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Lectures 1-10 notes BIOSC 0150 Zapanta - Foundations of Biology 1
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Lecture 1 What is Life Ch 112 Although there is no simple de nition of life most agree that organisms share ve fundamental characteristics 1 Energy 2 Cells 3 Information 4 Replication 5 Evolution A theory is an explanation for a general class of phenomena or observations that are supported by a wide body of evidence Theories have two components 1 Pattern something that occurs in the natural world 2 Process responsible for creating the pattern The cell theory states that all organisms are made of cells pattern and all cells come from preexisting ces process The cell theory was a challenge to the prevailing explanation of where ces come from caed spontaneous generation which was the belief that organisms could arise spontaneously under certain conditions A hypothesis is a testable statement to explain a phenomenon or a set of observations A prediction describes a measurable or observable result that must be correct if a hypothesis is valid Louis Pasteur wanted to determine whether microorganisms could arise spontaneously in a nutrient broth or whether they appear only when a broth is exposed to a source of preexisting ces He created 2 treatment groups a broth exposed to a source of preexisting cells and a broth that was not The spontaneous generation hypothesis predicted that cells would appear in both The acesfromces hypothesis predicted that cells would appear only in the treatment exposed to a source of preexisting cells The treatment exposed to preexisting ces lled with bacteria and fungi showing that the allcellsfromcells theory was correct for now Lecture 2 Chemical Foundations of Life Ch 212 Atoms Ions and Molecules The Building Blocks of Chemical Evolution All atoms consist of protons electrons and neutrons The protons and neutrons are found in the nucleus and the sum of them is an atom s mass number Atoms with the same atomic number number of protons belong to the same element and have the same chemical properties The number of protons does not ever vary but the number of neutrons can Forms of an element with different numbers of neutrons are known as isotopes The atomic weight of an element is an average of all the mass numbers of the isotopes based on their abundance Electrons move around nuclei in speci c regions called orbitals Each orbital can hold up to two electrons Orbitals are grouped into eves called electron shells Each electron shell contains a speci c number of orbitals An electron she comprising a single orbital can hold up to two electrons a shell with four orbitals can contain up to eight electrons The electrons of an atom ll the innermost shells rst then the outer ones Atoms are most stable when all orbitals are lled The outermost shell of each atom is the element s valence shell Eectrons found here are valence electrons The number of unpaired electrons found in an atom is called its valence One way that shells can be lled is through the formation of strong chemical bonds A strong attraction where two atoms share one or more pairs of electrons is called a covalent bond Substances held together by covalent bonds are called molecules Some atoms hold the electrons in covalent bonds much more tightly than others This property is called electronegativity which is caused by the number of protons in the nucleus and the distance between the nucleus and the valence shell 0 Electronegativity increases from left to right and bottom to top 0 An atom in a molecule with a high electronegativity holds electrons more tightly and therefore has a partial negative charge The other atom will have a partial positive charge 0 OgtNgtCH When two covalently bonded elements have equal electronegativities the result is a nonpolar covalent bond 0 Uncharged and nonpolar molecules do not dissolve in water When two covalently bonded elements have different electronegativities the result is a polar covalent bond Ionic bonds are created by the transfer of electrons in order to give the resulting atoms a full outermost shell An atom or molecule that retains a full charge is called an Ion o Positively charged ions are cations K o Negatively charged ions are anions Cl39 Molecular Formulas are compact but don t contain a great deal of information They indicate only the numbers and types of atoms in a molecule CH4 Structural Formulas indicate which atoms in a molecule are bonded together ll Properties of Water Water is vital for one reason It is an excellent solvent an agent for dissolving substances and getting them into solution Substances are most likely to come into contact with one another and react as solutes meaning when they are dissolved in a solvent like water Water is unique due to its 