Microbiology Notes: 2007

Wednesday, December 12, 2007

Final - the end!

We had the final for Microbiology today! IT is finished, we've made it to the end. I hope this sight has been helpful to all those trying to make the grade. For those of you that are taking Microbiology in the future here are my tips to you.

Review often (ideally after each class)
Answer the questions on the lab demo's right after the lab, if at all possible.
Do all the extra credit.

If anyone else who has taken the Microbiology class with Knipp wants to leave any tips feel free to give some advice in the comments!

Friday, December 7, 2007

Lecture 34, 12/7; Purification

Audio available here.

5 groups. On the test Mon. About 80 diseases that we are going to need to classify
Final – 140 questions and an essay. 150pts

• “Immunology” handout

o immunodeficiency – cant respond to the antigen. Burton’s disease, DiGeorge syndrome, SCID (sever combined immunodeficiency disease) – food must be autoclaved.

o Secondaray immunodeficiency diseases

• AID’s

o From ummunoppressive agents

• Irradiation

• Severe burns

o Auto-immune diseases - Respond to your own antigens

• Systemic Lupus Eritomas (SLE) – lupus. You respond to some of your own antigens

• Rheumatoid arthritis

• Type I, Type II diabetes

• MS

• Rheumatic fever

• Interleukin-2 (lymphokine, T cell product, CD4 +’s)

o 1 lymphokine affects b cells (responsible for antibody’s imunoglobulins). Helps with the proliferation of T cells.

o NK’s – natural killers. They are immune surveillance. They go through the body looking for things such as cancer cells (which have unique antigens).

• Type I hypersensitivity

o Response to pollen is caused by IgE. It causes the degranulation of the mast cells.

• Soil

o Urea to ammonia by the organism protease (ammonification)

o Nitrates – solid fertilizers

o Nitrogen fixation – rhizobium and legumes (symbiotic)

• Azotobacter and Klebsiella can do fix Nitrogen by themselves

• Bacterial photosynthesis – don’t have to know it
• Food poisoning and Water poisoning

o Don’t see milk borne diseases due to pasturization

o salmonella food poisoning

o fecal organisms

• enterococcus fecaelis

• e coli

o botulism – poorly canned foods

• food intoxication

o enterotoxin like staph aereus (fast acting food poisening)

o Botulism – get it from homemade canning

o Perfringens – associated with turkey

o e. coli o157: H7

• water purification

o Aluminum Potassium Sulfate – a protein precipitate. Mix it up let it coagulate and take the water off the top. It is then run through a sand filter. Microorganisms like to attach to the sand. From there chlorine is added. In places where this filtration process is worse they tend to add more chlorine.

• Sewage Treatment

o Use organisms to break down organic to inorganic substances

o aeration tanks

• zoogloea ramigera

o From the aeration tanks it is essentially the same process as water purification

• Bacterial Food Poisoning

o Staph aureus – custard and cream filled pastries and mayonnaise (projectile vomit)

o Clostridium perfringens - reheated meat like turkey

o Salmonella – poultry and eggs

o Clostridium botulism – turns things black. The exotoxin of clostridium is heat labile

• Exotoxins that are harmful

o Tetnus

o Salmonella typhi

o Botulism

o Neisserhea meningitidis

Thursday, December 6, 2007

Lecture 33, 12/5; Immunology

Here is the audio for this day's lecture.

• Org group exam Dec. 10 8am
• Big Final Wed 7:30. Dec 12
• Portfolio due Friday Dec 14

Flesh eating disease

Necrotizing fasciitis caused by Streptococcus pyogenes (p551 in text).

• 4-s → staphylococcal scolded skin syndrome (p548 in text)

staphylococcus aureus

• gas gang green

clostridium perfringens

• Immunology – classification of antibodies (handout from 11/28 titled “Immunology”)

IgG – most of the antibody is IgG. It comes from mom through placenta.

IGM – the macro antibody. Very large. It is a pintomer (5 IgG’s). Notable because it is the first antibody formed. Soaks up a lot of antigen.

IgA – a dimer, two monomers held together. Get it from mothers milk - colostrums. Coats GI tract of infant protecting from diarrhea. Also in other secretions such as saliva and urine. It is the secretory antibody.

IgD, IgE – look like IgG. In smaller concentrations. Antibody usually on surface of B cells and helps it recognize antigens. IgE protective against parasitic diseases. It is associated with hypersensitivity. Anaphylactic shock (adverse reaction to penicillin).

• Functional classes of antibodies (1st page of “Immunology” handout from 11/28)

Opsonins - Antibodies that make the antigen more susceptible to phagocytosis.

Antitoxins – antibodies that neutralize antitoxin toxins. We form them in response to a toxoid. Example – tetnus and diptheria. Shot lasts about 10 years

• Chemical makeup of IgG – composed of four peptide chains. Two “h” chains. Twice the size of l chains. They are all held together by disulfide bonds. There is some CHO on the H chain. Divalent – two antigen binding sights. An IgM can bind 10, that is why it is one of the first ones produced → it soaks up the antigen and takes it out.
• Fate of the foreign antigen (chart on p 5 of “Immunology” handout)

Initial or Primary response - IgG

Secondary or memory response or Anamnestic response.

• T cells mature in the thymus. B cells come from bone marrow.
• “The complex network …… defense mechanisms” (p2 from “Immunology” handout)

plasma cell - When it differentiates it forms all the immunoglobulins. IgG, IgM, IgD, IgE.

“T” helpers help b cells produce antibody’s. CD4 positives

Multiple myeloma – too much antibody produced

“T” killer. Virus antigen on outside of cell. T killer recognizes the viral antigen and kill the cell that is loaded with viruses.

delayed hypersensitivity (another type of T cell) – poisen ivy, TB tests. T cells also produce lymphokines that modulate the immune response. Example of lymphokine is interferon. There are three types of interferon’s; alpha beta antivirul, gamma (modulates reactions), and interleukin (come from leucocytes). We have 65 interleukin produced by different cells.

• VACCINES (p.7 of “Immunology” handout)

guardisil

rototeq – helps babies effected by diarrhea

Related Organism

• smallpox

Killed Organisms – dead suspension of something like:

• Cholera, whooping cough, polio (injectable. Discovered by Sulk), Influenza, rabies, typhoid fever, hepatitis A (havrix)

Attenuated Organism – living organism that is a strain of a disesease that is not harmful. Developled by Pasteur.

• MMR (measles, mumps, rubella), polio (oral), TB-BCG, Varivax (VZV)

Acellular (parts of organism)

• Capsule (HIB [Heamophilus Influenza Type b]

• Pneumovax - capsule of strep pneumonae

• Pili - whooping cough, purtussis.

Recombanant

• Hep. B. - Heptavax/Engerix

Toxoids

• Diphtheria, tetanus

• Havrix – hepatitis A vaccine, inactivated (p8 of “Immunology” handout)

• Immunodefiency diseases

AIDs

A gamma globulin anemia – b cell defect. Cant produce any antibody.
T cell defect – if your thymus doesn’t grow. Digeorges syndrome (???not sure??)

Severe combined immuno deficiency – b cell and t cell defects. SCID – bubble boy syndrome

Lecture 32, 12/3; Viruses, Immunology

Here is the audio.

