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JMU / Biology / BIO 280 / Why should we care about microorganisms?

Why should we care about microorganisms?

Why should we care about microorganisms?


School: James Madison University
Department: Biology
Course: Allied Hth Microbiology
Professor: J. herrick
Term: Fall 2019
Tags: Biology and Microbiology
Cost: 50
Name: BIO 280 Exam 2 Study Guide
Description: This study guide covers what will be on exam 2.
Uploaded: 10/20/2019
16 Pages 27 Views 10 Unlocks

Microbiology Exam #2 Study Guide / Summary

Why should we care about microorganisms?

Lecture 1 review (on last test): 

1. How we account for death rates:

a. Vaccinations  

b. Water source  

c. Antibiotics  

d. Sterile medical technique  

2. Infectious disease and parasitic diseases are one of the leading causes  of death worldwide

a. Nearly 15 million of the 57 million annual deaths are caused by  infectious diseases

3. Why we should care about microorganisms

a. They’re everywhere  

i. Gram of soil has 10^9 bacteria  

b. Human body has more bacterial cells than human cells  i. Skin, mouth, GI tract, respiratory tract, urogenital tract  c. Microorganisms live in extreme places  

i. Geysers and hot springs- hyperthermophilic

What does microbiology encompass?

ii. Very cold places  

iii. Deep sea hydrothermal vents  

iv. Hypersaline (salty) habitats (halophilic bacteria)  

v. Rock surfaces  

vi. Even other planets (ice on mars)  

d. Useful and beneficial  

i. Biotechnology  

ii. Agriculture  

1. Nitrogen fixation  

2. Nitrogen fixation  

iii. Food and chemical production  

iv. Mineral extraction  

v. Wastewater treatment  

vi. Bioremediation  

e. Basic scientific research  

i. Our understanding of chemical and physical principles  

come from microorganisms  

ii. Due to their use in the lab (easy to manipulate)  

What was carl woese's contribution to the classification system?

4. What does microbiology encompass??  

a. Study of microscopic organisms  

Lecture 2 Review (on last test) We also discuss several other topics like What was the declaration meant to be?

Evolution, identification, and classification of prokaryotes and  eukaryotes  

1. Microorganisms are too small to be seen with the naked eye  a. Most microbes encountered (in this class) will fall between  100um and 10nm in overall dimensions  

b. Microbes come in a variety of shapes and sizes  

2. The early evolution of microorganisms (from most recent to oldest)

a. Age of dinosaurs -> origin of metazoans -> origin of modern  eukaryotes -> origin of oxygenic phototrophs (cyanobacteria) ->  origin of life -> chemical evolution / formation of the earth  3. Cyanobacteria  

a. Algae blooms  

4. Prokaryotes: Eukaryotes: a. Single-celled or in chain clusters a. single celled or  multicellular  

i. Bacteria i. can organize  into tissues  

ii. Archaea b. fungi, plants,  protozoa, animals  Don't forget about the age old question of Marketing is not considered as what?

b. No true nucleus c. contains a true  nucleus  

c. No membrane bound organelles d. contains many  membrane bound .  


5. Eukaryotic cells cont.  

a. Most likely evolved from prokaryotic organisms by intracellular  symbiosis  

b. Some organelles originated from prokaryotic cells  

c. Endosymbiosis  

6. Taxonomy  

a. Primary concerns: classification, naming, aiding identification b. Orderly arrangement of organisms into groups  

c. Domain, phylum, class, order, family, genus, species  i. Most inclusive to least  

d. Based on judgement of scientists  

i. Constantly evaluated and revised  

7. Naming

a. Binomial system  

b. Genus and species  

c. Names are varied (discovering scientist, shape, color, disease it  causes)  Don't forget about the age old question of What are positive and negative couplings?

8. Phylogeny  

a. Natural evolutionary relatedness b/w groups of living things  b. Can be used to create a system of taxonomy  

9. Woese’s System  If you want to learn more check out How would mill respond to rousseau’s idea of what makes us free?

a. Domains: bacteria, eukarya, archaea

b. Determined by dna sequencing  

c. Archaea  

i. Prokaryotic cells  

ii. Unusual anatomy, physiology, and genetics  

1. Unique membrane lipids  

iii. Similar to eukaryotes rather than other prokaryotes  iv. Most are extremophiles*

Lecture 3 Review (on test one) 

