Cells & the Evolution of Life
Cells & the Evolution of Life BIOL 115
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DNA Replication Slide 2 DNA replication is a process that all cells must go through prior to any type of cell division When cells replicate their DNA they make two identical copies of their DNA from the original copy This process assures that the daughter cells resulting from cell division will each have a complete copy of the DNA necessary for the cell to survive As we will see DNA replication utilizes several different types of enzymes to link free nucleotides together into new strands of DNA Slide 3 During DNA replication DNA is unwound from its double helix the two strands are separated and each strand serves as atemplate for the synthesis of a new complementary strand which is built one nucleotide at a time Recall that when we use the term complementary we are referring to the complementary basepairing that occurs between the individual strands of the doublestranded DNA molecule 7 A base pairs with T and C base pairs with G In this way two identical molecules of DNA are synthesized from one original molecule and each new doublestranded molecule contains one parent strand and one newly synthesized strand of nucleotides Because each new molecule contains one of the original parent strands of DNA the process of DNA replication is referred to as semiconservative replication Slide 4 Replication of DNA begins at a speci c sequence of nucleotides in the DNA called an origin of replication The single circular chromosomes of prokaryotic organisms contain only one origin of replication In eukaryotic organisms however there are many origins of replication within each of their linear chromosomes Slide 5 Origins of replication serve as recognition and binding sites for a group of enzymes that together form a replication complex The replication complex is made up of several enzymes including DNA helicase singlestranded binding proteins RNA primase several types of DNA polymerase there are at least 14 types in humans and DNA ligase As DNA is replicated it moves through this replication complex and each of the enzymes in the complex play an important role in the synthesis of new DNA molecules As we describe the process of DNA replication in the following slides note how the names of each of the enzymes involved in this process are related to the role that they perform 7 it may help you to remember them more easily Slide 6 When a replication complex binds to an origin of replication one of the initial events that occurs is the partial unwinding of the DNA double helix and the separation of the two strands of the DNA molecule This is accomplished by both DNA helicase and singlestranded binding proteins DNA he licase unwinds the DNA double helix and separates the strands of DNA by breaking the hydrogen bonds between the complementary base pairs of each strand Singlestranded binding proteins bind each strand of DNA and prohibit the strands from reforming hydrogen bonds The separation of the two strands results in what is called a replication bubble which has a replication fork at each end DNA replication occurs at the replication forks and will proceed in both directions away from the origin of replication Because of this DNA replication is often referred to as bidirectional Slide 7 After the strands of DNA have been separated by DNA helicase and singlestranded binding proteins DNA replication begins by the synthesis of short strands of surprisingly RNA These strands called RNA primers are complementary to the template strands of DNA The synthesis of RNA primers is catalyzed by the enzyme RNA primase RNA primers act as their name suggests priming the synthesis of strands of DNA essentially like priming an engine with a small amount of gasoline As we will see the enzyme that catalyzes the formation of new strands of DNA requires this primer in order to start its work At the end of DNA replication however the RNA primer is degraded and replaced by DNA through the activity of one type of DNA polymerase Slide 8 Once an RNA primer has formed synthesis of a new strand of DNA may begin Remember that in the semiconservative replication of DNA each strand of the original DNA molecule acts as a template for the formation of a new complementary strand The synthesis of each new strand of DNA is catalyzed by DNA polymerase DNA polymerase lengthens the growing strand of DNA by adding nucleotides one at a time to the 3 end of the growing strand In fact DNA polymerase is only able to add nucleotides in the 5 to 3 direction and cannot build strands of nucleotides in the 3 to 5 direction Slide 9 As replication proceeds at a replication fork the antiparallel nature of DNA presents a small challenge As the DNA is threaded through the replication complex one of the template strands will separate in the 3 to 5 direction the other in the 5 to 3 direction From the template strand running in the 3 to 5 direction synthesis of a complementary strand will proceed smoothly and continuously because DNA polymerase is able to add nucleotides to the growing strand in the 5 to 3 direction This continuous strand is referred to as the leading strand However since DNA polymerase is only able to add nucleotides in the 5 to 3 direction synthesis of a new strand of DNA complementary to the 5 to 3 template strand is discontinuous In order to synthesize this complementary strand called the lagging strand DNA polymerase synthesizes short stretches of DNA in the 5 to 3 direction then jumps ahead toward the replication fork to synthesize another short fragment These short fragments of DNA are called Okazaki fragments Note again that each fragment of the lagging strand is initially synthesized as the leading strand of DNA is 7 initially an RNA primer is synthesized by RNA polymerase and DNA polymerase builds the strand by adding nucleotides to the primer in the 5 to 3 direction Slide 10 As the fragments of the lagging strand are synthesized by DNA polymerase several other enzymes in the replication complex work together to anneal the lagging strand into one continuous strand of nucleotides For example after each fragment is synthesized its RNA primer is removed and replaced with DNA by another type of DNA polymerase The complete DNA fragments are then covalently linked through the action of the enzyme DNA ligase Through the continuous synthesis of the leading strand and the discontinuous synthesis of the lagging strand the entire molecule of DNA is eventually replicated so that two exact copies of the DNA are made These copies are eventually segregated during cell division and distributed to daughter cells Energy Thermodynamics Slide 1 Energy is a word that we commonly use although many of us might nd it difficult to de ne We say that some people don t have any energy while others are energetic We also worry about wind generators for instance not producing enough energy on calm windless days But what is energy really And why is it important biologically Slide 2 We will define energy as the capacity to do work or in other words the capacity to exert a force on an object over a distance There are two basic types of energy potential energy and kinetic energy Potential energy is the energy of state or position Think of potential energy as stored energy For example consider water backed up by a large dam While the water isn t really doing anything it has the potential to move very quickly and with great force if the dam were removed Kinetic energy on the other hand is the energy of motion A freelyflowing river for example has kinetic energy in the movement of its water If we were to attempt to swim upstream in a river we would feel the force of the water resulting from its kinetic energy working against us Slide 3 It is important to consider the different forms potential and kinetic energy may take in order to fully understand their importance Potential energy for example may include the energy stored in chemical bonds Kinetic energy may include electric energy light and heat in addition to movement Also note that energy may be transformed from one form to another Potential energy may be converted into kinetic energy or kinetic energy may be converted into potential energy Slide 4 Regardless of whether we consider the energy in owing rivers or individual molecules all energy is governed by what we call the laws of thermodynamics The rst law of thermodynamics states that energy can neither be created nor destroyed rather it can only be transformed from one form to another as we saw on the previous slide If we go back to the example of a river and dam consider the potential energy of water behind a dam If the dam is removed the potential energy stored in the water is converted to the kinetic energy of owing water If the flowin g water encounters another dam downstream however its kinetic energy will be transformed back into potential energy A similar example could be given at the molecular level A carbohydrate for instance holds potential energy in its chemical bonds As those bonds are broken the potential energy could be transferred into the chemical bonds of another molecule or could be released as the kinetic energy of heat In either example the energy present is only transferred between forms or carriers it is not created or destroyed Slide 5 The second law of thermodynamics states that when energy is transferred either from one form to another or between carriers some of the usable energy will be lost In other words no transfer of energy is 100 efficient At the molecular level for example this means that if the potential energy stored in the chemical bonds of one molecule is transferred into the chemical bonds of another molecule the new bonds formed will contain less energy than the original bonds Slide 6 We can use the principles of the laws of thermodynamics to describe biological systems and to predict the outcomes of chemical reactions In any system the total energy is equal to the amount of usable energy plus the amount of unusable energy present We can relate these three amounts of energy by the equation delta G equals delta H minus Ttimes delta S where delta G is the change in free or usable energy delta H is the change in the total energy of the system called the enthalpy and T or temperature times delta S equals the change in unusable energy or entropy Slide 7 The gist of this equation is that if a reaction has a negative change in free energy seen as a negative delta G it will proceed spontaneously If a reaction has a positive change in free energy or a positive delta G it will require an input of free energy in order to proceed and so will not proceed spontaneously Reactions that lose free energy and therefore proceed spontaneously are called exergonic reactions Again these reactions have a negative value for delta G Reactions that consume free energy and so do not proceed spontaneously are called endergonic reactions These reactions have a positive value for delta G Slide 8 Last remember that chemical reactions are reversible and in many cases the reactants and products will reach an equilibrium rather than all the reactants being used up to form products The change in free energy or delta G of a reaction determines where the equilibrium point for a reaction lies For exergonic reactions those with a negative delta G the equilibrium will lie closer to the products For endergonic reactions those reactions requiring an input of energy equilibrium will lie closer to the reactants The reaction displayed here shows the conversion of two different forms of glucose phosphate The conversion of glucose lphosphate to glucose 