Biology UNIT 2 PDF

1.5 Million species - Scientists attempt to order the natural world by grouping and classifying all living organisms. As technology improves our classification improves hand to hand. - Darwin’s Theory of Evolution - Law can be improven but theory can not be imp...

1.5 Million species - Scientists attempt to order the natural world by grouping and classifying all living organisms. As technology improves our classification improves hand to hand. - Darwin’s Theory of Evolution - Law can be improven but theory can not be improven. - Organisms produce more offspring than can survive. Of the offspring that do survive, many will never reproduce. - Because more organisms are produced than can survive there is intense competition for limited resources, such as food, water, and shelter. - Natural Selection: Individuals that are best suited to their environment survive, reproduce, and pass their traits on to their offspring. - The species that are alive on Earth today are descended with modification from ancestral species that lived in the past Taxonomy: The branch of biology that classifies organisms and assigns each organism a universally accepted name. - Early Attempts at classification: - Organisms were first classified more than 2000 years ago by the Greek Philosopher, Aristotle: plants and animals. - Animal: he divided animals into three groups: Land, Water, and Air - Plant: Herbs, Shrubs, and Trees - The Problem: - Many organisms were placed in groups to which they had no real relationship with the other members of the group. - THe use of common names was very confusing. For example: catfish, jellyfish, shellfish. - Many new organisms were being discovered and needed to be classified. - Carlos saves classification - He classified system based on structural similarity, he thought that the organisms that looked alike were the most closely related - He placed an organism in a particular group and assigned it a scientific name. - This is called binomial nomenclature: the system of assigning a scientific name that consists of two parts. - He first divided all organisms into large groups that he called kingdoms. He based on two kingdoms: Plants and Animals - Then each subset was further subdivided until he had developed 7 levels of classification. - Kingdom - Phylum - Class - Order - Family - Genus  - Species - But recently we found level above the kingdom called a “domain” - The scientific name always consists of two words: - The genus and the species - All scientific names are in Latin. It is understood by all. - The Genus is capitalized but species is not - The two names are always written in italics or underlined. - Modern Taxonomy: Phylogeny - The evolutionary history of an organism - To show the evolutionary relationship between different groups of organisms, scientists construct phylogenetic trees. - Traditionally the morphology (structure) of the organism was the basis for its classification. Modern Taxonomy now takes into account more when attempting to classify an organism. - Morphology - Is classification based on the structure possessed by the organism - It is not the least important because of technology - Homologous structures are structures in different species that are similar because of common ancestry: ex: the bones found in the wing of a bird, the wing of a bat, the forearm of a human, and the flipper of a whale are homologous to one another. (similar structure but different function) - Analogous Structures - These are structures in different species that are similar in function but no in structure. Analogous structures are not derived from a common ancestor. (similar function different structure) - Vestigial Structures - A structure that is reduced in size and seems to be “left over” from a previous ancestor - Ex: Remnant of hip bone in whales are found in whales - Human Appendix and hip bone in whales - The fossil record gives us many clues as to the morphology of ancient species, but it is an incomplete record - Embryological Similarities - Similarities in embryological development provide evidence of phylogenetic relationships. - Some organisms show no similarities asd adults but are very, very similar as embryos. - On the basis of this shared embryological structure, reptiles, birds, and mammals are grouped together and are referred to as amniotes. - Cellular Organization  - Tctures provides evidence that organisms may be related. Ex: cell wall in plants - Biochemical Similarities - Similarities of chemical compounds found within cells can be used as evidence to show relationships between organisms. - A comparison between the proteins of two organisms serves as a “molecular clock” ; simple mutations occur all the time, causing slight differences in the DNA and the proteins being built. - When the proteins of two different organisms are compared, the number of differences in amino acid sequences is a clue as to how long ago two species diverged from a shared common ancestor - Evolutionary Relationships - Basically looking at common ancestors - Scientists now group organisms into categories that represent lines of evolutionary descent or phylogeny - Ex: 25 breeds of dogs all came from a wolf like ancestor - Genetic Similarities - Do the two organisms being compared have the same number of chromosomes? The same type of chromosomes? - Two organisms that bear no resemblance to one another anatomically may still be related to one another. Two different “looking” organisms may have similar genes in their DNA - Ex: humans have a gene that