1. Early microscopy  

a. Simple lenses  

b. Compound microscope  

i. Invented by Zecharias Janssen in beginning of 17thC  

ii. Magnification of 3x to 9x

c. Van Leeuwenhoek  

i. First observation of bacteria  

ii. Made his own microscope of magnification of 200x or more iii. Great resolution*  

2. Modern microscopy  

a. How it works:  

i. Refraction: bending of light rays. Lens bends light and is  made to focus it at a specific point  

ii. Results in an image larger than size of original (like a  If you want to learn more check out If we were the direct ancestors of chimpanzees, what would happen?
We also discuss several other topics like What are time series components?


b. Compound lens system  

i. Total magnification = product of mag of each lens (ocular x objective lens)

c. Magnification can continue to increase but the image won’t be  clear after a certain point because of resolution  

d. Theoretical limiting factors of resolution  

e. RP= “d”, the resolution distance or “resolution” (want it to be  small)

i. Made smaller by using illumination source with a shorter  wavelength  

ii. Also by making denominator larger  

f. Wavelength- illumination source  

g. Numerical aperture- measure of the light passing from the object and into the objective to maximize optical clarity and resolution  (for average lens= 0.94)

Lecture 4 Review (on test one) 

1. Most abundant biological molecule= WATER 

a. Aqueous environment plays a large role in determining how  macromolecules assemble to form structures in the cell  

b. Water is polar

c. It interacts w/ itself and other polar molecules and ions  d. Hydrophilic  

e. Hydrogen bonds

f. Hydrophobic (does not interact with non-polar molecules like oil)

i. Such as: hydrocarbons  

g. Hydrophobic molecules will interact with each other  

h. Amphipathic molecules (like phospholipids) have hydrophobic  and hydrophilic properties  

2. Macromolecules  

a. Organic chemicals- compounds containing both carbon and  hydrogen atoms  

b. Carbon is the fundamental element of life  

i. Has 4 electrons in its outer orbital  

ii. Can form single, double, or triple covalent bonds as well as  linear, branched or ringed molecules  

3. Carbohydrates  

a. Include sugars and polysaccharides  

i. CH2O2 (general formula)  

ii. Functions: structural support, nutrient and energy storage  iii. Subunits linked by glyosidic bonds  

b. Sugars- monosaccharides and saccharides  

4. Lipids  

a. Long, complex, hydrophobic, C-H chains triglycerides,  

phospholipids in membranes, steroids

b. Functions: triglycerides- energy storage, phospholipid- major cell  membrane component, sterols and steroids- cell membrane  components, waxes-waterproofing, resistance to immune cells  5. Proteins  

a. Predominant- macromolecules in cells  

b. Functions: support, enzymes, transport, defense, movement  c. Monomer: amino acids (there’s 20 of them)  

d. Structure:  

i. Polymer: peptide, polypeptide, protein  

ii. Subunits linked by peptide bonds  

iii. 4 Levels of Protein Structure:  

1. Primary- amino acid sequence  

2. Secondary- alpha helices and beta pleated sheets  

3. Tertiary- overall folding pattern of helices and sheets  

4. Quaternary- putting together of multiple ‘domains’ or

tertiary structures  

Lecture 5 Review (on test one) Bacterial Cell Envelope  

1. The cell envelope  

a. Made up of:  

i. Glycocalyx: polysaccharide, either slime layer or capsule,  biofilm formation,

ii. outer membrane

iii. cell wall: fundamental unit of the cell wall is a carb polymer (peptidoglycan)

1. peptidoglycan: 2 monomers are N-acetylglucosamine

and N- acetylmuramic acid

iv. cell membrane  

2. lysozyme  

a. Alexander Fleming  

b. Found in tears, saliva, nasal and sinus fluids

c. Breaks bonds between NAG and NAM monomers in  


3. Gram Positive vs Gram Negative  

Gram Positive  

Gram Negative

4. Lipopolysaccharide

a. Large, complex molecules composed of polysaccharides linked to lipid molecules  

b. Lipid portion is buried in the membrane, while polysaccharide  portion lies on the surface of the cell

5. Porins:

a. Outer membrane of Gm. Neg. bacteria restricts the passage of  many molecules into cell  

Lecture 6 Review (on test one) 

