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York University
Natural Science
NATS 1670
Motti Anafi

Friday September 7, 2012 Emerging infectious diseases Microbes: ◦ 99 % of microbes are not dangerous, but are actually healthy and can provide protection (trillions of microbes) (Life originated with microbes, and all forms of life are derived from microbes.) ◦ Microbes can form 1 of 3 symbiotic (means to live together) relationships with their hosts - Mutualistic, Commensal, and Parasitic ◦ In Mutualism both organisms benefit from the interaction ie. humans and intestinal bacteria, humans lack nutrients which are provided by the bacteria living in the intestine ◦ Commensal relationships are one-sided; one organism benefits the other does not ie. a spider builds a web on a plant and receives shelter but does not harm the plant ◦ In a Parasitic relationship one organism benefits and the other is harmed or destroyed ie. Tuberculosis bacteria living in human lungs live and multiply while harming or destroying the human ◦ This course will focus on the 0.1 % of microbes that are Parasitic and can pose a threat to our lives (disease-causing agents) Main purpose: ◦ Turning inorganic molecules (nitrogen, co2) into organic compounds ◦ Oxygen(Microbes generate more than half of the oxygen we breath in) ◦ Waste breakdown and decomposition ◦ Food production (making bread)(Bread is the result of a microbia fermentation of the sugar to produce carbon dioxide) as well as Beer and Cheese. ◦ Drug preparation (penicillin, insulin) ◦ Digestion and nutrition in animals and humans; helps make vitamins. Beneficial Roles of Microbes: ◦ Our body from inside to out is filled with Microbes they help us break down food and protect us from other pathogens ◦ They assist us in maintaining good health (if they disappear we may have problems) ◦ The natural microbial flora provides protection against more virulent microbes ◦ Studies have shown that a lack of bacterial flora in the gut can severely effect brain development in mice ◦ Used as digestion and nutrition in animals and humans (intestinal flora produce vitamin K) ◦ Turning inorganic molecules (nitrogen, CO2) into organic compounds (e.g. nucleic, amino acids) ◦ Responsible for oxygen, waste breakdown, and in food productions (to make bread, yeast is required) ◦ Ex: conditions such as temperature are used as mechanisms to make grapes into wine or vinegar ◦ Drug preparation (e.g. penicillin, insulin) ◦ In agriculture microbes help break down waste ◦ Used to make food such as cheese and bread ◦ We have microbes all over our body and this flora is our first defense against pathogens trying to enter the body. Microbes-Host Equilibrium ◦ Microbes have caused the most devastating epidemics in recent human history. (Ex: Spanish Flu, Bubonic Plague, smallpox) ◦ If our microbes are out of balance, they begin to harm us ◦ Infections are another example of a fatal microbe-causing death. Eg: Wounded soldiers are exposed to harmful pathogens, causing infection and ultimately death. ◦ Microbial diseases are often severe (e.g. Tuberculosis, HIV, Ebola virus, Sars) ◦ 1.7 billion people at the moment are infected with tuberculosis and is the most successful pathogen ◦ Diseases like tuberculosis are still active today because the microbes have are becoming more tolerant to the drugs that are given to cure them ◦ 28 % of individuals in Canada infected with HIV do not know about it and as a result is a successful virus ◦ As drugs advance, there will be more infections of HIV (more common) however at a lower fatality ◦ Reason why some microbial diseases cannot stay around is because it cannot evolve from a dead host. ◦ Other pathogens/microbes act sensitively within in our bodies so that they have a chance to be passed on to the next generation through reproduction or by being passed on. ◦ Two very successful microbial pathogens in terms of evolution are tuberculosis and HIV. Tuberculosis, is a bacterial infection where when the host is infected, they stay alive for apx. 30 years, coughing and spreading the harmful microbe to others. HIV is a microbial virus causing aids. It stays and infects the host for apx.7 years without showing signs or symptoms allowing the disease to be transmitted. This may result in full-blown aids causing death. ◦ TB and HIV are two examples of very successful pathogens in humans. Tuberculosis (TB) Primarily TB infection is asymptomatic, presenting most frequently with only a new positive reaction to TB skin test - a subcutaneous injection in the arm, if irritation and swelling take place to the area than the patient is sent for chest x-rays for confirmation of damage to the lungs. Most patients with active TB have pulmonary symptoms including productive cough, hemoptysis, chest pain and irregular lung sounds. More strains of TB are becoming more resilient to the use of drugs as treatment. Some short course therapies include: Isoniazid, Rifampin, Pyrazinamide, and Ethambuto ◦ The Ebola virus is located in Central Africa and can transmit through several host such as gorillas and humans, however transmission is limited and kept local ◦ When infected with the Ebola Virus, virus particles can be found in every part of the body. ◦ People infected with Ebola virus die very quickly making the time for transmission very low. ◦ However, the natural evolution of a microbe operates on its spreading capacity, not on its ability to cause a disease ◦ Ex: There are still SARS on beds however because infections are limited evolution of this pathogen is unlikely ◦ Ebola and SARs have a high incidence of quick mortality ◦ Death of an infected host compromises the survival of the infecting microbe. ◦ Natural selection favours