• Medically important human viruses
• HSV-1, HSV-2 → herpes, oral and genital
• RSV → respiratory sincicial virus. Mom can give it to the baby.
• EBV → mono and burkettes lymphona
• VZV → chicken pox and shingles
• HPV → human papiloma virus. Causes warts. Some strains are associated with cervical cancer. (this is why Guardisil is popular)
• Adenovirus → upper respiratory infections, not a cold
• HAV → Hep A virus. Fecal/oral → contaminated water/food. There is a vaccine for it.
• HBV → Hep B virus. Blood borne or semen. Linked with liver cancer. There is a vaccine for it.
• HCV → Hep C virus. Similar transimission to Hep B. Used to be called transfusion disease. No vaccine.
• Rotavirus → severe diarrhea in babies and toddlers. Rotateq combats this disease.
• Rubella virus → German measles
• Variola virus → supposedly eradicated. Smallpox
• Rabies virus → rabies. Bullet shaped virus. Most deadly.
• Measles virus → MMR takes care of it
• Influenza → old get vaccinated. Hypermutability – changes very quickly. This is why you need a flu shot every year.
• Hantavirus - Navajo flu → Comes from little white mice.
• CMV – Cytomegalo virus → Babies, toddlers, and AIDs patients are susceptible.
• Rhinovirus → common cold, 120 different strains (that is why there is no vaccine).
• Echo/Coxsackle viruses - Noro virus → Causes gastroenteritis. Cruise ship disease.
• Mumps virus → can move to testicles in guys. MMR vaccine takes care of it.
• St. Louis Encephalitis virus (SLE) → mosquito borne
• West Nile → mosquito borne
• HIV-1 and HIV-2 → takes out all T helper cells. Allows for opportunistic disease to come in.
• HTLV-1 and HTLV-2 - human T cell lymphoma viruses → Can cause cancer.
• AID’s related infections – sheet from handout showing diseases AID’s patients get with time.

o Bacterial skin infections are one of the first things you see.

o Thrush comes in (usually a good indicator of AID’s)

o Severe athletes foot

o PCP, histo, herpes, crypto

• IMMUNOLOGY

o Winter viruses are typically airborne

• 1st line of defense – Mechanical factors

o lysosymes – good against gram (+).

o Organisms can’t go through the skin EXCEPT for rabbit fever

o Mucus is sticky and holds organisms

o Normal flora – prevent pathogens from colonizing

• Second line of defense - Cellular factors

o If disease comes into bloodstream white blood cells will come to do phagocytosis (discovered by Meintchnekoff). Interferon was initially up to 10,000$ a shot.

o Inflammation – heat, redness, swelling, pain. This is the bodies way of localizing an infection.

• Third line; antibody formation. Takes 10-14 days

o Acquired immunity

• Types of acquired immunity

o Active immunity – we form the antibodies (long lasting)

• Artificially acquired - vaccines

Naturally acquired – infections

• Acute or sub-acute

o Passive immunity – someone else is forming the antibodies

• Artificially acquired – HBIG

• Immune globulin – immediate protection but does not last long (about a month). They are preformed antibodies.

• Naturally acquired – HgG and IgA

IgG is given from the mother to baby across the placenta. IgA is from mothers milk – it coats intestine of baby and prevents diarrhea in baby. Rototeq can cause this diarrhea.

• Classes of antibodies

o “Y” usually represents antibodies

o IgG – the most important one, we have the most of this in our blood. 80-85% of all the antibodies we carry is IgG. Major protective antibody in blood. If you run into an antigen it is IgG that will probably attach to it. It is also the one that comes from mom to baby over placenta.

Lecture 31, 11/30; Vectors, Toxins

Here's the audio.

• Opening
o Monday – pass in AID’s Week reflection paper
o AID’s cases have been about 40 mil. For the first time AID’s has decreased.
o Autclave 121C, 15 psi, 15-30min
o Filtration
o Sab-dex=molds
o EMB, McKoncey – gram (-) rods
o 3:20 what azide does?
o Ent fecalis – always ferments – nothing oxidated
o 100 colonies on a plate → 10^5 → positive for UTI

• Bacteria

o Salmonella typhi – typhoid fever

o Shigella dysenteriae - dysentarea

o Vibrio cholerae - cholera

o Campylobacter jejuni - gastroenteritis

o Escherichia coli

• protozoa

o entamoeba histolytica – amoebic dysentary

o giardia lamblia - giardiasis

o cryptosporidium parvum - cryptosporidiosis

• Viruses

o Hepatitis A virus (HAV) – fecal, oral

o Poliomyelitis virus (PMV) -

o Coxsackie/Echo/Norwalk – Norro (cruis ship disease)

• Bioremediation – pseudomonas
• Sewage treatment – bacteria are involved here
• Food poisoning
• “Infectious Disease” handout – mode of transmission

o Mode of Transmission

o Contact infection – STD’s

o Droplet infection

o Phomites are inanimate objects.

• Vectors

o Insects that move the organism from one place to another. Ex. Flies, mechanical vector → cholera

o Biological vectors – growth stage is in the vector. Lyme, malaria, west Nile.

• Portal of entry

o Elementary track

o Mom → baby = vertical transfer. Ex. AID’s, psyphylis, genital herpes

• If you’ve seen the antigen you’ve got antibodies.
• Typhoid Mary – Salmonella typhi

o Could have carried in gall bladder. Found in poop → no hand washing

• Study pathogens from two standpoints: transmission, how does it cause the disease – virulence factors
• Virulence factors – how do they cause disease

o invading tissue – invasive factors OR

o production of toxins – toxigenic factors

• Capsule – inhibits phagocytosis

o Strep pneumonae

o Klebsiella pneumonae

• Pillis

o Neisseria gohnerrhea

o Whooping cough – bordetella pertussis

• Highly uronidase (the spreading factor) – sometimes its structure sometimes its enzyme or secretion. It is an enzyme that breaks down highly uronic acid (this is whats in tissue that holds cells together, if this is broken down the organism spreads through the tissue)

o Usually think of staphs and streps

• Coagulase – Coagulase positive → staph aureus.
• Lukasiden – staphs and streps have a secretion that kills white cells. An accumulation of this dead white blood cells is puss.
• Hemolysin – break down red blood cells. Alpha and Beta hemolysis can only be seen on blood agar. Alpha is incomplete, Beta is complete. Streptococcus pneumonae is an alpha. Strep pyogenes - complete hemolysis.
• Toxins

o Exotoxins – from some gram (+). More lethal.

o Indotoxin – from gram (-)

• High fever = gram (-) infection
• Classical exotoxins

o Corinii

o Tetani

o Botulinum

• Staph aureus has an enterotoxin (under exotosin category). It affects the intestines. That enterotoxin is what causes staph food poisening.
• Shigella dysentari (gram -) – has an endotoxin
• Immunology
o Resistance (much broader) vs immunity (specific antibodies for a disease)
o Antigen – a substance, usually injected, producing protective proteins called antibodies. Vaccines are suspensions of antigens.
o Immunoglobulin (Ig’s) – new name for antibodies (protective proteins that are formed in response to antigens).
o An antigen has size - molecular weight of more than 10,000. It has to have chemical complexity. Proteins are very good antigens. Lipids → no . . . nucleic acids → no.
o Lupus – your respond to your own DNA

Wednesday, November 28, 2007

Lecture 30, 11/28; Immunology

Here is the audio for today's lecture.