6phosphate is energetically favorable compared to the reverse of this reaction because it is an exergonic reaction Therefore at equilibrium glucose 6phosphate is more common than glucose 1 phosphate Structure and Properties 0fDNA and Genes Slide 2 DNA is the fundamental genetic material of all types of life DNA is a completely informational molecule in that it stores the information needed to produce the proteins and enzymes necessary for all of the metabolic pathways found in an organism In this lesson we will discuss some of the important structural and organizational features of DNA and the genes found in DNA in order to better understand their role as the genetic material of life Slide 3 DNA is found in all living cells A few specialized cell types such as the red blood cells of animals only contain DNA in the early stages of their development In prokaryotic organisms DNA is found in an area of the cell called the nucleoid In eukaryotic cells it is bound by membranes in an organelle called the nucleus In addition certain eukaryotic organelles such as the chloroplast and mitochondria contain their own DNA Slide 4 Wherever DNA is found its basic structure is the same DNA is formed as a doublestranded molecule called a double helix Essentially a double helix is like a ladder that has been twisted around The legs of the DNA double helix are made up of a sugarphosphate backbone These backbones consist of alternating molecules of phosphate and sugar In the case of DNA the sugar is deoxyribose The linkages connecting phosphates to sugars are covalent bonds called phosphodiester linkages These covalent linkages make each individual strand of DNA very strong The rungs of the DNA double helix are composed of nitrogenous bases In DNA there are four nitrogenous bases adenine A cytosine C guanine G and thymine T Recall from our earlier lesson on macromolecules that the each nitrogenous base together with a molecule of deoxyribose and a molecule of phosphate makes up the fundamental subunit of DNA called a nucleotide Slide 5 The opposing strands of a DNA molecule are held together by the hydrogen bonds that form between the nitrogenous bases of each strand Remember that in DNA A always pairs with T and C always pairs with G in a process called complementary basepairing The weakness of the hydrogen bonds makes it relatively simple to separate parts of the two strands of DNA which is important in DNA replication and in transcription of DNA into RNA On the other hand when taken together the many hydrogen bonds in a DNA molecule combine to make the entire molecule a fairly stable structure although the strands may still be separated for example by exposure to high heat Slide 6 Another important feature of DNA is that the two strands that make up the DNA double helix are antiparallel That is to say that while they are parallel to each other the strands run in opposite directions One strand of a DNA molecule runs in a 3 to 5 direction while its opposing strand runs in the 5 to 3 direction The directionality of the strands of DNA is determined by the molecules of deoxyribose that help make up the sugar phosphate backbones For example if you are moving along a strand of DNA and each phosphate group is followed immediately by the 5 or number five carbon of deoxyribose you are moving in the 5 to 3 direction If the 3 or number three carbon of deoxyribose is encountered immediately after a phosphate group you are traveling in the 3 to 5 direction The antiparallel character of the DNA molecule has some important consequences in DNA replication which we will cover in a future lesson Slide 7 Most of the information in DNA is stored in segments called genes A gene is a specific sequence of nucleotides in a strand of DNA that codes for a specific polypeptide or sequence of amino acids Within a given molecule of doublestranded DNA genes may reside on either of the two strands Genes range in size from only a few hundred to several thousand consecutive nucleotides depending on the size of the polypeptide that they code for Slide 8 Genes also are generally anked by sequences of nucleotides that act to regulate their transcription or in other words sequences that regulate how often genes are copied into RNA In some cases there are sequences that bind molecules that inhibit the transcription of DNA In others there are sequences of nucleotides that bind molecules that promote transcription A common example found in both prokaryotic and eukaryotic organisms is the promoter region The promoter serves to help bind an enzyme called RNA polymerase The binding of RNA polymerase is necessary in order for transcription of the genes in DNA that code for proteins Slide 9 So how much DNA is in organisms and how many genes do organisms require to successfully survive and reproduce The amount of DNA found in organisms is quite variable A relatively simple organism such as the bacterium Escherichia coli contains around 47 million base pairs of DNA More complex organisms on the other hand can contain more DNA by several orders of magnitude Mammals for instance have on the order of three billion base pairs of DNA Certain salamanders and plants may have up to 150 billion basepairs of DNA Stretch this DNA out straight and it would measure several meters in length It s a pretty impressive packing job to get all of that DNA into a nucleus just one or two micrometers wide The number of genes in organisms follows a similar pattern to DNA more complex organisms generally have more genes although there are many exceptions to this rule E coll for example has a little over four thousand genes while singlecelled yeast has around six thousand Multicellular humans have somewhere between fifty and eighty thousand genes while certain plants such as rice may have several thousand more Slide 10 As you can imagine organizing the DNA in a cell can be a complicated endeavor In order to accomplish this DNA is packaged at several different levels First DNA in the cell is often wrapped around proteins called histones Histone proteins help to organize DNA and affect whether or not the DNA is available for replication or transcription When DNA is associated with histone proteins it is referred to as chromatin The individual units of DNA wrapped around histone cores are called nucleosomes Nucleosomes in turn may be coiled and packaged together more and more tightly to form a chromosome which is often visible under a light microscope In cells DNA is packaged loosely for the majority of the time so that it may be available for transcription which will be discussed in the following lesson or replication Tightly packed chromosomes form and are visible mainly when a cell is dividing such as during mitosis or meiosis The Great Truth Slide 2 You re probably familiar with the saying that some see the glass as half full while others see the glass as half empty It refers to how two seemingly opposite conclusions can be made about a single observation The same situation arises when observing the biological world Slide 3 One cannot help but be impressed by the diversity of life forms on the planet They vary in every imaginable way 7 shape size color 7 ying and not ying 7 2 legs six legs and no legs 7 single celled microscopic protists to blue whales 7 feathers fur and bald 7 and so many more ways Even within a single kind of organism there is exceptionally impressive diversity There are 900000 species of insects that have already been identi ed and probably 2 million species in total In the United States alone there are 11500 species of moths and butter ies1 But high levels of diversity are not found only in insects There are 200000 species are leafy plants like trees bushes and ferns that have been identified and even 4000 species of mammals There are so many different kinds of organisms on the planet that a person could conclude that organisms are mostly different from one another However a quite different conclusion would be reached if one considered the differences and similarities that exist at the cellular level in various species While there are certainly differences among cells from different species and from different tissues found in a single species there are also many features that are remarkably conserved and are common to all forms of life no matter their size shape or other characteristics Slide 4 So what are some of these features that are so highly common Well some of these common features you have already learned about All cells are made of the same kinds of macromolecules 7 nucleic acids lipids proteins and so on And remarkably these are all made from the same kinds of monomers 7 there are only 4 nucleotides in DNA only 4 nucleotides in RNA only 20 common amino acids in proteins and the basic structure of lipids is always the same No matter what species you choose to examine 7 from the smallest bacterium to the largest mammal 7 their composition and structure will be remarkably similar at the cellular level 1 http WWW si eduresourcefaqnmnhbuginfObugnos htm 2 http WWW cotf eduetemodulesmseseearthsysflrspecies html Slide 5 This remarkable similarity suggests that cells from all species must have many catabolic and anabolic functions in common As it turns out this is actually the case All cells must metabolize substrates and synthesize the monomers that are then used to make the macromolecules found in cells This could be done by a myriad of different pathways that differ among species 7 but this is not the case There are very few pathways for the synthesis of monomers that exist and they are common to all living organisms How can this be true Of course the answer to this question is unknown but the existence of common pathways that lead to the synthesis of common monomers that lead to the synthesis of common macromolecules constitutes some of the strongest corroborating evidence that support Darwin s theory of evolution and the parsimonious conclusion that life on earth as we know it evolved from simpler life forms through diversi cation and adaptive evolution In other words certain biological processes evolved early in the history of life on earth and have been conserved throughout evolutionary time Slide 6 Let s consider a simple example The heritable genetic information of cells is always encoded in deoxyribonucleic acid 7 DNA The code exists as triplets 7 sequences of 3 nucleotides Each triplet in DNA is always faithfully transcribed into a matching triplet found in messenger RNA Each of these mRNA triplets 7 which are called codons 7 encode a speci c amino acid This is always true in all organisms So perhaps when we look at the remarkable diversity of life forms on the planet we can see that the glass is both half empty and half full 7 there is an incredible diversity of life forms but there are also many features that have been conserved throughout evolution and can be found in all them Slide 7 Since the macromolecules and monomers that comprise cells are common to all life forms you might guess that the biochemical pathways by which they are produced are common to all life forms 7 and you would be right Of course not all organisms can do everything In some instances an organism cannot make some amino acids or vitamins that it requires and these must be supplied in its diet For example human cells cannot make the amino acid lysine and it must be consumed in the form of lysine containing proteins Nonetheless the cells of most organisms have most of the means to make what they need in order to grow and reproduce So you re probably thinking that since cells are so complex there must be a large number of biochemical pathways that lead to the synthesis of a