less or non-virulent microbes ◦ A well-adapted microbe can live in its host without causing significant damage ◦ Many microbial diseases can be viewed as a failure of the microbe to adapt to its host ◦ People that are "resistant" to diseases such as HIV are actually infected but are stopped in the body by certain human cell mutation I.e. Prostitutes can infect many of their clients without developing full blown AIDS themselves Kids need to be exposed to some types of bacteria before age 6. a sterol environment is not good for us it does nothing to build our immune system Sept 10 , 2012 Life Expectancy: - Life expectancy was below 50 years of age - Could not find many cases of cancer - Alzheimer disease was rare - Spanish flu made the life expectancy go below 40 years of age - Life expectancy is increasing all the time in Canada and the US - Over the years the population has been continuously increasing - In 1880, there was 63% countries with infectious diseases which were low income countries - Now 6% are low income countries - Started to understand basic rules of the immune system o Were able to make vaccines and antibiotics to fight infections - In the developing world, third world countries, there is a huge gap of life expectancy between developed countries o 1980s AIDS killed many young adults and from then on, life expectancy is very low o Infectious diseases are very high and therefore many people die at a younger age o 6 Billion dollars must be spent if we want to send vaccines and antibiotics to those countries o The money is available but we are just not helping o Bill Gates said his foundation would provide an additional $100M for the polio campaign, and Cameron urged other European countries to follow Britain’s lead o During the mid-1900s most scientist and policy makers were shifting their attention away from infectious diseases as vaccines and antibiotics made these diseases rare, at lease in the developed world - Started to think about cancer cures Away from Infectious Disease? - Vaccination was successful (take away smallpox by mid 1970s) - Antibiotics (used in WWII and then regular basis) o Find antibiotics against every pathogen - Infectious diseases appeared to be on the way out - 1969 US Surgeon General to Congress: o “its time to close the book on infectious diseases”  do not need the budget to look for more and cures and put money on cancer research - BUT microbes will never go away therefore you cannot say infectious diseases are not important Emerging Infectious Diseases - Will not disappear - Drug resistant strains o Tuberculosis  Pathogen that is very successful that has been present for thousands of years  Developed several antibiotics  Today there are 5 (must use 2/3 together)  Last couple of years, the disease became resistant  1.7 billion infected by Tuberculosis - Outbreaks of existing diseases o West Nile Virus (WNV) in North America o Flu (Swine H1N1)  Epidemic influenza - New disease-causing agent o HIV/AIDS  Jan 1981, first time physician made a unique diagnostic o Severe Acute Respiratory Syndrome (SARS)  Animals and humans o Ebola (70s)  New virus in Africa, killing many people (90% of people infected are killed) o Monkey Pox  Similar to small pox, from same family  2003, Human-Monkey Pox  Giant Gambian Rat -> Prairie Dog -> Humans  Africa -> Texas  Humans received it by being scratched or bitten by prairie dog pets  Symptoms include rash, fever, chills sores  Not usual fatal  Symptoms last 2-4 weeks  No vaccine  Not as strong as small pox September 12, 2012 How Mother Nature and Human Collaborate in Emerging Infections Disease Wild-life origin/reservoir Man-made amplifier AIDS Chimpanzee (SIV) Sexual activity, drug addiction, blood products (sharing needles) SARS Palm civet Restaurants, hotels, hospitals West Nile Virus (WNV) Wild Birds Tires from Africa Influenza Wild aquatic birds Poultry farms Monkey Pox Wild rodents in Africa Pet retailers and stores Disease Transmission Within Populations: Today vs. the Old Days - 4000 years ago, you had to walk - 2000 years ago, transmission was easier: started to use boats o This meant diseases/viruses could come from one country to another o Aboriginals were killed by million of viruses (small pox and measles) - Today, we can fly to other places (airplanes) o Very fast transportation o Viruses and diseases can be transmitted very quickly o EX: Swine Flu cases from New Zealand were found from Mexico Super-Spreading of SARS - Guangdong Province, China -> An hotel in Hong Kong -> 2 Hong Kong, 1 Vietnam, 3 Singapore (1 took a plane to Germany), 1 USA, 1 Ireland, 2 Canada - In Nov 2002, China realized there was “something” going on (400 people with certain conditions, seemed mild) = kept quiet about it = were WRONG - Physician who was taking care of people came to a conference and infected others (just by touching, sneezing, etc) - TRAVEL ALERT was issued - Half a year later, there were no cases of SARS Bioterrorism - Intentional release of bacteria, viruses, or toxins for the purpose of harming or killing civilians o AFTER 9/11: Letters containing anthrax (can find anywhere)  Post office was closed  Many changes occurred  Incubation period of 45 days  AMI building was first targeted  23 cases of Anthrax in US during 2001 (5 killed) - Inconclusive science: The methods the FBI used to investigate the anthrax letters were sounds, says, a new report, but not sufficient to establish their sources o Someone from the govt was MOST LIKELY the source of anthrax (the strand that infected people came from a government controlled lab) Potential Bioterrorism Agents: CDC Category A - Organisms o Anthrax  Used for bioterrorism  Top of the list o Plague (Bubonic Plague)  Someone can take the DNA and put it in a bacteria o Smallpox  We THINK it is eradicated o Tularemia  There are vaccines, and treated with a drug  PROBLEM: very aggressive pathogen o Viral hemorrhagic fevers  Very aggressive  Can be transmitted very quickly  Many viruses from this family o Botulinum Toxin  Most aggressive toxin  Tiny amount found in water or milk can kill hundreds of thousands September 14, 2012 - Features o Easily disseminated or transmitted person to person  Anthrax ??  