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Bacteria Prokaryotes are the most numerous organisms on Earth Prokaryotes Prokaryotes: are single-celled organisms that do not have a membrane-bound nucleus They live in every environment on Earth They are a major source of food for many organisms They also help many organisms digest food General Characteristics 1. 2. 3. 4. 5. 6. Unicellular Prokaryotic Nutrition modes: mainly absorption, some photosynthetic, some chemosynthetic Anaerobic and aerobic species Reproduction: fission or budding microscopic Carl Woese Discovered in the late 1970’s that prokaryotes made up 2 of the 3 domains of life Categorized based on ribosomal RNA analysis 2 Major Domains 1. 2. Archaea: means “archaic” or “ancient” Bacteria: Domain Archaea Not like bacteria, but more like Eukaryota Differ from bacteria in the make up of their cell wall, membrane lipids, their genetics & metabolism Cell walls do not have peptidoglycan (a protein-carbohydrate compound) Cell walls have different amino acids and different types of lipids Truth about Archaea Archaea were first discovered in extreme environments like swamps, salt lakes and hot springs Recently, scientists found Archaea genetic materials in samples of surface water from the North Pacific & Antarctic Oceans So, Archaea may be more common that once thought. 3 Broad Groups of Archael Bacteria 1. 2. 3. Methanogens Halophiles Thermoacidophiles 1. Methanogens Named for their unique way of getting energy – Convert H2 gas & CO2 into methane gas (CH4) Live in anaerobic environments)-like swamp bottoms (marsh gas), sewage, intestinal tracts of humans, cows, & termites Oxygen is poisonous to them A cow can belch 200 & 400 L Of Methane per day The methane that bubbles out at marshes are called marsh gas 2. Halophiles “Salt Lovers”-live in high salt concentrations like the Great Salt Lakes & Dead Sea High salt concentrations would kill most bacteria but favor the growth of halophiles b/c they have adapted to live in very salty water Aerobic organisms • Ex: Salt Lakes • Ex: Dead Sea 3. Thermoacidophiles Live in very acidic environments that have very high temperatures (ph less than 2) with temperatures (230 F); Found in hot springs (Yellowstone National Park), volcanic vents, hydrothermal vents of the ocean Requires sulfur anaerobes Hot Springs at Yellow Stone National Park • Hydrothermal Vent Domain Bacteria Most well known prokaryotes General Characteristics 1. Largest group of bacteria 2. Occur in many shapes and sizes 3. Have distinct biochemical and genetic characteristics Domain Bacteria Occur in different shapes and sizes Identified by basic shapes 1. Sphere: Coccus [round] 2. Rods: Bacillus [Rod Shaped] 3. Spirals: Spirillum [Spiral] Three Bacterial Cell Shapes Bacterial cells are also classified by their arrangements Diplo – Two Bacteria can occur in pairs diplo- bacilli or cocci Staphlyo – Clusters Staphylococci cause “staph” infections Strepto – Long Chain Streptococcus cause infections such as “strep” throat Some well known Bacteria Streptococcus mutans causes tooth decay by converting sugars to an acid That erodes the tooth Clostridium botulinum produces a poison causing food poisoning Treponema pallidum causes syphilis Gram Stain Used to group bacteria into 2 groups based on the structure of their cell walls 1. Gram-positive bacteria: appears purple because they retain the crystal violet stain Are simpler and have more peptidoglycan The stain retains purple dye and appear purple Gram-negative bacteria 2. Gram-negative bacteria: appears pink because the cell becomes counterstained by the safranin red stain Gram negative bacteria have cell walls that are complex and have small amounts of peptidoglycan It takes up the red dye of the Gram stain making it look pink Peptidoglycan Cell Wall Peptidoglycan Cell Wall Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 1. Cyanobacteria 2. Spirochetes 3. Gram-Positive Bacteria 4. Proteobacteria 5. Chlamydia Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 1. Phylum Cyanobacteria: (blue green bacteria) Photosynthestic Encased in a jelly like substance-live in colonies Some are made of chains of cells with special enlarged cells called heterocysts (fixes nitrogen into ammonia which plants use) Environmental note: Anabaena loves phosphates and nitrates-undergoes a population bloom (eutrophication)-following the bloom many die and become decomposed by heterotrophic bacteria which consume large amounts of oxygen causing fish kills Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 2. Phylum Spirochetes: Gram negative, spiral-shaped bacteria Some are aerobic, some anaerobic Moves by means of a cork-screw like rotation Live freely, symbiotically, or as parasites Treponema pallidum causes syphilis Borrelia burgdorferi causes limes disease Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 3. Phylum Gram Positive Bacteria Not all are gram positive Some gram negative in this group share molecular similarities Makes yogurt Found in oral cavity and human intestines Causes tooth decay Makes antibiotics (actinomycetes) Members include: streptococcal