UCF Microbiology Exam 1 (MCB3020)

Infuenza (Spanish Flu)

More Americans died than were killed during World War I, WWII, Korean and Vietnam wars combined (about 2 million)

Pandemic (world wide epidemic) that killed 50 million

Due to an antigenic drift

Small Pox

Over 300 million people killed, making it one of the biggest killers in history

Since the development of the vaccine no deaths reported since 1977 (said to be eradicated)

Categorized as a Biological Warfare Agent (30% mortality)

Black Plague

1/3 of the population of Europe (about 25 million) perished during one epidemic from 1346-1350

Antibiotics are available and control this disease

Categorized as a Biological Warfare Agent

New Emerging Diseases

Legionnaire's Disease (1976)

Lyme Disease

AIDS (1980s)

Hantavirus (1993)

Mad Cow Disease (1986)

Ebola (2015)

Asian Flu/H2N2 (1957), Swine Flu/H1N1 (2009)

Due to antigenic shift

Bird Flu/H5N1 (1997)

Due to antigenic drift

Severe Acute Respiratory Syndrome (SARS) (2002)

Antigenic Drift

Vaccine efficacy wanes with time as new surface antigens appear from mutations in genes encoding them. Changes to the flu virus that happen slowly over time. This causes the changes to the seasonal flu that require us to get vaccinated against the flu each year

Antigenic Shift

Results when two different flu strains combine and infect the same cell.

Viral Hemorrhagic Fever

Subgroup of dangerous and feared viral pathogens

Most lethal infectious agents known

Handled by the CDC under biosafety level 4.

Ex's:

- Hantavirus (endemic to the US)

- Marburg Virus (Germany)

Bacteria, Viruses, Fungi, Parasites

4 Kinds of Microorganisms that can lead to disease

Industrial Microbiology

Conversion of raw material to desirable end products by selected microorganisms. Utilization of microbes in manufacturing process. The old belief was the study of the fermentation process ==> production of beer and wine

Primary Metabolites

products are necessary for microbial growth (amino acids, alcohol, organic acids)

Secondary Metabolites

products are not necessary for microbial growth (antibiotics, steroids, etc.)

Agricultural Microbiology

Benefits from the cycling of nutrients. Bacteria forms nodules on legume's roots. Nodules convert N2 --> NH3 (called Nitrogen Fixation). Ammonia is then used for plant growth.

N2 -> NH3 -> NO3 --> (repeat)

Ruminant animals have MO's in their "rumen" vessels which allow them to digest nutrient poor cellulose such as grass.

Agricultural Microbiology can cause Disease

Microbial disease of plants can cause major economic loss.

Ex: contaminated food such as E.Coli or Salmonella from infected meat.

Jack in the Box - outbreak of E. coli 0157:H7 in hamburgers / 4 children died / 600 sick. Undercooked patties contained fecal material w/ bacteria

Blue Bell Ice Cream - listeriosis cases caused by Listeria monocytogenes - 10 people sick / 3 dead

Food Microbiology

spoilage, safety, production. Some food requires microorganisms

Ex: some dairy depends on key acids from microbial fermentation

Ex: fermentation of yeast alcoholic beverages and baked goods.

Glucose => 2 lactic acid => Proprionic acid + acetic acid = cheese / yogurt

Glucose => 2 Ethanol + 2CO2 => 2 Acetic acid = pickles / acohol

Energy Microbiology

Focuses on converting waste material into methane natural gas and ethanol. (biofuels)

Ex's: cellulose & cornstarch -> glucose fermented into alcohol

Biotechnology

Uses genetically modified microorganisms to synthesize products of high commercial value. Focuses on applying gene technology or recombinant DNA technology to develop products. Synthesis of an in vivo system of thousands of products useful to humanity. It makes a lot of gene products such as Interferon and Somatostatin.

Genentech

Uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients w/ serious of life-threatening medical conditions. First to produce somatostatin and insulin

Bioremediation

Uses living organisms to degrade pollutants in the environment . Bacteria can be used to degrade oil spills, PCBS (polychlorinated biphenyls), & trichloroethylene

Metabolism: nutrients become new cell material/waste & energy

Growth: increase in cell number

Evolution: Next generation has traces of parental cells

All cells include these properties

Motility: Self propulsion

Communication/Genetic Interchange: Sharing information among themselves

Differentiation: Modified cells that become specialized

Some cells include these properties

All cells have them. Cannot be changed.