• Be sure to have your lab number on your write up of AIDS week
• Lab practical next teus. About 80minutes.
o 8 lab 2
o 10 lab 3
o 12 lab 4
o 2pm+4pm either lab 1+5

• IMMUNOLOGY

o Back of page 2 from handout from 11/28 “Immunology”

o B cells are associated with plasms cells. Plasma cells produce all those antibodies. T cells tend to be regulatory in nature. We know cd4+. That is the cell that HIV likes. T-helper helps the B cells. HIV destroys the communication between these two cells.

o Side notes: candida albicans (budding)– thrush

• Toxoplasmosis – protozoan

• Valley fever - fungal

• PCP – fungal

• Herpes – virus

o Vaccines

• Cowpox vaccine is given instead of smallpox. They share antigens

• Engerix-b – recombinant vaccine

• Handout from 11/26 “Infection and Disease” - definitions

o Toxoids - diphtheria, tetanus

o vaccine – simple suspensions of antigens. When given to an individual the production of antibodies is stimulated

o virulence – capacity or ability to cause disease. Highly virulent organisms – rabies, ebola. Low virulence organism – candida albicans (must be given an opportunity to cause disease)

o zoonosis – diseases of animals that can be transmitted to man. Example – Lyme, Anthrax. Fungal zoonosis – ringworm, microsporum canis. Protozoan zoonosis – taxoplasmosis gondii. Prion zoonosis – mad cow disease. Viral zoonosis – rabies. Most of our emerging diseases are zoonosis.

o Nosocomial infections (from the hospital) – if you see puss it is either a staph or a strep. Bacteria that account for 70% of nosocomial infections (these are the main 4): E. coli → UTI, Staph aureus, enterococcus faecalis. pseudomonas aeruginosa – blue green puss

• STAGES OF INFECTIOUS DISEASE

o Incubation period – time of exposure to time of symptoms

o Prodromal stage – highly communicable, disease can spread easily at this stage.

o Clinical stage – peak symptoms

o Decline stage – first signs of recovery, could also become latent or hidden. Disease that does this → herpes. You are also are developing antibodies.

o Convalescent stage – return to recovery

• SUMMARY OF EVENTS IN THE TRANSMISSION OF DISEASE

o Portals of exit

• Feces

• Urine

• Discharges from mouth and nose

• Saliva – rabies, mononucleosis

• Blood

o Portals of entry: skin, respiratory

Tuesday, November 27, 2007

Micro Lab 11/27 - Review Session with Eric Wells

I recorded the review session with Eric during lab 3. Here is the audio.

DONT TRUST MY SPELLING!!!

• Selective – only grows certain types of organisms. Ex. EMB selects for gram – organisms and inhibits the growth of gram +.
• Differential – what organisms do when they grow. Ex. EMB is differential based on lactose fermentation
• Enriched media – don’t know exactly what is in it, really good for fastidious organisms (organisms that require a lot of ingredients)
• Chemically defined – all components are known. Organisms that grow on these are the complete opposite of fastidious. Ex. M-9, E. coli grows on this
• General purpose – use this if you want to grow an organism and don’t need anything special to do it
• NA Plates – general purpose. We used to isolate organisms from our body and from dust.
• TSA (triptic soy agar – has soybean digest and triptone which is a digestive kasin. Kasin is the protein that makes milk white)– general purpose. We used it to isolate organisms from our body and from dust.
• Nutrient Agar – has beef extract and peptone for nutrients.
• Motility test agar stab tube – differential, used to determine motility. Percent of agar used is 0.5%. The plates have 1.5% agar.
• Sab-Dex Plates – selective because they only grow fungi. High sugar and low pH around 6 which is great for fungi growth.
• Agar block plates – made with sab-dex. Used to identify different molds.
• Blood agar – enriched media. Differential because you can look at hemolysis. Alpha hemolysis – partial clearing of red blood cells. Two organisms that did that are streptimoni and strep salivarius. Beta hemolysis – complete clearing. Two organisms that do this are streptococcus pyogenes and staph aerues.

o How do you make blood agar/chocolate agar → start with a base (TSA,NA, Brain Heart infusion). Heat it and melt it. Cool it down to 35-40C before you add 5% sheep blood.

o Chocalate Agar is the same process except you cool it to 80C when you add the blood. This lyses the blood cells and turns it a chocalatey color.

• Chocalate Agar – enriched media. You can grow even more fastidious organisms on it. It is the same principle as cooking food → it helps the organism digest nutrients easier. You would grow strep pnemonea, any legionella, heamophilus influenza, neisseria gonohrrea.

• EMB plates – selective and differential. Selective because of the dyes (eosin and methaline blue → inhibit gram (+) this means they select for gram (-)). They are differential because of lactose.

o EMB – e. coli has metallic green sheen

o Klebsiella – gooey fish eye

o EA – looked normal

o Proteus Mirabilis – negative

o Staph Aureus – had trouble growing

o Ent. Feacalis – had trouble growing

o B. sub – had trouble growing but had endospores and survived.

• MSA plates – Mannitol Salt Agar. Mannitol makes it differential. Salt makes it selective. It differentiates based on mannitol fermentation. Also has pH indicator → phenol red. In the presence of an acid it turns yellow. Same pH indicator used in TSI slants and Urea agar slants. When it is basic turns red. A positive reaction on MSA is a yellowing of the agar, negative is still pink.

o It selects especially well for staphs. They can tolerate the high salt level. You can also grow entrococcus on it → positive but did not ferment as well as staph aeurues.

• M-ENT plates – extremely selective, only grow enterococci. The ingredient that makes this so selective is sodium azide. Similar to cyanide. It also has a pH indicator TTC → doesn’t make it differential just makes the colonies turn a red color when the grow making it more visible.
• BHI agar – enriched medium. Good for fastidious organisms. Can make blood/chocolate agar with it.
• Starch agar plates (NA plate with starch in it) – differential. We used them to differentiate organisms ability to break down starch. B. sub could break down starch. E. coli could not break down starch. We are ultimately testing for the presence of amylase → this breaks down starch.
• TSI slants – highly differential. Three sugars, has iron in it. Three sugars are lactose (10x), sucrose (10x), glucose (1x). Also has iron sulfate which helps with H2S production in some organisms. Has pH indicator Phenol red (yellow with acid, red with bases).
• 3 things to look for sugar fermentation, gas bubble production, H2S production.
• Only proteus do iron to H2S
• Skim Milk Agar plate – differential. NA plate with skim milk to give them some kasin. Testing for presence of a protease or kasinase.

o B sub – positive (has protease)

o E. coli

• Nutrient gelatin stab tubes – differential. Gelatin is a protein matrix – that’s what keeps it solid. If an organism has a protease it will break down that protein matrix. A positive reaction would be a liquid tube. Negative reaction – tube still solid. Used it looking at mostly gram (-)
• Plate Count Agar – like NA, general purpose
• Simmons Citrate Agar Slant Tubes – differential. Used for Gram (-) rods. PH indicator is Brohm Thymol. Starts out green – in a presence of a base it turns blue. We are testing for the ability of an organism to utilize citrate as a source of carbon. If they can they will grow. Also present are ammonium salts → if it grows it will use these salts (create ammonia). The ammonia then reacts with the Brohm Thymol and turn it from green to blue (blue is the positive reaction for this one). Used for gram (-)
• Urea Agar Slant Tubes – used for gram (-). Differential. Testing fro presence of urease. Urea broken down to CO2 and ammonia using a urease. The pH indicator is phenol red. In presence of a base it goes pink. Positive is pink.
• Mckonkey Agar Plate- just like EMB but with different ingredients. Used for gram (–) organisms. Unlike emb it selects for a more narrow range of organisms. Two of its ingredients make it selective – bio-salts and crystal violet (inhibit gram (+) org). The lactose makes it differential. It has a pH indicator – neutral red. When in the presence of acid it turns pink. Positive reaction is pink meaning lactose fermentation. Negative is clear/see through.
• MH - Muelerr Hinten Agar – tests for antimicrobial sensitivity. Has beef extract. General purpose.
• Enterotubes – differential. Results only meaningful if using gram (-) rods.
• Liquid broth
• Litmus milk – differential. grow tons of stuff. Looking for three things: lactose fermentation, curd formation (soft or hard), proteolisis (zone of clearing of kasin). Two ingredients = litmus and skim milk.
• Tryptone broth – used to detect presence of tryptophanase. Tryptone digest of kasin is rich in tryptophan. If an organism makes tryptophanase it breaks it down and results in indole. Put kovacs reagent in and it reacts with indole. If it is positive it will produce a red ring on top (negative- no reaction). Used a lot for gram (-).
• Nitrate broth – gram (-). It is differential. It is basically beef extract but rich in NO3. NO3→NO2→N2. Positive reaction is the gas bubble. Only one organism was able to make it through and do this → Pseudomonas Auriginosa
• Rabbit plasma (not as important) – differential. Staph aerues is (+). This means it produces coagulase
• 35min
• Lactose broth – differential. Used for water microbiology. Positive reaction is an air bubble. The air bubble in lactose broth comes from lactose fermentation. When you ferment lactose you make acid and a gas byproduct. This test is used to test for gram (-) rods because they will do this.
• MR-VP broth – what organisms do with glucose. Glucose could be fermented to organic acid which lowered the pH to 5ish. Methyl red is added after incubation - If glucose fermented red appeared in tube. OR . . . VP - glucose is converted into 2,3 butane diole. Barets reagent added to convert 2,3 butane diole into acetoine which would give tube a red color. Good test differentiating gram (-) rods.

o e. coli → positive for methyl red. Turned glucose into various natural acids

o e. a. → negative for methyl red

o Using the OTHER method

o E.a → positive. Made 2,3butane from glucose

o E.c. → negative

• M-9 – chemically defined. E. coli grows on it.