1. Within the cytoplasm  

a. Genetic material in prokaryotes  

i. Chromosome

b. Plasmids: extrachromosomal circular DNA  

i. Contains genes that aren’t necessary for survival but may  be useful  

ii. Can be transferred horizontally  

iii. Used as vectors for transferring DNA in genetic engineering c. Ribosome  

i. Used for constructing proteins from messenger RNA

ii. In 2 parts. Made up of proteins and ribosomal RNA  

d. Storage bodies and inclusions  

e. Genetic material  

i. Bacteria generally have a single large chromosome  

ii. Not bounded by membrane  

f. Storage bodies and inclusions: PHB, glycogen, sulfur,  


g. Endospores  

i. For survival, not reproduction  

ii. Toughest life form  

h. Significance of endospores:  

i. The two major genera: Bacillus and Clostridium

ii. Persistence and resistance of endospores contribute to the  pathogenicity of these species  

2. Bacterial Motility  

a. Run and tumble  

i. in response to an attractant, a bacterium will increase the  duration of its RUNS relative to the TUMBLES

b. flagellum- worlds tiniest motor

c. Eukaryotic motility structures:

i. Flagella and cilia  

1. Similar in composition but differ in size and function  

2. Flagella: either singly or in pairs, larger than bacterial

flagella, move in a whip like manner  

3. Cilia: only found in ciliates (protozoa), shorter and  

more numerous, function like oars

d. Other surface structures:

i. fimbriae and pili  

Lecture 7a Culturing *new info for test 2

1. The germ theory of disease and Koch’s Postulates 

a. What is postulate 1?

b. Postulate 2: the suspected organism should be grown in pure  culture  

i. Necessary because: non pure culture would confound  

interpretation: who’s causing what??  

ii. Problems: not all microorganisms can be cultured  

c. Postulate 3?

d. Postulate 4: the organism should be reisolated and shown as  the original  

i. Necessary because: there may have been something else  introduced or one may have made a mistake. If you treat  

something, you have to know what is causing it  

2. What are problems we inherent in studying microorganisms? a.




3. Studying microorganisms without a microscope  

a. Limits to microscopy—how does one study physiology, genetic,  etc?  

b. Most major discoveries in microbiology are not based on  anything one can see 

4. How to do it:  

a. Make billions of cells to study  

b. Pure cultures (aseptic technique)

i. Attained by isolating cells  

1. Methods: streak plate method  

ii. Goal: isolate colonies for further purification  

c. Media  

i. Liquid, semisolid, solid (big breakthrough)  

d. Chemical content of media (2 types)

i. Defined (synthetic) media- used for specific applications ii. Undefined/complex (non-synthetic)

e. Define Selective medium:

f. Differential medium- indicator has been added to allow one to  differentiate between various chemical reactions during growth  g. Mediums can be both selective and differential*

5. Culturing or microscopy are not the only ways to study  microorganisms*

Lecture 7b Nutrition and Growth 

1. Bacteria are highly evolved like other organisms!  

2. Classification of microorganisms by nutrition type  

a. Carbon source vs energy source  

i. Humans get both from the same source  

ii. Plants derive their carbon from CO2 and their energy from  light  

iii. What does “trop” mean?  

b. Classification by carbon source  

i. Heterotroph – C source is organic molecules  

ii. Autotroph—C source is CO2

c. Classification by energy source  

i. Phototroph—energy source is light  

ii. Chemotroph—energy source is chemicals  

iii. Chemoorganotrophs – organic chemicals  

iv. Chemolithotrophs—inorganic chemicals (minerals)  

3. Nutrient acquisition and transport  

a. Prokaryotes use exoenzymes to digest their food  

b. Facilitated diffusion- passive diffusion that does not require  energy input  

c. Active transport (molecular channels, group transport) uses  energy*

4. Microbial growth  

a. Exponential growth and how to calculate it  

b. Generation time (g) / Doubling time – the time required for a  population of cells to double or for one cell to become two  c. Calculating generation time:

i. There’s a direct, predicable relationship between the  

number of cells in a culture initially and the number there  after a period of exponential growth  

ii. Nf = (Ni)2n 

5. Bacterial growth curve  

a. Lag phase: period after inoculation of a culture before growth  begins  

b. Exponential phase: period of exponential growth  

c. Stationary phase: period in which growth ceases  

d. Death phase: period in which cells die off  

6. How do we measure growth?  

a. Total cell count (direct count/direct microscopic count)  

b. Viable count (plate or colony count)  

c. Measurements of cell mass or turbidity  

7. Using turbidity to estimate cell growth  

a. Measuring turbidity: measure cloudiness of a cell suspension by  light scattering  

b. Turbidity is proportional to cell number  

c. Can give us a relative measure of growth (if turbidity doubles, we know the total number of cells has also doubled  

