1. Animal

2. Plant

3. Monera

4. Protozoa

5. Fungi

The rise of living from the non living. 

Pasteur and Koch = Germ Theory of Disease

He found the cure for syphilis.  Found out that Salvarsan chemical killed the spirochetes.

"Magic Bullet" that targets the site of infection

Louis Pasteur

Did the swan- neck flask experiment and developed the Germ Theory of Disease that states that there is a germ behind every disease. 

Found the causes for Tb, anthrax, cholera, and rabies.

1. Carbon

2. Hydrogen

3. Sulfur

4. Oxygen

5. Nitrogen

6. Phosphorous

(SPONCH)

1. Lipids  = Fatty acids + glycerol

2. Protein = Amino Acids

3. Nucleic Acids = Nucelotides (Base/Sugar/PO4)

4. Carbohydrate (Polysaccharides) = Sugars

Cellulose

(but cant be digested by humans because of the B 1,4 bond)

1. Structural units

2. Energy

3. Important in the cell membrane they can attach to lipids and proteins on surface then can serve as receptors

Saturated = More hydrogens, no double bonds

Unsaturated = More double bonds, less hydrogens (MORE FLUID because the double bonds tilt the molecule so it dont compact well)

Protein

It accounts for 55% of dry weight of cells

1. Synthesis = Anabolism = Dehydration

2. Decomposition = Catabolism = Hydrolysis

3. Exchange = no net gain/loss of water

Peptidoglycan

Chitin

Exergonic

Endergonic

1. Enzymes

2. Regulate cellular processes

3. Structural support (ex: collagen)

4. Surface receptors (ex: glycoprotein)

5. Carriers

6. Transmembrane proteins that are involved in signal transduction

~ 300 A.A connected by peptide bonds (a form of covalent bond)

The NH2 from 1 A.A attachs to the COOH from another A.A

Held together by H-bonds between the A.A along with there peptide bonds from their primary structure. 

Alpha helix and Beta Sheets

1. Disulfide bonds (S-S = covalent bond)

2. Hydrophobic interactions

3. Van Der Waals interactions

Folding gives its properties

Temp (can melt H bonds)

pH (can affect polarity/charge)

1. Compound Light microscope = 1000-2000x magnification

2. Electron microscope = 100,000x Magnification

Fluorescent

UV light

SEM = surface of cell

TEM = cross section of the cell

It is good for detail of individuals structures, you can even view viruses. 

They use electron beam as the light source

1. Simple stain = one color

2. Differential stain = 2 colors

3. Negative stain = stain the background

1. Gram Stain

2. Acid fast stain

Flagella

Endospore

Capsule

What is the relative size of microbes?

What about RBC and Eukaryotes?

Micro = 0.5 to 2.0 microns

RBC = 7.5 microns

Euk = 20 microns

What types of shapes do the following have:

1. Cocci

2. Bacilli

3. Spirillum

4. Spirochete

1. Spherical

2. Rod

3. Spiral

4. Coil

Bacillus (anthrax)

Clostridium (tetanus, botulinum)

1. E. Coli

2. Salmonella

1. Capsule

2. Extracellular Polysaccharides

3. Slime layer

In the formation of the biofilm

Gram +

Gram -

NAG = N-acetylglucosamine

NAM = N-acetylmuranic Acid

1. Many layers of peptidoglycan

2. No outer membrane

3. Contains Teichoic and Lipoteichoic acid

4. No Lipopolysaccharrides (LPS)

1. Few peptidoglycan layers

2. Has an outer membrane

3. Has a Periplasmic space btwn the outer and cytoplasmic membrane

4. Has LPS

5. Has no techoic acid

6. Has porins for entry of molecules

1. Primary stain with a crystal violet

2. Add a mordant (Iodine) to intensify the primary stain

3. Decolorize via Alcohol or Acetone

4. Counterstain with a secondary stain - Safarin

RESULTS

Gram + retain the primary color cause of thick walls so they are purple

Gram - lose the primary color after decolorizing and are red/pink due to the counterstain

