Bio 1001A: Why evolution is true

envelope

outer glycoprotein layer surrounding the capsid of some viruses, derived in part from host cell plasma membrane.

capsid

the protective layer of protein that surrounds the nucleic acid core of a virus.

Evolution of AZT resistance

•mutations-->variation in AZT-resistance •AZT-resistance passed from 'parents' to 'offspring' •not all virions reproduce •when AZT is present, some forms (AZT-resistant) are more likely to reproduce than others (AZT-susceptible) •viral population changes over time

lecture 2 slide 3

" Average life expectancy decreased as a result of the HIV epidemic " HIV hit Africa much harder than any other place in the world

slide 15 lecture 2

" Blue=ones that are resistant to drug " A parent virion is going to give rise to daughter viral particles that happen to become more resistant; genetic evolution

Natural selection results in adaptation, not perfection

" Constrained by available genetic variation " Trade-offs betn competing demands (energy that is used for developing your immune system is energy you don't have available for reproduction; finite energy) " Environments vary over time (populations might be well adapted to environments that prevailed in the past but global warming is happening very fast so organism might not be able to adapt) " Environments vary over space " Evolutionary arms races with other organisms

lecture 2 slide 9 HIV lifecycle: hijack immune cells

" Extracellular form of virus: virion " Anti-retroviral therapies (ARTs) inhibit virus-specific enzymes " We can use this info to make drugs " Best way to make anti-viral drugs is to identify which steps the viruses make with which steps humans don't make " Reverse transcription is very error prone so there's a lot of mutations that occur from this step, this creates a genetic variationí raw material for genetic evolution -Virion (viral particle) enters host cell -Reverse transcriptase --> viral DNA -Integrase splices viral DNA into host DNA -Transcription, translation, new virions assemble and enter circulation -Immune system collapses

falsifiability

" Falsifiability means that a statement can be tested to see whether it's true or false " Matters of opinion cannot be falsified (subjective stuff) " Statements like "x exists" are often not falsifiable " "Some" paper is white is not falsifiable because maybe there's paper on mars that you haven't found yet ("Some x" is not falsifiable)

slide 20 lecture 2

" If we treat patients with drugs one at a time it is not enough

lecture 2 slide 8 Retroviruses disobey central dogma of molecular biology

" In order to replicate itself, the retrovirus takes this step: reverse transcriptase (no proof reading) (green arrow from RNA to DNA)

slide 14 lecture 2

" People that became resistant to AZT (took AZT for a long time there was a gradual change), the resistant form changed shape and could no longer pick up AZT molecule so the drug did not work

lecture 2 slide 5

" SIV is endemic in chimpanzees, but became epidemic (and then pandemic) as HIV in humans " HIV is epidemic: increasing population catches the diseases " HIV is also pandemic because it has a global geographic spread " The red tips indicate the HIV that infects humans; shows the spill over from chimpanzee to humans " Why did we get HIV from chimps?

lecture 2 slide 10

" To minimize side effects, target the virus-specific processes and enzymes

lecture 2 slide 7

" Viruses are weird " Retroviruses are associated with HIV-they have an RNA based genome, other cellular sources have DNA as their genome " Anti-viral drugs often have serious side effects...why? Anything you do to kill the virus is going to interfere with the host cell. Viruses use the host's machinery to do everything, they are parasitic.

lecture 2 slide 6

" Where do viruses fit in the tree of life? The vines that go around it because viruses are technically not alive but they depend on all sources of cellular life

lecture 2 slide 4

" Zoonotic disease: spill over from nonhumans to humans " Usually relatively harmless in the original (nonhuman) host; much more harmful in their new host (us) " The next big disease is probably going to come through zoonotic diseases " Zoonotic diseases are endemic " HIV came from another species in which a similar virus was endemic

three aspects of fitness that are important to understanding how evolution works

(1)Fitness is a relative concept. It doesn't matter in absolute terms how many offspring an individual leaves, only that it leaves more than others in the population. (2)A trait is only valuable if it increases fitness. We tend to think of traits such as being faster, stronger, bigger as valuable; however, they are only valuable, and thus selected for, if they increase reproductive success. (3)The traits that increase fitness may change. If the environment changes (e.g., climate change), those traits that previously increased fitness may not be advantageous any longer.