Things to know

• Gram reaction, shape
• Do they ferment lactose, do they make spores, do they make pigment

Ex. Psuedomonas aureiginosa – makes extracellular pyocyanin pigment

Serratia marcesins – makes intracellular prodigiosin

ML – makes pigment

Pseudomonas flourescens – makes pigment

• Know if they are bacteria, yeast or mold, ect. And any notable reactions.

Lecture 29, 11/26; Infectious Diseases, Micro Terms

Audio for today's lecture is available here.

Quote of the day: “I haven’t slept with anybody. I’m as pure as the driven snow.”

RANDOM
Lab test a week from Monday the 26th
Know the nitrogen cycle for the final
Microbes in the News
5 bonus points for going to a presentation this week about AIDS. Give him single page of what we learned – due next Monday Dec. 3.

LECTURE
Quick overview of handout from 11/26 “A STUDY GUIDE FOR MICROBIAL PAHTOGENS”

• Streptococcus pyogenes – strep throat. Sometimes called acute pharyngitis. Rheumatic heart disease or rheumatic fever. Gram positive cocci in chains. Beta hemalitic

• Puerperal fever – Semmelweis and Holmes

• Food Borne and Water Borne

• Botulism is food borne

• Shigella dysenteriae is water

• Vibrio cholerae – water

• Soil Borne and Arthropod borne

• Clostridium tetani – spores

• Borrelia burgdorferi – lyme, tics

• STD’s

• Chlamydia

• Clostridium difficile – pseudo membranous colitis. Overdose of oral antibiotics. All good guys in gut die and this organism takes over

• VIRAL

• Rhinoviruses - cold

• VZV – shingles

• FUNGAL DISEASES

• Pneumocystis carinii pneumonia PCP. → It’s a fungus.

• Other handout from 11/27/07 “Infection and Disease”

• Incubation period: time between exposure and first symptoms

o staphylococcal food poisoning has a short incubation period – 1-7hrs

o long incubation period – leprosy, AIDS

o streptococcal sore throat – 2-5days

• commonly reported diseases

o chlamydia

o gonorrhea

o salmonellosis

o AIDS

o Pertussis

o Varicella – chicken pox

o Lyme

o Giardiasis

o Shigellosis

o TB

• Infectious diseases summary on page 5 on handout from 11/26 “Infection and Disease” Page labeled → “Summary of Events in the Transmission of Disease”
• Definitions p 2 of handout 11/26 “Infection and Disease”

o Bacteremia – bacteria in the blood. Flossing can give you this if you break capillaries with the floss → Strep mutans

o Carrier – typhoid mary, patient 0 (history of AIDS)

o Disease – (look up in glossary). Tell diseases apart by symptoms.

o Endemic – low number but constant. Gonorrhea is an example.

o Endotoxin – Gram (-) organisms have it. Part of the cell wall.

o Enteropathogenic – causes problems in the intestine.

o Enterotoxin – has to do with the gut, intestine → diarrhea

o Epidemic – high number of cases. Example AIDS in Africa.

o Etiology – a.k.a. cause. Salmonella typhi → typhoid fever

o Exotoxin – toxin made inside the cell and then secreted

• Clostridium tetani – locks your jaw

• Clistridium botulinum – atoxin

• Corinii bacterium diphtheria – unique cellular arrangement

o Infection – something an organism causes. Localized infection (in one place) or systemic infections. Example of opportunistic → Candida albicans (doesn’t get started till something else happens) yeast infection.

o Nosocomial disease – from the hospital

o Pathogen – any organisms that can cause disease. Some are extremely virulent (doesn’t take many organisms to cause infection). Some are opportunistic and need many more organisms to cause and problems.

o Toxemia – toxins in the blood

o Toxoid – detoxified toxin. Example: used primarily in vaccines.

• Dpt vaccines; diphtheria and tetanus are both toxoids. They are given to us so that we will form antibodies against those organisms in case we ever see them. (fyi: “p” is for purtussis)

Friday, November 16, 2007

Lecture 28, 11/16 (Maybruck 13); Phosphorus

Here is the audio for today's lecture. It is on ly 16:00 min. long. The rest of the time we watched a video about the pneumonia outbreak in 1918.

Ill post the notes sometime before Monday.

Wednesday, November 14, 2007

Lecture 27 11/14 (Dr. Maybruck 12); Biosphere

Audio for todays lecture is available here.

SLIDE 1 handout 11/14
• Biosphere (1 giant ecosystem) – region of earth that contains living organisms

o Living organisms are supported by the interactions that are occurring between abiotic (non living matter) and biotic (living matter) processes.

• Levels of the Biosphere (ultimately connected together)

o Lithosphere – the land (and a few miles into the earth)

o Hydrosphere – aquatic

o Atmosphere – few miles into the air

• Ecosystem: Communities of organisms that are interacting with one another and their physical environment
• Community: populations interacting with one another and their environment
• Population: group of organisms of all the same species
• Habitats: location where the populations live
• Niche: poplulations occurring in the community serve a specific role

o Example: protozoans consuming bacteria

SLIDE 2 Components that make an ecosystem work
• Producers consumers decomposers → different trophic(feeding) levels.

o Primary – autotrophic organisms. Convert CO2¬ into glucose.

• Photoautotrphs – use the sun as an energy source to convert CO2 into glucose
• Chemoautrophic – found in hydrothermal vents. Get nutrients other than the sun

o Consumers and decomposers

• Heterotrophs – convert glucose into CO2. Consumers are ultimately responsible for consuming primary producers.
• Decomposers – consume primary and consumers. Consume them as dead organic matter.

Example: bacteria, fungi, invertebrates, scavenger animals

• Diagram on handout illustrating components of ecosystem

o Energy is lost going from step to step

o NOTE: energy is not cycled back into the system. Ultimately energy is lost through heat. What IS cycled is carbon and nutrients (elements).

SLIDE 3
• Example of energy lost

o Start with 100 energy

o Only 10 units of energy to the next level

o Only 1 unit of energy goes on to the secondary consumers

o Only .1 unit of energy goes to the final consumer

• It is important that the primary consumers are sustained – therefore we are sustained
SLIDE 4
• Carbon – considered separate from nutrients but still critical
• Essential Nutrients: nitrogen, phosphurus
• Liebig’s Law of the minimum – an organisms growth is going to be restricted when the elements (carbon, nitrogen and phosphorus) are not at levels required for the organisms growth.
• Biogeochemically cycle – ensures all trophic levels receive proper nutrients. The most important part of this cycle is biological processes.
• Notes on Carbon Cycle

o CO2 found in high concentrations in aquatic system and aquatic life

o Photosynthetic organisms that occur on land and have access to this CO2

o In aquatic life microorganism are the primary producers → algae, bacteria, protozoans

o Cow consumes glucose of the grass and converts it to CO2

o Autotrophic organisms break down glucose and produce CO2

o Limestone erosion: limestone is created from the shells of animals condensing together and being buried. Shells form from the combination of calcium and CO2 → forms calcium carbonate. This makes up the shell of the organism.