- Cell membrane

- Ribosomes

- DNA

- RNA

Invariant Structures

Some cells have them.

- Cell wall

- Mitochondria

- Chloroplast

Variant Structures

Metabolism

Cells take up nutrients, transform them, an expel waste.

1) Genetic (replication, transcription, translation)

2) Catalytic (energy, biosynthesis)

Final result = 2 new cells

Growth

Nutrients from the environment are converted into new cell materials to form new cells. Catalysts are used

Antibiotic Selective Pressure

Refers to the impact of antimicrobial use on a population of organisms, in which organisms that are resistant to the antibiotic gain a survival advantage over those susceptible to the antibiotic.

Differentiation

Some cells can form a new cell structure such as a spore. Responds to specific triggers

Motility

Self-propulsion through the use of flagella, fimbriae, and pili.

Genetic Exchange

Cells can exchange genes w/ each other by several mechanisms. Independent of evolution, accelerates adaptation to the environment.

Chemical Machines that carry out chemical transformations in the confines of the cell or coding devices which store and processes genetic information (DNA) and passes it off to offspring. They work together to support cell growth.

Cells can be viewed as

Population

Group of cells derived from a single parental cell

Habitat

Where the population lives, interactions can be beneficial, neutral, or harmful

Ecosystem

All living organisms living together w/ the physical and chemical components of the environment. Greatly influence by microbial activity. Can expand and contract, population size and makeup can change

4.6 bya

3.8-3.9 bya

2 billion years

Within 1st billion years

within 2nd billion years (2.6 bya)

2 bya

0.5 bya

Earth is how old?

Microbial cells appeared how long ago?

How long was earth anoxic? (had N2 and CO2)

When did photosynthetic organisms appear?

When did cyanobacteria appear?

Multicellular life appeared?

Plants and animals appeared?

1) Microscope

2) Sterilization and aseptic techniques (pasteur)

3) Pure Culture Methods (koch)

3 things imperative in development of MicroBio

Robert Hooke

First to coin the term "cell"

Described fungi and mold with his primitive microscope. Discovered microorganisms.

Antonie Leeuwenhoek

First to see microorganisms . Discovery of bacteria

Semmelweis and Lister

Had evidence of the importance of aseptic techniques. Their handwashing technique was ignored.

Robert Koch

Developed the germ theory, proving that microorganisms are the causative agents of a disease. Developed postulates. Worked with anthrax, mice, tuberculosis. Developed Agar to culture microorganisms in the lab. Developed Pure culture technique.

1) Pathogen should be present in all cases of disease, absent in health animals

2) suspected organism should be grown in pure culture

3) When culture is inoculated into animals, it should initiate disease

4) Organisms should be re-isolated & shown to be same as original

Koch's Postulates

sufficient but not necessary to establish causation

Solidifying agent allowing for isolation of pure culture

Solidifies at 40 degrees C

Melts / Liquifies at 100 degrees C

At 60 degrees Celsius it can be solid or liquid

Agar

Evolution

Process of descent w/ modificiation which generates new variety and species. Variation is due to mutation and natural selection.

Linnaeus System

Haeckel System - 3 Kingdoms

Stainer System

Whitaker System - 5 kingdoms, 3 levels of organization

Woese System - 3 kingdoms, now 3 domains

Classification Systems for Naming Bacteria

Phylogeny

permits grouping of organisms based on the evolutionary lines of descent by DNA comparison

Taxonomy

grouping of organisms for convenience of laboratory study and hence focuses on phenotypic differences

Animalia (motile)

Plantae (non-motile)

Linnaean System

("based on observations")

3 Kingdoms

Animalia

Plantae

Protista (cannot easily be placed into other kingdoms)

Haeckel System

Haeckel's Protista

Unicellular or multicellular organisms that do not develop into differentiated tissue. Includes algae, fungi, protozoa, bacteria including cyanobacteria

Animalia

Plantae

Higher Protista (eukaryotic: algae, protozoa, fungi)

Lower Protista (prokaryotic: cyanobacteria, bacteria)

Stainer System

Animalia ( ingestion, consumer)

