Cells & the Evolution of Life
Cells & the Evolution of Life BIOL 115
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This 13 page Class Notes was uploaded by Oma Larkin on Friday October 23, 2015. The Class Notes belongs to BIOL 115 at University of Idaho taught by Bruce Mobarry in Fall. Since its upload, it has received 10 views. For similar materials see /class/227880/biol-115-university-of-idaho in Biology at University of Idaho.
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Date Created: 10/23/15
Errors in the Code Slide 2 Mutations are not just the stuff of science fiction movies Mutations happen every day in all kinds of cells in all kinds of organisms A mutation is a change in an organism s DNA that can be passed on to other cells or offspring There are many different kinds of mutations that are categorized by where they occur We will look at somatic and germline mutations point and chromosomal mutations and spontaneous and induced mutations Slide 3 In a singlecelled organism any change in the DNA will be passed on to its offspring when the cell divides and gives rise to two new cells because each daughter cell receives an exact copy of the DNA For multicellular organisms two different types of mutations may arise Somatic mutations occur when the DNA in a non gamete cell is altered These mutations are passed on to daughter cells when the original cell divides during mitosis Somatic mutations may adversely affect the organism but cannot be passed on to the organism s offspring Skin cancer is an example of a somatic mutation Germline mutations are found in gametes or cells that give rise to gametes These mutations can be passed on to offspring but do not adversely affect the parent Down Syndrome when a gamete receives three copies of chromosome 21 is an example of a germline mutation Slide 4 Point mutations involve an alteration of a single base in a DNA molecule The rst of the 4 types of point mutations is called a silent or synonymous mutation Recall that the genetic code is redundant that is there may be more than one codon that codes for a specific amino acid For example there are four codons for leucine two codons for glutamic acid three stop codons and so on A silent mutation is one in which a base is changed but the resulting mRNA still codes for the same amino acid These mutations have no adverse effects on the organism because the conect protein is still synthesized Silent mutations are very useful in phylo genetics as we will see later in the course Slide 5 Missense mutations occur when a base in the DNA is changed resulting in a codon for a different amino acid The resulting polypeptide has one incorrect amino acid in its sequence These mutations usually have consequences for the organism because the resulting protein may not have the correct shape and therefore may not function correctly In many cases missense mutations cause a protein to function less efficiently than the correctly formed protein so an organism may be able to survive with this type of mutation Sickle cell disease is an example of a missense mutation Slide 6 Nonsense mutations have more serious consequences for an organism In nonsense mutations a base is changed such that a stop codon is inserted into the mRNA sequence Translation terminates prematurely leaving a truncated polypeptide sequence that may not form a functional protein The organism may be left without a protein that is essential to life Slide 7 Frameshift mutations involve the insertion or deletion of a base in the DNA sequence Remember that codons are like a series of 3letter words Inserting an extra letter in or deleting a letter from the sequence will move all of the other letters over one but the translation machinery is still going to read the sequence three letters at a time All of the codons after the insertion will code for different amino acids and the resulting polypeptide sequence will essentially be random This type of mutation also has serious consequences for the organism because essential proteins may not by synthesized Slide 8 There are also 4 types of chromosomal mutations 7 mutations that involve pieces of a chromosome rather than just a single base A deletion is exactly what it sounds like 7 part of the chromosome breaks into two pieces a segment of the chromosome is lost and the remaining pieces join together This type of mutation can have consequences similar to those arising from a frameshift mutation The 3letter codons will be out of register and will code for the wrong amino acid sequence Slide 9 When a chunk of a chromosome gets deleted as in the last slide what happens to it When homologous chromosomes break at different points and reconnect with the wrong partners as in this example one chromosome ends up with a deletion while the other has a duplication Slide 10 Sometimes a deleted piece of a chromosome will be ipped over before it is reinserted into the chromosome Now part of the genetic code is running in the opposite direction Any resulting protein would be seriously altered and probably non functional This type of mutation is called an inversion Slide 11 That broken piece of chromosome may meet another fate When a segment of chromosome breaks off one chromosome and is reinserted into a different chromosome translocation has occurred The example here shows a reciprocal I translocation N n 39 have 39 J segments This type of mutation can cause problems during meiosis Slide 12 How do all these types of mutations arise Spontaneous mutations occur because DNA replication while extremely accurate is not perfect Instability in the chemical structures of the nucleotide bases can lead to errors in base pairing during DNA replication Although proofreading catches most