BIOL 1305 Study Notes for Exam 1
BIOL 1305 Study Notes for Exam 1 BIOL 1305
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This 14 page Bundle was uploaded by Rachel Pankuch on Thursday September 10, 2015. The Bundle belongs to BIOL 1305 at University of Texas at El Paso taught by Horacia O Gonzalez in Summer 2015. Since its upload, it has received 140 views. For similar materials see General Biology in Biology at University of Texas at El Paso.
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Date Created: 09/10/15
BIOL 1305 General Biology Professor Horacio Gonzalez Email olgauaminersutepedu Week 1 Notes from Lectures Chapter 2122 Life Chemistry and Energy Chapter 2 All of the sciences are interconnected Atomic Structure is the Basis for Life All living and nonliving matter is composed of atoms 1 Atoms are composed of subatomic particles A Protons 1 charge a positive charge B Neutrons Zero charge are neutral C Electrons 1 charge a negative charge Charge controls reactivity and chemical reactions Charge a fundamental property of matter of subatomic particles that can be measured Atoms have volume and mass 1 Mass of one proton or neutron is an atomic mass unit or amu or 1 dalton One amu is equal to 17 X 10 24 grams 2 Mass of one electron 9 X 10 28 grams though this number is usually ignored The number of protons identifies which element it is If the number of protons equals the number of electrons the atom is electrically neutral Element a pure substance containing only one type of atom e1ements are arranged in the periodic table of the elements the symbol of the element in the periodic table is the abbreviation of the element s name in Latin Atomic Mass the mass of the protons and neutrons mass of the atom in daltons the average of isotopes for the element taking care to factor in the appearance of the isotopes in nature All elements except hydrogen have 1 or more neutrons Isotope atoms of the same element With the same number of protons but having a different number of neutrons Atomic Weight the average of mass numbers of the isotopes in their normally occurring proportions Electrons The behavior of electrons determines Whether a chemical bond Will form and What shape the bond Will have Outer shell electrons are balance electrons First electron shell 2 electrons max Second electron shell 8 electrons max Third electron shell 8 electrons max Atoms With unfilled outer shells tend to undergo chemical reactions to fill their outer shells to attain stability Octect Rule atoms With at least 2 electrons form stable molecules so they have 8 electrons in their outermost shells Atoms always try to have 8 electrons in the outer shells Bond Energy the strength required to pull atoms apart under physiological water conditions Chemical Bond attractive force linking molecules together to form molecules Ionic Attraction attractions of opposite charges has a 37 bond energy Covalent Bonds sharing of electron pairs has a 50110 bond energy covalent bonds are the strongest Hydrogen bonds sharing of a Hydrogen atom has a 37 bond energy Hydrophobic interaction interaction of nonpolar substances in the presence of polar substances especially water has a 12 bond energy van de Waals interaction of electrons of nonpolar substances has a bond energy of 1 Ionic Bonds Ionic bonds result from the electrical attraction between ions With opposite charges The resulting molecules are called salts Ions charged particles that form when an atom gains or loses one or more electrons Cations a positive ion that is missing electrons Anions a negative ion that has added electrons BIOL 1305 General Biology Professor Horacio Gonzalez Email Week 2 Notes from Lectures Chapter 23 3 Proteins Types of Bonding Covalent Bonding 2 atoms share pairs of electrons Carbon atoms have 4 electrons in their outer shells they can form 4 covalent bonds the degree of sharing electrons is not always equal Three ways of depicting bonding 1 Structural formulas 2 Ball and stick models 3 Spacefilling orbitals Properties of covalent bonds Orientation length angle direction of bonds between 2 elements are always the same Strengthstability covalent bonds are very strong Multiple bonds Single such as CH Double such as CC Triple such as NEN Electronegativity the attractive force atomic nucleus exerts on electrons depends on the number of protons and the distance between the nucleus and the electrons Oxygen has high electronegativity 34 and attracts electrons Potassium has low electronegativity 08 Nonpolar covalent bond when electronegativities of different atoms are similar and the charge is even CCC Polar covalent bond Two atoms with different electronegativities creates polarity charge is uneven uneven force of the atoms creates a partial charge electrons will be closer to the most attractive atom Hydrogen Bonding the attraction between the 839 end of the atom and the 8 hydrogen end of another molecule They form water molecules Important in the structure of DNA and proteins Provide exibility Water molecules form multiple hydrogen bonds with each other contribute to a high heat capacity A lot of heat is required to raise the temperature of water Evaporation has a cooling effect on the environment Hydrogen bonds give water cohesive strength cohesive strengthcohesion permits thin columns of water to move from roots to leaves Hydrophobic waterhating the interactions between nonpolar molecules nonpolar charge uniform a bond of repulsion ex Oil and water Hydrophilic waterloving In aqueous solutions polar molecules become