large number of basic cell components and you d be wrong Here s a great truth about cellular biochemistry All the components of cells can be synthesized from 12 intermediates that are formed during the metabolism of substrates In addition during the metabolism of substrates energy is conserved in the form of the highenergy phosphate bonds of ATP and reduced cofactors are produced as substrates are oxidized And these components 7 12 key intermediates ATP and reduced cofactors 7 are all that a cell needs in order to synthesize all of the monomers and all of the macromolecules that are found in cells At this level cellular metabolism in all life forms is remarkably conserved among species and remarkably simple Slide 8 These 12 key intermediates 7 as well as the ATP and reduced cofactors that are needed 7 are made in only 3 biochemical pathways in the cell namely glycolysis the Krebs cycle and the pentose phosphate pathway As shown on this slide all 12 of the necessary compounds occur as intermediates in these pathways and serve as the starting points for the synthesis of more complex compounds such as amino acids fatty acids nucleic acids and so on If you examine these 3 pathways carefully you will also see that ATP and reduced cofactors are also produced Thus not only are these 12 key intermediates ATP and reduced cofactors necessary for all cells they are also sufficient While organismal biology is amazing in its complexity cellular biology is elegant in its simplicity Slide 9 So in your study of basic processes in cellular biochemistry you will see nearly everything that occurs is directed toward the synthesis of these 12 key intermediates ATP and reduced cofactors Certainly there are differences among organisms in the ways these objectives are achieved and these fascinate some individuals but they are the ones who see the glass as half empty Others compare the ways cells achieve these objectives and are struck by the existence of common denominators and these are the people who see the glass as half full In our discussions of cellular biochemistry we will focus on the glass that is half full 7 the biochemical pathways and processes that have been conserved through evolutionary time that yield all the basic components that a cell needs to grow and reproduce in e 9 Species and their Fon nation Classification of Biological snan Audio Lecture 1 Explain relationships between organisms 2 Predict traits 3 Give unique names in e 55 Two Systems of C Nonevolutionary hierarchical classification Carl Linnaeus 1758 s Evolutionary classification An anging H y imo taxonomlc Fwe ngdum System Three Dumam System Eukarya E How do we Clam Org anisms39 Hentame trams mav be gous r swrm ar characters mhented from a common ancestor Derwed e tram dwffers from the ancestra Homop astwc trams mav resu t from Convergent evohmon ParaHe evommon Evohmonarv reversas Trails used in 1 ing Organi Examples of data used in classifying organisms o Fossils 0 Structural traits 0 Molecular stmctu re 91 Phylogenetic Trees mild my Kingdom Plantae The Prokaryotic Cell Cycle Slide 2 The prokaryotic cell cycle is a relatively straightforward process Essentially unicellular prokaryotic organisms grow until reaching a critical size using the 12 key intermediates to synthesize more cytoplasm cell membrane ribosomes cell wall and other cell constituents They then replicate their DNA segregate copies of the chromosome and divide by a process called binary fission to produce two new genetically identical daughter cells Slide 3 Most research suggests that the rate of ssion in prokaryotic organisms is largely controlled by environmental conditions For example most prokaryotic organisms have an optimum temperature range for cell growth When environmental temperatures are above or below the optimum cell division tends to decrease The rate of ssion is also dependent on suf cient nutrients in the environment Under ideal environmental conditions many prokaryotic species undergo binary ssion at a fairly rapid rate with generation times of one to several hours This can lead to an astonishing growth in population size over a relatively short period of time In some instances populations of prokaryotes may increase by a million or even a billion fold in a matter of days Slide 4 Replication of the cell s DNA prior to cell division is essential for the process of binary fission as each new cell must have an accurate and complete copy of the DNA in order to function properly Although prokaryotic DNA often appears as a tangled mass it is in fact organized as a single supercoiled circular chromosome Replication of the circular bacterial chromosome starts at a speci c location on the chromosome 7 the origin of replication called ori for short As replication proceeds the DNA is threaded through an assemblage of proteins called a replication complex that makes a second copy of the cell s DNA As the chromosome is replicated the two ori regions 7 one from each copy of the DNA are attached to the plasma membrane The two ori regions then move apart as more of the chromosome is replicated and new plasma membrane is synthesized and added between the points of attachment When DNA replication is complete there are two identical copies of the cell s DNA that have segregated to each end ofthe cell Slide 5 The nal step of ssion is called cytokinesis Cytokinesis is the physical division of one cell into two cells This process generally begins shortly after the replication of DNA Cytokinesis begins with a pinching in of the cell membrane As the membrane pinches inward to divide the cytoplasm new cell wall materials are synthesized and deposited in the plane of cell division Ultimately two genetically identical cells with complete cell membranes and cell walls are produced and the process of growth and ssion may begin again Slide 6 It may be surprising to learn that certain organelles in eukaryotic cells also go through the process of binary ssion just as prokaryotic organisms do For example chloroplasts and mitochondria both contain DNA single circular chromosomes 7 just like prokaryotic cells These organelles also replicate their chromosomes and undergo binary ssion within the cytoplasm of eukaryotic cells Based on this and other similarities between these organelles and prokaryotic organisms it is generally thought that chloroplasts and mitochondria were once freeliving prokaryotic organisms that were engulfed by larger cells at some time in the past The theory describing this phenomenon is called the Endosymbiosis Theory The Evolution of Populations I Slide 2 When we discuss evolution we often equate evolution and natural selection However natural selection is only an agent of evolution it is not evolution itself We de ne evolution as a change in the genetic constitution of a population Most simply then evolution may occur in two ways 1 by changing the frequency of the existing alleles of a gene or genes in a population or 2 by changing the alleles themselves for example by mutation or by introducing new alleles into a population There are many ways by which populations may evolve or by which the genetic makeup of populations may change These mechanisms of evolutionary change including natural selection will be discussed in the following lesson In this lesson however we will consider the characteristics of a hypothetical population that is not evolving Such populations are said to be in HardyWeinberg equilibrium Slide 3 Consider a large isolated population of a diploid species A particular gene called gene A is present in all members of this population Further gene A has two alleles 7 big A and little a 7 so that there are homozygous individuals AA and aa and heterozygous individuals Aa or aA within the population Now imagine if all of the individuals in the population mated randomly with other individuals in the population to produce many offspring Essentially this would be akin to putting all of the alleles of gene A from all of the individuals in the population into a hat and pulling out two at a time to represent new diploid offspring If enough offspring were produced eventually the same frequency of alleles present in the parental population would be present in the offspring population Slide 4 We can show this to be true by calculating the allele frequencies from generation to generation For example the frequency of each allele big A or little a may be calculated as the total number of that type of allele divided by the total number of both alleles Say our population has 40 AA individuals 40 Aa individuals and 20 aa individuals In total we have 100 individuals but 200 alleles since each individual has two alleles The frequency of the big A allele would simply be 40 x 2 since 40 homozygous individuals have two copies of big A plus 40 since the 40 heterozygous individuals carry only one copy of big A divided by 200 total alleles This gives an allele frequency of 06 or 60 for big A The same calculation can be performed for little a in this case to give a frequency of 04 or 40 At this point you may notice that the frequencies of the two alleles A and a add to equal one When the frequencies of the different alleles of a gene in a population are added they will always add to equal one Take a moment and think about why this is true When our hypothetical population reproduces at random ie when the gametes carrying one or the other allele are drawn out of the hat there is a 60 chance for big A to be drawn and a 40 chance for little a to be drawn As more and more offspring are produced then the new allele frequencies will tend toward the frequencies of the original population Slide 5 While it is not difficult to see how the allele frequencies remain the same it is also true that the genotype frequencies will remain the same from generation to generation This occurs because the genotype frequencies in large randomly mating populations are determined by the frequencies of alleles If the allele frequencies do not change genotype frequencies also will not change For example the odds in our r r 39 quot of r J 39 l J g 4 dominant offspring are equal to the odds of receiving two big A alleles There is a 60 chance that any offspring will receive one big A allele and a 60 chance that they will receive a second big A allele The odds of receiving both big A alleles are then 60 times 60 or 36 Alternatively the odds of producing a homozygous recessive offspring are obtained by multiplying the frequencies of little a and little a in this case to give 016 or 16 Genotype frequencies for entire populations are calculated using a special equation called the HardyWeinberg equation This equation is written as p2 2pq q2 1 where p2 and q2 are the frequency of homozygous genotypes and 2pq is the frequency of heterozygotes As you might guess p and q represent the allele frequencies of any gene with two alleles like gene A that we have been considering For example if p equals the frequency of the big A allele the frequency of the AA genotype is p times p or p2 The same holds true when q equals the frequency of the little a allele To determine the frequency of heterozygotes we multiply the allele frequencies of the big A allele by the frequencies of the little a allele and then multiply that by two since heterozygous individuals could be either Aa or aA As we have seen previously the allele frequencies in our hypothetical population are not changing from generation to generation It follows then by the HardyWeinberg equation that the genotype frequencies also will not change because the same allele frequencies will be plugged into the equation generation after generation Since allele and genotype