LEARNING OUTCOMES: TEST #1

Basic Knowledge:
 Basic building blocks of life (elements): Sulfur, phosphorus, oxygen, carbon, hydrogen, nitrogen
 Basic types of bonds/atomic interactions:
Type of Bond Interaction
Covalent non-polar A covalent bond is the sharing of electrons
between two atoms. In non-polar, there is equal
sharing between atoms with similar
electronegativity
Covalent polar When atoms have a different electronegativity
from one another, the electron will stay mostly
orbiting one atom with greater electronegativity.
Ionic Cations and Anions exists (Water molecule).
Bond is formed from differences in charges
within the molecule.
Hydrogen A bond formed between a slightly positive
hydrogen atom and a slightly negative atom.
VanderWaal Forces Are weak forces between individual molecules.
Molecular mass increases, vanderwaal forces
increases. Can have London Dispersion forces of
Dipole-Dipole.

 pH: Potential Hydrogen; higher the pH means more basic

 Osmosis: Diffusion of water across a semi-permeable membrane. Water will move from a lower
concentration to a higher concentration.
o Hypertonic: Higher concentration outside, fluid moves from in a cell to outside. Cell crenation
o Hypotonic: Concentration higher inside the cell, fluid moves into the cell and the cell bursts.
o Isotonic: Fluid concentration inside and outside of the cell are the same, no movement.
 4 classes of organic macromolecules: Carbohydrates, lipids, proteins, nucleic acids
o Carbohydrates are made of carbon chains
o Lipids are made of a glycerol molecule and fatty acid chains
o Proteins are made up of amino acids, has peptide bonding
o Nucleic acids are RNA, DNA
 Basics of Eukaryotic cell
o Nuclear envelope that surrounds the DNA forming a nucleus
o Ribosomes: Package proteins needed for cell division
o Endomembrane System: Work together to modify, package, and transport lipids and proteins.
o Mitochondria: Provides energy for the cell
o Chloroplasts: Found in plant cells that cause the plant to be green through photosynthesis. Also
found in eukaryotic algae.
 Biological information system DNA ->RNA -> protein
 Enzymes: Catalysts that speed up chemical reactions.

Microorganisms
Microbiology: The study of small living things
Symbiosis: “To live together”
 Commensal: One member of the relationship benefits without significantly affecting the other.
Example: Staphlococcus epidermis grows on the skin but does not harm.
 Mutualistic: Both members benefit from the relationship. Example: Bacteria in your colon thrives in the
warm environment and the bacteria releases vitamins that is absorbed into your intestines.
  Amensalism: Relationship where one thrives and the other is harmed or destroyed. Antibiosis.
Example: Bread Mold
 Parasitism: One organism lives on another, causing it harm and is adapted structurally to it’s way of
life. Example: Tuberculosis in the lungs
Pathogen: Causes disease
Non-pathogen: Does not cause disease
Opportunistic pathogen: Take advantage and cause infection where it would normally live. Example:
Pneumonia can normally live in the body but if the immune system is weak, then pneumonia can take
advantage.
Axenic: Parts that are microbe free. There are parts of the body that are axenic.

List and briefly describe the different sorts of organisms that are considered to be microbes/
microorganisms
 Microbe: A microorganism that causes disease or fermentation s/a bacteria
 Microorganisms:
o Bacteria – prokaryotic, cell wall made of peptidoglycan, reproduce asexually, can degrade plants
and animals
o Fungi – eukaryotic (each of their cells contain a nucleus with genetic materials, surrounded by a
distinct membrane), can be mold (reproduce sexually or asexually), or yeasts (reproduce
asexually by budding)
o Archaea – prokaryotic, cell wall made up of different chemicals, reproduce asexually, found in
extreme environments s/a hot springs
o Protozoa – single celled eukaryotic, capable of locomotion by flagella, cilia, or pseudopods. Ex:
Plasmodium: Malaria-causing protozoa
o Algae – photosynthetic eukaryotes, can make their own food from carbon dioxide
• List at least four reasons why microorganisms are important:
1. Can ferment into food and beverages
2. To produce vaccinations and antibiotics
3. Can degrade toxic materials like oil and petroleum
4. Symbiotic relationships
Human microbiome: The collection of microbes that inhabits the human body.