separated and surrounded by water molecules polar charge uneven van der Waals same types of molecules are attracted to each other with a weak force an atom by itself weak many atoms strong enough to have structure Functional Groups small groups of atoms with specific chemical properties confer properties to larger molecules presence of charge provides polarity to molecule Macromolecules most biological molecules are polymers Condensation removal of water links monomers together Hydrolysis breaking macromolecules with water Monosaccharides simple sugars one molecule of sugar Glycosidic linkages 2 monosaccharides covalently bonded by condensation reactions Pentoses five carbon sugars Ribose and deoxyribose are 5 carbon sugars but with very different chemical properties and biological roles ribose and deoxyribose are the backbones of RNA and DNA Ribose one OH molecule much more reactive less stable present in RNA Deoxyribose one H molecule a ribose Without one oxygen atom more stable less reactive present in DNA Hexoses six carbon sugars glucose fructose mannose and galactose Oligosaccharides several monosaccharides many have functional groups often bonded to proteins and lipids on cell surfaces serve as recognition signals Polysaccharides large polymers of monosaccharides chains can be branching Starches branched polysaccharides of glucose Glycogen highly branched polymer of glucose main storage molecule in mammals Cellulose most abundant carbon containing compound on Earth stable linear Polymers made by covalent bonding of smaller molecules called monomers divided into four groups proteins nucleic acids carbs and lipids Proteins formed by different combinations of 20 amino acids Nucleic Acids formed from four types of nucleotide monomers Carbohydrates formed by linking similar sugar monomers to form polysaccharides source of stored energy transport stored energy Within complex organisms structural molecules give organisms their shapes Lipids made up of lipid monomers held together by covalent bonding nonpolar molecules of hydrocarbons insoluble in water because of many nonpolar covalent bonds store energy have a structural role in cell membranes Triglycerides simple lipids composed of 3 fatty acids and 1 glycerol fatssolid at room temperature oi1sliquid at room temperature very hydrophobic very little polarity Fatty acids amphipathic nonpolar hydrocarbon chains attached to a polar carboxyl group Saturated fatty acids harder to break less reactive Unsaturated fatty acids easier to break more reactive Glycerol an alcohol with three hydroxyl groups Phospholipid two fatty acids and a phosphate compound bound to glycerol negative charge the phospholipid area of the molecule is hydrophilic in water form a bilayer Chemical Reactions occur when atoms have enough energy to combine or change bonding partners Reactants gt products Metabolism the sum of all chemical reactions happening in a biological system at any time involve energy changes creates disorder there are two basic types of metabolism anabolic and catabolic Anabolic link simple molecules and change them into complex molecules require energy Catabolic break down complex molecules into simple molecules stored energy is released most often destroys things Energy can be converted from one form to another some of the energy becomes unavailable for doing work there are different forms of energy potential and kinetic Potential energy stored energy is in a state or position Kinetic energy moving energy does work changes things Laws of Thermodynamics apply to all matter and energy transformations in the universe no energy transformation 100 efficient human cells are much more efficient than any human machine First Law energy is neither created nor destroyed Second Law disorder entropy tends to increase Chapter 3 Nucleic Acids Proteins and Enzymes Nucleic Acids macromolecules used in genetics are polymers specialized for storage transmission and use of genetic information include RNA and DNA DNA and RNA the skeleton is sugars and phosphate groups bonded together by phosphodiester linkages Phosphodiester linkages a covalent bond RNA dynamic compound ribose single stranded bases are attached to adenine guanine cytosine and uracil can be folded into 3D structures by hydrogen bonding DNA computer program deoxyribose double stranded strands are opposite bases are attached to adenine guanine cytosine and thymine hydrogen bonds between the purines and pyrimidines hold the two strands together is an informational molecule and has two functions gene expression and replication Both depend on the base pairing RNA and DNA are made up of nucleotides Nucleotides monomers with a nitrogencontaining base a pentose sugar and a phosphate group nucleotides are polar 1 Nitrogencontaining base are either pyrimidines or purines Pyrimidines singlering Purines two fused rings 2 Pentose sugar either ribose or deoxyribose 3 A phosphate group negatively charged A nitrogencontaining base and a pentose sugar is a nucleoside Adding a phosphate group makes the nucleoside a nucleotide the numbering of ribose carbons is the basis for the identity of the 5 39 and the 339 ends of DNA and RNA strands directionality comes from organic chemistry Complimentary base pairing base pairs are linked by hydrogen bonds DNA bases AT adenine with thymine AT double bonds are less strong CG cytosine with guanine CEG triple bonds more strong RNA bases AU adenine with uracil CG cytosine with guanine RNA and DNA are made up of polynucleotides the longest polymers