The Steps in HIV Infection of a Host Cell +draw diagram from tb

(refer to tb diagram)

lecture 2 slide 11+12 AZT

-AZT is a nucleoside analog - shaped ALMOST like thymidine -AZT solves the synthesis of DNA

slide 13 lecture 2

-People who were on AZT for a while became resistant and the viruses kept on replicating

Which is better for avoiding evolution of multi-drug resistance: Treat each patient with several drugs at the same time? Treat with one drug at a time, switch treatments only when necessary (after virus becomes resistant)?

A

homology

A characteristic shared by a set of species because they inherited it from their common ancestor.

polyhedral viruses +draw diagram

A virus in which the coat proteins form triangular units that fit together like the parts of a geodesic sphere.

bacteriophages/phages +draw diagram

A virus that infects bacteria. Also referred to as a phage.

how are viruses classfied

Although they are not considered to be alive, viruses are classified into orders, families, genera, and species using several criteria, including virus size and structure, genome structure (RNA or DNA, single stranded or double stranded), and how their nucleic acid is replicated. More than 4000 species of viruses have been classified into more than 80 families. The family names end in -viridae (Table 22.1) and may refer either to the geographic region where the virus was first discovered or to the structure of the virus. For example, Coronaviridae, the family to which the influenza virus and SARS (Severe Acute Respiratory Disorder) belong, is named for the "crown" of protein spikes on the capsid, as shown in the photomicrograph at the start of this chapter (corona = crown). Like some bacteria, some viruses are named for the disease they cause; these names can be one or two words, for example, herpesvirus or Ebola virus. Each type of virus is made up of many strains, which are differentiated by their virulence.

vestigial structures

An anatomical feature of living organisms that no longer retains its function.

fitness

An individual's reproductive success.

viral structure

Body plans of viruses video and figure 22.1 The nucleic acid genome of a virus may be either DNA or RNA and can be composed of either a single strand or a double strand of RNA or DNA. Viral genomes range from just a few genes to over a hundred genes; all viruses have genes that encode at least their coat proteins, as well as proteins involved in regulation of transcription. Genomes of *enveloped viruses* also include genes required for the synthesis of envelope proteins. Some viral genomes also include virus-specific enzymes for nucleic acid replication. Most viruses take one of two basic structural forms, helical or polyhedral. In *helical viruses* the protein subunits assemble in a rodlike spiral around the genome. A number of viruses that infect plant cells are helical. In *polyhedral viruses*, the coat proteins form triangular units that fit together like the parts of a soccer ball. The polyhedral viruses include forms that infect animals, plants, and bacteria. In some polyhedral viruses, protein spikes that provide host cell recognition extend from the corners, where the facets fit together. Both helical and polyhedral viruses can be enveloped in a membrane derived from the host's membrane. In enveloped viruses, proteins synthesized from the viral genome in the host cell are transported to and embedded in the membrane before the virus particle buds through the host cell. These proteins allow the virus to recognize and bind to host cells.

lecture 2 slide 2

Deaths caused by HIV and AIDS are decreasing

what IS the theory of evolution?

Descent with modification from a common ancestor. Evolution happens. allele frequencies in a population change from one generation to the next -All life is related through common ancestry. -Speciation: Lineages diverge into multiple daughter lineages -Evolution is variational, not transformational. Populations evolve; individuals do not -Gradualism and transitional forms -Selection generates adaptation, and explains much evolutionary change (but not all). Selection is not the only mechanism that can cause evolution

Why does a new vaccine have to be developed each year?

One reason for the success of this virus is that its genome consists of eight separate pieces of RNA. When two different influenza viruses infect the same individual, these RNA pieces can assemble in random combinations derived from either parent virus. The new combinations can change the protein coat of the virus, making it unrecognizable to antibodies developed against either parent virus. Being "invisible" to these antibodies means that new virus strains can infect people who have already had the flu caused by a different strain, or who had flu shots effective against only the parent strains of the virus. Random mutations in the RNA genome of the virus add to the variations in the coat proteins that make previously formed antibodies ineffective.

So What Actually Is Natural Selection?

