contains a huge aggregate of carbon hydrogen oxygen nitrogen and many other atoms The combination of these produces characteristics reactions and products that can only be described as living Fundamental characteristics of cells They are processes that define life These are growth reproduction and heredity metabolism including cell synthesis and the release of energy movement orand irritability cell support protection and storage mechanisms capacity to transport substances into and out of the cell Atoms They are the basic units of all matter containing three major components These components are Electrons negatively charged electrons e Protons positively charged p Neutrons uncharged neutral Protons and neutrons are the heaviest components are found in the nucleus of the atom The electrons orbit the nucleus The number of protons normally equals the number of electrons atoms is uncharged Elements It is a substance that consists of a single type of atom There are 92 naturally occurring elements and only 4 that make up 99 of all living material by weight These 4 are Carbon C 25 Hydrogen H 49 Oxygen O 25 Nitrogen N 05 Phosphorus and Sulfur makeup another 05 and all other elements account for less than 05 Till date there are 118 elements both naturally and artificially The unique properties of each element result from the number of protons neutrons and electrons it contains Atomic number is the number of proton ie of protons of electrons and Atomic mass is the sum of the number of protons and neutrons Electrons are arranged in orbitals space and shells and fill the orbitals and shells in pairs They can move from one orbital to another as they gain or lose electrons Each orbital contain a certain number of electrons The first shell orbital closest to the nucleus contains 1 orbital and maximum of 2 electrons The second shell contains 4 orbitals and up to 8 electrons The third shell can hold up to 18 electrons The fourth shell can hold up to 32 electrons The stability of an atom depends upon its outer orbital containing the maximum number of electrons if the outer orbital is not filled then it will fill by bonding with others to fill their outer orbitals atoms can either gain or lose electrons to others changing the environment when this happens Molecule is a chemical substance that consists of 2 or more atoms held together by chemical bonds Atoms that make up a molecule can either be the same or different elements eg HZNZ 2 of the same atoms H20 two different atoms Compound a molecule that consist of two or more different elements ie water and biological molecules protein sugar and fats are the most predominant substances in the living systems The molecular weight of a molecule or compound is the sum of the atomic weights of the atom Example molecular weight of N02 is 141616 46 3 chemical bonds that hold atoms together 1 Covalent bonds is a strong bond formed by atoms sharing electrons with other atoms filling the outer orbital of both atoms simultaneously The majority of the molecules associated with living things are composed of single and double covalent bonds between the most common biological elements which are C H O N S and P Example Carbon has 4 electrons but requires a total of 8 to fill its outer orbital Hydrogen has one electron and requires 2 to fill its outer orbital H2 CH4 Methane Two types of covalent bonds Polar One atom has a much greater attraction for electrons than the other electrons are shared unequally When atoms of different electronegativity form covalent bonds the electrons are not shared equally and may be pulled more towards one atom than another eg water Non polar Covalent bonds are formed between identical or different atoms that have equal attractions for a shared electron eg H H C H 2lonic Bonds Electron transfer among atoms no sharing occurs If electrons from one atom are attracted strongly by another nearby atom the e completely leave the first atom and becomes part of the outer orbital of the second without sharing The loss or gain of electrons leads to an atom that is electrically charged So basically the attraction between a and charged atom forms ionic bond Ionization is when ionic bond breaks and atoms separate into unattached charged particles called ions Ions atoms that gain electrons become negatively charged and are called Anions while atoms that lose electron becomes positively charged and are called Cations Ionic bonds are weak compared to covalent bonds These weak forces holds ions atoms and molecules together Example of ionic bond Nacl gt Na Cl Sodium has 11 electrons so it gives its last electron to Chlorine which has 17 electron so its outer orbital can be completely filled for stability Comright The McGrawHill Carmamiss Inc Permission ruquiled Em reproduction or display a Sodium atom Na Chlorine atom Cl 3Hydrogen bonds There is no sharing losing or gaining of electrons but instead it is due to attractive forces between nearby molecule or atoms Weak bonds results from the attraction of positively charged hydrogen atom in a polar molecule to a negatively charged atom N or Oin another polar molecule Hydrogen bonds are important in biological system and are weak bonds Water The most single most important molecule in the cell as well as the world All life organism depends on it It makes up 70 of all living organism by weight and it is known as a universal solvent because it dissolves so many compounds pH potential Hydrogen Concentration of H in moles per liter It is the measure of logarithmic scale of 0 14 in which the lower the number the more acidic the solution ie pH measures the degree of acidity pH 7 is the pH for which most bacteria live near neutrality Neutral pH 7 Acidic O 69 Basic 71 14 Acidophiles very acidic conditions Alkalophines very alkaline conditions Buffers added to growth mediums to maintain the pH near neutrality It is added to solutions because bacteria produce acids and bases when they degrade compound and this can halt the growth of the bacteria Inorganic compounds A chemical is inorganic if it does not contain both carbon and hydrogen It doesn t contain CC bond Examples are NaCl CaC03 COZ Organic compounds They are carbon compounds with the basic framework bonded of the element carbon bonded to other atoms It has C C or C H bonds Small molecules in the cell All cells contain a variety of small organic and inorganic molecules Positively charged ions required in minute amounts in order for certain enzymes to function negatively charged phosphate ions play a key role in energy metabolism Precursor metabolites Organic small molecules converted to the building blocks of larger molecules called macromolecules ATP Adenosine Triphosphate the storage form of energy in the cell It is