frequencies are not changing from generation to generation our population is not evolving Populations in these cases are said to be in HardyWeinberg equilibrium Slide 6 So how do we use the HardyWeinberg equation for real populations Scientists use HardyWeinberg equilibrium as a baseline or a null hypothesis against which to measure the genetic change of real populations As a null hypothesis Hardy Weinberg equilibrium is usually considered to rest on five assumptions 1 population size is large 2 mating is random 3 there is no migration into or out of the population 4 there is no mutation 5 there are no selective forces on the alleles under consideration If the frequencies of the alleles of a gene are changing it is clear that one or more of the above assumptions is incorrect Slide 7 As you might guess many characters in populations are evolving In fact HardyWeinberg equilibrium is more often the exception rather than the rule when investigating the genetic structure of populations What factors cause populations to evolve or drive populations away from HardyWeinberg equilibrium Any factor that causes the assumptions of HardyWeinberg equilibrium to be violated can be considered an agent of evolutionary change As we mentioned before natural selection is one factor that can cause populations to evolve There are others too such as mutation sexual selection gene ow and genetic drift that also play important roles in the evolution of populations We will discuss these mechanisms of evolutionary change in the following lesson SexLinked Inheritance Slide 2 While the concept of gender is very familiar to us it may be surprising to learn that the majority of sexually reproducing organisms on earth are functionally both male and female at the same time Most owering plants for example produce functionally bisexual owers which produce both male and female gametes Many other plants produce male and female reproductive structures in separate owers or cones but still on the same individual Some members of the animal kingdom such as the earthworms are also able to produce both types of gametes within the same individual Many animals however and a number of plants are capable of producing only male or female gametes in each individual These types of organisms are sometimes referred to as dioecious meaning two houses In dioecious species sex may be determined in a number of ways In some cases environment and nutrition affects the development of sexual characteristics In other cases such as in honeybees fertilization or lack thereof may determine gender In yet other organisms including humans sex is determined by special sex chromosomes which carry genes that code for male or female characteristics Slide 3 In addition to genderrelated characteristics sex chromosomes often carry genes that code for characters apparently unrelated to gender Such genes often show inheritance that deviates from Mendelian patterns because they are located on sex chromosomes In Drosophila for example sex is determined largely as it is in humans 7 females generally carry two X chromosomes while males carry an X and a Y chromosome It has also been shown that the gene for eye color is carried on the Drosophila sex chromosomes specifically on the X chromosome The allele of the gene that codes for red eyes is dominant over the allele that codes for white eyes Because this gene is located on the X chromosome however the results of crosses between redeyed and whiteeyed individuals may vary from Mendelian ratios depending on which parent has which character This is due to the fact that male parents only donate a Y chromosome which does not carry the gene for eye color to male offspring Whichever allele the male offspring receives from their female parent will be expressed in their phenotype regardless of the genotype of the male parent For instance in crosses between homozygous redeyed females and whiteeyed males all of the offspring have red eyes as would be expected When homozygous whiteeyed females are crossed with redeyed males however only the female offspring have red eyes while all male offspring have white eyes Slide 4 Sexlinked inheritance also has some important consequences for humans as a number of hereditary diseases or disorders such as hemophilia A and redgreen color blindness are linked to sex chromosomes In most cases sexlinked hereditary diseases are caused by recessive alleles of genes found on the X chromosome Heterozygous females therefore may carry the allele for the gene with no effect although they may pass it on to their offspring Males that carry the allele on the other hand will always be affected as there is no complementary allele on the Y chromosome to mask the effects of the recessive allele If males live to reproduce any daughters that they have will automatically carry the recessive version of the gene as a father can only donate an X chromosome to his daughter Any sons that they produce will not carry the recessive version of the gene as sons only receive the Y chromosome from their fathers Evolution of Populations 11 Slide 2 As discussed in the previous lesson evolution is de ned as a change in the genetic structure of a population Populations that are not evolving for a particular character or characters are said to be in HardyWeinberg equilibrium This equilibrium rests on ve basic assumptions as listed on this slide If any of these assumptions are violated in a population allele and genotype frequencies will change When this happens the population is no longer in HardyWeinberg equilibrium and is said to be evolving In this lesson we will take a closer look at the agents of evolutionary change that cause populations to evolve Slide 3 To start remember that our hypothetical population was isolated This means that no individuals are leaving the population and none are entering the population from the outside You could surmise that if one or several new individuals entered the population and contributed their alleles to the genetic makeup of the population by breeding the allele frequencies might change depending on the genetic makeup of the new individuals The magnitude of change would depend on the number of individuals entering their genotypes and the size of the population When individuals migrate between populations to contribute their alleles to new populations we call this gene ow Gene ow is one agent of evolutionary change Slide 4 We also stated that our population was large and that all members mated to produce offspring Because of this many individuals contributed their alleles to the offspring generation and the allele frequencies were maintained What might happen if the population was small though say a population with 10 members or 5 or 3 In a small population the consequences of not mating ie not contributing your alleles to the next generation may very well be that your alleles are lost permanently Essentially there is a smaller chance that other members will carry and contribute the same alleles in the same frequencies simply because there are fewer individuals The change in allele frequencies due to chance events such as missed mating opportunities is called genetic drift Genetic drift is a significant problem in the conservation of many endangered species A goal of most conservation plans is the maintenance of relatively high levels of genetic diversity in threatened or endangered populations The small size of endangered populations however often makes this very challenging Slide 5 Similarly consider how allele frequencies might change if our large population was suddenly reduced in size by half or by 90 There is a good chance that the allele frequencies in the resulting smaller population will differ to some degree from the original larger population As a result when the population reestablishes its original size allelic and genotypic frequencies will be changed This type of occurrence is not uncommon For example many populations go through such bottlenecks when a significant portion of the population is lost or separated due to a dieoff or a substantial environmental change Similarly a few individuals from a population may colonize a new habitat such as an island Again the genetic makeup of the resulting population in the new habitat will likely differ from the original population This phenomenon is a specific type of genetic drift called the founder effect It is believed that the diversification of the picturewinged fruit y on the Hawaiian islands is largely a result of the founder effect In this case there were likely at least 45 founder events where some members of a population on one island founded a new population on another island Slide 6 In our hypothetical population mating between individuals was also random with regard to gene A Because of this the chance of inheriting either of the alleles was based solely on the frequencies of each allele In most natural populations however mating is nonrandom in that potential mates are selected to some degree by their partners and vice versa Take a second to look around the computer lab for example Would you mate with just anyone of the opposite sex or would you be more inclined to specifically choose a mate based on various characters Similar mate selection processes occur in many types of organisms Nonrandom mating also known as sexual selection can greatly affect allele frequencies in populations over time Slide 7 We also assumed that in our population there was no benefit for individuals to have a particular genotype If for example there was an advantage to carrying and expressing one ofthe alleles of gene A we could expect that allele to increase in frequency over time because individuals carrying that allele would be more likely to survive and reproduce This is natural selection an agent of evolution that we have considered in more detail in a previous lesson Slide 8 Finally we did not consider what would happen if new unique alleles were introduced into the population such as a third allele of gene A This theoretically could happen by immigration of new individuals carrying the new allele into the population or by mutation of the alleles that already exist in the population Both of these processes can play significant roles in affecting the genetic structure of populations Mutations in fact are the ultimate source of genetic variation and help provide novel genetic material on which natural selection may act Although mutation rates are generally extremely low over many generations they play a significant role in the evolution of populations Slide 9 Although we have now covered a number of mechanisms of evolution individually it is important to realize that in natural populations these mechanisms do not generally act alone Rather evolution or the genetic change of populations is often the sum of several or even all of these processes working together In some cases certain processes may play more important roles than others but generally over time more than one of these processes contribute to the evolution of populations Take for instance the finches of the Galapagos Islands It is probable that the various species of finch on the island arose from a single ancestor species that colonized the islands from the South American mainland The founding population likely differed to some degree genetically from the mainland population resulting in a founder effect Over time the finches were exposed to different selective pressures resulting from the different habitats on the islands and so natural selection must have played a role in the diversi cation and speciation process You could probably also imagine that as the nches diversi ed different