Bubonic plague o High mortality rate  Ebola virus (90% of people infected are going to die)  Small pox (30% of people infected are going to die) o Public panic and social disruption  Healthcare has to be reorganized  Change protocols  MOST SUCCESSFUL towards bioterrorism o Cost of coping with Bioterrorism  Resources of the healthcare system  Spend billions of billions of dollars  ICU (Intensive Cure Unit)  Healthcare may reach its limitations  Research and development (R&D)  Open up 11 organizations against bioterrorism in U.S.  1997 = 5 million  2003 = 96 billion (AFTER Anthrax attack) & 2004 = 123 billion Smallpox (Variola major) - 1990 WHO declared Smallpox is DEAD - Have a very good vaccine (discovered 200 yrs ago) - Can only infect human beings o Much easier to vaccinate because animals are not infected - Severe symptoms - 30% - 40% people infected are likely to die - If smallpox comes back we are not as safe, since the 80s people have stopped using vaccines - People may die from taking the vaccine - U.S. army is prepared if smallpox does appear again o Have vaccines ready Possible Source of Smallpox as a Bio-weapon - Bio-weapon used against U.S. by Soviet Union - Used as a weapon in the past o Used by the “good guys”  French and Indian war  French offered Indians blankets that were used with those with smallpox  Indians got infected Factors that Affect the Emergence of Disease - Microbial adaptation o Antibiotics resistance  Toxins that were secreted from the bacteria is what affects humans - Human behavior o International travel  Moving from country to country within hours  Transmission moves very quickly o Sexual Activity  HIV/Aids - Human susceptibility to infection o Poverty, malnutrition, poor sanitation  EX: Cholera - Changing ecosystems o Climate and weather - Wars - Bioterrorism *when small pox infects the structures of the body (inflammation), is when people really get infected September 17, 2012 Anthrax Movie from PBS - 2001, October - Anthrax spores - Travels quickly and takes month to disinfect - FBI did not have the equipment to deal with Anthrax - A professional was the only one that could modify Anthrax - Someone in the “government, a scientist” was said to be a “traitor” - Searched his apartment, public accused him HOWEVER could not find any evidence - Hatfield becomes angry, and starts to become public o Insists he is INNOCENT - FBI believed Hatfield left the “evidence” in a pond o Found a plastic box with a hole in it o “A turtle trap” - Took 5 years until Hatfield was declared innocent - Ivans the man investigating the anthrax, become a suspect o Was seen to be in his office all the time o Did not find any evidence September 19, 2012 Some Basic Concepts in Biology The Cell - The cell is the basic unit of life o Unicellular  Made up of just one cell  Bacteria, yeast, etc o Multicellular  Made up of several to billion of cells  Digestive system, nerve system  Most plants and animals  These cells work together to help the organisms grow and survive (send messages to each other) The Unity of Life - All cellular life has many characteristics in common: o Have a CELL MEMBRANE: that separates the chaos outside a cell from the high degree of organization within the cell  Things inside the cell are very organized  For ex: on the surface of the membrane the same types of proteins that do the same things are found throughout the entire body  REGULATE the flow of nutrients and wastes that enter and leave the cell (channels and gates)  CONTAINS DNA as its genetic material  Several varieties of RNA molecules  PROTEINS  Most of the proteins are ENZYMES  Are composed of the same BASIC CHEMICALS: carbs, proteins, nucleic acids, minerals, fats and vitamins  REPRODUCE and are the result of reproduction  Require a SUPPLY OF ENERGY  ATP (general form of energy in all life on the planet) Diversity of Living Organisms Cell Structure: Prokaryotic and Eukaryotic - Eukaryotic: there is a nucleus in cell o Place where we store DNA, where DNA is expressed, certain activities are done in the nucleus - Prokaryotic: no nucleus - Cytoplasm: can find a lot of enzyme activities and organelles - Nucleus: storage site of genetic information, the site of DNA replication - In Prokaryotic organisms, you will find: o Cilia and Flagella for movement o Cell Wall: protects against mechanical and hypertonic stress o Cytoplasm: region where many metabolic reactions occur and find organelles o Ribosome: sites of protein synthesis o Nucleoid Region: storage of genetic information Prokaryotes Eukaryotes Nucleus No Yes RNA Processing No Yes Organelles No Yes Cell Wall Yes No (animal cells) Cell Size (small to large) Viruses, Bacteria, Yeast, Animal Cell, Multi-cellular organism - Electron Microscope (Virus) - Light Microscope (Bacteria, Yeast, Animal cell) - Naked Eye (multi-cellular organism) Prokaryotes Diversity of Bacterial Shape - Rod-like (Bacillius) o E.Coli - Spherical (Coccus) - Spiral (Spirillum) - Vibrio Cholerae – curved (vibrio-shaped), rod o Comes to life after disasters o Common pathogen September 21, 2012 Diversity of Prokaryotes: Environmental Conditions - Temperature o Grows best below 20C (Psychrophiles)  Most are not human pathogens  More food related o Grows best between 20-50C (Mesophiles)  Affect our health especially if its around 36.5C (optimal)  Most pathogens fall underneath this temp o Grows best above 50C (Thermophiles)  72C is optimal for many pathogens - pH (acidic or basic environments) o Grows well at pH of 1 to 2 (acidic) (Acidophiles)  H. Pylory (grows in gastric juices) o Grows best near neutral pH o Grows well at pH of high as 9 (basic) - Moisture o Most cells require a minimum moisture content o Water  Related to the development of life o Some cells can stay alive in the near absence of moisture (spores) - Salt o Most cells require a moderate level of salt o Some cells can exist in very high salt concentrations (Halophiles) - Oxygen Availability o Require oxygen for growth (aerobic) o Require lack of oxygen for growth (anaerobic) - Nutrient Availability o Most microorganisms require organic and inorganic nutrients to grow and survive o Cyanobacteria grow in the absence of key nutrients: eg. Can convert CO2 from air into organic cellular molecules The Evolution of Life on Earth - 3.8 billion years ago – first evidence of life? - 4.3 billion years ago – first water? - 4.4 billion years ago – first solid rock? - 4.5 billion years ago – moon forms - 4.5 – 4.6 billion years ago – earth formation begins Origin of Life: (Prokaryotes) Halophiles, Methanogens, A/Unicellular Thermacidophiles Archaea Eykarya EuBacteria UniversalAncestor UniversalAncestor UniversalAncestor - Vents are one of the most extreme environments on Earth, but can be used as laboratories to study life on and beneath the seafloor Archaea - Morphologically, the two kingdoms of Prokaryotes appear similar, however, they have major biochemical differences - Most archaea live in extreme environments o Thermoacidophiles  Hot sulfur springs where they experience high temperature and low pH o Methanogens  Live in methane-containing environments o Halophiles  High salt environments - Members of the Archaea are not human pathogens “It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is most adaptable to change” - Charles Darwin September 24, 2012 Diversity of Microbes – Other than Prokaryotes Viruses - Viruses are complex of nucleic acids and proteins - Use fxns of the host cells on which they are parasites - Not considered life form - Have the capacity for replication in animal, plant, and bacteria cells o 8% of our genome are made up of genetic DNA from viruses - The viral parasite causes changes in the cell - Directing the host cell’s metabolism to the production of new virus particles may cause cellular death What are Viruses? - Nucleic acid genome: o DNA or RNA - Protein Coat o Protection, entry into the cell  RNA is very fragile, can be destroyed extremely quickly - Lipid envelope in some viruses o Give some advantage on how to enter the cell - Small o 10-400 nm - Obligate intracellular Fungi - ex. Yeast o Eukaryotic, unicellular organism o 5-10 um in siz o oval shape o involved in human diseases such as:  yeast infections  opportunistic infections (eg. AIDS) o most commonly used in the food industry  under aerobic conditions used as a baker’s yeast to make bread  under aerobic conditions used for alcohol production  yeast is found on the grapes – wine - ex. Molds o filamentous fungi with a mycellial structure  mycelium is a highly branched system of tubes that contain mobile cytoplasm with many nuclei o molds are used for production of citric acid and antibiotics  used to fight bacterial cells  the mold Penicillium produces penicillins o involved is allergic reactions o Aspergillus – group of diseases that affect people with weak immune systems, ex. AIDS  Cause of certain infections, fever, chest pain, sinus infection  Opportunistic infection - Ex. Protozoa o Unicellular, motile, relatively large (up to 50 um) eukaryotes that  Lack a cell wall, only cell membrane  They cause a number of human diseases  Eg. Malaria o But have beneficial roles  Digestion  Removing bacteria from wastewater September 28, 2012 Flow of Information Translation • Proteins • DNA • (activity) • (information • RNA storage) • (information carrier) Transcription Phenotypes (physicalfeaturesand fuctionaltraits of organism) Definitions: - Atom: the smallest chemical unit of matter - Molecule: two or more atoms held together by chemical bond (methane, CH4) DNA (deoxyribonucleic acid) - DNA is the molecule responsible for transmission to information from one generation to the next in most forms of life on this planet - Exceptions are some viruses that use RNA (ribonucleic acid) as their hereditary molecule, and prions that apparently use proteins as their hereditary molecule Nucleotide Structure ( - Phosphate group, nitrogenous base, sugar - Nucleotides are monomers that consist of a sugar - Phosphodiester bond: nucleotides polymerize to produce nucleic acids through formation of a phosphodiester linkage b/t the phosphate group on the 5’ carbon of one nucleotide and the –OH group of the 3’ carbon of another Nucleic Acid Structure - DNA’s primary structure consists of a sequence of nitrogen-containing bases, which contain information in the form of a molecular code - Adenine, Guanine, Thymine, Cytosine (A-T and G-C through hydrogen bonding) *john kryk website* DNA Structure: - The two stands are “antiparallel” (opposite directions) - Strands are held together by complementary base pairings - One strand runs 5’ to 3’ while the other runs 3’ to 5’ - 3’ = carbon #3 and 5’ = carbon #5 - Sugar-phosphate “backbone” - Two DNA strands combine to make a double helix - Bases are attached to the sugars - Pyrimidines and purines - C - G come together via 3 hydrogen bonds - A - T come together via 3 hydrogen bonds - Ex: FOR DOUBLE STRANDED DNA G = 35% C = 35% (70%) A = 15% T = 15% (30%) - In