study guide- first microbio exam

1. What are microbes? Microbes are beasties or animalcules we found moving in the water.

How are they categorized? Microbes are categorized by a taxonomic system; Bacteria, Archaea, Fungi, Protists, Algae, Small Multicellular Animals, and Viruses.

Be able to give the defining characteristics of each of the 3 Domains. The 3 Domains are Bacteria, Archaea, and Eukarya and they are prokaryotes and have no membrane bound organelles or no nucleus

Any Kingdoms discussed. The 4 Kingdoms discussed are Protists, Animals, Plants, and Fungi which are eukaryotic and has a TRUE nucleus and other membrane bound organelles

The six major groups of microorganisms we talked about or from your General Biology course?! Bacteria and Archaea ~ prokaryotes, unicellular, lack nuclei, smaller than eukaryotes, found everywhere (needs moisture), reproduces asexually (no partner needed). Although both are prokaryotes, there are 2 different kinds; Bacteria’s cell walls have peptidoglycan (a type of polysaccharide) and Archaea has cell walls with peptidoglycan. Fungi ~ eukaryotic, have membrane bound organelles and have nucleus, obtain food from other organisms (heterotrophs), and have cell walls. Protozoans (protists) ~ eukaryotes, unicellular, similar to animals; need nutrients & cell structure, live freely in water; some inside animals, most reproduce asexually, but some may reproduce sexually, locomotion by (moving to a place to another) by pseudopodia (fake foot), cilia, and flagella. Algae ~ have an unclear classification but perhaps protists, they are eukaryotes, they are multicellular or unicellular, they also do photosynthesis, then do simple reproductive structures, they are categorized based on the pigmentation, storage, or size/shape.

Also be able to give some examples of organisms in each microbe category mentioned in our notes. Bacteria- E.coli, Archaea- Euryarchaeota, Fungi- Agaricus, Protist- Ciliate, Algae- Diatom, Small Multicellular Animals- Bryozoans, and Viruses- Norovirus.

Recall information you learned in the homework assignment about Domains & Kingdoms, too.

Who was Leeuwenhoek and what were his contributions to microbiology? He was early “microbiologist” and his contributions were making microscopes
When was the Golden Age of Microbiology? The Golden Age of Microbiology was in the years 1857-1907
What 4 major questions were being examined at that time? Is spontaneous generation of microbial life possible? What causes fermentation? What causes disease? How can we prevent infection & disease?
What is spontaneous generation and who is it attributed to? Spontaneous generation is when living things can arise from nonliving matter and it is attributed to Aristotle.
What (and whose) experiments supported spontaneous generation? Aristotle’s experiment about ants popping up during your picnic. Needhams Experiment on the idea that animals did not arise out of nowhere but maybe microbes did.
Which debunked spontaneous generation as one of the processes by which life arose? Redi’s Experiment on meat in a jar with different lids. Spallanzani’s experiment that needham didn’t execute his experiment previously, accurately.
How did each of those experiments support or debunk spontaneous generation? For Aristotle, he questioned how did the ants appear during your picnic? This supported the spontaneous theory. Redi rejected the theory because of the idea that food can be outside and animals will try to appear but only once the food is exposed to the air. Needhams supported the idea but questioning of tiny microbes was spontaneously growing. Spallanzani’s had critiques against Needham that he didn't seal jars right enough or used enough heat to kill the previous microbes.
What is the scientific method? The scientific method is observation to question then question to hypothesis then hypothesis is tested through experiments, then results confirm or don’t confirm hypothesis. Confirmed hypothesis become theory or law and if not confirmed then it is modified.
What is the connection between the study of microbiology and the scientific method? The study of microbiology connected with the scientific method by understanding the trial and errors when researching tiny microbes that were being studied in microbiology.
Why was the development of the scientific method so important for the study of microbiology and science, in general? The development of the scientific method is important for the study of microbiology because it was so new at this time, having a procedure to help us find out what is the truth helps us learn more about our world correctly.
Be sure to know and understand the contributions of the following scientists:
1. Redi- Redi conducted an experiment that showed that spontaneity was not real. His meat in a jar method with different kinds of coverings showed us how nothing really grows on the meat unless exposed to the air.
2. Needham- Needham conducted an experiment that led him to believe that microbes could arise on meat but we just couldn’t see it.
3. Spallanzani- Spallanzani’s experiment conducted that Needhams experiments had many mistakes and could have been tested better for some accurate results, meaning rejecting spontaneous generation.
4. Pasteur- Pasteur conducted an experiment on the reason of why yeast was reproducing in grape juice, his conclusion was that just enough heat kills bacteria and still allows yeast to make alcohol which is known as pasteurization. He also developed “germ theory of disease” which was that specific microbes were responsible for diseases which are pathogens. Lastly, he was also known as the “Father of Microbiology”
5. Koch- Koch studied the agents of disease, etiology. Prove that bacteria caused Anthrax and examined colonies of microorganisms. He also came up with the “gold standard” of studying disease—such as important ones like “microbe must be present in every case of the disease” or “when you then take that agent and introduce it to a healthy person, then the host should get the symptoms/disease”
6. Gram- Gram developed staining technique in 1884 which involves the series of dyes
7. As well as recognize some of the other contributions made by other scientists during the Golden Age of Microbiology (the ones I specifically mentioned in our lectures)- We talked about
  1. Semmelweis (handwashing)
  2. Listers’s (Antiseptic Technique)
  3. Nightingale (Cleaning wards/clothes & nursing)
  4. Snow (Infection control & epidemiology)
  5. Jenner’s Vaccine (Field of immunology)
  6. Enrlich’s “magic bullets” (Field of chemotherapy)
What are Koch's 4 postulates and what is their function and how do they work/how used? Koch’s 4 postulates are 1. Suspected causative agents must be found in every case of the disease & be absent from healthy hosts, microbes must be present in every case of the disease, 2. Agents must be isolated & grown outside the host, 3. When you then take that agent then introduce it to a healthy person, then the host should get the disease/symptoms, agent must cause the disease when a healthy person is inoculated with it, 4. The same agent must be found in the diseased experimental host. All must be in order!
What is the germ theory of disease? That microbes are responsible for diseases
What is a pathogen? A specific microbe causes specific disease
What is etiology? Is the causative agents of disease
What is industrial microbiology? Industrial microbiology is when we use microbes to intentionally make products, for example using yeast or bacteria to improve foods. ex. Grape Juice
What 4 questions are being examined today in microbiology and what fields of science are associated with each one? The 4 questions being examined today are 1. What are the basic chemical reactions of life?, this is in biochemistry, 2. How do genes work?, this is in gene therapy, 3. What roles do microbes play in the environment?, this is in environmental microbiology 4. How do we defend against disease?, this is in vaccines, serology, and immunology.