phenotypes could have resulted in different mating behaviors As a result sexual selection likely played a role in the diversi cation process In addition there is always the possibility that favorable mutations could have occurred in the DNA of certain individuals on the island resulting in their increased tness and contribution to the gene pool of their populations Diffusion and Passive Transport Slide 2 Biological membranes play a vital role in controlling how substances move into and out of the cell The phospholipid membrane and its embedded proteins act as both a barrier to and a connection with the world outside the cell In this module we are concerned with the processes that move atoms ions and molecules across the membrane without requiring any energy input We will investigate passive transport processes including simple diffusion osmosis and facilitated diffusion Slide 3 In order to understand what makes substances move anywhere in the first place it is important to understand the concept of a gradient In simplest terms whenever there is more of something in one place than in another a gradient exists Think of your house on a cold day On the outside of the wall there s a lot of cold air On the inside of the wall there is warm air A temperature gradient exists between the cold air outside and the warm air inside If you open the door cold air will come into the house and warm air will go out of the house Leave the door open long enough and the air outside and inside will reach the same temperature What has happened Temperature equilibrium has been reached through diffusion of the warm and cold air molecules and the temperature gradient has been erased In the absence of any barriers substances will tend to diffuse so that a state of equilibrium or even distribution of the substances is reached It is important to note that in the process of diffusion no energy input is needed The random motion of the molecules will tend toward equilibrium Slide 4 Diffusion can occur across a membrane if the membrane is permeable to the substance that is diffusing Biological membranes are semipermeable or selectively permeable meaning that some substances can pass through the membrane but others can t In general molecules that are lipidsoluble will pass directly through the phospholipids that make up a large part of the membrane Polar and charged molecules cannot pass directly through the phospholipid portion of the membrane To move these types of molecules across the membrane we will see that the proteins embedded in the membrane have several important functions Even though it is a polar substance water can readily diffuse across biological membranes but it must do so by way of protein channels In some cases water moves through special protein channels called aquaporins Water may also be carried through certain integral membrane proteins along with other molecules Diffusion of water is called osmosis Remember that diffusion will always occur down the concentration gradient from the area of higher concentration to the area of lower concentration In the case of osmosis it is important to remember that it is the concentration of water that is being considered not the concentration of solute Consider the situation illustrated on this slide A solute is dissolved in water A selectively permeable membrane separates two solutions with different solute concentrations and is impermeable to the solute itself The solution in the right half of the tube initially contains a higher solute concentration than the solution in the left half of the tube In this case water will move across the membrane from the area of its higher concentration but lower solute concentration to the area of its lower concentration but higher solute concentration The resulting solutions have equal concentrations of both solute and water Slide 5 The selective permeability of biological membranes and the solute concentrations inside and outside of a cell have important implications for cell shape and function If the solute concentrations inside and outside of a cell are too different the cell may not be able to function An isotonic solution is a solution with the same solute concentration as is found inside the cell A cell in an isotonic solution experiences no net movement of water into or out of the cell Remember that water molecules are still diffusing across the membrane but they are traveling equally in both directions so the water and solute concentrations remain the same inside and outside the cell A hypotonic solution has a low solute concentration compared with the concentration inside the cell A cell in a hypotonic solution experiences net movement of water into the cell and the cell will swell In cells with cell walls such as cells of plants prokaryotes or fungi the cell wall prevents the cell from bursting and this swelling helps maintain turgor pressure in plants and helps the cell grow In animal cells on the other hand there is no cell wall and cells in a hypotonic solution may swell to the point of bursting A hypertonic solution has a high solute concentration compared with the concentration inside the cell A cell in a hypertonic solution experiences net movement of water out of the cell and the cell may shrivel and lose many of its cellular functions As you can see it is important for a cell to be in an environment with the proper tonicity in order to maintain proper shape and function Slide 6 Ions and molecules that cannot pass directly through the phospholipid membrane may move across the membrane through special protein complexes in a process called facilitated diffusion Keep in mind that in facilitated diffusion just as in simple diffusion and osmosis the movement of molecules is always down the concentration gradient and no energy input is needed The protein complexes simply provide an appropriate opening in the membrane for specific molecules to pass through Ion channels provide a good example of protein channels Each type of ion channel is specific to the type of ion that can move through it and these channels are gated meaning that some type of signal is needed to open them When the appropriate signal is received the shapes of the proteins in the channel change to allow the ion to pass through The direction of net movement of the ions will depend on the relative concentrations of the ion inside and outside of the cell Slide 7 Carrier proteins also act in facilitated diffusion These proteins actually bind the molecule that is being transported across the membrane change shape in response to the presence of the molecule and then release it on the other side of the membrane After the molecule is released the proteins return to their original shape and are ready to accept another molecule Slide 8 In summary passive transport processes may involve simple diffusion osmosis and facilitated diffusion These processes are called passive transport because they do not require any input of energy While facilitated diffusion will involve channel or carrier proteins in every case of passive transport the net movement of substances will be down the concentration gradient toward a state of equilibrium DNA Proofreading and Repair Slide 2 DNA replication is an amazingly accurate process As DNA polymerase adds nucleotides to a growing strand of DNA it inserts an incorrect base on average only once in every 104 to 106 bases This is an error rate of one in ten thousand to one in one million bases Even more astonishing DNA polymerase maintains this low error rate while working at an incredible rate of speed In E coll for example DNA polymerase builds new strands of DNA at rates of over one thousand nucleotides per second Remember though that the majority of mutations or changes in DNA have a neutral or negative effect on the organism It is essential then that organisms minimize the number of mutations occurring in their DNA as much as possible Cells utilize numerous repair processes to safeguard their DNA from damage Some of these processes are found in all types of cells while others may be highly specific to certain cell types All repair mechanisms are energyrequiring which perhaps underscores the importance to organisms of maintaining the integrity of DNA in a cell In this lesson we will discuss three of the basic mechanisms that organisms use to reduce the error rate of DNA replication proofreading mismatch repair and excision repair Slide 3 As DNA replication proceeds the replication complex through which DNA is threaded simultaneously builds a new strand of DNA and proofreads its work Proofreading involves many of the enzymes of the replication complex but DNA polymerase 111 plays perhaps the most important role When DNA polymerase III inserts an incorrect nucleotide in a growing strand of DNA it usually recognizes its mistake immediately removes the nucleotide and replaces it with the correct nucleotide This proofreading mechanism alone greatly reduces the error rate of DNA replication Slide 4 After DNA replication is completed a second mechanism similar to the proofreading mechanism scans the new strand of DNA for errors missed by proofreading When errors are found incorrect nucleotides are removed and replaced by DNA polymerase This mechanism is called mismatch repair Together with the proofreading mechanism mismatch repair reduces the error rate of DNA replication to around one incorrect base pair in a billion Slide 5 During the life of a cell there is always the potential for damage to the cell s DNA which in turn could result in the production of nonfunctional proteins The DNA may be exposed to different mutagens for example such as chemicals or ultraviolet light which can chemically alter nucleotides To guard against this type of damage specialized enzymes continuously scan the cells DNA for any damage such as mismatched base pairs or even extra nucleotides When damage is encountered short stretches of DNA may be removed or excised These stretches are then replaced with the proper nucleotides through the activity of DNA polymerase and DNA ligase This type of repair is called excision repair Slide 6 Considering the highly effective and energyconsuming repair mechanisms that cells use to repair their DNA one might ask why errors in DNA occur at all or why evolution hasn t produced absolutely perfect proofreading and repair mechanisms Recall however that mutations are truly the source of novel genetic material Without mutations constantly altering the DNA of organisms species could not evolve and adapt to changing environments And without evolution a species ultimately would not be able to survive On the other hand since many mutations have adverse effects a mutation rate that is too high could have disastrous consequences for individual organisms It is believed therefore that mutation rates have evolved over time to fall in between the extremes of no mutations hence no evolution and too many mutations hence the death of individual organisms In this way mutation rates allow a balance between the evolution of species and the survival and reproductive success of individual organisms Measuring Genetic Divergence Slide 2 In recent years scientists who study evolution have turned to molecules to learn about the timing of evolutionary events This concept of a molecular clock rests on the assumption that neutral mutations accumulate in DNA at a relatively constant rate Of course the DNA sequences of genes are expressed as polypeptide sequences so it is also possible to approach the molecular clock idea using protein sequences This slide shows a plot of amino acid substitutions in cytochrome c a protein involved in the respiratory chain vs the