d. Measure using a spectrophotometer  

e. Chemostat- a device for continuous culture  

8. Environmental effects on microbial growth  

a. Important to distinguish b/w effects on VIABILITY and effects on  GROWTH (including reproduction)  

b. Important factors: temp, pH, water availability, O2

9. Effects of temp on growth rate

a. Each microorganism has a minimum, maximum and optimum  b. Organisms can be classified by their optimum temp  

c. Examples:  

i. Boulder spring (boiling spring) in Yellowstone National Park ii. Growth of thermophilic cyanobacteria in grand prismatic  spring, Yellowstone

iii. Psychrophile grows at below freezing temp (-12 degrees C) Lecture 8 Control 

Physical and chemical control of microorganisms  


1. “control”- limiting exposure to infectious agents  

a. Microorganisms are part of our environment  

b. Infection can be controlled by limiting exposure to infectious  agents  

2. Sterilization- removal or disinfection of all viable microorganisms  

3. Disinfection- removal or destruction of pathogens (not spores) from  non-biological areas

a. Off of non-biological related things (table)

b. Could be disinfectant wipes

4. Antiseptics- destruction or inhibition of vegetative forms from the body  a. Can be used on bio related things

b. Could be a hand sanitizer  

5. Sanitization- any cleansing technique that mechanically removes  microorganisms  

a. Usually soaps  

b. We want to limit exposure by getting it off of us (doesn’t need to  be dead, just away from us)  

c. Most important line of defense against infection (1st step)  6. “cide”- refers to killing

a. “bacteriocide” kills bacteria  

b. Fungicide kills fungi, etc.  

7. “static”- means to stand still  

a. An agent which prevents growth but doesn’t kill  

b. Stops from growing  

c. Bacteriostatic, fungistatic, virustatic, etc  

Factors that determine the effectiveness of a control method 

1. The number of microorganisms  

a. Death curve  

b. Decimal reduction time  

2. Agents: temp and pH of environment, concentration of the agent,  mode of action of the agent, presence of interfering compounds or  inhibitors of the control agent  

3. Moist heat methods  

a. Boiling water  

b. Pasteurization (temp below boiling to kill specific pathogens)  i. Ultra-high temp  

c. Steam under pressure  

i. If pressure increased, higher temps can be reached  

4. Effects on cellular proteins  

a. Physical methods: radiation  

b. Ionizing: knocks electrons off atoms  ions  

i. Damaged DNA and proteins by breaking bonds, exposure  hazard to humans, penetrates solids and liquids, used to  sterilize fruits and veggies, now meats too  

c. Non-ionizing*-- excites atoms but does not ionize  

i. Damages DNA, relatively safe to use, does not penetrate  solids or liquids well, surface disinfection, water treatment d. Other physical control methods  

i. Sonication—disruption using sound waves  

ii. Filtration  

5. Chemical control agents  

a. Many kinds but most function by: disrupting membranes and  altering protein and or nucleic acid structure  

b. Effectiveness is determined by: concentration and contact time  

6. Halogens:  

a. Mainly chlorine is used now

b. Iodine ‘iodophors’ are the most common iodine compound used  in hospitals  

c. What are the main chlorine forms?

d. Effective against?  

e. Limitations: ineffective at an alkaline pH

f. Unusable light and O2 cause breakdown  

7. Phenols: 

a. Affect protein function and or disrupt membranes  

8. Alcohols: 

a. Ethanol  

b. Isopropanol – more microbicidal but also more toxic (rubbing  alcohol)  

c. Destroys cell membranes and can coagulate proteins because it  is a dehydrator

9. Hydrogen peroxide:  

a. O2 forms free radicals which are toxic to cells  

b. Also breaks down H2O and O2  

10. Aldehydes  

a. Effective disinfectants and even sterilants  

11. Gases:  

a. chlorine dioxide gas disrupts proteins  

b. ethylene and propylene oxide  

i. very effective sterilant  

12. detergents:  

a. all solubilize membranes and disrupt proteins  

b. ionic and non-ionic

13. heavy metals: 

a. mainly mercury and silver  

b. form ions that complex w/ cell components, stopping growth  c. disadvantages:  

i. toxicity

ii. allergenic

iii. microbes can develop resistance  

Lecture 9  

1. Terms  

a. Antimicrobial chemotherapy: when a drug is used to control  an infection

b. Antimicrobial drugs: a class of compounds which inhibit or kill  microorganisms.

c. Antibiotics -- natural antimicrobial drugs.