1 Small shape 2 Bent shape 3 Highly polar covalent bonds 4 Overall polarity Hydrogen bonds are the weak electrical attractions between the partially negative oxygen of one water molecule and the partially positive hydrogen of a different water molecule Water can form four hydrogen bonds at a time Hydrogen bonding gives water unique properties Cohesion is the attraction between E molecules Cohesion is responsible for surface tension Adhesion is the attraction between unlike molecules Water has a high speci c heat the amount of energy needed to raise 1 gram of a substance by 1 degree 0 Water molecules have a slight tendency to ionize hydrogen ions H and hydroxide ions OH39 which allows it to act as both an acid a proton donor and a base a proton acceptor Higher pH is basic and lower pH is acidic The pH of pure water is 7 o The pH of a solution is the negative of the base10 log of the hydrogen ion concentration pH ogH H antilogpH 1039pH Compounds that minimize changes in pH are called buffers because they reduce the impact of adding acids or bases on the overall pH of a solution This helps to maintain homeostasis Lecture 3 Chemical Foundations of Life cont Ch 235 lChemical Reactions Energy and Chemical Evolution oChemical reactions involve the making andor breaking of chemical bonds The initial or reactant molecules are shown of the left and the resulting reaction product is shown on the right When the forward and reverse reactions proceed at the same rate the quantities of reactants and products remain constant although not necessarily equal A dynamic but stable state like this is chemical equilibrium oEnergy is de ned as the capacity to do work or supply heat This exists as a stored potential or as an active motion Stored energy is called potential energy An object gains or loses its ability to store energy because of its position 0 An electron in an outer shell has more potential energy than an electron in an inner shell 0 Potential energy stored in chemical bonds is called chemical energy Kinetic energy is the energy of motion Molecules have kinetic energy because they are constantly in motion 0 The kinetic energy of molecular motion is called thermal energy o The temperature of an object is measured by how much thermal energy its molecules possess Low temp means its molecules are moving slowly and high temp means its molecules are moving rapidly 0 When two objects with different temperatures come into contact thermal energy called heat is transferred between them The First Law of Thermodynamics states that energy cannot be created nor destroyed but it can be transferred or transformed from one type of energy to another The Second Law of Thermodynamics states that systems tend to proceed from a state of order to a state of disorder 0 Entropy is a measure of disorder randomness of a system Chemical reactions are spontaneous reactions if they are able to proceed on their own without energy 0 Reactions tend to be spontaneous when 1 The product molecules are less ordered than the reactant molecules 2 The products have lower potential energy than the reactants Chemical processes proceed in the direction that results in increased entropy and lower potential energy ll Investigating Chemical Evolution Approaches and Model Systems The prebiotic soup model proposes that certain molecules were synthesized from gases in the atmosphere or arrived via meteorites The surface metabolism model suggests that dissolved gases came in contact with minerals lining the walls of deepsea vents and formed more complex organic molecules Ill The Importance of Organic Molecules Carbon has great importance in biology because it is the most versatile element on Earth Because of its four valence electrons it will form four covalent bonds resulting in an almost limitless array of molecular shapes Molecules that contain carbon bonded to other elements are called organic molecules The carbon atoms in an organic molecule furnish a skeleton that gives the molecule its overall shape oThe critically important H N 0 P and Scontaining groups found in organic compounds are called functional groups Amino Groups tend to attract a proton when in solution acting as a base They are polar Carbonyl Groups are found on aldehyde end and ketone middle molecules They are polar Carboxyl Groups tend to drop a proton when in solution acting as an acid They are polar Hydroxyl Groups act as weak acids and may drop a proton Because they are polar molecules containing hydroxyl groups will form hydrogen bonds and tend to be soluble in water Phosphate Groups carry two negative charges The charge dramatically affects the structure of the molecule it is attached to Phosphates that are bonded together store chemical energy that can be used in chemical reactions They are nonpolar Sulfhydryl Groups consist of a