time at which various organisms diverged in evolutionary history According to this plot cytochrome c has evolved at a fairly constant rate Slide 3 We can also use the accumulation of neutral mutations in different species to infer a number of things about how species are related to each other In conjunction with fossil and lllUll 39 39 39 39 data 1 can help determine where lineages split and how closely or distantly related different species are The more differences there are in their molecular sequences the more distantly related two species are But let s back up a little What exactly are neutral mutations Why can we say that they accumulate at a constant rate What are molecular sequences and how do we measure the differences in those sequences Slide 4 Let s start with neutral mutations Think back to our lesson on mutations Many point mutations in DNA have no effect on the amino acid sequences produced by transcription and translation either because they occur in parts of the DNA that don t encode genes or because they occur in positions that don t change the amino acid produced Remember that the genetic code is redundant that is there are usually several codons that code for the same amino acid These silent or synonymous mutations are also called neutral mutations because they have no effect on an organism s ability to survive and reproduce Even some mutations that do cause changes in the amino acid sequence of a protein may not have any effect on the protein s ability to function properly For instance the substitution of one nonpolar amino acid for another may not change the protein s shape or function These mutations can also be considered neutral mutations because they just don t give natural selection anything to work with Neutral mutations are free to accumulate in a population and may eventually become part of the genome ofa species On the other hand we have nonsynonymous mutations 7 mutations that cause changes in genes that do affect an organism s ability to survive and reproduce Now natural selection can get into the act Most nonsynonymous mutations are disadvantageous and are quickly removed from the population usually by the death of the organism carrying the mutation Occasionally nonsynonymous mutations are advantageous and these mutations may be quickly fixed in the population If we want to talk about the rate at which a mutation will become fixed in a population we can see that nonsynonymous mutations are usually fixed or eliminated rapidly while neutral mutations may be fixed over a longer period of time The result shown in this slide is that we see fewer nonsynonymous mutations than synonymous mutations fixed in a population for a given period of time Slide 5 During the past several decades molecular sequencing capabilities have exploded As a result DNA RNA and protein sequences are easily accessible via the intemet We are often interested in comparing similar sequences among various organisms to see what parts of a gene or polypeptide have changed and what parts have been conserved through evolution An important part of this process is alignment For either a nucleic acid or amino acid sequence it is important to find some starting points where we are confident that the sequences line up There may be nucleotide insertions or deletions that have accumulated over time in the sequences in different species that make this process tricky so there are a lot of software algorithms to help solve this problem Once we have some sequences properly aligned we can begin to look at the similarities and differences among them To estimate the degree of divergence among different organisms a similarity matrix can be constructed In this matrix the number of different amino acids are shown above the line and the number of identical amino acids are shown below the line The simplest assumption is that the more differences there are between sequences the longer the organisms have been evolving separately Slide 6 Here is an interesting comparison of amino acid sequences As we mentioned before cytochrome c is an important constituent of the electron transport chain in mitochondria It is found in all eukaryotic organisms By comparing aligned sequences of cytochrome c from different organisms we can begin to get an understanding of how species have diverged over the course of time We can also see what parts of the amino acid sequence are absolutely vital to the proper functioning of the protein Invariant positions in the sequence must represent amino acids that cytochrome c simply can t do without To get back to the idea of how mutations accumulate in a sequence proteins that are absolutely essential to the functioning of an organism evolve slowly while less essential proteins can evolve more quickly To get down to a finer scale parts of an amino acid sequence that are essential for the functioning of a protein the invariants in the cytochrome c sequences for example evolve very slowly if at all Slide 7 Similarity matrices can be used to study DNA sequences as well For instance scientists can look at the similarity matrix for a gene that is common to many organisms and calculate relative times of divergence With the explosion in published DNA sequences and computer programs to compare them whole genome comparisons are becoming possible Recent research has shown that the total genomes of chimpanzees and humans differ by only about 15 Using the molecular clock theory researchers have estimated that humans and chimpanzees shared a common ancestor around 4662 million years ago Slide 8 Just as the choice of characters is important in constructing phylogenies based on morphology the choice of molecules is very important in looking at where and when organisms may have diverged from one another To do broad studies of many kinds of organisms it is obviously important to use a molecule that all of those organisms have We looked at cytochrome c sequences in many different kinds of eukaryotes For even broader studies of both prokaryotes and eulmryotes ribosomal RNA is a popular tool It has the advantages of being ubiquitous in all living organisms and having some portions that evolve extremely slowly Most mutations in rRNA cause problems with translation and are quickly removed by natural selection These types of slowly evolving molecules are useful for looking at ancient lineage splits On the other hand mitochondrial and chloroplast DNA have proved useful in studying recent evolutionary divergence because they accumulate mutations relatively rapidly Meiosis Slide 2 In a previous lesson we discussed a type of cell division called mitosis that involved the division of one parent cell into two genetically identical daughter cells This type of cell division is important in the growth and asexual reproduction of many types of organisms Mitosis however is somewhat limiting for cells in an evolutionary sense because it results only in the production of genetically identical individuals or clones Without a mechanism to increase genetic variation species have difficulty adapting to changing environments Many species counter this difficulty by constantly generating genetic variation through sexual reproduction which involves combining the genetic material from two different organisms to produce new genetically unique offspring At the foundation of sexual reproduction is a process of cell division that results in the production of genetically variable cells This process is called meiosis Slide 3 Although meiosis like mitosis is a process of cell division it differs from mitosis in several key aspects First meiosis involves two rounds of cell division instead of one and so results in the production of four daughter cells from each parent cell Only one round of DNA replication occurs prior to cell division however so the four daughter cells produced by meiosis contain only half of the chromosomes from the original parent cell For instance if a diploid cell undergoes meiosis it will produce four haploid daughter cells Finally a process called crossing over occurs in meiosis During crossing over homologous chromosomes physically exchange segments of their DNA This mechanism is an important way by which meiosis generates genetic variation Slide 4 Both rounds of cell division in meiosis contain essentially the same stages as mitosis prophase metaphase anaphase and telophase We refer to the rst round of cell division in meiosis as meiosis I and the second round as meiosis II The stages are similarly named For example prophase of meiosis I is called prophase I metaphase of meiosis II is called metaphase II After meiosis I the cells of some organisms move directly into meiosis II In other types of organisms meiosis I and meiosis II are separated by a short period called interkinesis In the following slides we will discuss some of the key aspects that occur during meiosis I and meiosis II and how they differ from the corresponding stages in mitosis to produce four genetically distinct daughter cells Slide 5 During prophase of meiosis I the DNA of the cell is condensed into chromosomes and homologous chromosomes pair tightly together in a process called synapsis Recall that prior to meiosis the cell has undergone DNA replication Because of this each chromosome consists of two identical sister chromatids The chromatids of homologous chromosomes become physically connected at points called chiasmata singular chiasma Crossing over occurs at chiasmata when segments of DNA are exchanged between homologous chromosomes Crossing over results in a recombination of genetic material meaning that the sister chromatids of the homologous chromosomes become genetically distinct from each other This is the first way by which meiosis generates genetic variation In the illustrations on this and the following slides note that each member of a pair of homologous chromosomes is indicated by a different color Each color represents the genetic material ie the chromosomes donated by one parent When pieces of chromosomes are exchanged this is indicated by the different colors as well Slide 6 During metaphase I homologous chromosomes line up at the equatorial plate in the plane of cell division At this point each homologous chromosome will become attached to kinetochore microtubules from only one end of the cell Because of this arrangement during anaphase I the homologous chromosomes each with two chromatids separate and move to opposite ends of the cell recall that in mitosis it was the sister chromatids that separated and moved to opposite ends of the cell In this way each ofthe two new cells formed in meiosis I will have one of each type of chromosome but only half the total number of chromosomes as the parent cell For example a diploid cell going through meiosis I will produce two daughter cells each with one set of chromosomes instead of two Meiosis I therefore results in a reduction in the ploidy level or the number of sets of chromosomes Further while each end of the cell will receive one member of each pair of homologous chromosomes exactly which member it receives is a random process This random assortment of homologous chromosomes into daughter cells during meiosis I is a second mechanism employed by meiosis to produce genetically diverse daughter cells Slide 7 In some species anaphase I is followed by telophase I and cytokinesis during which time nuclear envelopes reform around the condensed chromosomes at each end of the cell and the cell divides into two daughter cells In some organisms there is an interphase between cytokinesis of meiosis I and the beginning of meiosis II called interkinesis During this stage each of the daughter cells will