d. _synthetics-- man-made antimicrobials. Antibiotics which have  been chemically modified are called _semisynthetic.

e. broad spectrum agents

f. narrow spectrum agents

2. where do antimicrobials come from?  

a. Alex Fleming’s discovery of penicillin  

b. Of the thousands discovered, a few are useful  

3. How they work:  

a. Five main approaches:

b. Inhibition of cell wall formation -- e.g. penicillins and  


c. Inhibition of cell membrane function (less common) e.g.  polymixin  

d. Inhibition of dna synthesis -- e.g. ciprofloxacin

e. Inhibition of protein synthesis -- e.g. tetracycline, erythromycin f. Inhibition of nucleic (folic acid) synthesis -- e.g. sulfa drugs 4. Main Families of Antibiotics  

a. B lactam antibiotics

b. 4 types: penicilins, cephalosporins, carbapenems and  


c. They all have a b-lactam ring

5. Inhibition of cell wall synthesis: b-lactam anibiotics

6. Nucleic acid synthesis inhibitors  

a. Trimethoprim  

b. Sulfanilamide (metabolic analogs)  

7. Protein synthesis inhibitors  

a. Tetracyclines  

b. Macrolides  

i. Erythromycin – ribosome binding antibiotic derived from  streptomyces erythraeus  

c. Aminoglycosides – also derived from streptomyces but also  ribosome binding but bactericidal  

d. Fluoroquinolones  

i. Introduced about 15-20 yrs ago  

ii. Synthetic  

iii. Broad spectrum especially against gram- negatives  

iv. Primarily binds to and interferes w DNA gyrase – DNA  complex for DNA replication

8. 2 newer classes of antibiotics  

a. Synercid and Zyvox  

Antimicrobial drugs  


a. Antibiotics prescribed in wrong situations  

b. Not finishing the prescription  

c. Use of antibiotics in food (agriculture)  

d. The bacteria are developing a resistance to antibiotics not to us

10. Antimicrobial ‘arms race”  

a. Development of resistance has led to an arms race

i. We develop a new class of antibiotics  

ii. The microorganism that is targeted develops resistance to  it  

iii. We develop a modification of the antibiotic  

iv. The microorganism develops resistance to all forms of the  antibiotic  

v. And so on

11. Mechanisms of antimicrobial resistance  

a. Enzyme inactivation  

12. Host / drug reactions (adverse or side effects)  

a. Tissue toxicity  

b. Allergic reactions  

c. Disruption of normal flora  

13. Picking the right antimicrobial drug  

a. Identify the agent  

b. Determine the susceptibility of the agent  

i. Kirby Bauer  

ii. Minimum inhibitory concentration  

Lecture 10 Microbial Genetics 

1. Levels of Structure and Function of the Genome

a. Genome- sum total of genetic material of a cell (chromosomes  +mitochondria/ chloroplast and or plasmids  

i. Genome of the cells-DNA  

ii. Genome of viruses – DNA or RNA  

b. DNA complexed w/ protein constitutes the genetic material as a  chromosome

2. Genes  

a. Chromosomes are subdivided into genes  

i. Cite on the chromosome that provides info for a certain cell function  

ii. Segment of DNA that contains the necessary code to make  a protein or RNA  

b. 3 basic categories of genes:  

i. Structural genes

ii. RNA coding genes  

iii. Regulatory genes  

3. RNA

4. DNA  

5. Growth (polymerization) of a single DNA strand  

a. DNA polymerase reads from 5’ to 3’  

b. Antiparallel arrangement of the two strands of a DNA molecule  c. The base component of a nucleotide – a purine  

d. The base component of a nucleotide – pyrimidine

e. In a cell, the amount of adenine = the amount of thymine and  the amount of cytosine = the amount of guanine  

6. DNA secondary structure


7. DNA replication – first steps  

a. Synthesis takes place simultaneously but in opposite directions  on the two DNA template strands

b. Begins at a single replication fork when a double stranded DNA  molecule unwinds to provide the two template strands  

c. Synthesis continues on one template strand of DNA and  discontinues on the other  

8. Flow of genetic info in cells:  

a. DNA  RNA  Protein  

9. Promotor region- where RNA polymerase binds to initiate transcription  a. One gene  one protein  

10. DNA Transcription  

a. Template strand is being transcribed  

b. Promotor region is the part of the sequence (nucleotides)  11. Genetic Code  

a. Represented by the mRNA codons and the amino acids they  specify  

b. Code is universal among organisms  

c. Code is redundant

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