species, causes strep throat Clostridium botulinum: makes toxins in botulism (used medically to treat painful muscle spasms and frown lines on the face) Anthrax is caused by the rod Bacillus anthracis which is used as a biological weapon Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 4. Phylum Proteobacteria: Largest & most diverse bacteria Divided into several subdivisions: A. Enteric Bacteria – Gram negative, heterotrophic, found in animal intestinal tracts, aerobic or anaerobic, Escherichia coli (E.coli) found in human intestines; makes vitamin K, aids in the break down of nutrients, Salmonella-disease causing protobacteria B. Chemoautotrophs: – Gram negative, extracts energy from minerals – Lives symbiotically – Rhizobium and Azotobacter-fix nitrogen in the soil. Live in nodules inside the roots of legumes which is important to the success of plants – Called Nitrogen Fixation C. Other Proteobacteria: – Some cause disease like Rocky Mountain Spotted Fever – Helicobacter plyori causes stomach ulcers – Agrobacterium causes tumors in plants Important Bacterial Groups 5 major phyla (actually 12 phyla exist) 5. Chlamydia Gram-negative-coccoid bacteria Live only inside animal cells (rely for protection and nutrients) The cell walls do not have peptidoglycan Chlamydia tramchomatis causes chlamydia---an STD The importance of bacteria Soybeans have nodules on their roots that convert nitrogen gas to ammonia that is used by the plant Foods & Medicines some foods would not exist without bacteria Swiss cheese Distinctive flavors Nitrogen fixing bacteria vinegar Crispy Pickles sauerkraut Biology of Prokaryotes Structure & Function Nutrition & Metabolism Prokaryotes have many ways of getting carbon and energy from the environment Heterotroph Photoheterotroph Chemoheterotroph Uses light energy but gets its carbon from other organisms Obtains both energy and carbon from other organisms Autotrophs Photoautotroph Uses light energy and gets carbon from CO2 Chemoautotroph Extracts energy from inorganic compounds and uses CO2 as a carbon source Reproduction: binary fission Prokaryotes reproduce asexually by binary fission ANTIBIOTICS Antibiotics affect bacteria with certain cellular activities – Penicillin: blocks the ability to build new cell wall material – Tetracycline: blocks protein synthesis Antibiotics are made naturally by some fungi & bacteria They kill neighboring bacteria or fungi that compete for resources Antibiotic Resistance A big worry for modern medicine Bacteria may become resistant to antibiotics by – Mutations in bacterial DNA give bacterium resistance – Mutant bacteria multiply & take over the population and stop the antibiotic’s curing power Viruses In 2003, some people in China started showing symptoms of a new illness. These symptoms were similar to those of pneumonia. The condition was highly infectious. Soon, scientists found that the disease was caused by a virus. They called the disease severe acute respiratory syndrome, or SARS What is a Virus? You’ve probably had the flu—influenza—at some time during your life. Nonliving particles called viruses cause influenza. Viruses are composed of nucleic acids enclosed in a protein coat and are smaller than the smallest bacterium Viruses are interesting to scientists because they cause many diseases and are useful tools for genetic research Did You Know… Viruses are not alive because they lack some of the key characteristics of living organisms – 1. They do not have cytoplasm or organelles – 2. They cannot carry out cellular functions like metabolism and homeostasis – 3. They do not grow as cells do by dividing into two – 4. They cannot reproduce outside a host cell – 5. They must enter a living cell and use the host cell’s ribosomes, ATP, enzymes, and other molecules to reproduce Virus Size and Structure Viruses are some of the smallest particles that are able to cause disease They vary in size and shape Capsids and Envelopes A capsid is the protein shell that encloses the viral genome Capsids are built from protein subunits called capsomeres A capsid can have various structures Viral Shapes Consist of an inner core of nucleic acid surrounded by 1 or 2 protein coats or capsid The human flu virus may have another layer called a viral envelope surrounded by an outercoat Contains DNA & RNA but never both The arrangement of proteins give different shapes to viruses RNA Capsomere DNA Membranous envelope RNA Capsid Head Capsomere of capsid DNA Tail sheath Tail fiber Glycoprotein 18 250 nm 70–90 nm (diameter) 20 nm 50 nm (a) Tobacco mosaic (b) Adenoviruses virus Glycoproteins 80–200 nm (diameter) 50 nm (c) Influenza viruses 80 225 nm 50 nm (d) Bacteriophage T4 Shapes Polyhedral viruses (polio virus) resembles small crystals Tobacco mosaic viruses-small cylinders T-4 –looks like a lunar landing module Nucleic acid Capsid Viral Envelopes Some viruses have membranous envelopes that help them infect hosts These viral envelopes are derived from the host cell’s membrane and contain a combination of viral and host cell molecules The envelope is formed from the nuclear membrane or the cell membrane of the host cell as the viral capsid buds from the host cell Classification of Viruses 1. 