prepare for a second round of cell division by synthesizing enzymes cell membrane and other components necessary for meiosis II It is important to note however that DNA is not replicated during interkinesis as it is during interphase of the mitotic cell cycle Slide 8 Meiosis II involves cell divisions that are essentially identical to mitosis During meiosis II each ofthe two cells produced during meiosis I will divide resulting in a total of four daughter cells At prophase II the chromosomes of each cell re condense and the nuclear envelopes begin to break down The chromosomes line up on equatorial plates during metaphase II and the sister chromatids of each chromosome are pulled apart to opposite ends of the cell during anaphase II just as they are in mitosis The assortment of the genetically variable sister chromatids into daughter cells is a random process similar to the assortment of homologous chromosomes in meiosis I And as in meiosis I the process of random assortment aids in the generation of genetic diversity among the daughter cells produced by meiosis This is the third way by which meiosis generates genetic variation After the chromatids have moved to separate poles of the cells they begin to decondense while nuclear envelopes reform in telophase II A second round of cytokinesis resulting in the four final daughter cells follows telophase I Slide 9 To review let s brie y look again at the specific processes in meiosis that result in four genetically unique daughter cells First DNA is exchanged between homologous chromosomes during the crossing over events of prophase I resulting in genetically variable sister chromatids Second the homologous chromosomes of meiosis I and the sister chromatids of meiosis II are randomly assorted into daughter cells prior to each cell division This assures that while each daughter cell has a complete set of chromosomes it will differ genetically from the chromosomes of the other daughter cells Slide 10 So how exactly does meiosis play a role in sexual reproduction In sexual reproduction the genetically variable cells produced by meiosis in two different individuals combine The resulting cell called a zygote develops into a new genetically unique individual As an example consider the egg and sperm cells of animals Both of these cell types are produced by meiosis and so carry unique genetic material from the parent that produced them When these cells fuse to form a zygote during fertilization the resulting cell will carry only half of the chromosomes from each of its parents and so will differ to some degree from both of them However as we know from meiosis it is purely chance as to exactly what genetic material from each parent ends up in each e g or sperm cell When a number of offspring are produced the odds are that each offspring will be genetically distinct from all of the other offspring In this way the process of meiosis generates the genetic variability that is the cornerstone of sexual reproduction and which is essential for the process of evolution Slide 11 In addition meiosis plays one other important role in sexual reproduction Remember that because of the reduction in chromosome number that occurs during meiosis I each gamete produced contains only half of the chromosomes from the parent that produced it When gametes combine the resulting zygote will then contain the same total number of chromosomes as each of its parents If a reduction in chromosome number did not occur during meiosis I each time a zygote formed it would have twice as many chromosomes as its parents In a short time of course this could cause major difficulties for the survival and reproduction of cells and organisms Through the reduction in chromosome number that occurs in meiosis I meiosis acts to maintain the ploidy level or number of sets of chromosomes of sexually reproducing species Horizontal Gene Transfer in Prokaryotes Slide 2 Before we explain horizontal gene transfer some background on prokaryotic organisms is required Prokaryotes represent all singlecell organisms that are not eukaryotic and can be subdivided into two majors groups the Bacteria and the Archaea Humans and other animals plants and fungi are examples of eukaryotic organisms Slide 3 Prokaryotic cells are about 1 micrometer or less in size and the cells come in a few different shapes Unlike in the eukaryotes the doublestranded chromosome of prokaryotes is not surrounded by a membrane prokaryotes do not have a nucleus They have about 1 1000 of the DNA of human cells Prokaryotes play important ecological roles including cycling elements in the soil atmosphere and water They present disease challenges to humans animals and plants Prokaryotes also play a central role as tools for biotechnology In this lecture we will mainly focus on the group of the Bacteria Slide 4 Prokaryotes usually reproduce asexually by cell division also referred to as vertical gene transfer The division of single cells into two identical offspring produces clones or genetically identical individuals Prokaryotes can grow rapidly Escherichia 001139 can double every 20 minutes In addition to this asexual cell division prokaryotes have several mechanisms through which they may acquire new genes by horizontal gene transfer Slide 5 There are three wellknown mechanisms of horizontal gene transfer in Bacteria 0 Transformation is the process by which bacteria take up extracellular DNA from their environment These DNA fragments may recombine with the host chromosome permanently adding new genes This mechanism was discovered more than 75 years ago and was at the basis for the discovery that DNA is the heredity factor in all living organisms A second mechanism of gene transfer is transduction During transduction viruses carry genes from one bacterial cell to another Viruses are obligate intracellular parasites needing the biochemical machinery of living cells to reproduce Viruses that infect bacteria are called bacteriophages Many get their genetic material into the cell by attaching with tail assemblies that then inject the DNA into the cell During the lytic cycle when the host cell breaks open some bacteriophages package some of the host bacteria s DNA Cells that are subsequently infected by such viruses get a segment of DNA from another bacterium which can recombine with the chromosomal DNA of the host and thus alter its genetic composition Several bacteria can conjugate Conjugation is the exchange of genetic information DNA by direct cellcell contact Physical contact is initiated by a pilus which is a fine tube produced by the donor cell Before we can discuss conjugation we must introduce another kind of genetic element called a plasmid Slide 6 Plasmids are genetic elements that replicate independently of the host chromosome Almost all known plasmids are doublestranded DNA and most often circular They typically ca1ry genes that are only required by the host under specific conditions For example genes that confer antibiotic resistance to their host are often found on plasmids in the presence of antibiotics only the resistant bacterial cells will survive Plasmids can also carry genes that code for a wide variety of other functions such as resistance to heavy metals and UV light degradation of organic compounds including environmental pollutants production of antibiotics and production of virulence factors Slide 7 Conjugation is the process whereby a plasmid is replicated and transferred to another cell by celltocell contact It was first demonstrated in 1946 by Joshua Lederberg and Edward Tatum Some but not all plasmids are conjugative This means that these plasmids have the required genetic information to govern their own transfer Some plasmids are transferable to a broad range of bacteria They are called broad host range plasmids The conjugation process is as follows First the plasmid initiates conjugation in the Donor cell bacterium with plasmid by making a pilus that makes contact with the Recipient cell bacterium without plasmid Next a copy of the plasmid is transferred to the Recipient which then becomes a Transconjugant recipient cell with new plasmid Plasmids can have 1 to about 40 copies per cell Slide 8 Transposable elements found in most organisms move genes among plasmids and chromosomes They facilitate gene transport within an individual cell and are sometimes also called jumping genes Long transposable elements that include one or more genes are called transposons Transposons have contributed to the evolution of plasmids They often carry genes that encode antibiotic resistance or degradation of pollutants Recently several other mobile genetic elements have been found in bacterial chromosomes such as the pathogenicity islands which code for virulence factors Trans cription Slide 2 Recall the lesson about macromolecules where the structure of DNA and RNA was discussed Pause the audio lecture for a moment and study the figure shown here and see if you can determine the difference between the two types of molecules You should have noticed two differences in the nucleotides the type of sugar present and the base pairing RNA has ribose sugar DNA has deoxyribose Base pairing is the same in both molecules except that the thymine base in DNA is replaced with uracil in RNA Both thymine and uracil have the ability to pair with adenine You will also have noticed that DNA is represented as a double strand whereas RNA is a single strand molecule Slide 3 The figure here shows three different processes where information is transferred 1 Replication 7 DNA can be replicated using the existing information contained within the strands of DNA 2 Transcription 7 one of the DNA strands acts as a template for the production of RNA Three different types of RNA are produced messenger RNA mRNA ribosomal RNA rRNA and transfer RNA tRNA 3 Translation 7 when messenger RNA mRNA is read the information encoded in the strand is translated to produce polypeptides which eventually become proteins In eukaryotic cells both processes of replication and transcription take place in the nucleus translation takes place in the cytoplasm In prokaryotes which have no nucleus all three processes are completed in the same location the cytoplasm This lesson will focus on the process of transcription Slide 4 The diagram on the left shows that transcription and translation in a prokaryote takes place in the cytoplasm In a eukaryotic cell shown on the right hand side the two processes are separated TRANSCRIPTION takes place in the NUCLEUS translation in the cytoplasm Slide 5 Messenger RNA is the only class of RNA that carries information necessary to build a polypeptide Most of the genes on the DNA molecule encode for mRNA Some genes on the DNA strand encode ribosomal RNA the main component of ribosomes Recall that ribosomes are the subcellular structures necessary for the assembly of polypeptide chains Yet other genes on the DNA encode the information necessary to produce transfer RNA As the name implies tRNA transfers individual amino acids to the ribosome where they are assembled into polypeptides according to the information encoded in the mRNA Slide 6 The process of transcription can be divided into three phases initiation elongation and termination During the initiation phase the enzyme RNA polymerase binds too a specific sequence of nucleotides the promoter on the DNA molecule This interaction causes the two DNA strands to unwind in that area exposing the DNA template strand Somewhere between 10 and 20 bases are exposed at any one time The DNA molecule winds back into a double helix once the bases have been transcribed Slide 7 During the second step elongation of the