SLIDE 5
• Nitrogen cycle [how do we get nitrogen to primary producers]

o Plants prefer to have ammonium rather than nitrate. They would have to break nitrate to ammonium.

o Ammonium and nitrate are inorganic sources of nitrogen.

• Animals consume organic matter which is where the nitrogen is.
• Primary producers get inorganic nitrogen through thee different methods

o Precipitation – “butloads” of nitrate

o Erosion of rock (which is weathered by precipitation)

o Ammonification, nitrification, denitrification, and nitrogen fixation

SLIDE 6 - ammonification

o When the heterotrophic organisms is consuming nitrogen and it has excess it will release the extra ammonium into surroundings → ammonium pool

o Precipitation, weathering and excretion also contribute to the ammonium pool

Slide 7 nitrification

o Overall purpose is to turn CO2 into glucose.

o CO2+H20 → CHO+O2

o Nitrosomonas (chemoautotrphic)

• CO2+NH4→CHO+NO2 (nitrite)

o Nitrobacter

• CO2+NO2(nitrite) → CHO+NO3 (Nitrate)

Slide 8 denitrification

o Looking at heterotrophic bacteria (convert glucose to CO2)

o These bacteria have an anaerobic metabolism.

o Animal respiration

• CHO+O2→CO2+H2O

o Denitrification (anaerobic process)

• CHO+NO3(nitrate) → CO2+N2 (nitrogen gas)

Slide 9 Nitrogen fixation (another example of a anaerobic organism)

o Nitrogen fixing organism get it from denitrification or from the atmosphere

o CHO+N2 → CO2+NH4

o Mutualistic – intimate association with benefits for each organism

• Rhizobia infects roots of legumes resulting in root nodules. This creates anaerobic environment in root. When the nitrogen gas goes into the root it is converted to ammonium and then the plant can use it. The plant gets ammonium the organism gets nutrients.

Tuesday, November 13, 2007

Lecture 26, 11/12 (Maybruck 11); Viruses

Audio for lecture on 11/12 is available here.

• Slide 1 handout from 11/9

o Regulation of gene expression at the level of translation: Inhibit gene expression of a dominant protein. This is done by regulating translation. Bacteria do it using antisense RNA. Antisense RNA will complimentary bind its sequence to a specific mRNA sequence. This forms an RNA double stranded. RNA must be single stranded in order for it to translate. We use antisense DNA because it is easier to manufacture. Antisense DNA makes its way into the nucleus of the cell where it binds to a specific sequence and translation can no longer occur (double stranded → doesn’t work AND the double stranded nucleic acid doesn’t leave the nucleus. Translation usually occurs in the ER)

o Another therapy is triplet DNA therapy regulation at transcription level: DNA strand that is complimentary to template strand. This is important because in transcription it only reads off the template strand DNA. This prevents DNA polymerase from attaching, binding and reading.

• This process in its early stages – trouble getting DNA into nucleus

• Can be used for cancer

• Slide 1 11/12 VIRUSES

o Ways to tell a virus is alive: growth, heredity, metabolism, protective mechanisms, transport of substances

o A virus cant do this stuff independently → it can do it once it infects a cell. Virus should be considered as infectious particle.

• Slide 2 Virus size

o Virus size are less than .2 um → VERY small

• Slide 3 virus structure

o Virion – completed virus particle which has two parts

• Outer covering – consists of a capsid and an envelope

 Capsid (made with same protein subunit called capsomer) comes in two different forms: helical and Icosahedron.

• Helical form - Capsids bind to one another and extend in a condensed helix. It manifests itself in a rod → called a naked virus.

• Icosahedron – a polyhedron (3-d structure that contains sides that are polygons – a polygon has three straight sides and three angles). Icosahedron is made up of twenty polygons. This formation is called a facet. The facets are made up of 20 capsomers. As a result of this geometric formation there are 12 equally spaced corners. At each corner is 5 capsomers called penton center.

 Envolope

• Taken from the cell host. The envolope provides additional protection for the genetic material AND aids in release of genetic material into cell host.

• Central core – consists of genetic material and enzymes

o All viruses will have a capsid and genetic material meaning they also must have an outer covering and central core.

• Slide 4 genetic material of viruses

o Viruses contain either DNA or RNA (not both)

o Viruses also use single stranded nucleic acids as their genetic code.

o Because viruses are very small their genetic material must be concise. Hepatitis B has 4 genes (Human eukaryote has tens of thousands of genes). Those genes in a virus must code for synthesis of the viral capsid and genetic material, produce protein products that will regulate the actions of their cell host, they need to code for genes that will help package the virus (virion).

• Slide 5 viral multiplication

o 1st step – absorption

o viruses attack specific cells. They determine it based on receptors of the cell host. This can help us characterize viruses into these categories:

• restricted: example hep B → only infects liver cells

• intermediate: example polio virus → infects intestinal cells and nerve cells

• broad: example rabies virus → infects a bunch of eukaryotic cells

• slide 6

o it needs to release its genetic material into the cell host. This can be done by endocytosis (similar to how an amoeba eats food). Food vacuole is formed. Food vacuole is bombarded with enzymes and breaks down the capsid. As a result genetic material is released into the cell.

o It can also transfer its DNA by merging. As it merges it will spread open and genetic material is released.

• Slide 7 synthesis and assembly

o Double stranded DNA virus can recombine into our genome and creates potential for cancer.

o RNA polymerase transcribes viral DNA → it then moves to the ER where it is translated → proteins are then brought back in to the cytoplasm.

• Slide 8 viral release

o There will either be cell lyses or exocytosis.

o Cell membrane is critical to life of cell

Lecture 25 11/9 (Maybruck 10)

I was absent for this lecture. If anyone has notes/audio that they would want to post - let me know via a "comment".

Thanks

Friday, November 9, 2007

Micro Extra Credit 3

LECTURE 10/31 is UP!

AND . . .

Here is a possible extra credit article "Fuel Without the Fossil" from the New York Times.

Wednesday, November 7, 2007

Lecture 24, 11/7 (Dr. Maybruck 9); Bacterial Genetics

Audio for today's lecture is available here.

• Slide 1 (handout from 11/5) tools and techniques for biotechnology applications: Plate hybridization

Plate hybridization - Helps identify specific DNA sequence associated with an organism

You use plate hybridization in order to determine if an organism is present and is harmful by looking at the DNA.

Take your food sample and streak a plate –-> incubate plate for a day → bacteria grow. From this growth we do gene analysis.

Place nitrocellulose on top of the colonies (so that they touch) that have grown. Pull the membrane off and it contains smears of the colonies that had grown on the plate. Next you lyse the cells and denature the DNA. Denaturing the DNA causes it to separate into single strands. You then expose the membrane to a gene probe. The gene probe is a sequence of DNA that will complimentary bind to the gene of interest (the one that has the toxins). If there is no harmful gene then the gene probe will not bind. The gene probe has a radioactive label that emits energy. The photographic film picks up the radioactive label (if it is bound to the DNA in one of the colonies) and a mark appears on the photographic film. You can then take the photographic film, lay it over the original colony again, and determine which colonies have the genes of interest.

• Slide 2 – PCR

Polymerase chain reaction allows us to amplify specific sequences of DNA.

Components of a test tube:

First thing you need is your DNA fragment that you wish to amplify. Then you need DNA polymerase which is responsible for synthesizing the new complimentary strand of DNA (semiconservitive replication). DNA polymerase will not add complimentary bases to make a new strand of DNA without primers. When making a complimentary new strand of DNA you need nucleotides.

The above components will be put into a thermocycler (instrument that cycles through temperatures).