False, it is the opposite

+ = violet

- = red

Cell wall

sensitive

+

Biological membranes are a 2D liquid made up of lipids and proteins that diffuse more or less easily than others.  PHOSPHOLIPID BILAYER

SEMI PERMEABLE

Facilitator protein

Conformational Change

Cytoplasm

Equal

(Equilibrium)

Energy Dependent

Inside (1000x more than outside)

1. Proton Gradient

2. Charge Gradient

Phosphotransferase System

Gluc comes into the cell and gets PO4+ via PEP

(is highly regulated)

Catabolism = releases energy

Anabolism = uses that energy to make new cells

Defined = You know the exact # of material and you need a buffer to maintain pH

Undefined (complex) = You dont know the # and is uses proteins derived from plants and animal extracts as the buffer

Oxidation

Reduced

ATP

Lose Electrons = ___________

Gain Electrons = ____________

Oxidation

Reduction

(LEO the lion says GER)

Coupled

Electron Carrier Proteins

1. NAD+---------> NADH

2. NADP+-------> NADPH

3.  FAD-------> FADH2

In Glycolysis (makes PEP first)  and the Kreb Cycle (makes succinly CoA)

Oxidative Phosphorylation

ETC

1. Membrane maintains electrochemical gradient

2. Cells use energy released in redox rxns of ETC to make PMF

3. H+ propelled by PMF, flow down electrochemical gradient via ATP Synthases to make ATP

AKA Oxidative Phosphorylation because proton gradient created by oxidation of components of ETC

1. Anaerobic Respiration

2. Aerobic Respiration (most preferred)

3. Fermentation

Oxidized

2

2

2

Glycolysis

Alcohols

Acids

Acetyl CoA

CO2

Pyruvate Dehydrogenase

The release of CO2

There is 2 CO2 released

1. Succinyl-CoA

2. ATP, ADP

3. PEP

False;

Prokaryotes = Cytoplasm

Eukaryotes = Mitochondrial Matrix

Amphibolic = Can be used for both anabolic and catabolic processes

Example = Glycolysis and Kreb Cycle

1. Regenerate NAD+ and FAD

2. Pump H+ out of cell, but comes back in via ATP Synthetase, this creates PMF

3. Make lots of ATP

4. O2 is reduced to H2O

1. NADH Dehydrogenase

2. O2

In Fermentation there is no Kreb Cycle or ETC

It uses an organic molecule as the terminal e- acceptor and makes ATP via SLP.  It also only make 2 ATPs

Anaerobic Respiration = Occurs with the ETC but different e- acceptor than O2.  It uses inorganic molecules and makes ~ 34 ATPs

Oxidative Phosphorylation

(aka chemiosmosis)

2 ATP

2 FADH2

4 CO2

6 NADH

Both undergo Glycolysis, Krebs and ETC

ATP is made via Oxidative Phosphorylation

Electron carriers are re-oxidized

Sun

Oxidation of organic/inorganic compounds

Inorganic compounds

Organic compounds

Apoenzyme

Cofactor or Coenzyme

Holoenzyme

 It is the amount of time it takes for the bacteria to 2x

Measured during the log phase

1. Lag Phase

2. Log Phase

3. Stationary Phase

4. Death/ Log Decline Phase

Lag phase = acclimation, where preparation occurs and the synthesis of necessary enzymes

Log phase = Exponential growth where you get the max rate of growth

Stationary phase = Waste builds up and the # of cells dividing = # cells dying

Death phase = cell death

Absorbance

higher

more

1. Hyperthermophiles: grow at 80 C

2. Psychrophiles: grow at 20-40 C and 0 C

3. Mesophiles: Optimal growth at 37 C

Temp: if 2 hi or low can denature protein by affecting H bonds

pH:  Changes enzymatic activity by changing the shape of the protein

1. Fermentation

2. Anaerobic Respiration

3. Aerobic Respiration

Formation of oxidizing agents such as:

Superoxides

Peroxides

Free radicals

(All can lead to cell damage)

Selective = select on group against others

Differential = Different groups will grow in different colors

If fermentation has occured the pH will b lower. Use phenol red indicator to determine when fermentation has occured.