single stranded, if G is 35%, A is unknown because there can be anything there due to the fact that is SINGLE STRANDED October 1, 2012 Erwin Chargaff Experiment - Discovered the pairing rules of DNA letters, noticing A matches T and C and G. Two Functional Roles of DNA - Duplication: the molecule must be replicated and transmitted in each cell division o Each daughter cell contains almost identical copies of DNA molecules as compared to its mother cell - Information: the molecule contains information expressed in the sequence of the nucleotides o The sequences are transcribed into RNA to release their information DNA Replication The DNA is opening like a zipper. Two strands are attached to one another but you can open it up and then create another strand of DNA on the single stranded molecule. The molecule that can open up the zipper of the DNA are called DNA helicases; they know how to separate the 2 strands of the DNA We can start with the double stranded and then end up with the single stranded molecules and now each base is open to be read by the appropriate nucleotide DNA Replication - DNA polymerase catalyzes addition of deoxyribonucleotide units to a DNA chain - DNA polymerase is a template-directed enzyme that synthesizes a product with a base sequence complementary to that of the template - DNA polymerases catalyzes the formation of a phosphodiester bond efficiently only if the base on the incoming nucleotide is complementary to the base of the template strand - The new DNA chain is assembled directly on a preexisting DNA template - The template DNA must be bound to a primer strand having a free 3’ - The chain-elongation reaction catalyzed by BDNA polymerases from 5’ to 3’ of the elongated DNA Okazaki Fragments - Because the original DNA strands are complementary and run antiparallel, only one new strand can begin at the 3’ end of the template DNA and grow continuously as the point of replication moves along the template DNA - The other strand must grow in the opposite direction - The other strand of this discontinuous replication is the production of a series of short sections of new DNA called Okazaki Fragments - The RNA primer is replaced by DNA October 3, 2012 Beginning Notes: - Information can be found on the sequence of the nucleotides in DNA - Our life cells use four different options: A, C, T, G 3’ direction. ◦ this RNA is complementary to the DNA template strand Transcription begins near promoter sites and end at terminator sites. NOTE: ◦ Bases in nucleotides of the RNA strand form pairs with the bases in DNA strand. ◦ RNA nucleotides contain sugar ribose which has 2' hydroxyl group of the last nucleotide. ◦ During the reaction, a pyrophosphate ion is released and broken down which release energy that fuels transcription. ◦ Termination is the last step to the process where RNA transcript is released from the template. DNA rewinds completely. ◦ RNA polymerase: synthesizes an RNA transcript using one strand of NA as the template ◦ This strand is the template strand, and the other one is non-template strand. RNA polymerase synthesizes the RNA strand in the 5' --- 3' direction. This RNA is complementary to the DNA template strand. Transcription begins near promoter sites and ends at the terminator sites. 3 steps of transcription: ◦ Initiation ◦ Longation ◦ Termination October 5, 2012 Initiation: How does Transcription begin?  The enzyme RNA polymerase binds to a specific site in DNA (promoter) with the help of transcription factors Whole process  Outside of membrane, there is a site to recognize chemicals  The response to the chemicals is inside the membrane  Polymerase separates the base pairs of DNA forming a transcription bubble  Ribonucleotide triphosphate diffuses into the active site and base pairs with the complementary base of the template  Second ribonucleotide pairs with the template and is joined to the first base by a phosphodiester bond  RNA is only using the template strand  Polymerase than copies the DNA in a separate fashion separating the DNA base pairs ahead and forming base pairs behind. The RNA is elongated as the polymerase transcribes the gene. Elongation and Termination  After the enzyme RNA polymerase binds to the promoter, it catalyzes the production of an RNA molecule  The base sequence of the RNA produced is complementary to the base sequence of the DNA template strand  Transcription ends with a termination phase. RNA polymerase encounters a transcription termination signal that causes the RNA to from a unique structure that help to dissociate from the DNA and from the RNA polymerase The RNA is processed differently in prokaryotes and eukaryotes  Prokaryotes lack nuclear envelope  Hence, prokaryotic mRNA is formed in the cytoplasm Proteins  Are the active players in most cell processes  Involved in essentially all sub-cellular, cellular, and developmental functions in living organisms  Major classes of proteins: o Enzymatic: catalysts in biochemical reactions (DNA/RNA polymerases) o Regulatory: control of gene expression, intercellular signaling (transcription factors) o Structural: cellular or organismal anatomy Amino Acids  The building blocks of proteins (monomers)  An a.a. consists of a central carbon atom (alpha carbon), linked to an amino group, a carboxylic acid group, a hydrogen atom, and a distinctive R group (the side chain)  Twenty kinds of side chains varying in size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and their ability to be further modified  Proteins are built from a repertoire of 20 amino acids  The amino acid sequence of a protein determines its three-dimensional structure  The remarkable range of fxns mediated by proteins results from the diversity of these 20 building blocks October 10, 2012 Protein Synthesis Translation  Process of converting info stored in nucleic acid sequences into proteins  Genetic Code: the ribosomes read mRNA sequences in 3-base codons Components  mRNA: the template that is used to specify amino acid sequence  Ribosomes: a complex of proteins and rRNA molecules  Transfer RNA (tRNA): small (70-80 nucleotides) RNA molecules that serve as adapters b/t codons in mRNA and a.a. Transfer RNA (tRNA):  tRNA anticodon recognize the codon in mRNA  the hydroxyl (3’) end of each tRNA is linked to the carboxyl group of a specific a.a The Genetic Code  Triplet Code: 61 a.a.