3 steps occurring in one cycle of PCR (the more cycles the more DNA molecules)

• denaturization – heat can be used to separate the DNA strands to separate at 94ºC

• priming – temperature is cooled to 50-65ºC. this causes the primers to bind were they need to. This is important because DNA polymerase wont start adding new nucleotides until there is a primer there.

• Extension – temp is increased to about 70º which causes DNA polymerase to come in and start making new strand of DNA.

Thermos aquaticus – thermophile. Organism able to survive in extreme heat.

• Taq polymerase – used often in PCR because its polymerase is used to being at hot temperatures.

Video explanation titled “Polymerase Chain Reaction” – available on blackboard

• Slide 3 DNA sequencing

DNA sequencing: Gives us an idea of what we are dealing with

Sanger dideoxy method of DNA sequencing

• Dideoxy nucleotide is missing an oxygen from its 3 carbon sugar.

In a test tube you have: gene, primers, DNA polymerase, 4 nucleotides (G,C,A,T), 1 modified nucleotide (this is the dideoxy nucleotid missing oxygen from its 3 carbon sugar)

Once the modified nucleotide is added to the chain then nothing will add on afterwards.

Video titled “SANGER SEQUENCING” available on blackboard

• Slide 1 (handout 11/7)

Recombinant DNA is taking the genetic material of one organism and incorporating it into the DNA of another

This is a natural occurrence among bacteria. It is called transformation.

We can use this to our benefit as we can make organisms make proteins, Make transgenic organisms and amplify DNA.

Monday, November 5, 2007

Lecture 23, 11/5 (Maybruck 8); Operons + Bacterial Genetics

You can get the audio for lecture on 11/5 here.

• Review of last class - check out the animations on blackboard.
• Slide 1 (handout from 10/26) Lactose operon: inducible operon

Operons (structures found in bacteria (prokaryotes)) – grouping of genes that are adjacent to each other and are involved in coding for one particular phenotype

Their transcription will be regulated together

Lac operon (inducible operon) – the only way that transcription is going to occur is if lactose is present.

Promoter region – where RNA polymerase is binding. Once it binds there it will start transcribing (3’-5’ direction). This is what operons are regulating – with the help of an operater region. This is found “downstream” of the promotor. (downstream indicates that it is in the direction that transcription occurs – 3’-5’ . . . upstream is the opposite.)

If you want transcription to happen in lac operon you must get rid of repressor protein. The repressor protein has two binding sites one binds to the operating region. Once bound it prevents RNA polymerase from transcribing. The other binding site will bind to lactose. Lactose is the inducer of this operon. Lactose binds to repressor protein and causes it to change protein form. This protein can no longer bind. This allows rna polymerase to begin transcribing. The only time this operon will transcribe is when lactose is present.

What is being transcribed in this operon?

• Beta-galactosidase : this enzyme is responsible for breaking down lactose into galactose and glucose.

• Slide 2 arg operon: repressible operon

Arg operon – responsible for a group of genes that are responsible for building the amino acid argenine. RNA polymerase comes along and transcribes Arg operon. Argenine acts as a repressor. It associates with a repressor protein (which has two binding sites like the other one). One site is for argenine the other is for the operator region of that operon. When argenine is no longer available to bind to the repressor protein the repressor protein will move away from operater region and allows transcription to occur once more.

• Slide 1 Application of bacterial genetics (handout11/5/07)

Biotechnology – manipulating the biochemical processes of an organism to benefit humanity.

• Example: insulin → there are bacteria that make our human insulin

• It can also help us identify different bacteria

• Slide 2 restriction endonucleases

Restriction endonucleases - Internal cutting of DNA

The restriction endonucleases are bacteria’s immune system. They try to stifle viruses attempt to inject their DNA into the bacteria.

They always cut palindrome sequences.

Sticky ends and blunt edges

• Sticky ends created by restriction endonucleases. They occur when the DNA is split. These sticky ends go on and bind to other complimentary pairs.

• Blunt ends are cut clean

Sticky ends are used in a process called recombinant DNA. Recombinant DNA splices foreign DNA.

Restriction fragment length polymorphism (RFLP)– a piece of DNA that has been cut by a restriction enzyme. We can use the RFLP to distinguish between different organisms.

• Slide 3 analysis of DNA + getl electrophoresis

Polymorphisms – the subtle differences that are occurring between the different nucleotide sequences of the organisms.

EcorI cuts up certain base pair sequences consistently for different organisms. The cuts leave certain lengths which cause it to be identifiable.

Gel electrophoresis helps identify cut pieces

• Add the samples (cut pieces) to gel wells.

• The gel is exposed to an electrical current which creates a negative charge at one end and a positive charge at the other end. The positive charge is always away from the wells. DNA has an overall negative charge to it. This means that it will want to move away from the negatively charged wells.

• The fragments then spread out through the gel. Smaller fragments migrate faster. Large fragments move slower.

• From there you can compare electrophoresis tests to compare and classify different organisms.

Sunday, November 4, 2007

Lecture 21, 10/31 (Maybruck 6); Bacterial Genetics

Here is the audio.

• Slide 1 of handout from 10/29 – bacterial genetics replication, transcription, and translation

o The study of bacterial heredity discusses passing of traits to subsequent generations and evolution of genetic material (more on slide one of handout from 10/29)

• Slide 2 levels of structure and terminology

o Genome – total amount of genetic material in a cell

• In bacteria and eukaryotes and viruses the genetic material is DNA. In a retrovirus it would be RNA (ex. HIV)

o Chromosome – includes genes that are critical for the survival of the bacteria/cell.

• We have diploid chromosome sets (two copies). 23 chromosomes 2 copies . . . 46 total

• Haploid have only one copy.

• Chromosome is supercoiled to save space. For it to be copied it will be unwound by a DNA gyrase.

o Plasmids – another type of genetic material. Plasmids help but are not essential. They allow the bacteria to adapt to a certain situation

o Gene – a specific sequence of nucleotides. Found within the chromosome they are a specific sequence of nucleotides that will code for a protein.

o Genotype – genetic makeup of a gene. Genotype is a specific nucleotide sequence of that gene.

o Phenotype - The protein that was produced by the gene produces a trait and that is called the phenotype

• Slide 3 DNA

o Basic unit of DNA is a nucleotide.

o Nucleotide – includes nitrogenous base which defines the type of nucleotide we have, They have a phosphate group and a sugar group.

o Hydroxyl group lacking on the ribose sugar of DNA. If you see a hydroxyl group you know you have an RNA.

o Each separate strand of the DNA (nucleotide) is covalently bound – unequally shared electrons.

o The phosphate group is covalently bound to an adjacent nucleotide at the #3 carbon.

o sugar phosphate linkage occurs on outside of helix

o you ultimately get the double helix

• slide 4 DNA

o purines: adenine and guanine

o pyrmidines: thymine and cytosine

o two colons two hydrogen bonds 3 colons three hydrogen bonds. A::T G:::C

• slide 5+6 DNA replication in bacteria: a semiconservative process

o semiconservative - formation of a new DNA molecule from old DNA strands

o STEP 1

• uncoiling the DNA using DNA gyrase

• separating the DNA molecule into 2 strands – helped by the enzyme helicase (which goes to “A” “T” rich area which is the origin of replication) and single stranded binding proteins (without these the hydrogen bonds would reattach). The A::T rich sight is the origin of replication – it is easier for the helicase to break down the bonds here.

• The area where the strands are being split is called the replication fork.

• Slide 7 DNA replication in bacteria: a semiconservative process

o In order for the synthesis of new nucleotides to be added to the old DNA strand to form a new DNA strand you need RNA primase and DNA polymerase III.

o DNA polymerase III – before it can add new nucleotides it needs a primer (RNA primase). It works down the strand adding nucleotides according to what it reads on the old strand. It can only read DNA strand in 3’-5’ direction. SO in order for it to replicate 5’-3’ direction it waits for helicase to open up the two DNA strands wide enough so that an RNA primer can get in. The DNA polymerase III uses it to replicate in the opposite direction.

o RNA primase – adds complimentary RNA nucleotides

o Processing of the lagging strand creates okazaki fragments.

o DNA polymerase I (repair polymerase) - removes all of RNA primers and replace it with the correct complementary nucleotides in the newly synthesized strand.