2. By whether they have RNA or DNA as their gnome and whether their gnome is double stranded or linear or circular. Based on the nature of the capsid and on the presence or absence of an envelope ex: SARS is a coronavirus. Corona is the Latin word for “crown” –the envelope protein looks like a crown How are they named? Viruses are not given names 1. Often named after the disease they cause EXAMPLE: RABIES VIRUS Poliovirus AIDS VIRUS How are they named? 3. Code Numbers are 2. The organ or used to name several tissue they infect viruses infecting the EXAMPLE: same host ADENOVIRUSES Example: T-1 T-7 adenoid tissue in the 7 viruses that infect back of the throat the intestinal bacteria E.coli (T stands for Type) Bacteriophage Bacteriophages, also called phages, are viruses that infect bacteria They have the most complex capsids found among viruses Phages have an elongated capsid head that encloses their DNA A protein tail piece attaches the phage to the host and injects the phage DNA inside T-4 Bacteriophage is a virus that infects bacteria T-4 Attachment to a Host Before a virus can replicate, it must enter a host cell virus recognizes and attaches to a host cell when one of its proteins interlocks with a molecular shape that is the receptor site on the host cell’s plasma membrane. General Features of Viral Cycles Once a virus has entered a cell, it begins to manufacture viral proteins The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules Viral nucleic acid molecules and capsomeres spontaneously selfassemble into new viruses These exit from the host cell, usually damaging or destroying it DNA 1 Entry and uncoating VIRUS 3 Transcription and Capsid 2 Replication manufacture of capsid proteins HOST CELL Viral DNA mRNA Viral DNA Capsid proteins 4 Self-assembly of new virus particles and their exit from the cell Replicative Cycles of Phages Phages are the best understood of all viruses Phages have two reproductive mechanisms: the lytic cycle and the lysogenic cycle The Lytic Cycle The lytic cycle is a phage replication cycle that ends in the death of the host cell The lytic cycle produces new phages and lyses (breaks open) the host’s cell wall, releasing the progeny viruses – A phage that reproduces only by the lytic cycle is called a virulent phage – Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA Lytic Cycle: To Break Down 1. Attachment 4. Assembly: nucleic 2. Entry: once inside acid & coats are the virus destroys assembled into new the host DNA viruses 3. Replication: it 5. Release: host cell reprograms the cells breaks open & new metabolic activity to virus particles are copy the virus genes released 1 Attachment 2 Entry of phage 5 Release DNA and degradation of host DNA Phage assembly 4 Assembly Head Tail Tail fibers 3 Synthesis of viral genomes and proteins The Lysogenic Cycle The lysogenic cycle replicates the phage genome without destroying the host Phages that use both the lytic and lysogenic cycles are called temperate phages The viral DNA molecule is incorporated into the host cell’s chromosome This integrated viral DNA is known as a prophage Lysogenic Cycle 1. 2. 3. Begins like the Lytic Cycle Instead of destroying the host cell the DNA becomes part of the host New DNA does not interfere with normal functions of the host cell 4. Every time the host cell reproduces, virus is reproduced 5. Can continue undetected for many years, but can pop out at any time then the virus starts killing the host cells. Replicative Cycles of Animal Viruses There are two key variables used to classify viruses that infect animals – 1. The nature of the virus (single- or double- stranded DNA or RNA) – 2. The presence or absence of an envelope • An animal virus with an envelope uses it to enter the host cell RNA -Retrovirus The broadest variety of RNA genomes is found in viruses that infect animals Retroviruses use reverse transcriptase to copy their RNA genome into DNA HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome) Provirus-DNA Viral DNA that is integrated into the host genome is called a provirus Unlike a prophage, a provirus is a permanent resident of the host cell The host’s RNA polymerase transcribes the proviral DNA into RNA molecules The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new viruses released from the cell Evolution of Viruses Viruses do not fit our definition of living organisms – Since viruses can replicate only within cells, they probably evolved after the first cells appeared Candidates for the source of viral genomes are plasmids (circular DNA in bacteria and yeasts) and transposons (small mobile DNA segments) – Plasmids, transposons, and viruses are all mobile genetic elements Where are Viruses found? Viruses are found everywhere… Some have been linked to cancers, animals, in plants Ex: Tobacco mosaic virus Viral Diseases in Plants More than 2,000 types of viral diseases of plants are known; these have enormous impacts on the agricultural and horticultural industries Plant viruses have the same basic structure and mode of replication as animal