in the world Oligonucleotides have about 20 monomers and include small RNA molecules important for DNA replication and gene expression Genome the complete set of DNA in a living organism Genes DNA sequences that encode specific proteins and are transcribed into RNA not all genes are transcribed in all cells of an organism Base sequences reveal evolutionary relationships BIOL 1305 General Biology Professor Horacio Gonzalez Email Monzalez utenedu Week 3 Notes from Lecture Proteins and Enzymes Proteins Type of macromolecule quotMajor Functions of Proteins Enzymes catalytic properties Defensive Proteins antibodies HormonalRegulatory Proteins control physiological processes Receptor Proteins receive respond to molecular signals Storage Proteins store amino acids provide protection Structural Proteins physical stability movement the skeleton Transport Proteins carry substances like hemoglobin Genetic Regulatory when how and to what extent a gene is expressed Amino acids monomers of proteins Composed of an a carbon a carboxyl group C 0039 a R side chain and an amino group H3N 20 amino acids Grouped according to the properties of the R groups The R group differs in each amino acid Amino and carboxylic acid functional groups act as both bases and acids Amino acids work together Does not need memorizing for exam R groups provide functionality and diversity Disulfide bridge or disulfide bond covalent bonds between Cysteine side chains Peptide linkages when amino acids are linked in condensation reactions Oligopeptides short 20 or fewer polymers of amino acids Polypeptides Proteins many 51 amino acids in insulin to 34 350 in titin Polymerization of a polypeptide chain takes place in the amino to carboxyl direction Lillte a sentence the capitol is the N terminus and the period is the C terminus Structures of Amino Acids Primary structure amino acid monomers are joined by forming polypeptide chains Linear sequence of amino acids genetic code controls the directionality connection of the amino acids Covalent bonding Secondary structure polypeptide chains form a helices or 3 pleated sheets a helices exible connected by hydrogen bonds 3 pleated sheets folded connected by hydrogen bonds Tertiary structure polypeptide chains fold forming specific shapes Stabilized by bonds all bond and disulfide bridges Interactions between R groups Ionic interactions form salt bridges Very sensitive to H in the environment Quaternary structure 2 or more polypeptide chains assemble to form larger protein molecules Ionic and hydrophobic interactions as well as hydrogen bonds Weallt interactions allow small changes aiding in protein s function tetramer 4 polypeptide sub units Representing Proteins by using a spacefilling model stick model or ribbon model Denaturing when heat or chemicals are used to disrupt weaker interactions in a protein destroying the secondary tertiary structure Temperature concentration of H high concentrations of polar substances and nonpolar substances are factors of denaturing Catalysts substances that speed up reactions without altering the reaction Most biological catalysts are enzymes proteins and a few are RNA molecules Transition state reactants after an input of energy activation energy or Ea Enzymes Lower the activation energy Catalyze reactions by Reducing strain substrate bonds stretched creating an unstable transition state Substrate orientation bringing substrates together so bonds can form Adding chemical groups may directly involve R groups in the reaction pH affects enzyme activity Acidic side chains generate H become anions Basic side chains attract H become cations Temperature affects enzyme activity Warming increases rates of chemical reactions If the temperature is too high then noncovalent bonds can break and inactivate the enzyme Active site a specific site on the enzyme Substrates reactants that bind to the active site Cofactors inorganic ions Prosthetic groups permanently bound to their enzymes Non organic groups Coenzymes add remove chemical groups from substrate Organic groups can participate in different reactions Rates of Catalyzed Reactions Saturated all enzyme molecules bound to substrate molecules Turnover molecules of substrate converted to product per unit of time Metabolic pathways the product of one reaction is substrate for the next First step is the commitment step other reactions then happen in sequence Homeostasis maintenance of stable internal conditions Inhibitors can bind to enzymes slow reaction rates Natural inhibitors regulate metabolism Artificial inhibitors treat diseases kills pests study enzyme functions Reversible more common in cells Competitive competes with a substrate for the active site Noncompetitive binds somewhere other than the active site causing a distinct change in enzyme shape and function Irreversible inhibitor binds covalently to a side chain in the active site permanently inactivates the enzyme Allosteric regulation and site when a nonsubstrate molecule binds to an enzyme somewhere other than the active site activates or inactivates the enzyme Kinases enzymes that regulate responses to the environment by using organisms Law of mass action the higher the H concentration the more the reaction is driven to the left to the less hydrophilic form Isozymes catalyze the same reaction but have different composition and physical properties Feedback inhibition when the final product acts as a noncompetitive inhibitor of the first enzyme and shuts down the pathway
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