sulfur atom bonded to a hydrogen atom They link to one another via disulfide SS bonds Functlunal Grnups Hyman iI EeEb wi quot39CHG 5 U3 I CazWWI C Amine W NH Phi 5111am 3933 3 Sul iydxyl SH Class Elf Mnlecules Almhnls Aldehde Ketunes C 311 I qrhc Acids Arm39nes Grgemin PhD sphates Tl39liuls Fumula H DH Rmemr e R SH Lecture 4 and 5 Proteins Ch 314 Acetaldehyde H B H E 3 H hif f Ii E H H Acetnne H 339 5 5 H PCquot m iiquot i H H H Acetic Acid H H i f H EWH i quotu H H Me iylamjrm Hi I I a E H migh39DH I ICEquot 1 hw 39393939 u39 H 3quot E Phn 5111 glycerin acid 5 at HWC g EH 1 H H M captne 39wnnl Amino Acids and Their Polymerization Modern cells produce proteins made up of 20 different building blocks called amino acids All 20 have a common core structure It 9 HN C COH Amino Carb oxylic Acid Group Group Di carbon Side Chain The Rgroups or side chains vary from a single hydrogen atom to large structures containing carbon atoms linked into rings Each is unique 0 NONPOLAR Glycine G gt Gly Aanine A gt Ala Vaine V gt Val Leucine L gt Leu lsoeucine l gt He Methionine M gt Met Cysteine C gt Cys Phenyaanine F gt Phe Trptophan W gt Trp Proline P gt Pro Not charged or electronegative cannot form h bonds 0 POLAR Serine S gt Ser Threonine T gt Thr Tyrosine Y gt Tyr Asparagine N gt Asn Glutamine Q gt Gln Partially charged can form hbonds o ACIDIC Aspartate D gt Asp Glutamate E gt Glu Negative charge can form hbonds and ionic bonds 0 BASIC Lysine K gt Lys Arginine R gt Arg Histidine H gt His Positive chard can form hbonds and ionic bonds Nonpolar side chains are hydrophobic meaning they do not interact water They tend to coalesce in aqueous solution Polar side chains are hydrophilic and interact and dissolve in water A molecular subunit like an amino acid nucleotide or sugar is called a monomer Many monomers bonded together create a polymer The process of linking monomers together is called polymerization A macromolecule is a large molecule made up of smaller molecules 0 A protein is a macromolecule Monomers polymerize through condensation reactions dehydration reactions This is named as such because the newly formed bond results in the loss of a water molecule The reverse reaction hydrolysis breaks polymers apart by adding a water molecule Amino acids polymerize to form a protein The CN covalent bond that results from the condensation reaction is a peptide bond The peptide bonded backbone has 3 key points 1 Rgroup orientation The side chains present in each residue extend out from the backbone making it possible for them to interact with each other and water 2 Directionality There is an amino group on one end of the backbone the Nterminus and a carboxyl group on the other end called the Cterminus Amino acid sequences are written N to C 3 Flexibility Although the peptide bond itself can t rotate the single bonds on either side can making the structure exible 0 O O 0 ll 0 HQN CIlliC NH CHliC NH CH CWOH k J J Y Y Nterminal Cterminal When fewer than 50 amino acids are linked together it is an ogliopeptide Polymers containing 50 or more are polypeptides What Do Proteins Look Like The unique sequence of amino acids is the protein s primary structure Hydrogen bonding between backbone atoms in a polypeptide leads to secondary structure The bonding occurs between the oxygen on to CO group of one amino acid and the hydrogen on the NH group of another 0 The oxygen atom in the CO group has a partial negative charge due to its high electronegativity while the hydrogen atom in the NH group has a partial positive charge because it is bonded to nitrogen which has a high electronegativity 0 Hydrogen bonding between sections of the same backbone is possible only when a polypeptide bends in a way that puts CO and NH groups close together This forms two possible structures 1 An alpha helix in which the polypeptide s backbone is coiled They form when hydrogen bonding occurs between residues that are 4 amino acids apart 2 A betapleated sheet in which segments of a peptide chain bend 180 degrees and then fold in the same plane Which one forms depends on the peptide s primary structure the geometry and the properties of the amino acids in the sequence The overall shape or tertiary structure of a polypeptide results from interactions between Rgroups or between R groups and the backbone Five types of interactions involving side chains are important 1 Hydrogen bonds form between polar Rgroups and opposite partial charges either in the peptide backbone or other Rgroups 2 Hydrophobic interactions In an aqueous solution water molecules interact with hydrophilic polar side chains which forces the hydrophobic nonpolar side chains to coalesce 3 Once hydrophobic side chains are close to one another they re stabilized by electrical attractions called van der Waals interactions 4 Covalent bonds can form