Chemistry (Ch. 2)

Why is it important to study the chemistry of microbes? To understand the molecules because they makeup cell structure and help cells to function
Define and give examples (where appropriate) of:
1. matter- anything that takes up space and has mass
2. element- matter made of 1 type of atom
3. atom- smallest chemical units of matter
4. electrons- negative charge
5. neutrons- neutral charge
6. protons- positive charge
7. isotopes- atoms with the same number of protons, but different neutrons (Carbon-12= 6 protons and 6 neutrons
8. molecule- 2+ atoms held together by chemical bonds
9. compound- molecule composed of >1 element bonded together
10. different types of bonds
  1. Covalent Bonds- = sharing of electrons by two atoms, strongest bonds
  2. Ionic- loss of electrons by 1 atom to more electronegative partner in compound, forms a bond between the 2 atoms, weaker than covalent bond, commonly forms compounds that are salts (NaCl) cations- positively charged electrons 7 anions- negatively charged electrons
  3. Hydrogen- weak ionic bonds, rises from attraction of + and - charges between H & other atoms, extremely important for stabilization of large 3-D molecules, ex. DNA, Enzymes, and Antibodies
  4. Polar- water= H₂O
  5. Nonpolar covalent- sharing of electrons equally between two atoms
  6. Peptide- short chain of amino acids linked by peptide bonds
  7. Electronegativity-= attraction of an atom, the greater the pull its nucleus exerts on electrons
  8. Organic compounds- one or more atoms of carbon are covalently linked to atoms of other elements, mostly hydrogen, oxygen, or nitrogen.
  9. Electrolytes- Sodium Chloride (NaCl) which forms electrolytes, critical for life, stabilize compounds, act as element carriers, allow elements gradients within cell
What are the four major macromolecules necessary for life? Carbohydrates, Proteins, Lipids, and Nucleic Acids
Be able to define each,
1. Carbohydrates (CHO)- the major source of energy for cells and structural components of bacteria, archaea, plants, fungi, and some protists.
  1. Has 3 types of carbohydrates
    1. Monosaccharides- one hexagon shape and simple sugars with a short lifespan in the cell. They break down quickly giving energy for metabolic processes or link to form disaccharides or polysaccharides
    2. Disaccharides- two hexagons, 2 monosaccharides linked together. They are short-term energy storage, when the cell requires the energy, the bond between 2 sugars is broken to release energy.
    3. Polysaccharides- complex carbs (many hexagons), many monosaccharides bonded together. Long term energy storage which provides structural support for cells and fiber for digestion in animals
2. Proteins (CHON)- Large molecules composed of small subunits called “amino acids”, they regulate chemical reactions (enzymes), transport, build structures, and are made for defense and offense (antibodies)
3. Lipids (CHO)- They are C,H,O but H>O compared to carbs and they don’t break down easily in the water. They are also somewhat diverse for example, some types of lipids are
  1. Oils, Fats, and Waxes
    1. Fats and Oils function as long term energy storage and contain more energy than carbs or protein, (ex.1 gram fat = 2x more energy than 1 gram carb). Most composition of fats is that 1 glycerol = 3 fatty acids and that fatty acid = hydrocarbon
    2. 2 Types of Fats are Saturated (3 fatty acids all in a straight line and should be solid in room temp; ex. Butter) and Unsaturated (at least 7 fatty acid bends b/c of double bond, the double line causes a kink in the fatty acid and at room temp it is liquid; ex. Fish or Plant oil).
    3. Waxes have no glycerol and instead have long chains of C’s with hydroxyl (-OH) groups and fatty acids are all saturated. They function by helping some microbes resist desiccation & other external factors (ex antibodies) and they prevent them to dry up and protect it from outside harm
  2. Phospholipids- They are structurally similar to fats=glycerol + fatty acid chains (usually 2) + phosphate group (PO₄)- basic components of cell membrane. (Ex. Hydrophilic head, hydrophobic tail, the strands on the end are fatty acids).
  3. Steroids- They are very different from fats in structure & function and rings of C bonds, (ex. Cholesterol- which are an essential molecule in the body and present themselves in phospholipid membranes that surround animals' protists cells which makes them more fluid). They play a role in microbial metabolism and are present in cell walls of fungi.
4. Nucleic Acids (CHONP)- They function by storing and transmitting hereditary information
  1. 2 Types
    1. DNA (deoxyribonucleic acid) which stores info and is inherited. Also has very long molecules which are made up of single units which are…
      1. nucleotides: they have 3 parts, a phosphate group, a pentose (5-carbon sugar), and a nitrogenous base
    2. RNA (ribonucleic acid) which transmits info (transfer)
  2. 2 types of nitrogenous bases
    1. Pyrimidines- Cytosine (found in both DNA & RNA), Thymine (found in DNA), and Uracil (found in RNA)
    2. Purines - Adenine and Guanine (both found in DNA and RNA)
5. What is a monomer? A molecule that bonds with other monomers to form a polymer
6. Polymer? A large molecule made up of many smaller units called monomers
7. What is dehydration synthesis? When water is getting or forced out of the process of a reaction from a larger molecule from smaller units
8. Hydrophilic/hydrophobic? Hydrophilic is when something is water loving and hydrophobic is when something is water fearing.
9. Be able to compare and contrast DNA and RNA. DNA has deoxyribose and RNA has ribose, DNA stores genetic information and RNA transfer information, DNA is a double helix and RNA is a single line, DNA has A,G,C,T and RNA has A,G,U,C, and that DNA is hereditary and RNA is not
What is ATP and how is it related to nucleic acids?ATP is a nucleotide derivative, (basically, a couple of nucleotides added with phosphate) which would break off a phosphate group to release energy, pop it back on, store energy again which is very important because it carries much of its energy, and you can always pop it on and off, as long as you have phosphate