RNA transcript RNA polymerase moves along the DNA template reading the strand from 339 to 539 The nucleoside triphosphates found in the nucleus of eukaryotes are added as nucleotides to the 339 end of the RNA strand until it grows to a designated length Note that the new RNA strand is being produced from its 5 39 to 339 end making it antiparallel to the DNA template The energy required for the reaction is provided by the hydrolysis of pyrophosphate into two molecules of inorganic phosphate Pyrophosphate is produced when a nucleotide is added to the RNA transcript How fast is this process Estimates show that about 60 nucleotides per second are transcribed Think about this at this rate of transcription how long will it take to make a large protein consisting of 1200 amino acids Remember that 3 nucleotides encode 1 amino acid Slide 8 Observe the gure shown on slide 8 and note that base pairing between RNA and DNA is the same as in the double stranded DNA helix The exception is that the thymine base of DNA is replaced with uracil in RNA Both thymine and uracil have the ability to pair with adenine Slide 9 The enzyme RNA polymerase will continue to read the DNA template until told to stop The termination phase as in initiation involves a specific sequence of bases forming a termination site on the DNA template Once these bases have been read the RNA transcript is released In eukaryotes when a messenger RNA transcript is released it is referred to as pre mRNA since it requires further processing before it is ready to translate the information into a polypeptide Slide 10 The first step in modifying the premRNA transcript is the alteration of the ends A modified guanine nucleotide forms a cap at the 539end Once in the cytoplasm this cap will help bind the mRNA to a ribosome At the other end of the premRNA transcript adjacent to the termination site a series of adenine nucleotides forming a poly A tail is attached by enzymes to the 339 site Both cap and tail modifications prevent the degradation of the mRNA by hydrolytic enzymes Slide 11 The premRNA has one last processing step before it is considered mature mRNA ready for translation The premRNA transcript is made up of exons and introns Exons are regions of the transcript that are eventually expressed during translation Introns are noncoding regions This figure shows an intron sandwiched between two exons Snurps bind to each end of the intron When the snurps come together with other proteins they form a splicesome snipping out the intron Before the mRNA is ready to go to the cytoplasm all of the introns are snipped out of the transcript The remaining exons are pasted together forming mature mRNA that is now ready for export through the nuclear pores Introns are degraded in the nucleus Mendel s Discoveries Slide 2 Gregor Mendel was an Austrian monk who lived in the middle of the 19th century A fair amount about Mendel s life is known from history including the fact that some of his lowest grades received in school were in biology Despite his academic shortcomings however Mendel s work as a scientist uncovered some of the most fundamental concepts of genetics and provided a basis for many of the major advancements in biology that were to come in the following century Slide 3 Over a period of about nine years Mendel performed breeding experiments on bean plants by collecting data on the hereditary patterns of a number of different characters of the plants such as the color of fruits and owers the shape of seeds and fruits and the size of plants Mendel s studies involved crossing bean plants that were truebreeding for different forms of various characters For example one of Mendel s crosses involved breeding plants that always produced smooth seeds with plants that were true for wrinkled seeds The outcome of this cross is shown in the illustration Mendel called his truebreeding plants the parental generation or P Crosses between two parents result in the first filial generation or F1 for short These F1 progeny were then allowed to selffertilize producing a second filial generation or F2 Mendel measured the characters under study as they occurred in both the F1 and F2 generations and then used a fairly simple mathematical explanation to describe the results that he found As we will discuss in the next few slides Mendel s results led to the discovery of two fundamental laws that govern heredity not just in bean plants but in all sexually reproducing organisms Slide 4 Mendel s rst experiments described the heredity patterns of single characters such as ower color or seed shape Crosses performed to follow the inheritance of a single character are called monohybrid crosses Invariably in these crosses the F1 generation displayed only one trait or version of the character that was present in the parental generation For example when Mendel crossed purple owered plants with white owered plants only purpleflowered plants were observed in the F1 generation When plants with smooth seeds were crossed with plants with wrinkled seeds only smoothseeded plants were observed in the F1 generation Mendel called the traits that appeared in the F1 generation dominant traits The traits that did not appear in the F1 generation were called recessive traits When Mendel allowed the F1 generation to selfpollinate the recessive traits reappeared in the resulting F2 generation However as shown in the table the dominant and recessive traits always appeared in the ratio of three dominant phenotypes to one recessive phenotype Slide 5 Mendel explained these results by reasoning that each plant had two units of inheritance for any given trait Plants could then theoretically have three possible combinations for a character they could have two dominant units two recessive units or a dominant and a recessive unit Furthermore when the adult plants formed gametes through the process of meiosis each of the units separated so that each gamete carried only one unit This means that when gametes from separate parents combined and developed into a new plant the offspring would have one unit of inheritance for a character from each of its parents Today we call Mendel s units of inheritance genes and the different versions 7 dominant and recessive 7 different alleles of the same gene As you follow through this lesson note that different genes are denoted by letters The dominant allele of a gene is represented by a capital letter while the recessive allele is denoted by a lowercase letter For example the gene for ower color is represented by the letter w The dominant allele that results in purple color is a capital W the recessive form that corresponds to white color is a lower case w Individuals with two of the same alleles are termed homozygous and are represented as WW or w while individuals with different alleles are termed heterozygous and are represented as Ww Mendel s truebreeding plants therefore were homozygous for certain characters such as ower color When these homozygous parental plants produced gametes all of the gametes from a given parent contained the same allele When gametes from two different parents combined the resulting offspring were heterozygous In appearance however only the dominant trait was observed because the F1 plants carried the dominant allele which was expressed over the recessive allele Slide 6 When Mendel s F1 generations produced gametes equal numbers of gametes contained dominant and recessive alleles When these gametes combined there would be an equal chance of each of the following allelic combinations in the offspring genotype dominantdominant dominantrecessive recessivedominant and recessive recessive However the physical appearance of the F2 plants would be observed in the ratio three dominant to one recessive because three of the possible allele combinations contain dominant alleles one contains only recessive alleles This three to one ratio is the ratio which Mendel observed At this point you should note that the physical appearance or phenotype of an organism is determined by its genetic makeup or genotype In addition different genotypes such as the homozygous dominant and heterozygous conditions can lead to the same phenotype Slide 7 The results from Mendel s first experiments led to the formation of Mendel s rst law the law of segregation The law of segregation states that during the formation of gametes the alleles of a gene separate so that each gamete only receives one allele for each gene Slide 8 Mendel s second set of experiments involved measuring the heredity patterns of two characters at a time This type of cross is called a dihybrid cross For example Mendel crossed plants that were truebreeding for seeds that were both round and yellow with plants truebreeding for green and wrinkled seeds The results Mendel obtained were similar to those of his first experiments although they were a little more difficult to interpret due to the inclusion of two characters rather than just one In the F1 generation all of the plants displayed both of the dominant traits found in the parental generation In our example the F1 generation all produced smooth yellow seeds In the F2 generation Mendel always found that the traits in question appeared together in a 933l ratio In other words out of every sixteen F2 plants measured nine had both dominant traits six had only one of the dominant traits and one displayed both recessive traits Slide 9 To explain the results of his dihybrid crosses Mendel proposed that not only did the alleles of each of the two genes segregate during gamete formation as he had shown in his first experiment but the two genes assorted independently of each other as well For example take a look at the F2 results in the illustration If you add up only the round seeds compared to the wrinkled seeds you will find 12 round and 4 wrinkled seeds This of course is a three to one ratio as is expected from Mendel s first law The same is true of the yellow and green seeds However when the characters of seed shape and color are considered together the resulting 933l ratio can only be explained if the two genes for these characters have behaved independently of each other during gamete formation When this occurs gametes with all possible allele combinations RY Ry rY and ry are formed with equal probability When these gametes then combine to form offspring the offspring are produced in a 93 31 phenotypic ratio Slide 10 The results of Mendel s dihybrid crosses led to the formulation of Mendel s second law called the law of independent assortment This law states that during gamete formation the alleles of different genes assort independently of one another Due to this any gamete may receive any combination of the alleles present in the organism Recall that Mendel s first law the law of segregation dealt with the segregation of different alleles of the same gene The law of assortment describes the assortment of the alleles of different genes Slide 11 Mendel s work helped lay the foundation for modern genetics and his discoveries and conclusions have largely stood the test of time However as we will see in the following lesson there are a number of exceptions to Mendel s second law and a number of examples where the phenotype of an organism is not so clearly defined by strictly dominant and recessive alleles of genes In fact many researchers consider it amazing that all seven of the characters that Mendel chose for study displayed such clear patterns of dominantrecessive heredity The exceptions to Mendel s rules of course have presented some of the major challenges to geneticists since Mendel s discoveries
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