is the code for building a protein called myosin. This protein is a primary component of our muscles. Yeasts (which have no muscles) have the same gene. The gene in yeasts produces the same myosin protein as it does in humans. In yeasts, this protein is used to move materials around the inside of the cell - The more similar the DNA sequences of two species, the more recently they shared a common ancestor, and the more closely they are related. - The more two species have diverged from one another the less similar their DNA will be - Cladistics - Cladistics is a relatively new method of classifying organisms. - Cladistics identifies the characteristics of organisms that are evolutionary innovations - These “innovations” are new characteristics that arise as living organisms evolve over time - Cladistics uses features called “shared characters” and “derived characters” to establish evolutionary relationships.  -Shared character: a feature that all members of a group have in common. Examples include feathers in birds and hair in mammals. (common ancestry) - Derived character: a feature that evolved only within the group under. - An example of derived character might be the feathers in birds - Birds are the only animals to have feathers. It is therefore assumed that feathers evolved within the bird group and were not inherited from a distant ancestor. - Clades: - Term is used to describe a group of organisms that include an ancestor plus all of its descendants - Clades do not use the traditional Linnaean category names such as phylum, class or order. - Relationship between the organism in a clade can be represented by a diagram called a cladogram. That is what a cladogram is. A diagram that shows the evolutionary relationships among a group of organisms. - Kingdom Comparison - Barriers Between the species. What factors keep the species apart? - Species: breed, reproduce, offspring fertile, viable. - Barriers - Prezygotic - Before sperm meet egg - These barriers prevent fertilization from occurring; species remain isolated before mating or fertilization. - Types of isolation: - Temporal - Isolated in time - Behavior - Many organisms, especially in the animal kingdom, will not mate unless certain behaviors. - Mechanical - Physical Characteristics difference - Habitat - Geographical barriers - Many organisms simply do not come into contact with one another - gametic - Bullfrog eggs may be fertilized by the sperm of the leopard frog. The eggs develop to a point but do not survive. There is too much difference in the chromosome  - Postzygotic - After sperm meet egg - These barriers prevent hybrid offspring from surviving or reproducing - Types: Hybrid inviability - The zygote, embryo or offspring produced is inviable (unable to survive), and dies early in its development. - - Hybrid sterility - Hybrid Sterility (infertile) The hybrid offspring is sterile (infertile and cannot breed). This is usually because the sterile cannot produce normal gametes during meiosis. - Hybrid breakdown - The hybrid can reproduce, but subsequent generations are infertile or have reduced ability to breed - Dichotomous Classification - A dichotomous key is a guide for the classification and identification of a living organism. By asking a series of questions to which there are only two possible answers with respect to the object to be identified, the key leads users toward the proper identification. Viruses and Bacteria Virus: - An extremely small (electron microscopic) infectious particle that is nonliving. - The word virus comes from the Latin word meaning “poison” - A viruses is active only when inside a living cell - When removed from a living cell it ceases all activities but retains its ability to infect the cell. - They may be crystallized and stored indefinitely but even after long periods of time they retain: their ability to infect a living cell. - Viruses vary widely in terms of size and structure, but they all have one thing in common. They enter living cells and use the machinery of the cell to produce more viruses - Part of the viruses - Capsid - Base plate - Tail fibers - Sheath - Collar - DNA or RNA - Viruses are non-cellular - They are not made of cells and have no cell parts - Viruses consist of two parts - DNA or RNA surrounded by a protein coat - Capsid: The protein coat that surrounds the DNA or RNA - The capsid is made of proteins that enable the virus to enter a host cell. The capsid has a particular shape that must match receptors on the surface of a host cell - When the virus attaches to these receptors, the cell is “tricked” into letting the virus inside. - All viruses are parasites - Parasites live in or on other living organisms, causing them harm - All viruses require a host - The host is the living organism the parasite live on - Since viruses must bind precisely to proteins on the cell surface, they are highly specific to the cells they infect - Plant viruses can only infect plant cells - Animal viruses can only infect animal cells - Viruses of eukaryotes are usually tissue specific. - Ex: Human cold viruses infect only the cells lining the upper respiratory system, ignoring all other tissues - Bacteriophages are viruses that infect only certain types of bacteria - - Viruses are not affect by any known antibiotic - Anything that will kill the virus will also kill the host. - Viruses: Are They Living or Nonliving? (LIVING) - They can reproduce but only inside a living cell  - They can mutate or change - They have DNA or Rna. Their genome may consist of only four genes