Describe in general terms the human gut microbiome and explain briefly how it can be disrupted, giving
an example:
 Serve to protect the body with vitamins, folic acid, and flatus
 Antibiotic use can diminish normal human microbiota and this can cause colonization by pathogenic
microbes
Koch’s Postulates: Koch identified anthrax bacterium. Steps taken to prove the cause of any infectious disease
1. The suspected causative agent must be found in every case of the disease and be absent from healthy
hosts.
2. The agent must be isolated and grown outside the host.
3. When the agent is introduced to a healthy, susceptible host, the host must get the disease.
4. The same agent must be found in the diseased experimental host.
Microorganisms: Taxonomy, cell structure and function, identification

List and Describe the characteristics of life:

Cell Theory: Cell is the basic unit of life, all organism come from preexisting cells

Theory of Evolution: Happens by population changes

 Evolution can occur through selection
 Population: Individuals of the same species that live together

 Linnaeus assigned a species a genus and a specific epithet this is bionomial nomenclature

Eukaryotic: Eukaryotes have a membrane called a nuclear envelope surrounding their DNA, forming a
nucleus which sets eukaryotes in domain Eukarya.
 The term eukaryote comes from Greek words meaning “true nucleus.” Besides the nuclear membrane,
eukaryotes have numerous other internal membranes that compartmentalize cellular functions.
 These compartments are membrane-bound organelles—specialized structures that act like tiny organs to
carry on the various functions of the cell.
 The cells of algae, protozoa, fungi, animals, and plants are eukaryotic.

Prokaryotic: The distinctive feature of prokaryotes is that they can make proteins simultaneously to reading
their genetic code because a typical prokaryote does not have a membrane surrounding its genetic material
(DNA).
Species: Similar organisms that interbreed and produce viable offspring via sexually or asexually
 Bacteria can be separated into coccus, bacillus, spirilia, flaginated, comma shaped (Vibrio cholera)
  Ex: Enterococcus faecalis is fecal bacteria, and Enterococcus faecium are the same genus different
species
Structure & Function on bacteria:
 Plasmid: Small molecules of DNA that replicate independently – can be circular in prokaryotic cells
 Cell Membrane: Phospholipid bilayer, hydrophilic and hydrophobic areas
o Allow chemicals or molecules into or out of the cell
o Passive, active, facilitated diffusion
 Cell Wall: Provides structure and shape to the bacterial cell and protects it from osmotic forces. Can
resist with antimicrobial drugs
o Composed of peptidoglycan
o Gram positive (have thick wall) or gram negative walls (have thin wall)
 Glycocalyx: Gelatinous, sticky substance that surrounds the outside of the cell. Composed of
polysaccharides, polypeptides, or both. They are made internally and make themselves onto the surface
of the cell.
 Pilus (pili)/fimbriae: Projections adhere to one another and to substances in the environment –
important for biofilms to help stick
 Flagellum (flagella): Propel beyond the glycocalyx, to move the bacterium forward in the environment
o Can move towards environment through positive taxis, or away by negative taxis
o Can be due to chemotaxis or phototaxis. Ex: Positive chemotaxis
 Endospore: Produced inside the cell and released to the outside
o Affects pathogenicity (making it more pathogenic) and durability
o Bacillus and Clostridium
Mycobacterium tuberculosis: Has a waxy wall that protects it from drying. Causes TB in the lungs, airbourne
Mycobacterium pneumoniae: Pneumonia found in the lungs
Klebsiella pneumoniae: Can be in the lungs or UTI
Streptococcus pyogenes: Gram Positive, causes strep throat, airbourne, highly contagious
Staphylococcus aureus: Can cause a range of skin viruses such as pimples, boils, meningitis, pneumonia
Escherichia coli: Gram negative, facultative aerobic, found in the gut,
Neisseria gonorhoeae: Gram negative, causes STD gonorrhea

Clostridium: Is an endospore. Ex: C.Difficile, C. Tenani, C.Botulium, C. Perfingens