LAB Material Reminder:

Laboratory Safety & Microbial Contamination (Lab 1)

What are some of the important "rules" for working with microbes (re: microbiology lab procedures signed sheet)?- No food or drinks, closed toed shoes, pants, keep in lab items away from your mouth/eyes/nose, no application of domestics, and no cell phones. At the start of the lab make sure to wash your hands, wipe your bench, then at the end put away supplies and empty biohazard contents, then wipe the table and wash hands. Tie up your hair and wear eye protective gear if needed, don’t bring all personal items to the table, label everything, use pipettes correctly and not by mouth.
Why are those rules in place? To help us prevent cross contamination or any harm to our own body. To make sure labs go as safely as possible and results come out accurately.
What are some sources of contamination- some sources of contamination are not hand washing, sneezing, coughing, bodily fluids
routes of transmission- some routes of transmission of sneezing in open air, coughing without cover, or accidentally letting bodily fluids touch others
factors affecting host susceptibility- not being careful around others who may be sick or protecting yourself from them. Proper handwashing and coverage
ways to reduce all of those things- Hand wash properly, face coverings and hand coverings if needed, understand when to quarantine, and take care of overall health
What did the handwashing lab demonstrate - both generally and specifically- The lab showed how quickly and easily the contamination was able to spread and despite having a napkin, not all the germs were killed or removed. But once sprayed we were able to see it starting to disappear. Only with the black light of course, another thing was that when handwashing you were able to see how much of the germs were sticking on small crevices of your hand. Then see how many seconds were not as effective as others and that you can’t really clean your hands completely with just water. You need soap.

Microscopy (Ch. 4 & Lab 2)

What are the parts of the compound microscope and each of their functions? The Arm, The Stage Adjustment Knobs (fine and course), The Base, Ocular, Rotating Nosepiece, Objective Lenses, Stage Clips, Stage, Abbe Condenser, Iris Diaphragm, and Illuminator
Make sure you understand how microscopes work and be sure you know how to properly use a microscope to see both eukaryotic and prokaryotic cells, as well as how you calculate magnification of an object you are looking at, etc.- to change magnifications we have the red 4x, the yellow 10x, the blue 40x, and the white 100x.
Related to #2, what are the "rules" associated with working with microscopes (re: microscope rules- Some rules for microscopes are to make sure you have two hands when grabbing the microscope, the base and arm. Make sure when rotating the nosepiece you are holding on the rubber knob when turning. Make sure the stage clips are on top of the slide without damaging them. Make sure to use lens wipe to only cleans the lens, nothing else.