or up to a hundred genes. - Viruses Are They Living or Nonliving? (NON-LIVING) - They are non-cellular. - They have no metabolism. They have no food or energy requirements. - They can be crystalized and dehydrated and stored indefinitely. They come to “life” only when injected inside a living cell. - The two reproductive possibilities: - Once a virus is inside a host cell, two different processes may occur. - Some viruses replicate themselves immediately, killing the host cell. - Other viruses replicate themselves in a way that does not destroy the host cell. - Those are called The lytic cycle and The lysogenic cycle - The Lytic Cycle - In a lytic infection, a virus enters a cell, makes copies of itself, and causes the cell to burst. - Ex: Bacteriophage T4 is a bacteriophage that causes a lytic infection. - Attachment. - Entry. - Synthesis - Assembly - Release - Lysogenic Cycle - The host cell makes copies of the viral genetic material indefinitely - The virus incorporates its DNA into the DNA of the host cell. The viral DNA is then replicated along with the host cell’s own DNA. - Lysogenic viruses do not kill the cell right away; a lysogenic virus may remain inactive for some period of time. - Prophage: The viral DNA embedded into the host cell’s DNA - The prophage may remain part of the host for many generations before becoming active - Eventually, certain environmental conditions (chemical, radiation) may trigger the switchover from the lysogenic cycle to the lytic cycle. - Comparison of Viruses and Cells  Characteristics Viruses Cells Structure Have DNA or RNA and a Cell membrane, protein capsid cytoplasm, nucleus, cytoplasmic organelles Reproduction Only within a host cell Reproduce independently either sexually or asexually Genetic code DNA or RNA DNA Growth and NONE Yes, in multicellular development organisms Obtain and use no yes energy Respond to the no yes environment Change over time yes Yes - Battle against viral disease lies in the use of vaccines - Vaccines: Contain a harmless variation of the pathogen (virus) - Our immune system launches a response to the harmless form, thereby learning to recognize it the next time that we are exposed to it - When we are exposed to the “real” pathogen, our immune system can respond much faster since it has already learned to recognize the pathogen. Bacteria - Bacteria are prokaryotes - A prokaryotic cell: does not have a true nucleus or membrane-bound organelles. - Prokaryotes dominate the biosphere. Their collective biomass outweighs all eukaryotes combine by at least 10 fold - Some are harmful and cause diseases, but most bacteria are benign or beneficial. A relatively small number of species cause disease. - They are stressful because of theri rapid cell division ( reproduction) and their great metabolic diversity. They can double their numbers every 20 minutes and live in environments that support no other forms of life. - Until recently, all prokaryotes were placed in a single kingdom called the Monera kingdom. - However, biologists now recognize that there are such great differences between two distinct groups of prokaryotes that they should be placed into separate domains. - Classification of Prokaryotes - The bacteria are separated into two different domains - 1.Domain: Archaea - 1. Kingdom: Archaea - 2. Domain: Bacteria - 2. Kingdom: Eubacteria - Archaea - Under a microscope, Archaea looks very similar to the eubacteria. They are: equally small, lack nuclei, and have cell walls. - Chemically, the Archaea are very different - The Archaea lack the peptidoglycans found in the eubacteria. They also have different membrane lipids - Further, the DNA sequences of key archaeal genes are more like those of eukaryotes that those of eubacteria - They live in extremely harsh environments, such as: Swamps, salt lakes and hot springs. - Three Archaeal Groups: - Methanogens - These archaea have a unique way of getting energy. They convert hydrogen gas and carbon dioxide into methane gas - Oxygen is poisonous to these archaea. They must live in anaerobic environment such as deep fresh water, marine mud, swamp mud and sewage - Methanogens also thrive in the digestive tracts of cows and termites. A cow can release 200 to 400 liters of methane gas per day. - Halophiles - These are the “salt loving” archaea. - These organisms live in environments that have very high salt concentrations such as the Great Salt Lake and the Dead Sea. - Thermoacidophiles - These archaea live in very acidic environments that have very high temperatures, such as the host springs in Yellowstone National park. - These organisms can thrive in temperatures of 110C and at a pH of less than 2 - They are often found around “black smokers” which are hydrothermal vents that leak very hot, dark  colored, acidic water. Large communities of worms, calms, and crabs live near these vents and utilize the thermoacidophilic archaea as a primary source of food. - Eubacteria - These are the “true” bacteria - There is great variety in the organisms that belong to this kingdom. These bacteria are found in every environment on Earth. - The eubacteria have a cell wall that contains a polysaccharide called peptidoglycan - Bacteria are found almost everywhere the best environment for growth has - Suitable temperature 80-100f - Moisture - Suitable food source - Darkness - Space to grow - Bacteria are very large in comparison to a virus - Prokaryotes are identified by several characteristics - 1. Shape - 1. Cocci are spherical - 2. Bacilli are rod shape - 3. Spirilla are spiral