-codons for 10 a.a. o 3 stop codons, to terminate protein synthesis  A universal code that is used in the nuclear genome of most organisms  Complementary anti codons are present in tRNA molecules which are specifically linked to a.a.  With 4 bases in RNA, the 3 base codons, there are 64 possible codons, but only 20 a.a. Thus, the genetic code is degenerate, where some a.a. specified by more than one codon (up to 6) October12, 2012 1. Translation Initiation: to begin translation, and small ribosomal subunit along with the initiating tRNA, assemble onto the mRNA 2. Translation Elongation: with the initiator tRNA placed at the P site of the ribosom, elongation can proceed. The next aminoacyl-tRNA enters the ribosome at the A site. The amino acid at the P site is transferred to the tRNA at the A site. The ribosome moves one codon farther along the mRNA, releasing the empty tRNA. The A site is now free for the next incoming tRNA. The cycle is repeated as the ribosome travels along the mRNA resulting ina growing polypeptide chain. 3. Translation Termination: translation termination is triggered by a stop codon in the mRNA. Stop codons are recognized by release factors, which help release the fully-synthesized polypeptide chain from the ribosome. Translation  In translation, the sequence of bases in the mRNA is converted to an amino acid sequence in a protein  Each a.a. is specified by three bases (a codon) in the mRNA, according the a nearly universal genetic code  Ribosomes catalyze translation of the mRNA sequence into protein  Inside ribosomes, mRNAs are translated to proteins via intermediary molecules called transfer RNAs (tRNA)  Transfer RNAs carry a.a. and have a three-base pair anitcodon, which binds to an mRNA codon  The a.a. carried by the transfer RNA is then added to the growing protein via formation of a peptide bond Moving Down the mRNA  Translocation, which occurs when the ribosome moves down the mRNA in the 5’ to 3’ direction, moves the empty tRNA into the E site, movies to the tRNA containing the growing polypeptide into the P site, and opens the A site to expose a new mRNA codon  The three steps in elongation repeat down the length of the mRNA: o Arrival of a.a. loaded to tRNA o Peptide bond formation o Translocation October 15, 2012 Polyribosome  Polyribosome are strings of ribosomes  Assembled along a mRNA to increase the rate of protein production SECOND MIDTERM: The Length of the DNA  Human DNA of one cell is ~2 meters long  10 cells are produced in human lifetime o 2 x 10 km of DNA Mutations  In the living cell, DNA undergoes frequent chemical change, especially when it is being replicated  Most of these changes are quickly repaired  Those that are not result in a mutation DNA Repair  Mutations can result from the incorporation of incorrect bases during DNA replication  Most such spontaneous changes in DHA are temporary because they are immediately corrected by processes collectively called DNA REPAIR  Most damage to DNA is repaired by removal of the damaged bases followed by resynthesis of the excised region The Molecular Basis of Mutation  A mutation is any change in an organism’s DNA sequence  Proteins, encoded by the genotype, produce the phenotype  Hence, DNA mutations affect phenotype only when the mutation is expressed (DNA -> RNA -> Protein) and the resulting protein functions abnormally  Not all mutations affect the protein’s ability to function and thus do not generate a phenotye  One of the most common types of mutation is the point mutation, a change in a single nucleotide  Point mutations can result from errors in DNA replication or from exposure to mutagenic toxins. October 17, 2012 NOTES ON PAPER October 19, 2012 Mutated Genes can Induce Cancer Mutated Genes -> Cancer What is Cancer?  Cancer is an essence of a genetic disease  It’s caused by mutations of genes o Mainly somatic non-heritable Origin of Mutations  Spontaneous  Physically induced (UV light)  Chemically induced  Physically and chemically = environment Epidemiology of Cancer Tobacco and Lung Cancer The Smoking Gun  The class of mechanism of lung carcinogenesis is based on the fact of that carcinogens in the tobacco end up causing DNA mutations  Tobacco smoke consists of approximately 60 known components that have adverse biological affects Adler (1912): “primary neoplasm of the lung are among the rarest forms of the disease” COPD (Chronic Obstructive Pulmonary Disease) 22% of Canadians aged 15-19 years old, were smokers in the year 2001 Tobacco and Cancer  Lung cancer is the leading cause of cancer deaths in the U.S. and Canada  In 1992, the U.S. Environmental Protection Agency classified tobacco smoke as the most dangerous cancer-causing agents in humans  In the U.S., nearly 150,000 people die prematurely each year from tobacco- related cancers and many more from other non cancer diseases (~500,000)  Lung cancer is almost entirely preventable, since the vast majority of cases are due to cigarette smoking 30% of all cancer deaths is due to smoking Smoking accounts for ~80% of all cases of lung cancer Second-hand Smoking  Kills 70,000 