Plantae (photosynthesis, producer)

Fungi (absorption, decomposer)

Protista (eukaryotic, unicellular) / Algae, Protozoa

Monera (prokarytic, unicellular) / Bacteria, Cyanobacteria

Whittaker's Kingdom's

Based on genetics and evolution

Eukarya (eukaryotes)

Bacteria (prokaryotes)

Archaea (prokaryotes)

Woese's Domains

Woese rRNA sequencing

Cell DNA is extracted -> PCR makes many copies of the rRNA gene -> Gene is sequenced -> Sequence is aligned to other organisms -> Similarity is assigned -> Phylogenetic Tree

Archaea Phylum: Euryarchaeota

4 Groups of Organisms

1) Methanogens (anaerobes)

2) Extreme Halophiles (NaCl)

3) Thermoacidophiles / Thermoplasmatales (High Temp, Low pH

4) Hyperthermophiles (> 80 C)

Archaea Phylum: Crenarchaeota

Mostly hyperthermophiles & anaerobes

- Uses H2 as energy

chemolithotrophs or chemoorganotrophs

5 Kingdoms:

Monera, Protista, Fungi,Plantae,Animalia

3 Domains:

Bacteria, Archaea, Eukarya

3 Domains and 5 Kingdoms

Morphology & Size: simple or negative stain

Differential Stain: Gram stain, due to different cell wall structure

Structural Stain: spores, capsule, flagellum

Staining Properties

1) Crystal Violet

2) Iodine

3) Decolorize w/ alcohol

4) Counterstain with safranin

Gram Stain Steps

Nomenclature

ex: Pseudomonas aeruginosa

Genus and Species are the major taxonomic groups

- 1st letter of genus CAPITALIZED

- Species not capitalized

- Both names ALWAYS italicized or ALWAYS underlined, not both.

Prokaryotic Cells

They do not contain organelles. NO nucleus, coupled transcription/translation. DNA is found in the cytoplasm and it is circular.

Louis Pasteur

Recognized optical isomers, disproved spontaneous generation , used swan neck flask. He developed anthrax, cholera, and rabies vaccines. Confirmed the germ theory of disease

Prokaryote

Cell wall

Cytoplasmic Membrane

Nucleoid

Cytoplasm

Plasmid

Ribosomes

Organic Molecules/Inorganic ions

Mainly Circular DNA

1 Chromosome w/ 1 copy of each gene (haploid)

Plasmids

Eukaryote

Cell wall (plants, fungi)

Cytoplasmic membrane

Mitochondrion

Nuclear membrane

Nucleus

Ribosomes

Endoplasmic Reticulum

Cytoplasm

Golgi Complex

Chloroplast

DNA linear / packaged by proteins / diploid

Algae, Protozoa, fungi, slime mold, plant and animal cells.

Eukaryotic Types

Bacteria and Archaea domains. DNA in cytoplasm, couples transcription and translation

Prokaryotic Types

Viruses:

- DNA or RNA

- Protein Coat

Viroids:

- Only RNA

- NO protein Coat

Prions:

- Only Protein

- No protein coat or RNA/DNA

Acellular Microorganisms

Viruses

-Acellular

-Smaller than cell, lacks attributes

-Only alive when they affect host

- Lack metabolic activity

- Contain genome

- NO RIBOSOME

- Disease causing

- Sometimes helps cell by changing genome

Proteins (informational)

Nucleic Acids (informational)

Lipids (noninformational)

Carbohydrates (noninformational) / Polysaccharies

4 Main Macromolecules

Covalent Bond

forms when 2 atoms come bvery close together and share one or more of their electrons.

Ex's: C=C, C=O, N=N, P=O,

C=O-N-H, cytosine, phenylalanine

Hydrocarbon

Nonpolar, do not form H bonds, and are insoluble in water

Higher the Number of bonds = Shorter & Stronger

Bond Strength and Size

Purine: Adenine, Guanine

Pyrimidine: Cytosine, Thymine, Uracil

Purines vs Pyrimidines

Amine: formed in water combined w/ H+ ion to make it POSITIVELY CHARGED

Amide: combining an acid & amine. UNCHARGED

Amine Vs Amide

Van der Waals Forces

- atoms approach each other and create non-specific bond

- Transient unequal distribution of electrons

H Bonds

- donor is electronegative

- H is acceptor

- polar

- intra or intermolecular

Hydrophobic Forces

Ionic Bonds

Weak Non-Covalent Bonds

Weak Non-covalent bonds:

Hydrophobic Forces

Ionic Bonds

1) Nonpolar molecules do not contain ions, possess dipole moment, or become hydrated

- Covalent bonds CC, CH, most common nonpolar bonds

- Decreases hydrophobes from interacting w/ water

- Important in protein Folding

2) Bonding electrons not shared, electron goes w/ more electronegative element. Do not have fixed orientations

- Polar

- stronger in the absence of water

- weak in aqueous solutions & salt

1) Lipids

2) Polysaccharides

1) Storage for excess carbon, prevents unrestricted movement of polar molecules

2) Important in cell wall, some are storage for carbon and energy

Carbohydrates

Organic compounds of C1H2O1. Monosaccharides. Pentoses are structural backbone of nucleic acid. Hexose are monomers of well wall polymers and energy storage. Derivatives have OH group replaced. D form predominates. Bound together by glycosidic bonds.

Glyceraldehyde

Ribose

Glucose

Dihydroxyacetone

Ribulose

Fructose

Aldoses (3,5,6)

Ketoses(3,5,6)

Enantiomers

Optical isomers that have the same molecular and structural formula. Cannot be superimposed. D or L depending on rotation to right or left.

L- Amino Acids (D in peptidoglycan)

D - Sugars (L cell wall of bacteria & archaea)

Most predominate isomers in Biological systems are

Polysaccharides

Held together by covalent glycosidic bonds (a or b). Diff. bonds give diff properties.

Complex forms

Glycolipid

Glycoprotein

Glycogen, starch:

important in carbon and energy storage in plants, animals, and bacteria

Alpha-1,4-glycosidic bond Glucose

Cellulose: found in plant and algae cell walls

Beta-1,4-glycosidic bond Glucose

When C that carries aldehyde/ketone group reacts w/ any OH group on a second sugar molecule.

1) glucose + glucose

2) glucose + galactose

3) glucose + fructose

Disaccharides:

Maltose

Lactose

Sucrose

Fatty Acids

Monomers that make up lipids found in Bacteria and Eukarya. Hydrophobic (methyl) and Hydrophilic (ionized)regions

Phytane

What are lipids in Archaea made of?

Simple Lipids

3 fatty acids esterified to glycerol (c3 alcohol)

- known as a triglyceride , formed by removal of water btw acidic carboxyl group and OH group of glycerol.

Complex Lipids

simple lipids with 2 fatty acids and additional elements such as phosphate group.

- known as Phospholipid

Oleic Acid (C18/ Unsat)

Stearic Acid (C18 / Sat)

Palmitic Acid (C16/ Sat)

Common Fatty Acids

dolichol phosphate

used to carry activated sugars in the membrane-associated synthesis of glycoproteins and some polysacccharides.

1) cholestrol

2) testosterone

2 main steroids

1) found in many membranes

2) male steroid hormone

Glycolipid

composed of hydrophobic region w/ 2 long hydrocarbon tails, a polar region containing 1 or more sugar residues, and no phosphate.

Pentose:

- RNA: Ribose

- DNA: Deoxyribose

N Base:

- Purine: A, G

- Pyrimidine: C, T, U

Phosphate

*Base attaches to sugar at C1 & on base N1 pyrimidine, N9 purine

phosphoester bond btw sugar and phosphate

Nucleotides

DNA

RNA

Nuceloside Triphosphate

or Nucleotide

ATP is what?

Pure As Gold

Adenine

Guanine

Glycosidic Bond: N9

Purines

Cytosine

Thymine (methyl group)

Uracil

Glycosidic Bond: N1

Pyrimidine

Thymine

Normally found in the keto form. Can be found in enol form where it will triple bond w/ guanine. Leads to spontaneous mutation.

Enol = OH--=

Keto = O=C

Nucleic Acid

Polymer made up of nucleotides. Backbone has sugar and phosphate molecules alternating & joined by covalent 3'5' phosphodiester bond. Synthesized by polymerase

5' to 3' direction

DNA/RNA synthesis occurs in which direction?

DNA

carries the genetic blueprint for the cell