Plant and animal breeders have applied the basic facets of inheritance from parents to offspring for thousands of years. By selectively breeding only those individuals with desired characteristics, they enhanced those traits in future generations. Although the mechanism of heredity was not yet understood, Darwin understood that selective breeding could produce for example, bigger beets, plumper pigs, and prize-winning pigeons. A good example of the power of selective breeding is the development of corn (maize). Corn is actually derived from an ancient Mexican grain called teosinte. Over thousands of years, farmers selected the teosinte kernels for replanting that were the largest, easiest to eat and most exposed on the cob. The result of this selective breeding is that, today, a typical cob of corn looks nothing like teosinte (Figure 16.9). Darwin referred to selective breeding as *artificial selection*, since humans were selecting the characteristics they wanted in the offspring by choosing parents with those traits. Darwin didn't see why a similar process of selection couldn't also work in nature, but the issue was the mechanism: how would it work? Darwin started to understand that a major aspect of evolutionary change must reside within a *population*—a group of individuals of a species that live together in a specific place. By understanding this, Darwin could see how Lamarck was wrong. Individual organisms don't evolve over their lifetime. But a population could. It is the population that has the capacity to change from one generation to the next. Darwin thought about two specific attributes of a population: its size and the amount of variation within it. First, Darwin observed that, while organisms have a huge capacity to reproduce, limiting resources constrain the size of a population. From this, Darwin hypothesized that individuals within the population compete for limited resources (Figure 16.10). Second, Darwin observed that individuals within a population are not identical but differ in certain traits (e.g., size, colour, behaviour), and that these traits tend to be inherited. This in turn led to Darwin hypothesizing that organisms with traits that allow them to outcompete others for limiting resources would leave more offspring. For Darwin, this thinking came together into a single idea, natural selection: individuals with certain inherited traits are better able to survive and reproduce than individuals without those traits (Figure 16.10). Individuals in the population that lacked such traits would die leaving fewer, if any, offspring. Thus, advantageous traits would become more common in the next generation. In other words, from generation to generation, the mechanism that is causing a population to change, or evolve, is nature selecting for (But keep in mind, this is a purposeless process. It's not like nature has some "grand plan" that species are marching towards. Rather, individuals with an advantage in a given environment do better) a set of traits that gives an individual an advantage over others in the particular environment that the population inhabits (Figure 16.11). What is remarkable about natural selection is that Darwin had discovered a mechanism for evolutionary change that no one had ever envisioned, much less documented.

artificial selection

Selective breeding of animals or plants to ensure that certain desirable traits appear at higher frequency in successive generations.

where did viruses come from?

Several different hypotheses have been proposed. Currently, there's no real consensus as to which hypothesis about viral origins is correct. Some biologists have suggested that, because viruses can duplicate only by infecting a host cell, they probably evolved after cells appeared. They may represent "escaped" fragments of DNA molecules that once formed part of the genetic material of living cells or an RNA copy of such a fragment. The fragments first became surrounded by a protective layer of protein with recognition functions, and then these fragments escaped from their parent cells. As viruses evolved, the information encoded in the core of the virus became reduced to a set of directions for producing more viral particles of the same kind. More recent hypotheses suggest that viruses are very ancient, with virus-like particles predating the first cells. The first viruses originated from the "primordial gene pool," the pool of RNA that is thought to have been the first genetic material.

natural selection

The evolutionary process by which alleles that increase the likelihood of survival and the reproductive output of the individuals that carry them become more common in subsequent generations.

biogeography

The study of the geographic distributions of plants and animals.

latent phase

The time during which a virus remains in the cell in an inactive form.

Viruses, Viroids, and Prions: Infectious Biological Particles

Viruses, viroids, and prions, non-cellular, elegant in their simplicity, highjack the machinery of cells of both prokaryotes and eukaryotes.

helical viruses +draw diagram

a virus in which the protein subunits of the coat assemble in a rodlike spiral around the genome.

enveloped viruses +draw diagram

a virus that has a surface membrane derived from its host cell.

"Mutation proposes, selection disposes"

genetic variation is continuously arising, regardless of environment changing the environment affects the fate of genetic variation

lecture 3 slides 13-22

look on word notes sept 18

You can fool most of the virions most of the time...

High error rate for reverse transcriptase creates variation in viral population vary in affinity for nucleoside analogs like AZT Using antiviral drugs provides an advantage to drug-resistant variants When antiviral drugs are used, drug-resistant variants increase in frequency

why are some viruses good?