Red = 7 Pink = 9 and Yellow = 5

1. Ribose vs Deoxyribose

2. Uracil vs Thymine

3. single stranded vs double stranded

5' -----> 3'

3' OH end

Leading (continous)

Lagging

1. Lacks proofreading activity

2. Does not need a helicase

3. Does not need a primer

4. Slower

5. Puts in U instead of T

It is normally off, and it has to be activated by an inducers.  This type of operon controls catabolic enzymes

Ex: Lactose Operon.  If no glucose then turned on because there is high # of lactose

It is normally on and transcribed continually until it is deactivated by repressors.  This type of operon controls anabolic enzymes.

Ex: Tryptophan operon.  If Tryp is present then operon is turned off

Protein

RNA

1. Universal

2. Remains unchanged

3. Start codon = AUG (Methionine)

4. Stop codon = UAA, UAG, UGA

If its ionizing then it induces breaks in both strands that are hard to repair in chromosomes.

If its nonionizing then it could still form thymine dimers

1. Nucleotide analogs

2. Nucleotide-altering chemicals

3. Frameshift mutagens

Base-pair substitution

Missense

Nonsense mutations

no protein is made

All repairs via DNA Polymerase

Finds error, removes it, fills gap with correct base.

Thymine dimers

The wrong base is removed and is replaced with a new base

Organisms replicate their genomes and then pass it down to the next generation.

Example from parent to daughter

1. Transduction = DNA is transfered with the help of viruses

2. Transformation = cells pick up DNA from lysed cells

3. Conjugation = Donor transfers plasmid to recipient via pilli

To modify genomes of organisms by natural and artificial processes for practical processes.

You can eliminate unwanted phenotypes

Combine beneficial traits to make  a valuable organism

Make products that humans need

1. Mutagens

2. Reverse Transcriptase

3. Restriction enzymes

4. Vectors

5. Synthetic nucleic acids

6. Gene libraries

Vectors are tools for inserting DNA into a host.  They can be viruses, plasmids, transposons

They are small enough to make in lab

Can survive inside the cell

Contain gene markers that are recognizable

Ensure genetic expression of gene

1. PCR

2. Separation of DNA molecules

3. Insertion of DNA into cells

4. Clone Selection

Polymerase Chain Reaction

Used for multiplying/ amplifying DNA in vitro

(Was used for West Nile virus and Bacilius Antracis to ID the source of spores)

1. Gel electrophoresis = separate based on charge, size and shape

(the smaller the faster it will travel)

2. Southern Blot

1. Transduction

2. Transformation

3. Conjugation

Can use vectors

1. Electroporation = Make the membrane more responsive

2. Protoplast fusion = fuse 2 cells membranes

3. Injection = gene gun and microinjection

1. Genome mapping

2. Drug development

3. Vaccine Development

4. Agricultural applications

5. Provides info on metabolism, growth

6. Relate DNA sequence to protein synthesis

7. Transgenic organisms

1. Establishment of Health Department in 1900s = Made water treatment systems that controlled Cholera

2. Creation of antibiotics = Controlled Pneumonia

3. Vaccinations = Eradicated smallpox

1. STDs

2. Upper Respiratory Disease

3. Gastroenteritis

1. AIDS

2. Respiratory Diseases

 3. Intestinal Diseases ( virus = rotavirus, bacterial = Salmonella, Campylobacter)

4. Deseases caused by lack of Immunization = Tetanus

Methillicin Resistant Staphylcoccus Aureus

(The pathogen is resistant to the antibiotic)

This is a 2 billion dollar problem in hospitals and accounts for 20000 deaths a year.