people in the U.S. In a pregnant mother, three generations are directly exposed to the same environmental conditions at the same time, Spontaneous abortion and other defects in babies born to smokers (especially mother) If smoking is so bad, why is it still so common? - For making money Why did women start smoking and why? During the 40s the tobacco company used psychoanalysis manipulations to try and convince women to smoke. Prior to, a woman smoking in public was actually considered “taboo”. “Tobacco companies deduct the cost of advertising and promotion from their taxes as a business expense, which saves them in excess of $1 billion dollars a year” In 1997, tobacco companies spent almost %5,.7 billion dollars to promote and advertise their products. This represents an increase in spending of almost 16 times since 1970, when advertising on radio and television was banned. While tobacco products have been mass. Should our govt support businesses that their products are causing such a huge damage to our society? What should be the criteria to illegalize such an activity? October 22, 2012 Evolution  The change in the inherited traits of a population of organisms through successive generations  Mainly by changes of DNA sequences: mutations  Charles Darwin: “it is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is most adaptable to change”.  Survival of the Fittest/Strongest Cells The Cell Theory  Developed during the mid 1600s o The discovery microscopy  All living organism are made of cells  New cells are created by old cells dividing into two  Cells are the basic building units of life The Eukaryotic Cell  The cell surface o Plasma membrane  Integral membrane proteins o Cytoplasm  Mitochondria  Endoplasmic reticulum  Vesicles such as lysosomes o The nucleus Plasma Membrane Function of Cell Membranes  Separate the inside of the cell from the outside environment  Organize the cell from inside  Separate cells from one another  Provide a surface on which chemical reactions occur  Regulate the passage of materials into/out of cells Membrane Structure  The struc. of phospholipids is responsible for the basic fxn of membranes as barriers b/t two polar (water) compartments  How? o Hint: oil and water cannot be mixed  Both inside and outside of cell are made of water  Phospholipids have a hydrophilic and a hydrophobic part Most naturally occurring phospholipids form bilayers spontaneously when they are dispersed in water. Why?  For the same reason that drops of oil in water will form a larger drop Structure of Plasma Membrane  Why phospholipids form bilayers spontaneously when they are dispersed in water? o The “head” group, the phosphate and glycerol, is polar and hydrophilic  Associate with water  The hydrophilic portion is associated with water from the both sides of the membrane o The long “tail” is nonpolar and hydrophobic  Repelled by water  The hydrophobic portion of two molecules or more tend to associate with each other  Like drops of oil in water October 24, 2012 Notes on Paper October 26, 2012 Vesicle  A pocket made of membrane that is separated from the cytoplasm  A carrier of molecules in and out of the cell without crossing the membrane Penetration of enveloped viruses by endocytosis  Make cells more susceptible  Easy for viruses to enter The origin of Mitochondria  The mitochondria have many similarities to bacterial cell: o Double cell membrane like some bacteria o Circular DNA o Genes without introns (to be discussed) o Small ribosomes o Similar size to prokaryotic cells  The has led many biologists to theorize that mitochondria are the descendants of some bacteria which was endocytosed by a larger cell billions of years ago, but not digested Lysosomes  Are the cells’ garbage disposal system, the “clean-up crew”  Breaking down molecules into their base components using strong digestive enzymes Nucleus Structure  Outer membrane, inner membrane, rough ER, chromatin, nucleolus, nuclear pore  The nucleus, the largest organelle, contains the DNA, RNA, proteins  The DNA is packed into chromosomes, an assembly of DNA and proteins  The nuclear envelope surrounding the nucleus consists of two membranes  This envelope has large pores that allow RNA and other macromolecules to leave or to enter the nucleus  On the inner surface there are attachment sites for the DNA molecules  The nucleolus is a spherical body located within the nucleus that contains primarily RNA and proteins Polio – (Video: The Polio Crusade) A infectious disease which was derived from the West, that in most cases has no symptoms. It was caused by a virus, which invades the nervous system. This disease can invade the brain and spinal cord, which can lead to paralysis, disability or death. The most severe cases were in the 1950s in the United States. Symptoms: ◦ Abortive polio – people who have the illness but don’t suspect anything because the symptoms are much similar to flu-like symptom- therefore having minor symptoms such as mild breathing problems, fever, cough, sore throat etc.