of these errors some slip by Chromosome breakage leading to translocations and inversions can occur during meiosis also giving rise to germline mutations Mutations may be induced that is they may be caused by some environmental factor that alters the DNA It is pretty common to hear that certain chemicals are carcinogenic Usually the reason they are carcinogenic is that they are also mutagenic or mutation causing These types of chemicals may alter the base pairing properties of the nucleotide bases or interfere with a base s ability to pair at all Different types of radiation such as Xrays and ultraviolet radiation are wellknown mutagens and are sometimes used in genetic experiments to induce mutations Slide 13 Mutations are occurring inside our bodies every day The frequency of mutations in DNA replication is about 1 mutation in 104 base pairs but proofreading and repair reduce that frequency to about 1 mutation in 109 base pairs Still with all the cells in our bodies and the rate at which they divide at least during some parts of our lives that seems like a lot of mutations Why aren t we all Xmen Remember that we have an enormous amount of DNA in each of our cells but not all of it contains genes that are expressed Some parts of our DNA simply don t contain genes while other parts may contain genes that aren t switched on Mutations being random often occur in the parts of our DNA that don t contain genes Also due to the redundancy in the genetic code many mutations are silent and don t affect protein synthesis Mutations are important in evolution because they provide genetic variability on which natural selection can act Remember that mutations are random 7 some are advantageous many are neutral but many are harmful to an organism Harmful mutations are usually lethal and less likely to be passed on to the next generation If the mutation provides an advantage for the organism it can be passed on to subsequent generations eventually becoming part of the gene pool for the species Natural selection however is not random and selects the individuals best suited to their environment An Overview of Differentiation and Morphogenesis Slide 2 Take a moment and think of any type of organism What did you think of A human A tree A sh A bacterium Whatever type of organism you thought of when you visualized it in your head it had a particular shape correct Virtually all types of organisms have a particular shape or morphology This is true whether you are considering different types of mammals plants algae or even prokaryotes As organisms develop their shape or morphology also develops in a process called morphogenesis Morphogenesis shapes multicellular organisms their tissues and organs and even the individual cells of singlecelled organisms Morphogenesis is a highly regulated process although it is more exible or plastic in some types of organisms than others compare plants to humans for example Even with plasticity however there are basic developmental processes in different organisms that hold true pretty much all of the time Humans for instance always develop with two eyes and a nose in the middle of their face two arms connected to their shoulders and two legs connected to their hips Even many bacteria though singlecelled always develop the same way 7E 001139 always develop as rodshaped cells Leptospira always develop as spiralshaped or coiled cells But what are the mechanisms that are responsible for morphogenesis What processes do we have to thank for not being born with eyes on the bottoms of our feet Slide 3 Morphogenesis is controlled at the cellular level in large part due to a process called cell differentiation Cell differentiation refers to a cell taking on its mature form and role for an organism A cell becomes differentiated by producing specific proteins from the DNA template that allow it to develop into its mature form Further in their mature form cells produce proteins that are specific to the cell s role in the organism As an example compare your kidney cells your liver cells your muscle cells and your blood cells All of these cells ultimately came from the same zygote that you started out as yet through the process of differentiation they have developed to perform very specific functions inside of your body They perform their functions by producing and using specific proteins coded for in your DNA Slide 4 At this point you might be wondering if morphogenesis controls the development of the shape of organisms and cell differentiation greatly affects morphogenesis what processes control cell differentiation As we will see in the following lessons cells receive signals from their internal and external environment that affect what genes in their DNA are turned on and what genes are turned off at specific times A cell s communication with its environment followed by the selective transcription of genes allows cells to differentiate and organisms to develop Cell signaling involves a multitude of chemical reactions and cell differentiation is only one possible outcome of these reactions There are completely differentiated cells in our bodies that constantly receive and respond to signals For example fullydifferentiated pancreatic cells still respond to the signal of increased levels of sugar in the blood This signal sets off a number of other signaling pathways that lead to the production of enzymes that help you metabolize the sugar you are ingesting Slide 5 In many organisms the genes involved in development are organized in a hierarchy Certain genes act early in development and are responsible for turning on other genes that act slightly later in development Those genes in turn are in part responsible for turning on yet other developmental