 C.Botulinum – act on the nervous system and disrupt it. Doesn’t affect food taste; causes blurred vision,
abdominal cramping, some skeletal muscle function and can stop diaphragm – will lose ability to breath
 C. Tetanus – Produces a different type of neurotoxin – cause muscle contraction; keep tensing; lock jaw,
affect breathing and hyperventilation leads to death
 C. Perfingens – can be on your skin, you can get cut and it goes into your cut, you lose oxygen to that
area of the wound that will generate gangrene and kill healthy tissue

Describe the basic structure of an archaeal cell, noting how it differs from a bacterial cell.
Describe where archaea are found in humans: Found in the colon, mouth, and skin. However, they were
once seen as extremophiles living in harsh conditions.
List 3 ways that archaea may contribute to human health and/or disease:
 Contribute to gut health
 Increase risk of inflammatory disease
 Increase risk of periodontal disease
 Prevent cardiovascular disease by breaking down chemical that causes CVD
Briefly describe gram staining, and how it relates to bacterial cell wall structure: Tells difference between
negative and positive
1. Soak the slide with violet
2. Stain is iodine to get it to stick, acts as a glue to hold the dye in place
3. Stain is to decolorize some of the cells; uses ethanol or acetone
4. Is flooded with safranin then rinsed so you can see the gram positive cells that are purple and the
gram negative cells are pink
Describe the general cell structure of a fungal cell, explain how it differs from a human cell, and name 2
human fungal pathogens.
 Are eukaryotic cells
 Fungal cell walls are made up of chitin or other polysaccharides
 Candida albicans is found in the gut, mouth or vagina and it is commercial
o A yeast infection
o Lives in warm, moist place
o Opportunistic

Describe briefly several methods that can be used to identify microbes in the lab – list 5 different
staining Gram stain, the acid-fast stain, the endospore stain, Gomori methenamine silver stain, and
hematoxylin and eosin stain.

 Gram staining
 Acid fast staining: Stains mycobacterium and Nocardia – cells that have large waxy lipid in their cell
wall
 Endospore staining: Bacilius and Clostridium – tetanus, gangrene, anthrax. Heat then colourize with
safranin
 Gomori methenamine silver stain:
 Hemotoxylin & eosin staining:

List and briefly describe the different sorts of organisms that are considered to be
microbes/microorganisms.

Viruses and Prions:

Describe the basic features/structures of viruses:
Describe the characteristics used to classify/categorize viruses, and where differences exist: Nucelic acid,
presence of an envelope, shape, and size.

Explain why viruses are classified as obligate parasites: Viruses must carry out their reproduction by taking
over a host cell therefore parasitizing them.

Identify several important viral diseases of humans: Measles, polio, tetanus, whooping cough.

Compare and contrast latent vs. lytic infection:

Lytic Replication cycle:
 Attachment: Of the virion to the host cell. This depends on the chemical attraction and fit between
attachment proteins on the phages tail fibers and complementary receptor proteins on the surface of the
surface of the host’s cell wall.
 Entry: Of the virion or it’s genome into the host cell. T4 has attached to the bacterium’s cell wall.
o T4 releases lysosymes that weakens the peptidoglycan of the cell wall. Genome is injected into
the tube and into the bacterium
o After entry, viral enzymes degrade the bacterial DNA into its constituent nucleotides.
 Synthesis: Of the new nucleic acids and viral proteins by the host cells enzymes and ribosomes.
o After losing its chromosomes the bacterium stops synthesizing its own molecules and
synthesizes viruses
o mRNA is transcribed from viral DNA instead of cellular DNA
 Assembly: Of new virions within the host cells
o Capsomeres accumulate within the cell they spontaneously attach to one another to form new
capsid heads
o This requires little to no enzymatic activity
o Transduction – when capsid assembles around left over host DNA by inserting phage DNA.
 Release: Of new virions from the host cell.
o Newly assembled virions are released while lysis completes its work on the cell wall and the
bacterium is integrated
o Plaques – bacteriophages “bacterial eater”
o Attachment to release is known as “burst time”
Lysogeny: Infected cells grow and reproduce for many generations before they lyse
 Viron randomly contacts an E.Coli cell and attaches its tail. Viral DNA enters; virus remains inactive
(prophage)
 Phrophage remains inactive by coding for a protein that suppresses prophage genes
 Fusing two pieces of DNA – prophage is replicated each time
 All daughter cells of the lysogenic cell are infected
 Inductive agents are usually the same physical and chemical agents that damage DNA molecules
 Synthesis
 Assembly
 Release
 The cell becomes filled with virions and breaks open