between the side chains of two cysteines through a reaction between the sulfhydryl groups These disul de bonds create strong links between distinct regions of the same polypeptide or two separate polypeptides 5 Ionic bonds form between groups that have full and opposing charges Hydrophobic interaction Polypeptide strand ti Hyd roger bund lDisLilfide bridge liretween cysteine molecules a v v 39 1 quot pm GHQ ECH GHQ willybet GH2 e I m li lb ltd Details at band associated with tertiary structure The combination of polypeptides gives a protein quaternary structure They are held together by the same types of bonds and interactions in tertiary structure Proteins with 2 polypeptide subunits are called dimers and with 4 are called tetramers lll Folding and Function Proteins fold spontaneously requires no energy because it is energetically favorable for hydrophobic amino acids to fold into the center and for hydrophilic ones to be on the exterior where they can interact with water Denaturation of proteins occurs by treating them with compounds that break hydrogen and disul de bonds Folding is often facilitated by speci c proteins called molecular proteins ons and small molecules can act as regulators that allow proper folding of proteins in response to certain signals Certain proteins can be folded into infectious disease causing agents They are called prions IV Proteins Are The Most Versatile Macromolecules In Cells Proteins are crucial to most tasks required for cells to exist Cataysis Many proteins are specialized to catalyze or speed up chemical reactions They are called enzymes Defense Antibodies attack and destroy viruses Movement Motor proteins and contractile proteins move the cells itself or move large moleculescargo inside the cell Signaing Proteins are involved in carrying and receiving signals from cell to cell Structure Structural proteins make up body components Transport Proteins allow particular molecules to enter and exit cells or carry them throughout the body Enzymes bring reactant molecules called substrates together in a precise orientation so the atoms involved in the reaction can interact This is done on the enzyme s active site Lecture 6 Nonenzymatic Protein Functions Ch 454 amp 5123 How Are Oxygen and Carbon Dioxide Transported in Blood Mammalian red blood cells are bags lled with approx 280 million copies of the oxygencarrying molecule hemoglobin Oxygen and C02 are not soluble so they must be transported n blood 985 of the oxygen is bound to hemoglobin Oxygen moves from areas of high partial pressure to low partial pressure Measured in mm Hg Hemoglobin is a tetramer Each of the four polypeptide chains binds to a nonprotein group called heme Each heme contains an iron ion Fe2 that can bind to an oxygen molecule Therefore each hemoglobin molecule can bind up to four oxygen molecules at 4 its 100 An oxygenhemoglobin equilibrium curve plots the percent of oxygen saturation based on the partial pressure of oxygen in tissues It is sigmoidal Sshaped The binding of each successive oxygen molecule to a subunit of the hemoglobin molecule causes a conformational change in the protein that makes the remaining subunits more likely to bind This is called cooperative binding Makes hemoglobin exquisitely sensitive to changes in the partial pressure of oxygen of tissues When the partial pressure of C02 is high the pH of blood drops The decrease in pH alters hemoglobin s conformation such that it s more likely to release oxygen at all values of partial pressure of oxygen 0 This is known as the Bohr shift ll Adaptive Immunity Recognition The adaptive immune response is based on interactions between speci c immune system cells and a speci c an gen An antigen is any foreign molecule that can initiate an immune system response Antibodies are proteins produced and secreted by B lymphocytes that bind to a speci c part the epitope of a speci c antigen The leukocytes that carry out the major features of the adaptive immune response are called lymphocytes B cells produce antibodies Bcell receptors are proteins called immunoglobulins and are crucial to the adaptive immune response 0 B cells consist of two polypeptides The smaller is called the light chain The larger is twice the size and called the heavy chain Each BCR has two copies of each held together by disul de bonds 0 Light chains and heavy chains from different Bcells have one segment in common the constant C region and a segment that is unique to each Bcell the variable V region Helper Tcells assist with the activation of other cells in the immune response lll Adaptive Immunity Activation MHC Major histocompatibility proteins are antigen presenting proteins on the surface of Bcells that bind small peptide fragments of antigens and present them to Tcells BCell Activation 1 Bcell receptors bind to a