genes that act yet later in development This hierarchical organization of genes is referred to as a regulatory cascade Slide 6 As we move through the following lessons on cell differentiation and morphogenesis our focus will largely be on the cell differentiation and morphogenesis processes as they occur specifically in several types of organisms such as humans the fruit y Drosophila melanogaster and the mouseear cress Arabidopsis thaliana These organisms represent both classic and contemporary examples of differentiation and morphogenesis As research progresses however it is also becoming clear that the pathways present in these organisms are found in large numbers of related organisms and can give important insight into the evolutionary histories and patterns of many forms of life Biological Membranes Slide 1 Biological Membranes Slide 2 Biological membranes play several roles that are essential to life Membranes are active structures surrounding cells and most eukaryotic organelles such as the endoplasmic reticulum the Golgi apparatus vacuoles and the nucleus Membranes aid in the regulation of the internal environments of cells and organisms by controlling what materials move into and out of cells and organelles and often are important sites of chemical reactions and energy transformations Slide 3 Membranes are often described by the uid mosaic model According to the uid mosaic model membranes are largely composed of a fluid or exible bilayer of lipids which contains a mosaic of other types of molecules such as proteins and carbohydrates The uidity of the lipid bilayer allows many of the proteins and carbohydrates associated with the membrane to move around to different locations on the surface of the cell or organelle Slide 4The most abundant molecules in biological membranes are a type of lipid called phospholipids Phospholipids have both hydrophilic heads and hydrophobic tails Each of these two regions interacts differently with the aqueous environment normally found in and surrounding cells Slide 5 See the arrangement of the different parts of the phospholipids in relation to their watery environment The hydrophilic heads of phospholipids form hydrogenbonds with water while the hydrophobic tails aggregate together due to nonpolar interactions These different regions in turn give stability to membranes and prohibit all but small uncharged molecules from moving directly through the lipid bilayer In addition the separation of the hydrophilic faces of the membranes by a hydrophobic interior prevents any ip op of molecules from one side of the membrane to the other This allows the interior and exterior sides of a membrane to differ in composition and function to some degree Slide 6While membranes are composed primarily of phospholipids their lipid composition may vary For example the fatty acids that make up the hydrophobic tails of the phospholipids can be either saturated or unsaturated The ratio of saturated to unsaturated fatty acids may vary over time in a membrane This can help maintain the uidity of membranes at different temperatures In addition cholesterol may account for up to 25 of the lipid composition of membranes Slide 7 Proteins and carbohydrates also play important roles in membranes Typically membranes contain about 1 protein molecule for every 25 lipid molecules although proteins may account for nearly 50 of membrane composition in some cases Membrane proteins are generally of two types peripheral and integral Peripheral membrane proteins are loosely associated with and active on only one side of membranes Peripheral proteins may be bound to the hydrophilic heads of the membrane phospholipids or to segments of integral membrane proteins that extend outside of the membrane Slide SIntegral membrane proteins are active on one or both sides of a membrane In either case these proteins are at least partly embedded in the hydrophobic interior of the membrane Some integral proteins span the membrane from one side to the other Note that since these proteins span the membrane they must have both hydrophilic and hydrophobic regions Both integral and peripheral proteins associated with membranes may be active in transporting molecules across the membrane in recognizing chemical signals or as enzymes involved in chemical reactions such as the reactions of photosynthesis and respiration Slide 9Carbohydrates account for less of the composition of membranes than do lipids or proteins but nonetheless play important roles for the cell or organelle Membrane carbohydrates are typically short polysaccharides covalently linked to either membrane lipids or membrane proteins When a carbohydrate is linked to a membrane lipid this structure is referred to as a glycolipid When a carbohydrate is linked to a membrane protein this complex is called a glycoprotein Note that the polysaccharide portion of the glycoprotein in this illustration consists of only several monosaccharides Both glycolipids and glycoproteins play important roles in communication between the cell and its environment This usually involves the binding of chemical signals in the environment or the binding of molecules on the surfaces of adjacent cells Metronome of Genetic Variation Slide 2 When we use the term genetic variation what exactly are we talking about Genetic variation refers to differences in the sequences of nucleotides that make up the DNA of different organisms Genetic variation occurs between different species and between different populations and individuals of the same species Slide 3 Ultimately genetic variation comes from mutations Remember that mutations technically are heritable changes in the DNA of organisms As we learned earlier in the semester while mutations occur