( almost 95% of people have this form of symptoms ) ◦ Meningitis- a more serious form of the disease where it one may contain neurological symptoms – can lead to paralysis ◦ . Paralytic polio- (rare case) but the most severe that could result in permanent disability or death Vaccination -There is no cure for the disease, although vaccination was the best way to protect the people. On April 26, 1954 – first vaccination given to children in the US. No one was aware if the vaccination was going to work, because there no evidence. Although, about a year later the vaccination was proved to work after 20 years of research to avoid polio. But even after there were cases where the vaccine was found to be contaminated with polio. By 1957, the vaccine decreased polio by 50% of the American population. And finally by 1962, they invented a oral vaccination, which ultimately decreased the chances of one attaining polio. October 29, 2012 - Covered with a cloud of microbes from day 1 - Microbes are very important to our health, doing good for us most of the time ◦ Help us to be healthy, to have appropriate vitamins - Microbes are an important part to our immune system (against more aggressive microbes, play defense) ◦ Ex. - taking long term antibiotics = secondary infections (yeast) , cloud of microbes surrounding you are destroyed by the antibiotics therefore making you prone to infection - Microbes also boost the immune system - Animals ingest microbes through feces to boost their immune system - Microbes protect us from allergies - Skin acts as barrier against harm, if barrier broken and antigen recognized immune system triggered - Harmful microbes can enter through the nose, eyes, mouth, and cuts  Hygiene Theory : In order to have a strong immune system, you need to be expoesd to microbes from a very young age. Infectious Diseases and Host Defense: - Immunology: the study of our protection from and response to foreign invading organisms and altered host cells ◦ good against virus cells ◦ Cancer cells know how to escape from the immune system ,and sometimes actually it should be blamed for the initiated of cancer cells.(20% of cancer is a product of chronic inflammation = cancer is initiated) ◦ viruses: in many cases, activating the immune system is the only way to fight the disease (Ex. - small pox is gone because we were able to adapt our immune system to disease) ◦ many vaccines to prevent viruses, few drugs to fight them ◦ bacteria: synergism between antibiotics and the immune system (for the antibiotics to have effect, you need to have a good immune system) Balance between Infection and Immunity: - Immune system's job is to recognize “self from non-self” and destroy abnormal molecules and cells (The Merck Manual) - When we feel fine, there is a balance between infection and immunity Infection - amount of pathogens Virulence is balanced with Immunity - host defense mechanisms = no infections Breaking the Balance: ◦ When the amount of pathogens is increased = less balance with immunity = DISEASE ◦ Some people are born with weak immune systems (certain enzyme isn't working) = decrease in defense mechanisms ◦ Too much immunity is not good for you = when immune system is working against the wrong target (Ex. - allergic reactions)(eg.pollen,chalk,etc)(One reason may because you live in a really clean environment and rarely are exposed to dust.) ◦ Autoimmune disease: when the immune system can't recognize body as itself, normally immune systems can recognize the body (immune system is turning against itself Ex. - immune system attacking joints, heart, kidneys, etc.) -> immune system sometimes misses the point ◦ Acute imflammation - sepsis: aggressive reactions (acute inflammation - quick reaction) immune system is overreacting against pathogens, so sever that the main damage is from the immune system ◦ Chronic inflammation - cancer: long term inflammation (Ex. - Hep. B) + Immunology is the study of our protection from response to foreign invading organisms and altered cells. Viruses: in many cases, activating the immune system is the only way to fight the disease Bacteria: synergism between antibiotics and the immune system November 12, 2012 Immunity vs. Autoimmunity Balance between Infection and Immunity  Infection = amount of pathogens virulence  Immunity = hose defense mechanism  There is a problem if the immune system cannot work properly  People with malaria What happens if the immune system is too strong?  Works against systems that do not harm us  Allergy  Autoimmune disease  Acute inflammation-sepsis  Chronic inflammation – cancer November 14, 2012 Our immune system- intro - 3 stages o Anatomical and physiological barriers  Skin  Low stomach pH o Innate immunity (basic immunity)  Circulation (white blood cells) o Adaptive immunity - Normal flora and anatomical barriers o Skin  An outer layer of intact skin  Normal flora  Flushing (sweat)-clears bacteria  Fatty acids- “soap” o Gastrointestinal tract  Peristalsis  Low pH(acidity)  Bile salts-“soap” o Nasopharynx and eye  Mucus, saliva, tears  Flushing  Lysozyme- destroy bacterial cells(in tears) Nonspecific Specific Speed: immediate Effects after few days No immunologic memory–healing Leads to a state of immune memory- process stays the same with same problem happens again immunity problem over time stops it (chicken pox) Specificity limited: 1 cell can Specificity improves during the recognize many pathogens course of response. 1 cell can recognize 1 pathogen highly diverse Specific (adaptive) immunity- response to infection - 1. Infection innate immunity disease  recovery adaptive immunity - 2. Infection innate immunity no disease adaptive immunity - 3. Vaccination adaptive immunity Adaptive immunity re-infection doesn’t happen b.c of immunity November 16. 2012 Organs of the Immune System  The immune system is found throughout the body and is made up of many different cells, organs, and tissues  The lymphoid system is divided into: o Bone marrow  The factory for hematopoietic stem cells o The thymus  Instructs certain lymphocytes to differentiate into thymus- dependent (T) lymphocytes  Peripheral lymphoid organs o Lymph nodes o The spleen o Mucosal and submucosal tissues of the digestive and respiratory tracts Cells of the Immune System  Hematopoietic stem cells o Lymphoid cells  B-cells  Plasma memory  T-cells  Helper cytotoxic suppressor
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