What is a nosocomial infection?

What are some contributing factors?

A disease acquired while in a hospital.

1. Old age, weakened Immune system

2. A breakdown of barriers (burns, cuts, etc)

3. Chemotheraphy

4. Antibiotic resistant bacteria

5. Get 1 infection every 14 extra days

6. 1/20 infected or 1/400 deaths = 20000/yr

7. 2 billion $ a year

1. Patients are already ill, have impaired defenses

2. crowding = more infections

3. Most virulent forms are in hospitals

4. Newborns lack functional immune system

5. Drug resistant pathogens

Which pathogens is most common in UTIs?

Which are most common in surgical infections?

1. E.Coli

2. Pseudomonas Aeruginosa

1. S. Aureus

2. Streptococcus

Bacteria capable of causing disease (only a small # are pathogens)

Usually: Mycobacterium Tuberculosis (TB)

and

Yersenia Pestis

A pathogen that normally doesnt cause harm, but does so in immune compromised people.

Ex:  Pseudomonas Aeruginosa

What is ID50?

What happens if you have a lower LD50?

ID50 = Infectious Dose 50

The number of organisms required to make 50% of the population sick

If LD50 is low then there is high virulence

LD50 = Lethal Dose 50

Is the number of microbes that can kill 50% of the population that has the disease.

If LD50 is high then you have low virulence.

State Koch's Postulates?

What does it prove?

1. Observation = Signs and symptoms

2. Isolation = Pure culture

3. Re-infection = in an healthy person

4. Re-Observation and Re-Isolation = compare

Proves the etiology of the disease. One disease from one microbe

1. Mycobacterium Leprae (leprosy) = grows to slow

2. Treponemma Pallidum (syphillis) = cant grow outside of host

3. Polymicrobic infections

Top: Normal individuals who are healthy . There are few microbes that are capable of causing disease. So here is there is hi LD50 and ID50

Side:  Individuals with impaired defenses

Bottom:  Immunocompromised individuals. Many microbes can cause disease. So here there is a low LD50 and ID50.  (ex: Chemo patients, HIV peeps, diabetes peeps, etc)

1. Invasion

2. Producing toxic products

1. No invasion

2. Minimal Invasion

3. Highly invasive

It is highly toxic; usually food borne toxin

Ex:  Clostridium Botulinum

or

S. Aureus

Potent toxin

Ex: Corynebacterium Diptheria

or

C. tetani

Little or no toxin made

Ex:  Shigella

M. Tuberculosis

1. Attachment

2. Obtaining nutrients

3. Avoiding host defenses

1. Proteins

2. Fimbriae

3. Pili

(Ex.  N. Gonorrhea has a specific pili for attachment)

What do you call the Iron binding proteins in Bacteria?

What about in the host cells?

Bacteria = Siderophores (Is a virulence factor)

(used to try and steal the hosts Iron)

Host = Transferrin, Lactoferrin

1. Avoid antibody

2. Avoid the phagocytic cells

1. Rapid antigenic change (changes it pili so wont recognize it)  - N.Gonerrhea, Borrelia

2. Precipitate Antibody by binding to Fc portion (inactivates it)  - Staphylcoccus Aureus

1. Leukocidins

2. Survival within the cell

3. Antiphagocytic capsule

Leukocidins

Staphyloccus Aureus

1. Mycobacterium Tuberculosis

2. Salmonella typhi

A:  Required for toxic activity

B:  Required for entry into cell (you want antibodies to inhibit the attachment)

Surfaces

Neurotoxins

C. Diphtheria

A portion of the dimeric protein inactivates the Elongation Factor 2 thus inhibits protein synthesis

C. Tetani

Constant contraction (ex: lock jaw)

The A portion of the tetramer increases the adenylate cyclase activity thus increases cAMP.  The increase in cAMP increases the flow of ions out of the cell and thus water too. 