• Slide 8

o DNA ligase – connects okazaki fragments

o Freesciencelectures.com video DNA replication process

• Slide 9 transcription and translation overview

o Gene has a specific sequence of nucleotides that’s going to code for a protein. That DNA within the gene has nucleotides that can be grouped into 3’s (triplets). Each of those groups will code for a specific amino acid. We get a protein that rolls over the DNA and creates an exact copy of the gene in RNA (mRNA). RNA’s grouped together as three is known as a codon (in DNA it is a triplet) which codes for a specific amino acid which is what proteins are made of.

o DNA → RNA = transcription

o mRNA → amino acids = translation

• Slide 10 RNA

o Look at diagram on the handout.

o RNA uses uracil (in pyrimidine group) instead of thymine

• Slide 11 RNA (1 strand of covalently bound nucleotides)

o mRNA – RNA that is involve in coding for a protein. Provides an exact copy for a gene.

o tRNA – parts of tRNA that complimentary bind to one another making it look like it has two strands. This creates hairpin structures. On one of the hairpin structures there is a triplet nucleotide sequence. That nucleotide sequence will bind to a specific sequence of mRNA. At the other end of the tRNA a specific amino acid will be attached.

• tRNA brings the specific amino acid of the mRNA to the codon. It knows because of the anticodon which complimentary binds to the codon.

Lecture 22, 11/2 (Maybruck 7); Translation + Transcription regulation

Audio for lecture on 11/2 can be heard here.

• Slide 1 (handout 10/29/07)

RNA are the work horse of the DNA, they are responsible for construction of proteins. The mRNA has the blueprint of the nucleotide sequence associated with the gene. (main difference between DNA and RNA is uracil (in RNA) instead of thymine which is found in DNA)

tRNA (transfer RNA) – single stranded nucleotide sequence (characteristic of all RNA). It has specific areas that are complementary to each other where it folds on itself forming hairpin loops. On a hairpin loop there is a span RNA nucleotides (3) that are referred to as anticodon. This is the compliment to the codon.

On a gene there are 3 consecutive bases that code for a specific amino acid. The gene is coding for a protein. That protein consists of a bunch of amino acids all linked together. With every three nucleotides in DNA will code for a protein. The three nucleotides link together is referred to as a triplet. In RNA this is called a codon. . . . You have a triplet that is coding for a specific amino acid within mRNA that grouping of three nucleotides is referred to as a codon.

Anticodon also codes for a specific amino acid. The tRNA knows which amino acid to bring over due to complimentary binding between the codon and anticodon.

The function of the tRNA is to bring the amino acid over to the mRNA which is within the ribosome.

• Slide 2

Ribosomal RNA – involved in being part of protein synthesis

• Slide 3 bacterial genetics: Transcription

RNA polymerase only reads one strand which is the 3’ to 5’ strand. The strand that it reads is referred to as the template strand.

RNA polymerase begins transcribing when it sees a certain pair of sequences. RNA polymerase binds to promotor region (which is made up of a couple different nucleotide sequences) and begins transcribing.

Continues to transcribe until it gets to the termination DNA sequence → end transcription.

• slide 1 of bacterial genetics: details of translation and transcription regulation (handout from 11/2/07)
• slide 2

you want genes to be selectively expressed. If all genes were expressed at the same time there would be energy lost by the bacteria.

You can regulate gene expression during replication, transcription and translation.

mRNA codons specifying for amino acids

genetic code – a way of translating the nucleotide sequence of a gene into the correct amino acids (amino acids make protein and in turn exhibit a trait).

20 amino acids and 64 codons

• this means codon usage will be redundant in formation of a particular amino acids

• slide 3 translation – protein synthesis

translation is happening on a ribosome

in prokaryotes it is referred to as a 70s ribosome. The “s” stands for Svedberg units. “S” units measures the sedimentation rate of a particle during centrifugation. The larger the particles the larger their “S” value.

Characteristic of a ribosome – there are spots in it for tRNA (settles within the 50s) and mRNA (settles within the 30s)

There is an “E” site an “A” site and a “P” site

3 stages in translation – initiation, elongation, termination.

• slide 4 translation

initiation (formation of a protein – the adding together of amino acids) – starts with one codon – methionine (always first amino acid that is translated).

There are different tRNA’s with different amino acids that try to get into the slots. The only ones that get in are the ones with anticodons that will bind to the codons. For example an AUG looks to bind with UAC.

CUG (codes for lucine) looking to bind with something that has an anticodon for lucine.

Ribosome is mixture of protein and RNA

• slide 5 translation

elongation

dipeptide strand - peptide strand of two amino acids bound together (the beginning of the building of the protein)

the ribosome moves down the mRNA and moves in 5’ to 3’ direction.

As it (ribosome) is moving in 5’ to 3’ direction (elongation) the dipeptide moves from both tRNA’s to just one tRNA. It is moving to the one located in the “A site” of the ribosome. The tRNA in the “A site” then moves to the “p site”. The one in the “a site” (bare of amino acids) moves to “e site”. Once in “e site” it is released into the surrounding. Now tRNA that was in “a site” is in the “p site” and has two amino acids associated with it (a dipeptide).

this process made a polypeptide strand that has two amino acids in it.

A site – where the new tRNA’s with amino acids are going to be added

P site is where elongation is occurring

E site is where tRNA is being discarded

Protein synthesis: termination

Stop codon stops translation

• slide 6 regulation of protein synthesis at the level of transcription

operon – grouping of genes right next to each other. Also are working towards expressing one particular phenotype

Transcription regulation in the operon is handled by two general processes: induction or repression

• inducible regulated operon – regulates transcription – transciption is off. This means that transcription must be induced to get going.

• repressible regulated operon – (always on) to turn this off it needs a molecule to repress it.

Examples

• Catabolic (breaking something down) operons – are usually inducible. Example → glucose.

• anabolic operons – associated with repressible regulated operons. molecule has to be present to turn transcription off.

Monday, October 29, 2007

Micro Extra Credit 2

Microbes talking to each other, get the article for extra credit folder here in the news.

Lecture 20, 10/29 (Dr. Maybruck 5); Microbial Drug Resistance

Audio for lecture 20 on October 29th.

• Slide 1 Chemotherapy for viral infections (Handout from 10/26)

Selective toxicity is difficult to achieve with viruses

Antiviral drugs target points in infectious cycle of viruses

• Preventing virus entrance into cell

• Preventing viral replication (duplication of DNA), transcription (synthesis of RNA) and translation (synthesis of proteins).

Viruses can use our own proteins to make their DNA.

With our drugs we are trying to prevent the life cycle of the virus. Try to keep the virus from entering the cell.

• Slide 2

Different drugs involved in inhibiting viral replication

• Viral thymine kinase → turns precursor guanine into guanine

• Acyclovir (“false” guanine) – mimics the precursor guanine. Once it is added to the DNA it prevents extra nucleotides from joining to the strands

• Azidothymidine (AZT) – mimics thymine. Reverse transcriptase grabs AZT nucleotide and binds it to the Adenine.

• Nevirapine – non nucelotide reverse transcriptase inhibitor. It bonds to the reverse transcriptase and prevents its function.

• Slide 3 drug resistance

Methocillin resistant staphylococcus aureus (MRSA) – developed resistance (“acquired resistance”) to Beta-Lactam drugs. Common hospital infection.

Why do they have this resistance

• Some have an Intrinsic resistance – ex. organisms that are responsible for creating the antibiotic.