randomly in DNA not all mutations are equal Some mutations have no effect at all on the proteins that an organism produces This may be either because the mutation occurs in a noncoding region of the DNA or because a codon is changed but still codes for the same amino acid On the other hand some mutations can have significant effects on the protein produced and even on the organism that is producing it Remember as an example the single mutation in the 5 hemoglobin gene that can result in sickle cell anemia Because different mutations have different effects on organisms it should not be too surprising that they have different evolutionary fates In general mutations with negative or deleterious effects are removed from populations by natural selection Beneficial mutations are often fixed into the gene pool of r r 39 quot Neutral quot with little or no affect tend to accumulate very slowly over time Slide 4 While different types of mutations are fixed or lost from populations at different rates mutation rates themselves are stable over time That is to say that mutations occur with great regularity much like the ticking of a metronome We refer to this regular occurrence of mutations over evolutionary time as the metronome of genetic variation Think about it mutations are occurring in the cells of our bodies and in the cells of all other types of organisms at a relatively regular rate 7 tick tick tick tick At some point a mutation will occur that has extremely negative effects on an organism As a result the organism might die before it reproduces and the mutation is immediately removed from the population Tick tick tick tick Alternatively as the metronome ticks away a mutation might occur that confers some type of advantage As a result an organism might reproduce effectively and pass on the new allele to further generations Mutations occur regularly but how they are treated in an evolutionary sense depends on the magnitude and direction of change they represent for the fitness of the organism Slide 5 In an evolutionary sense one of the most significant types of mutations is called gene duplication Gene duplication technically can occur at many different levels from the duplication of part of a gene to the duplication of an entire gene to the duplication of the entire genome In fact duplication of the entire genome has been an important process in speciation particularly among plants and some amphibians Some types of such polyploidy can give rise to reproductively viable individuals because all of the chromosomes are duplicated It should be noted however that in the majority of cases large changes to an organisms genome have catastrophic effects leading to severe defects or death Individuals that ca1ry duplicate copies of single or several genes however often do survive The extra copies of a gene generally continue to function like the original gene ensuring that there will always be plenty of that gene product You might also imagine though that accumulating extra copies of a gene also frees the copies to some degree from selective pressures as long as at least one copy remains functional As a result copies may accumulate mutations fairly freely In some cases so many mutations may accumulate that the copies become nonfunctional pseudogenes Alternatively a copy may accumulate mutations to the point that it acquires a new function Slide 6 One of the strongest lines of support for the importance of gene duplication in evolution is the presence of gene families Gene families are thought to have come about by gene duplication followed by mutation This illustration shows the hypothesized evolution of one such gene family the globin family The globin family contains several genes that code for different types of myoglobin and hemoglobin molecules in vertebrates Myoglobin the oldest of member of the globin family stores oxygen in muscles Hemoglobin of course carries oxygen in the bloodstream The different polypeptides that make up hemoglobin and myoglobin appear to have evolved by gene duplication from a single original myoglobinlike gene Presently in humans there are several types of 39 39 39 39 and J g39 39 39 39 39 produced that are essential to our development and survival because they are produced specifically in different tissues and at different stages of development This demonstrates the importance of gene duplication in evolution Slide 7 Gene duplication has likely also played a significant role in the expansion of genome size over evolutionary time In other words genome size differs between organisms to some degree because of gene duplication The graph on the left shows a comparison of the number of coding genes in a variety of organisms As we might expect it takes more genes to keep a relatively complicated organisms like a pufferfish going than it does to keep a relatively simple organism such as yeast on top of its game Although there are many exceptions to this rule in a broad sense we find this type of pattern to hold true the more complex the organism from singlecelled to multicellular from prokaryote to eukaryote the more genes it uses to direct its development respond to signals reproduce and so on The graph on the right shows that total genome size for many organisms is out of proportion to the number of genes that are actually expressed While a higher vertebrate like a mouse or a human has about 20 times as many genes as a bacterium its total genome size measured in base pairs may be tens of thousands of times larger than a bacterium s Clearly there must be an enormous amount of noncoding DNA in the genomes of some organisms Researchers are just beginning to understand the purpose of some of the noncoding DNA It is likely however that at