No antibiotics is need, just rehydrate

Fever

Hypotension

1. Mucous membranes (GI, Resp, Uri, Eye) 

2. Skin

3. Parenteral route

4. Vector Transmission

Entering the body by other means than the alimentary tract. 

Entry via subcutaneous, intramuscular, or IV

Entry via an insect

Ex:  Rickettsia Prowaskii = body lice

They are aka adhesins. Specific attachment

Genetic exchange

Promote blood clotting

Prevent Phagocytosis

An organ for locomotion

aka H-antigen

Capsule

K Antigen

What are virulence factors?

List the different forms of virulence factors.

Anything that facilitates a disease. Can be the prescence of the bacteria in the body, something the organism makes, or something it possess.

1. Pili

2. Capsule (K-Antigen)

3. Flagella (H-Antigen)

4. Cell Wall

1. Inhibit Phagocytosis = S. Pneumonia

2. Inhibit Lysosomal fusion = TB

3. Escape Lysosome = Plague

4. Lives w/in Lysosome = Salmonella

5. Kill Phagocyte = S. Aereus

Transmission, spread, control and prevention of infectious diseases in populations.

(All aspects of disease except treatment)

Endemic = Disease stays in pop at low frequency

Epidemic = Sudden outbreak in above levels
Pandemic = An epidemic over a wide area (worldwide)

Mortality = Reported deaths due to the disease

Morbidity = All reported cases of disease;  illness + deaths

Inanimate

Animate = Humans (ex: gallbladder)

Carriers

1. Airborne-borne = Most common, travels > 1 m (ex: Cold, Flu, TB)

2. Anthropod- borne = Carried by vector (ex: Thphus fever from body lice)

3. Direct contact = STDs

4. Food-borne = Preformed toxins (ex: Botulinum)

5. Water-borne = ex: Cholera

1. Proteases = inactivate host defense

2. LPS = Lipid A stimulate cytokine release, damages host cells

3. Capsules = Prevent phagocytosis

4. Vary surface antigens = H and K

5. Superantigens = Excess cytokine production

6. Cross reactivity

1. Staphylococcus - can tolerate it

2. Corynebacterium

1. GI = Lactobacilli

2. Small Intestine = Enterococci

3. Large Intestine = Entercocci

4. Upper Respir. Tract = Strep and Staph

5. Urethra = E. Coli, Proteus

6. Vagina = Lactobacilli

Mutualism

Antagonism

It has natural defense mechanisms

1. High Salt concentration

2. Low moisture

3. Fatty acids

4. Low pH

It has a tight layer of cells.  The top layer is dead cells that is constantly shedded.

Makes it hard for microbes to attach

Eukaryotic mRNA have the following modifications:

5' Cap

3' Poly A tail

Introns removed

Plasmids = DNA molecule that can separate independently of chromosomal DNA

Transposons = sequences of DNA that move within a genome

1. Glycocalyx

2. Adherence proteins

3. Lipoteichoic acids

4. Fimbriae (pili)

Intra = Microbes live inside cells where they are protected from Ab, phagocytes, etc. They dont move as much  (Ex: Chlamydia = obligate intracellular parasite)

Extra = Bacteria is in the blood not the cells. So they are constantly under attack, but have more motility

non specific attachment

sweep away fluids/particles

Gram +

Immune system activation

They are all virulence factors

Capsules = prevent phagocytosis

Flagella = locomotion

Endospores = Survive harsh conditions

1. Fast in, fast out

2. Mimic host antigens

3. Stay within host cells

4. Infect priviledge sites

5. Bind to host antibodies upside down

6. Antigenic variation

Restriction Fragment Length Polymorphism

It is the difference between samples of homologous DNA molecules that come from differing locations of restriction enzymes sites