composed of the following sugar ribose purine adenine and 3 phosphate groups ATP is an energy rich molecule because of the bonds thatjoin the phosphate and when broken there is much energy given off and inorganic phosphate is formed Macromolecules superstructures of life Organic compounds produced by living things or components of living things All macromolecules are polymers formed byjoining together small molecules Dehydration synthesis water is removed from its subunits to form macromolecules Hydrolysis water is added back to break down macromolecules into its subunits 4 classes of macromolecules 1Proteins Polymers of amino acids Catalyze all reactions of the cell required for life Structure contains ribosomes the protein building machinery in all cells Takes nutrients in the cell Turns genes on and off Cell movement by flagella Amino acid subunits Proteins are composed of numerous combinations of 20 major amino acids AA AA are building blocks of protein 0 The properties of protein depends on its shape which in turn depends on the arrangement of amino acids that make up the protein AA contains methyl CH3 which is non polar and therefore doesn39t interact with water molecules Hydrophobic means not readily soluble in water water fearing Hydrophilic means readily soluble in water water loving Side chains labeled R gives each amino acid its unique characteristic properties Side chains determine polar or non polar solubility properties of protein its shape and how it interacts in the cell Amino acids that make up proteins are held together by peptide bonds Peptide bonds are unique covalent bond linkage formed when the carboxyl group of one AA reacts with the amino group of another AA with the dehydration of water Polypeptide chain is a chain of AA formed when a large number of AA are joined by peptide bonds A protein is a long polypeptide chain Protein structure and diversity Protein has 4 levels of structure 0 Primary structure a secondary structure tertiary structure quaternary structure Diversity Protein has a unique shape a distinctive pattern of pockets and bulges allowing proteins to react only with molecules that complement or fits its particular surface like a lock and key providing the functional diversity required for many thousand of cellular reactions Enzymes serves as a catalyst for all chemical reactions in cells and nearly all reactions requires a different enzyme Protein Denaturation Protein must have its proper shape in order to function When a protein is denatured bonds within the protein and the protein loses its shape and no longer functions Conditions that causes the protein to denature high temperature heat high or low pH acids and alcohols certain solvents some disinfectants bonds within the proteins Most bacteria cannot grow at high temperatures because their enzymes are denatured at very high temperatures Denaturation can be reversed in some cases like if a solvent is removed a protein may refold to its original shape 2Carbohydrates comprise of a heterogeneous group of compounds of various sizes that play a variety of important roles in the life of all organisms It contains carbon hydrogen and oxygen atoms in a ratio of 121 These roles of carbohydrate include It is a common food source from which organisms can obtain energy and make cellular material Metabolism Two sugars form a part of the nucleic acids DNA and RNA certain carbohydrates serve as a reserve source of food in bacteria nutrient and energy sources sugars form a part of the bacterial cell wall structural support and protection Types of carbohydrates Monosaccharides simple sugar a single molecule Examples are the common 6 carbon sugars glucose galactose and fructose Sugars can be drawn in 2 forms linear and ring form Ribose and deoxyribose ribose without oxygen sugars in nucleic acids Disaccharides Consist of two monosaccharide joined by a covalent bond between their hydroxyl group Most common are lactose and sucrose table sugar Polysaccharides consist of five or more monosaccharide subunits Most abundant organic molecule on earth examples are Cellulose polymer of glucose and principal constituent of plant cell walls glycogen storage product of animals and bacteria Dextran synthesized by bacteria as a storage product Peptidoglycan source of structural support to the bacterial cell wall 3Nucleic Acids carry genetic information in all cells Information is decoded into the sequence of amino acids in protein molecules Types of nucleic acids Deoxyribonucleic acid DNA All of the cell39s properties are determined by its DNA Information is coded in the sequence of nucleotides The code is then converted into a specific arrangement of amino acids that make up the protein molecules of the cell Nucleotides is composed of three units Nitrogenous base which are adenine and guanine 2 purines two rings cytosine and thymine 2 pyrimidines single ring Deoxyribose sugar and a phosphate group Nucleotides play additional roles such as carry chemical energy in their bonds part of certain enzymes serve as a specific signaling molecules Nucleotides are joined by a covalent bond between the phosphate and the sugar Each pair of bases is held together by weak hydrogen bonds Base pairs that bond are complementary to each otherGuanine G to Cytosine C Adenine A to Thymine T resulting in 1 strand of DNA complementary to the other strand Ribonucleic acid RNA involved in decoding the information in the DNA into a sequence of amino acids in protein molecules Structure contains Uracil in place of Thymine and the sugar ribose in place of deoxyribose sugar It is considerably shorter and exists as a single chain of nucleotides 4Lipids heterogeneous group of molecules that are slightly soluble in water and very soluble in most organic solvents Two groups Simple Lipid Contains carbon hydrogen and oxygen and may be liquid or solid at room temperature Fats are common simple lipids and consist of glycerol bound to a fatty acid molecule with long chains of C atoms bonded to H atoms with a COOH on one end Fatty acids are stored in the body as an energy reserve by forming triglycerides Compound Lipid contains fatty acids and glycerol and other elements other than C H amp O Phospholipids are phosphate molecules in addition to fatty acids and glycerol further linked to other polar molecule such as acohos sugar and one certain AA referred to as a polar head group and is soluble in water Importance of Phospholipids Occurs in double layers biayer of unit membrane in the cytoplasmic membrane The structure of the biayer produces the essential properties of the cytoplasmic membrane Structure of phospholipids hydrophilic head soluble in water ong fatty acid chain of C amp H and hydrophobic tai water insoluble