least some of this noncoding DNA arose from duplication processes Slide 8 We have now looked at genetic variation on several levels from differences in single nucleotides to differences in entire genomes All of this genetic variation ultimately came from mutations Mutations do not work alone though to generate all of the genetic variation that we see In fact the variation that results from mutations is maintained and even ampli ed in species in a number of ways Sexual reproduction is one of these ways As we have discussed previously the gametes found in sexually reproducing organisms are produced by meiosis During meiosis crossing over between homologous chromosomes and the independent assortment of chromosomes occurs This results in genetically variable gametes Then after scrambling around the genetic material of an individual by meiosis that genetic material is combined with material from another individual The end result of sexual reproduction is that offspring differ from their parents and from each other providing genetic and phenotypic variation for natural selection to work with Slide 9 Sometimes the genetic variation in a species is spread out in various distinct populations or subpopulations Plants for example are especially likely to respond to different environmental conditions such as soil type microclimate and grazing The traits that are selected for in one location then may differ from the traits selected for in another so that individual populations are adapted to differing environments The different selective pressures in each environment therefore contribute to the maintenance of the genetic variability of the species as a whole Slide 10 Finally natural selection can in some cases preserve genetic variation by maintaining different forms or polymorphisms of a species This occurs when the fitness of a certain form of a species is linked to the fitness of other forms of the same species For example it is possible to find different coloration patterns within the same geographic region in individual species of garter snakes Some members of the species have prevalent spotting while others are striped In turn the different forms or polymorphisms are linked to different behavior patterns Striped garter snakes avoid predation by slithering away quickly from predators Spotted garter snakes on the other hand depend on remaining still and camou aged to avoid predators In this species of garter snake both coloration patterns are maintained because they both are effective in helping the snakes avoid predators In this sense both patterns contribute to the overall survival of the species In other words two patterns work better than one This type of selection where different polymorphisms of a species are maintained is called frequencydependent selection Pattern Formation and Morphogenesis Slide 1 Pattern Formation and Morphogenesis Slide 2 As multicellular organisms develop patterns become evident in the spatial organization of tissues and organs Spatial organization is relatively easy to describe visually in many cases In humans for example the heart always develops within the chest cavity the kidneys always develop on either side of the lower back and so forth The molecular interactions that cause such patterns on the other hand are often much more dif cult to determine Fundamentally developmental pattern formation is controlled at the genetic level 7 speci c genes code for proteins involved in development As we have seen the regulation of these genes and their phenotypic effects are controlled by hierarchical developmental genes which are thought to be activated by a variety of environmental cues such as the signal transduction that occurs at the time of fertilization Recall that after the moment when two gametes fuse a series of events including rapid cellular division and subsequent shapechange in the developing embryo result in a mature embryo where most cells are generally destined to be of one type or another and the basic tissues and organs are already de ned Let s focus now at some of the processes of pattern formation and morphogenesis that occur later in embryo development and during the adult life of an organism that cause more phenotypic change Slide 3 The development of the cells and tissues of plants and animals is often in uenced by their location in the organism In such cases cells receive positional information in the form of different chemical signals that direct development Chemical signals received by cells initiate signal transduction pathways which ultimately result in the differential expression of developmental genes Signals may be a variety of substances and may travel long or short distances within the organism Signals that travel only to neighboring cells usually have a localized effect Often times the cells that receive the initial signal send another chemical signal back to the cell This process of backandforth communication can be seen clearly in the development of the vertebrate eye As you can see in the gure there are two main groups of cells involved in eye formation The bulges of cells from the optic vesicle send signals to the neighboring cells that induce them to form a structure called the lens placode In turn the cells of the lens placode then induce the cells of the optic vesicle to form an optic cup This relay continues as the lens placode develops into a lens and eventually induces cells on the surface of the embryo to form a cornea This process of neighboring cells sending and receiving signals resulting in formational changes is frequently referred to as induction Slide 4 The avian wing provides another good example of how positional information can affect development The wings of birds develop from