speci c antigen 2 Fragments of the antigen bind to MHC proteins on the B cells 3 Helper Tcells are activated by MHCpeptide complexes 4 Helper Tcells release cytokines 5 Cytokines activate Bcells to replicate and produce large numbers of antibodies Lecture 7 Nucleic Acids Ch 412 I What is a Nucleic Acid 0 Nucleic acids are polymers made up of monomers called nucleotides which are made of a phosphate group a vecarbon sugar and a nitrogenous base The phosphate is bonded to the sugar molecule which in turn is bonded to the nitrogenous base The phosphate group is bonded to the 5 carbon In Ribonucleotides the sugar is ribose Ribose has an OH group bonded to the 2 and 3 carbons In deoxytibonucleotides the sugar is deoxyribose Deoxyribose has an H instead at the 2 carbon and an OH at the 3 The nitrogenous bases belong to structural groups called purines and pyrimidines Purines have a nine atom ring structure with C and N in the 2 rings and pyrimidines have a six atom ring structure with C and N in the single ring Purines adenine guanine Pyrimidines Thymine cytosine uracil PURINES Adenine A Guanine G PYRIMIDINES I o illl2 c HN4SCH HN3 c2 6CHl c2 6c 1 1 0 ll 0 N H H H Uracil ll Thymine T Cytosine C Nucleic acids form when nucleotides polymerize which involves the formation of a bond between a hydroxyl on the sugar component of one nucleotide and the phosphate group of another nucleotide The result of this condensation reaction is called a phosphodiester anage The sugarphosphate backbone of a nucleic acid is directional A DNA or RNA strand always has an unlinked 5 phosphate on one end and an unlinked 3 hydroxyl on the other DNA and RNA sequences are always written 5 to 3 which is also the way it is polymerized DNA deoxyribonucleic acid is a polymer of deoxyribonucleotides and contains a deoxyribose sugar and bases A G C and T RNA ribonucleic acid is a polymer of ribonucleotides and contains a ribose sugar and bases A G C and U H DNA Structure and Function Lecture 8 Nucleic Acis cnth Complementary base pairing means the number of purines in a given DNA molecule is equal to the number of pyrimidines Chargoffs rule A amp T C amp G DNA is comprised of two strands one oriented 5 to 3 template strand and the other oriented 3 to 5 complementary strand This means they are antiparallel If the antiparallel strands are twisted together to form a double helix the coiled sugarphosphate backbones end up on the outside of the spiral and the nitrogenous bases on the inside Primary structure is the base pairing Secondary structure is the double helix DNA can store and transmit biological information required for the growth and reproduction of all cells This information is contained in the sequence of the bases Complementary base pairing provides a simple mechanism for DNA replication Each strand can serve as a template for the formation of a new complementary strand minimal al39 hawpaired Faraml strands unwind and summits at W paints alurguthle DIEM quota i minimum 39arm n mammalian forks parental alnmd provides a template that mmoi and blinds wmplementarsr A wilh TIT anti with Eugmrpihmpham bandit harm of daughhr strands moaned Each Ema mulmuln canals11 of one parental and Elian d u h tBlf Minna IE I l maul uf Bernieme E 39 ireplloatl 434 RNA Structure and Function Like DNA RNA has a primary structure consisting of a sugarphosphate backbone formed by phosphodiester linkages and a sequence of four types of nitrogenous bases However the sugar is ribose and thymine is replaced with uracil The secondary structure is the complementary base pairing A amp U C amp G The presence of the OH group on ribose makes RNA much more reactive and much less stable than DNA The bases of RNA typically form hydrogen bonds with complementary bases on the SAME strand lt folds over forming a hairpin structure that has a stemandloop I S Li 9 1 Tel Leiin The tertiary structure is formed when secondary structures form into more complex shapes RNA is an information containing molecule Messenger RNA mRNA is synthesized from a DNA template and carries the genetic information to the ribosome for protein production Because RNA has a degree of structural and chemical complexity it is capable of catalyzing a number of chemical reactions Ribozymes are enzymelike RNAs capable of catalyzing a number of chemical reactions In Search of The First Life Form The RNA World Hypothesis states that chemical evolution led to the formation of a molecule that could replicate itself RNA is a more likely candidate than DNA because it is less stable Lecture 9 The Central Dogma Ch 1613 I What Do Genes Do Gene expression is the process of converting archived information into molecules that actually do things in the cell Alleles that do not function at all are called knockout mutants Creating these and analyzing their effects is one