However, not all viruses are pathogens. Many viruses actually benefit their hosts; for example, infection by certain nonpathogenic viruses protects human hosts against pathogenic viruses. The "protective" viruses interfere with replication or other functions of the pathogenic viruses. Some viruses also act to defend their host cells. For example, one of the primary reasons that bacteria do not completely overrun this planet is that they are destroyed in incredibly huge numbers by viruses known as bacteriophages, or phages for short (phagein = to eat). Viruses also provide a natural means to control some insect pests, such as spruce budworm. Viruses are vital components of ecosystems and may be the dominant entity in some ecosystems, such as the oceans. We don't yet fully understand their roles in these ecosystems, but it is clear that they affect nutrient cycling through their effects on prokaryotic organisms. For example, in certain regions of the ocean, a few genera of cyanobacteria dominate the marine phytoplankton, making major contributions to global photosynthesis. Bacteriophages infect these cyanobacteria, causing high levels of mortality, thus influencing cyanobacterial population dynamics as well as the release of nutrients from bacterial cells. But these viruses also help keep photosynthesis going in their cyanobacterial hosts, as recently discovered by Nicholas Mann and colleagues at the University of Warwick. One of the proteins that make up photosystem II is very susceptible to light-induced damage and so is constantly being replaced by newly synthesized molecules. As long as the cell can make new protein quickly enough to keep up with damage, photosynthesis can continue, but if the rate of damage to photosystem II exceeds the repair rate, the rate of photosynthesis will drop. When these bacteriophages infect cyanobacteria, they shut down their host's protein synthesis. Without continued synthesis of the photosystem protein, photosynthesis should slow down following infection; but it doesn't. How is the photosynthetic rate maintained? Mann and his colleagues found that the virus's genome includes genes for this protein; expression of these viral proteins enables the repair rate to keep up with light-induced damage, allowing the cell to photosynthesize. Although the virus is doing this for "selfish" reasons (i.e., to ensure that its host has sufficient resources for the virus to complete its life cycle), the outcome of this association is that much of the carbon fixed on Earth may be facilitated by virus-controlled photosynthesis.

The Source of Variation in a Population Is Random Mutation

Many of the traits possessed by an organism are inherited because they have a genetic basis: they are coded by DNA. It is the variation in DNA sequence that ultimately gives rise to individuals within a population having different inherited traits. While some traits (e.g., wrinkled versus smooth peas) result from variation in the sequence of a single gene, others (e.g., the shape of a finch's beak) are influenced by the variation in sequence of many genes. Although all organisms within a population have the same set of genes, the DNA sequence of any particular gene in any particular organism may be different due to past *mutation*—a random and heritable change in the DNA sequence. Mutations arise as an inevitable consequence of the imperfect nature of DNA replication as well as from the effects of certain physical, chemical, and biological agents. You can think of mutation as supplying the raw material for natural selection to work with—the differences in traits among organisms. It is critical to understand, however, that while mutations are the source of variation, they do not determine the path of evolution. Because mutations are undirected, they can occur anywhere in the genome: in essential genes required for life, or in a DNA sequence that has no function. Thus, some mutations are beneficial to an organism because they increase fitness. Other mutations may be harmful and lower fitness, while many others are "neutral," having no effect on fitness.

Influenza

Symptoms: runny nose, sneezing, coughing, sucking on lozenges, appears to have a feaver A respiratory illness caused by the influenza virus that can spread through coughing and sneezing. At any given time, 5-15% of the global populatio of people exhibit the symptos of influenza, and each year about 500,000 people die from influenza A. Recent research has shown that new strains of influenza A arise each year from just a few initial sources in East and southeast Asia and then spread around the world. As influenza viruses travel through populations around the world, they evolve, changing so much that the vaccines we developed in previous years are no longer effective, and new vaccines must be developed. Understanding the global pattern of influenza migration will help the World Health Organization to develop effective vaccines. Knowing which strains cause the initial outbreak in Asia allows scientists to formulate vaccines to target these strains, offering people in other regions some protection from the illness.

Why are viruses not on the tree of life? (characteristics of viruses)

That is because they lack many of the properties of life shared by all organisms and so are not considered to be living organisms. For example, viruses cannot reproduce on their own and they lack a metabolic system to provide energy for their life cycles; instead, they depend on the host cells that they infect for these functions. For this reason, viruses are infectious biological particles rather than organisms. So a virus, while able to evolve, is not a cell: it does not have cytoplasm enclosed by a plasma membrane, as do all known living organisms.