shaped or curved - 2. The materials composing the cell wall - - 3. The way they move - Some bacteria are motile and others do not move at all - Some move by means of flagella, which are whip like structures used for movement - Some lash or snake forward - Others glide slowly over a layer of slime they secrete. - 4. The way they obtain energy - Most bacteria are harmless or beneficial - Nodules of nitrogen fixing bacteria around the roots of plants - Some are pathogenic (cause diseases) - Staphylococcus - Streptococcus - Structures seen in the prokaryotic cell 1. Capsule 2. Cell wall 3. Plasma membrane  4. Cytoplasm a. The cytoplasm does not contain any membrane bound organelles b. The Chromosome consists of one single, circular continuous molecule of DNA. c. The cytoplasm is filled with many ribosomes 5. Flagella 6. Pili 7. Ribosomes 8. Chromosomal DNA 9. Plasmid DNA - The capsule may be present outside of the cell wall. It is composed of a gluey polysaccharide - It enables prokaryotes to adhere to their: substrate or to other individuals in the colony - Some capsules protect against dehydration - Some capsules shield pathogenic bacteria form: attack by their host’s immune system - Pili are shorter and thinner than flagella - Pili serve to attach bacteria to: - A food source - The surface of a liquid - Another bacteria during reproduction - Plasmid DNA - A small circular piece of DNA that is separate from the chromosome. A plasmid is generally one gene - Metabolic Diversity: how do bacteria obtain energy? - MOST bacteria are heterotrophs - They do not have the ability to make their own food - The heterotrophic bacteria are further divided into - Saprophytes - Saprophytes live on dead organic matter - He is very important as decomposers - Parasite - A Parasite is an organism that invades plants and animals and live off of them - Host: the organism that the parasite is living off - A few bacteria are autotrophs. They have the ability to make their own food  - Photoautotrophs - Photosynthetic organisms that use light energy from the sun to convert carbon dioxide and water into organic module glucose and oxygen - Chemoautotrophs - Use the energy from inorganic reaction as a source of energy to build molecules of glucose - Growth and Reproduction - If conditions are favorable for growth bacteria can grow and divide at incredible rates - Many bacteria can divide every 20 minutes (under ideal conditions) - If reproduction continued unchecked at this rate, a single prokaryotic cell could give rise to a colony. - IN REALITY, PROKARYOTIC REPRODUCTION is limited by - The eventual exhausted of food supply - Being poisoned by their own metabolic waste - Competition from other microbes - Being consumed by other organisms - Binary Fission - Two identical daughter cells are formed - Binary fission is a type of asexual reproduction where: one cell undergoes cell division to form two cells - Conjugation - A type of bacterial reproduction - During conjugation, a hollow bridge forms between two bacterial cells - Through this tube genes move from one cell to the other (they exchange gene) - There is no increase in numbers, but they have redistributed the genetic information. The transfer of genetic information increases genetic diversity in future populations - Now they can go back to binary fission and increase their numbers - The importance of Bacteria - Bacteria are vital to maintaining the living world - The prokaryotes can easily survive without the eukaryotes, by the eukaryotes are totally dependent on prokaryotes - Bacteria are decomposers - All living things depend upon a constant supply of: carbon, nitrogen, and other essential elements. - These essential elements must be recycled when an organism dies. - Bacteria are decomposers that help to recycle these essential chemical elements. - When an organism dies, it is attacked by bacteria and broken down into simpler materials. \  - Nitrogen Fixation - Plants and animals must have nitrogen to build amino acids. Amino acids are need to build proteins - Nitrogen gas makes up about 80% of Earth’s atmosphere, but plants and animals are not capable of using nitrogen gas directly. - In a process called nitrogen fixation, bacteria are able to convert nitrogen gas into nitrates, a form that plants can use. - N2 -> N03 that is what bacteria do - Plants take up these nitrates through their roots and use them to build plant proteins - Animals eat the plants and convert the plant proteins into animal proteins. - When an organism dies, bacteria decompose the organism, returning this nitrogen to the ecosystem to be used again. - Human uses for bacteria - Bacteria are used to produce a wide variety of foods and beverages. Ex: sour cream, yogurt, cheese. - Some bacteria can digest oil and are helpful in cleaning up oil spills - Bacterial Diseases in Humans - Some bacteria are pathogens - A pathogen is a disease causing agent - Bacteria produce disease in one of two ways - Other bacteria: release toxins or poisons in the body of the host - Some bacteria: damage the cells and tissues by breaking down the cells for food. - Vaccines - Many of these diseases caused by bacteria can be prevented with the use of vaccines (both bacteria and viruses) - Antibiotics - They are compounds that kill bacteria - They are effective against bacteria but have no effect on viruses. - Symbiotic Relationships between organisms - Symbiosis is a close and permanent association between organisms of different species. - Mutualism (+ +) - Commensalism (+=) - Parasitism (+-)