of the most common research strategies in studies of gene funcUon Beadle amp Tatum developed the onegene oneenzyme hypothesis which stated that each gene contains the information needed to make an enzyme They tested this by mutating genes in the bread mold Neurospora crassa and observed that defects in particular genes resulted in the mold s inability to produce speci c compounds Srb amp Horowitz also tested this They new that organisms synthesized arginine in a metabolic pathway made of several steps If a colony could grow in the presence of arginine but failed to grow without arginine they concluded that it couldn t make its own arginine II The Central Dogma of Molecular Biology Genes contain the information for all of the proteins in an organism The genetic code is information coded in the base sequence of DNA Messenger RNA mRNA carries information out of the nucleus from DNA to the site of protein synthesis ribosome The enzyme RNA polymerase synthesizes RNA according to the information provided by the sequence of bases in a particular stretch of DNA The Central Dogma summarizes the ow of information in cells It states that DNA codes for RNA which codes for proteins DNA gt RNA gt proteins The sequence of bases in DNA specifies the sequence of bases in RNA which specifies the sequence of amino acids in a protein Transcription is the process of copying hereditary information in DNA to RNA Translation is the process of using the information in nucleic acids to synthesize proteins Ill The Genetic Code The genetic code is a triplet code with a three base sequence called a codon specifying a single amino acid AUG is the start codon which signals that protein synthesis should begin at that point on the mRNA molecule There are 3 stop codons which signal the end of the protein coding sequence UAA UAG and UGA They do not code for any amino acid The genetic code is redundant because all amino acids except Met and Trp are coded for by more than one codon Lecture 10 Viruses Are They Alive Ch 3612 l Why Do Biologists Study Viruses A virus is an obligate or necessary intracellular parasite that enters a host cell to use its biosynthetic machinery in order to reproduce and synthesize viral proteins Virulence is a tendency to cause severe disease An epidemic is a disease that rapidly affects a large number of individuals over a widening area A pandemic is an epidemic that is worldwide Human immunode ciency virus HIV causes Acquired immune de ciency syndrome AIDS HIV infects Helper Tcells and destroys them These cells are the ones that produce Bcells which stimulate the production of antibodies Therefore people with AID die from bacterial fungal or other viral infections that would normally not be fatal ll How Do Biologists Study Viruses A virus particle or virion consists of genetic material DNA or RNA the viral genome It also has a protein coat called a capsid that surrounds and protects the genome It can also help recognize and release the virus when it enters the cell Some viruses also have a membranelike envelope around the capsid which came from the host cell HIV and Ebola are envelope viruses Enveloped viruses bud from a cell through the cell membrane Nonenveloped viruses burst out of the cell Viruses infect their host cells in one of two ways 1 Replicative Growth Lytic Produces the next generation of virions Kils host cell 2 Enter a state of dormancy that suspends virion production Lysogency Aows the virus to coexist with the host for a period of time replicates the viral DNA each time the cell divides HV Viruses gain entry to cells by binding to a speci c molecule on the cell wall or plasma membrane The viral genome can then be uncoated at the cell surface by binding to CD4 receptor on Tcells Otherwise the viral genome can be uncoated in an endosome Viruses can t manufacture their own proteins and must exploit the host cell s biosynthetic machinery to produce viral proteins Viruses must copy their genetic material to make a new generation of virions DNA viruses depend on the hostcell DNA polymerase to replicate their genomes RNA viruses use a viral RNA polymerase called RNA replicase which synthesizes RNA from an RNA template 0 HIV is an RNA virus Some RNA viruses are retroviruses where the RNA genome is transcribed to DNA by a viral enzyme called reverse transcriptase Breaks Central Dogma Reverse transcriptase is a DNA polymerase First it makes a singlestranded complementary DNA cDNA from a singlestranded viral RNA template Then it removes the RNA strand and synthesizes the complementary DNA strand resulting in doublestranded DNA that can be inserted into the host cell genome An incubation period is the time from infection with the virus to the onset of symptoms ncubation period of Ebola is 2 to 21 days
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