Darwin and the Galápagos Islands (Natural Selection Leads to Adaptation and Increased Fitness)

The Galápagos Islands are home to four distinct species of mockingbird (genus Nesomimus), which are found on specific islands of the group (Figure 16.12). During his visit to the Galápagos, Darwin collected mockingbirds from different islands, but it wasn't until he got back to England that someone pointed out that the birds from different islands were distinct species. Based on this work, Darwin developed the concept of descent with modification. It was clear to Darwin that the underlying similarity of the mockingbirds indicated that birds from all the islands shared a common ancestor (Figure 16.12a) but that, over time, each species had developed distinctly different traits (beak size and shape, coloration). The simplest scenario to explain this is that a popluation of one species of mockingbird came from mainland South America and colonized most of the islands at around the same time. Over thousands of years, the populations that developed on different island became less and less alike—their traits diverged. On each island, specific traits would become uniquely modified compared to the traits of birds inhabiting other islands. And all the species become distinct compared to the ancestral mockingbird species from the South American mainland. Darwin's work on mockingbirds would be complemented by even more detailed study of the many species of finches that inhabit the Galápagos Islands. The evolution of different species of birds on the Galápagos Islands is tied closely to the fact that the islands within the group have different habitats (food sources, microclimate) (Figure 16.12b), which resulted in natural selection favouring a different set of traits on one island compared to another. The inherited aspects of an individual that make it better suited to a particular environment than other individuals are referred to as adaptation. From generation to generation, a species becomes better adapted to a specific environment as a consequence of natural selection. The impact of Darwin's observations on the Galápagos Islands was that he extended his ideas about speciation in mockingbirds and finches to a broader sense of how evolution operates in all species across the globe. The underlying homology that huge numbers of species possess indicates that all life on Earth shares a common ancestor; and evolution leading to huge speciation over millions of years explains the tremendous diversity of life we witness on Earth today. Closely related to adaptation is the concept of fitness. Darwin characterized those individuals with the set of traits that led to greater survivorship and reproductive success as "fitter" compared to others. In the context of evolution, the term fitness describes an individual's reproductive success—an organism has higher fitness than another if it leaves more surviving offspring.

generation time

The average time between the birth of an organism and the birth of its offspring. or average difference in age between a parent and its offspring

treating and preventing viral infections

Viral infections are typically difficult to treat because viruses are, for much of the infection, "hidden" inside host cells and use host cell machinery to replicate (Somewhat ironically, the more genes a virus has (the more of its "own" proteins it travels with), the easier it is to design drug treatments for. Tiny genomes like HIV's are very challenging to treat because the virus uses host enzymes almost exclusively). These agents do not respond to antibiotics and other treatment methods. Research efforts have focused on development of vaccines and on preventing infection by viruses that cause serious or fatal diseases. As a result, many viral infections are allowed to run their course, with treatment limited to relieving the symptoms while the natural immune defences of the patient attack the virus. Some viruses, however, cause serious and sometimes deadly symptoms on infection; for these, the focus has often been on prevention through vaccine development (e.g., measles, polio). Viruses that use their own polymerases (e.g., RNA viruses such as influenza;Including retroviruses like HIV ... that is good news for us) provide more obvious targets, so researchers have spent considerable effort developing antiviral drugs to treat them. Many of these drugs fight the virus directly by targeting a stage of the viral life cycle.

Viroids and prions

Viroids and Prions Are Infective Agents Even Simpler in Structure than Viruses. Viroids, which infect crop plants, consist of only a very small, single-stranded, RNA molecule. Prions, which cause brain diseases in some animals, are infectious proteins with no associated nucleic acid.

What Is a Virus? Characteristics of Viruses

Viruses are non-living infective agents consisting of a nucleic acid genome (A genome is an organism's complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism) enclosed in a protein coat (capsid). Some capsids might be enclosed within a membrane, or envelope, derived from their host cell's membrane. Recognition proteins that enable the virus to attach to host cells extend from the surface of infectious viruses. The structure of a virus is reduced to the minimum necessary to transmit its genome from one host cell to another. Viruses reproduce by entering a host cell and directing the cellular machinery to make new particles of the same kind. Viruses Infect Bacterial, Animal, and Plant Cells by Similar Pathways. Viruses May Have Evolved from Fragments of Cellular DNA or RNA. Viruses may have evolved after cells and descended from nucleic acid fragments that "escaped" from a cell. +look at photo chapter 22 roadmap below 22.4 Different viruses vary tremendously in how much harm they do to the host (think of Ebola versus the common cold). Viruses also differ wildly in how fast they evolve. For this reason, some viral diseases can be prevented by a single dose of vaccine; others, like influenza, require a new vaccine each year; and others may never be candidates for vaccine development.