Acquired resistance can be looked at two ways:

• →SPONTANEOUS BENEFICIAL MUTATION

• Gene is a specific sequence of nucleotides that is going to code for a protein that protein then produces a certain trait.

• Mutation – a change in the specific nucleotide sequence that will be passed on to the next generation

3 types of mutations: lethal, neutral and beneficial.

Lethal mutation ex. Hexokinase – involved in first step of glucolosis. If it were tainted than glycolosis could not happen resulting in death.

Neutral – a mutation that results in neither beneficial or lethal. Ex eye color

Beneficial mutation – increasing that populations ability to reproduce and survive.

• Point mutation – a change in a few nucleotides

• Natural selection – picking a trait that benefits the population and passing it on

• Directional selection – an example of natural selection. This is associated with antibiotic resistance. Environmental pressures cause the organism to begin selecting a trait in the population that will be passed on from one generation to the next. Penicillin is an example of an environmental pressure.

• →HORIZONTAL GENE TRANSFER

Conjugation

• Two microorganisms (of different species) will share information (make a copy of the plasmid) by joining up through conjugation

• Slide 4 specific mechanisms of drug resistance

Enzymes are made to inactivate drug

Beta lactamases – example of an enzyme produced by bacteria that will inactivate the effects of penicillin and cephalosporins. This is one way that MRSA functions (it produces beta lactamase)

• Slide 5 specific mechanisms of drug resistance

Impermeability of cell to drug

Gram negative bacteria

Active transport pump uses energy to pump out the drug

• Slide 6 specific mechanisms of drug resistance

Producing an alteration in the target of the drug.

Erythromycin

• Prevents movement of mRNA through the ribosome

Fungi don’t produce binding substrate at all

Penicillin binding protein (PBP) – a protein that is used by bacteria to build their peptidoglycan cell walls. This protein readily binds to penicillin and is not a builder of the cell wall. MRSA will alter the attaching sight and the penicillin binding protein will continue to build the wall.

Alteration of metabolic pathway

• sulfinimide
changes way the dihydroteric acid is formed

Sunday, October 28, 2007

Lecture 19, 10/26 (Maybruck 4): Chemotheraputic Drugs

Audio for lecture on 10/26 available here.

• Slide 1 Antimicrobial target: nucleic acids(handout from 10/4)

o naladixic acid – inhibits function of DNA gyrase. DNA gyrase unwinds DNA and allows for efficient storage of the chromosome. It also allows for DNA synthesis ot occur

• slide 2 Antimicrobial target: Protein synthesis

o protein synthesis involves four primary parts: two ribosomal subunits (50s and 30s → unique to prokaryotes), tRNA and mRNA.

o Aminoglycosides – attach to 30s ribosomal subunit which causes the tRNA to misread the mRNA. In turn the protein is incorrectly formed and is nonfunctioning.

o Tetracycline – attaches to 50s ribosomal subunit and prevents tRNA from binding to that sight. (tRNA is bringing amino acids over to ribosomal subunit to create a protein). Considered a semisynthetic drug.

o Chloramphenicol – prevents bonding of amino acids together. Prevents peptide bond.

o erithromyacin – binds to 50s portion of subunit and prevents mRNA from sliding through the ribosome. This is where tRNA reads the mRNA and figures out what to bind where and form protein. Because mRNA can’t slide through – protein isn’t made.

o NOTE: Cells need to be metabolically active in order for the above antibiotics to function

• Slide 3 Antimicrobial target: Cell membrane

o These two drugs can work on a cell that is not metabolically active.

o Polymyxin (broad spectrum) – targets cell membrane. Acts as a surfactant, integrates into cell → disrupts it → cell dies.

o Chloroquine – little bit more selective then polymyxin. An anti-malarial drug. The causative agent of malaria is the protozoan plasmodium.

• Life cycle of plasmodium – mosquitoe → to human → to liver → attack red blood cells. Plasmodium brings nutrients (hemoglobin) into food vacuole.

• Uses enzymes to break down majority of hemoglobin. Doesn’t like the iron cofactor “heme”. Instead it converts iron into hemozoin (Hz). Chloroquine inturupts this function. Plasmodium will be unable to detoxify “heme” and the cell becomes toxified.

• Slide 4 Antimicrobial target: Folic acid synthesis

o Folic acid synthesis is unique to bacteria and protozoans.

o Folic acid is a precursor of DNA RNA and proteins. We get our folic acid from food we consume. Bacteria and protozoans make it for themselves.

o We prevent folic acid synthesis in a bacteria/protozoans with competitive inhibition of an enzyme.

o 2 examples:

• Hexokinase enzyme is responsible for taking glucose, binding it to phosphate and forms glucose 6 phosphate → initial reaction in glycolysis. Take an enzyme that is similar to glucose and present it in a greater concentration. This will take the place of the actual glucose and in turn prevent the process from occurring.

• Folic acid synthesis forms a dihydroteric acid (which is only formed using Para-aminobenzoic acid (PABA)). PABA binds to pteridine synthetase and forms precurusor to folic acid. We create a “pseudo”PABA that outcompetes the actual PABA. Drugs used are sulfonomides and trimethoprim.

• Slide 5 antibacterial drug groups: penicillin and related

o Penicillin (penicillium chrysogenum) – prevents synthesis of the peptidoglycan cell wall.

o Semi–synthetic antibiotic: what we would be prescribed. It is the modified version of the real thing. Causes it to become broad spectrum

o Alpha – hemolyses: when bacteria reduces iron or the “heme” group. Cause pnemonia

o Beta – hemolyses: involved in rupturing red blood cells. Cause strep throat.

• Slide 6

o Cephalosporin – Cephalosporium acremonium (similar to penicillin but induces fewer allergic reactions) – removes enteric bacteria (bacteria that colonize intestines) Ex. E. coli.

o Salmonella is another example → prevents water absorption.

• Slide 7 animoglycoside tetracycline, and chlorampheniccol

o See slide 2

• Antimicrobial Chemotherapy part II
• Slide 1

o Fungi are eukaryotic making their removal “tricky” because their functions at a molecular level are similar to ours.

o Target ergosterol which is in the cell membrane of fungi cells. Ergosterol is similar to cholesterol. Function of ergosterol is to support the cell.

o Macrolide polyene antibiotics target the ergosterol.

o It is used to attack Histoplasmosis (fungal infection that causes respiratory problems)

o Griseofulvin – targets cyctoskeleton of fungi cells. In particular it attacks the microtubules. This keeps the cell from forming properly. Drug is used to treat fungi infections in the hair skin or nails.

• Slide 2

o Azoles – prevents ergosterol synthesis. Fights off Cryptococcus meningitis. Meningitis affects the meninges in the spine.

o Flucytosine

• Fungi use this flucytosine analog to build the DNA strand. This in turn prevents DNA synthesis.

• Used to combat candidal cystits (a yeast infection associated with bladder)

Slide 3 drugs specific to the removal of protozoans

o Metronidazole – removes anaerobic microorganisms

• Upon administration to the individual the drug becomes inactive – a prodrug. In turn the protozoans injest this and then it become active in the protozoans. Once in the protozoan it interferes with DNA structure.

o Entomeaba histolytica amoeba - Fecal contamination is a source of this protozoa. Protozoan in the cyst form is resistant to stomach acid. It then progresses to the large intestine and turns into trophozoite form. In this form it inhibits water absorbtion by the large intestine.

Friday, October 26, 2007

Micro Extra Credit

For those of you who may be behind in your 100 article extra credit thing, here is an interesting article I found today. (I will be posting links to more articles as I find them)

French Dirt May Kill MRSA

Researchers said that a type of French clay can kill several disease-causing bacteria, including M. ulcerans, which is known as a "flesh-eating" bacteria, and the so-called super bug, MRSA.

Wednesday, October 24, 2007

Lecture 18, 10/24 (Maybruck 3); Control of Microbial Growth