Describe the process of infection of an animal cell by a virus:

 The same steps of attachment, entry, synthesis, assembly, release however there is a difference in the
replication
 Attachment: Have glycoprotein spikes or other attachment molecules on their capsids or envelopes
 Entry: Direct penetration, membrane fusion and endocytosis
 Synthesis: Positive ssRNA act directly as mRNA
o Retroviruses don’t use their genome as Mrna
 Assembly AND Release: DNA viruses that are then released from the host cell from the nucleus into the
cytosol
o Almost 24 hour process with a bacteriophage it takes 25 minutes
o Enveloped animal viruses are released via budding
o Herpes and Chicken Pox may remain dormant

Describe the general life cycle and biology of Rhinoviruses and Herpes Simplex Virus 1, relating life cycle
to illness in humans:
 Rhinoviruses are 50 % of common colds: Cause polio, food and mouth disease, HEP- A
o Only one virus can cause a cold
o Takes advantage of endomembrane system
o Mucous keeps building up especially in 37-degree temp. If ingested, stomach will digest and
cannot cause cold in stomach
 Herpes Simplex Virus 1: Enveloped, double straded DNA
o Causes oral, and genital herpes
o Can be both lytic and lysogenic
o Latency affects peripheral nervous system, trigeminal nerve
o Forms episome in nucleus
o Responds to cell stress and creates mRNA that makes proteins and causes replications
o Cold sores come and go

Define prion, and describe the model of infection involved in prion diseases: Prion PrP acts as a bad
influence, clumping and can cause these to propagate in the brain and neurons stop working.

Describe variant Creutzfeldt-Jakob Disease (vCJD) and how it may be linked to BSE (Bovine Spongiform
Encephalopathy - "mad cow" disease):
 Ingestion of infected tissue, transplants of infected tissue, or contact of infected tissue with mucous
membranes
Comparison:

Biofilms
Explain what a biofilm is and its clinical importance:
 Aggregates of many bacteria living together on one surface
 Biofilms release acid that can cause dental caries
 Biofilms are found on shower curtains as soap scum
  They form due to synergistic relationships (benefit) – they get more living together

Identify features of biofilms that differentiate it from a planktonic lifestyle:

 Biofilm is colony whereas planktonic is single

Describe the stages of biofilm formation, and major features of bacteria growing in biofilms:
1. Planktonic bacteria swimming around and at a point they will
2. Attach to the surface and will hold on if the environment is good
3. Secrete matrix components
a. Polysaccharides, proteins, create a new microenvironment, tightly attached
4. Quorum sensing molecules are released – a way of communication
5. Biofilm matures; water channels specific shaper, attract more microorganisms
6. Some cells detach and become planktonic again and can make more to establish new biofilm

Describe several medically important biofilms, including several microorganisms that can form biofilms:
 S.aureus
 Lactobacillus – keeps pH in vagina low
 Helobacteria, IBD – may contain biofilms
 Proteus vulgaris - found in kidney infection

Explain problems faced in treating biofilm infections:

 They are difficult to diagnose because it is mostly opportunistic bacteria
 More resistant to antibiotics
 Resistant to immune response

Diagnose a biofilm infection given specific symptoms/characteristics and propose proper

treatment/prevention:
 Dental caries: IV antibiotics for blood infection, pulling teeth, health teaching to parents about dental
caries cause, eliminating sugar – this is what feeds biofilms (metabolism and growth)
o S&S include sensitive teeth, tooth ache
Microbial Growth
Define “microbial growth”: Growth of the microbe.
Describe the major factors that microorganisms require to support metabolism and growth:
 Carbon, energy, and electrons
 Organic sources s/a plants for carbon
 Organic molecules such as sugar or inorganic molecule such as ions for sources of electrons
 Glycolysis can be used
 Human cells can ferment however we are not anaerobic b/c our brain still needs carbon dioxide
Distinguish between anabolism and catabolism:
 Anabolism requires the building up or synthesis of molecules
 Catabolism is the breaking down or destruction of molecules