a bud of tissue on either side of the early embryo As the wings develop different chemical signals from three locations 7 the tip of the developing wing the wingbody junction and the surface of the wing 7 diffuse through the wing tissue As these signals originate from different locations their concentrations in different areas of the developing wings will differ The varying concentrations of these signals in turn signal each cell and tissue of the wing how to develop This assures that feathers muscles tendons and bones form in the appropriate locations Since these types of signals affect the physical shape or morphology of the wing over a relatively large distance and are based on differences in concentration of signals they are termed morphogens Slide 5 It is also important to note the role of apoptosis or programmed cell death in pattern formation As organisms develop certain cells such as those that comprise the webbing between the digits of early human embryos or chicken embryos are genetically pre programmed to die The selective death of cells often plays an important role in determining the final shape of different parts of organisms bodies It may help to think of it as a sculpting tool that removes tissue not normally present in the adult form So if webbing is present in vertebrate animals such as chickens salamanders and humans but is then removed by apoptosis what happens in the development in animals that retain the webbing Let s look at ducks as an example Scientists have determined that there is a mutation in a regulatory gene that controls the inhibition of apoptosis This gene called the Gremlin gene is expressed in the webbing of duck limbs but not chicken limbs and is assumed to be responsible for the presence of webbing in adult ducks Slide 6 You may think that organisms don t change much once they begin their lives as self dependent individuals For many animals this seems to be the case But for some animals particularly invertebrates and for virtually all plants dramatic phenotypic changes continue to take place throughout much if not all of the organisms life You have heard of the classic example of caterpillars changing into butter ies This is an example of a process called metamorphosis which is really used to describe any major change in form from one developmental stage to the next What s particularly interesting in the case of animals that undergo metamorphosis is that the adult form is often different in both structure and function So how does this change occur Many scientists speculate that what actually happens is a dedifferentiation of the cells in the larvae In essence the cells of the caterpillar backup developmentally and can therefore receive signals to become something different These cells do not back up completely For instance those cells destined to be on the surface of the organism in the embryo usually remain on the surface in the adult form after metamorphosis is complete Slide 7 This process of cellular dedifferentiation is not unique to organisms that undergo metamorphosis Consider the examples of a plant and a salamander These organisms are both able to heal and sometimes regrow structures when damage occurs Creating new growth involves cells at the point of injury dedifferentiating into more poten cells These cells which are usually multipotent receive new growth signals and can replace the structure that was damaged If an herbivore devours a portion of a plant say a flower most plants can either grow another ower in its place or replace the ower with some other type of plant tissue If a predator catches a salamander and rips its limb off during an escape dedifferentiated cells create a new limb Slide 8 The ability to change after the early stages of development and pattern formation have been completed is called phenotypic plasticity Having a reserve of cells capable of dedifferentiation is a handy way of maintaining phenotypic plasticity but is not the only way in which organisms change once they have reached their adult forms In animals there are examples where different temperatures can result in a fish zygote developing into a female rather than a male Some species of moths develop into a specific color based on which season the larvae hatch in But plants are often considered the master of morphing Unlike animals plants do not sequester specific cells to become the only reproductive part of the organism in other words sperm and egg are not the only part of a plant that can create new growth Plants have undifferentiated cells that can actively grow and divide throughout their life These meristems as they are called can form new stems roots leaves and owers as long as the plant lives So when a plant encounters a particular environmental change the response can lead to much larger phenotypic responses than other types of organisms can muster As a starter most plants can grow towards light towards the ground or any other structure and they can extend their roots to reach water resources Slide 9 It should be clear now that development begins with the moment two gametes fuse in the process of fertilization and does not stop when an organism hatches germinates or is born There are many other processes of pattern formation and morphogenesis that must occur for the organism to reach its adult form Take a moment to think about the similarities and differences in the development and pattern formation of the multicellular organisms we have discussed here Another thing to consider at this point is how cell signaling differential gene expression and cellular differentiation are involved in the process of developing a complete organism It s really quite amazing
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