viruses Tobacco Mosaic Virus First plant virus to be identified There are more than 400 viruses that infect a variety of plants Virus can stunt the growth or yield a loss in the host plants Plant viruses require wounds, or insect bites to enter and infect the host Tobacco Mosaic Virus Vaccine A vaccine is a harmless derivative of a pathogen that stimulates the immune system to mount defenses against the harmful pathogen – Vaccines can prevent certain viral illnesses – Viral infections cannot be treated by antibiotics – Antiviral drugs can help to treat, though not cure, viral infections Emerging Viruses Viruses that suddenly become apparent are called emerging viruses – HIV is a classic example The West Nile virus appeared in North America first in 1999 and has now spread to all 48 contiguous states Epidemic and Pandemic In 2009 a general outbreak, or epidemic, of a flu-like illness occurred in Mexico and the United States; the virus responsible was named H1N1 H1N1 spread rapidly, causing a pandemic, or global epidemic Three processes contribute to the emergence of viral diseases – The mutation of existing viruses, which is especially high in RNA viruses – Dissemination of a viral disease from a small, isolated human population, allowing the disease to go unnoticed before it begins to spread – Spread of existing viruses from animal populations; about three-quarters of new human diseases originate this way Some Other Well known Viruses Small Pox 30% of infected die Vaccines not administered to public since 1970’s No treatment, only preventative vaccine Used as a biological weapon The last case of smallpox in the United States was in 1949 Hepatitis Is an inflammation of the liver Can be caused by 5 different viruses – Hepatitis A & E: can be spread by fecal contaminated food and water – Hepatitis B, C, & D are spread by sexual contact, by contact with infected blood an serum, and by the use of contaminated needles – Symptoms: fever, nausea, jaundice, and liver failure Caused by Hepatitis B Influenza A, B, & C Influenza types A or B viruses cause epidemics of disease almost every winter. In the U.S. influenza epidemics can cause illness in 10% to 20% of people average 36,000 deaths and 114,000 hospitalizations per year Influenza Pandemic of 1918 http://www.youtube.com/wa tch?v=rbYwNOcKqqc&feat ure=channel AIDS Virus HIV is the virus that causes AIDS. AIDS is a serious condition in which the body's defenses against some illnesses are broken down. Herpes Virus The virus Herpes simplex causes the common sexually transmitted disease genital herpes There are two types of Herpes Simplex, and both can cause genital herpes Most babies are born through c-section HPV Genital Warts:one of the most common types of sexually transmitted diseases Virus that causes them called the human papillomavirus http://www.thesahara.net/ verrucas_plantar_warts.ht m Bubonic Plague During the 1300s - a massive epidemic swept through Europe, killing one-third of the population by some estimates, and subsequently changing the course of European history. Referred to as The Black Death, Caused from being bitten by a rodent flea that is infected with the disease Polio Virus Phase 3: Muscle weakness and muscle It enters through the mouth & is contagious. paralysis, difficult swallowing, nasal Phase 1: Fever, headache, sore throat, voice, difficulty spewing, breathing malaise(general bodily weakness and discomfort). Phase 2: Meningitis, fever, severe headaches, stiff neck and back, muscle pain. SARS Originated in Asia in 2003 Stands for Acute Respiratory Syndrome and can be contracted by close person to person contact. When first introduced into the United States, SARS was thought to be a chemical weapon. Ebola Virus Ebola Virus, common name for several strains of virus, three of which are known to cause hemorrhagic fever in humans, which is characterized by massive bleeding and destruction of internal tissues. Chicken Pox Chicken pox is a rash illness caused by a virus. Chicken pox usually occurs in childhood. More than 90% of Chicken pox cases occur in children less than 12 years of age. Shingles Chicken pox and shingles are caused by the same varicella-zoster herpesvirus The virus multiplies in the lungs and travels to blood vessels in the skin The painful shingles rash, caused By a herpes virus, is limited to an Area of the skin innervated by a Particular nerve branch Ex: on the side of the chest Anthrax Caused by the bacteria Bacilli Anthrax most commonly found in wild &domestic lower animals (cattle, sheep, goats, camels, antelopes They ingest spores from soil It can occur in humans when they are exposed to infected animals Or when anthrax spores are used as a bio-terrorist weapon Yellow Fever Yellow fever is a serious viral infection, transmitted by mosquitoes in tropical regions There are no medicines that are effective against this virus Emerging Viral Diseases Are illnesses caused by new or reappearing infectious agents that typically exist in animal population— often in isolated habitats—and can infect humans who interact with these animals. Ex: Ebola virus also called hemorrhagic fever