List the major factors that affect growth of microorganisms and explain how they affect growth:
 Temperature
 pH level
 Osmotic pressure
Distinguish among aerobic, anaerobic and facultative anaerobic bacteria:
 Aerobes: Use oxygen in aerobic respiration
 Obligate aerobes: Must use oxygen
 Anaerobes: do not use oxygen for respiration
  Obligate anaerobe: oxygen is poisonous; lack enzymes to break down toxic form of oxygen
 Facultative anaerobe: Normally needs oxygen, but can live without it so switch to fermentation
 Microaerophiles: Do require oxygen but amounts lower than atmosphere lower than 20% eg: H.pylori
at 2-10%
Distinguish among the following types of microorganisms:
 Psychrophilic: Grow best at temperatures below 15 degrees and even below 0, they will die above 20
degrees. Example: Algae, fungi, archae, bacterial that live in snow fields, ice and cold water
 Mesophilic: 20-40 degrees; these are human pathogens – thermoduric means they can survive briefly in
periods on higher temperatures
 Thermophilic: Grow above 45 degrees – composts, hot springs
 Hyperthermophilic: Grow in water above 80 degrees

Distinguish among the following types of microorganisms:

1. Neutrophilic
2. Alkalinophilic
3. Acidophilic
4. Halophilic
5. Barophilic

Define and be able to identify

 Antagonistic: Microbe harms/kills other
 Synergistic: Individuals support/benefit
 Symbiotic relationships: Become interdependent on each other

Describe the role of healthcare professionals in the collection of clinical samples/specimens: Human
material such as saliva, feces, CSF, blood – transported by a medium, Patient must get a clean catch

Describe and justify the general precautions that must be observed during collection, handling and
transport of clinical specimens: Proper PPE must be worn. Gloves, and face mask are a must where there is
fluid contact

Explain how specimen contamination and improper transport and storage can affect the end result: Can
alter the genetic material, it can change state, contamination by air or HCP, immediately refrigerate 2-8 degrees
to reduce growth

Explain what is meant by generation time and exponential growth:

 Generation time: time required to grow and divide – this depends on various growth factors
 Exponential growth: binary fission, growth that divides
Interpret a growth curve and identify the clinical relevance:
 Plots population overtime
 Lag phase – cells are adjusting; can last for hours to days
 Log phase – rapid chromosome replication, growth, and reproduction

Microbial Growth Control (in the Environment):

 Sterilization: the removal or destruction of ALL microbes – does NOT apply to proteins
 Aseptic: an area free of contamination of pathogens
 Disinfection: use of chemical or physical agents such as alcohol or bleach
 Degerming: removal of all mibrobes from surface via scrubbing
 Sanitization: disinfecting plates and utensils using steam, hotwater, or chemicals
 Pasturization: use of heat to kill pathogens and decrease spoilage to food and beverages
  Cidal: will destroy all microbes
 Static: will inhibit further growth
Explain Microbial Death Rate and its clinical relevance: the rate can be calculated to see permanent loss
under ideal conditions- within the first minute of treatment, the weakest die first. Broth will be sterile when all
the cells are dead
Antiseptic: chemical used on skin or tissue
Disinfectant: Are more concentrated and can be left on the surface for longer
List several physical methods used to inhibit growth of microorganisms:
 Heat – high temps denature proteins
 Moist heat – boiling
 Dry heat – occurs in oven
 Freezing – decreases microbial growth
 Desiccation – drying out, inhibits liquid s/a syphilis
 Lysophilization – combining freezing and drying to preserve microbes – prevents the formation of
large, damaging ice crystals
 Filtration – HEPA filters
 Osmotic pressure – preserves honey, jerky, jams, jelly
 Radiation – particulate high speed particles, electromagnetic
List several chemical methods used to inhibit growth of microorganisms
 Phenolics – denature proteins s/a with vomit
 Alcohols – bacterialcidal, fungicidal, virucidal against enveloped viruses
 Halogens – iodine, chlorine, bromine, fluorine
 Oxidizing agents – peroxides, ozone, peracetic acid preventing metabolism
 Surfactants – decrease attractions amount molecules such as soaps and detergents
 Heavy metals – copper to control algae growth
 Aldehydes – crosslink functional groups, what’s used in hospital rooms
 Gaseous agents – ethylene
 Enzymes – lysozyme
 Antimicrobials – antibiotics