Exam 1- Microbiology Study Guide PDF

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Exam 1 Study Guide Ch. 1 Introduction to Microbes 1. Name and define the two primary cell types. Which appears first in the fossil record? Approximately when (in billions of years) does each appear? Prokaryotes- bacteria and archaea - unicellular; 4 billion yrs ago(1st)- no nucleus, no membrane bound organelles; Eukaryotes- fungi (yeast and molds), protozoa, helminths (infectious worms)- multicellular --2 billion yrs ago- has nucleus, membrane bound organelles: 2.

Define: microorganisms (microbes). Which are noncellular?

A microorganism or microbe is an organism that is so small that it is microscopic (invisible to the naked eye). All prokaryotes are microorganisms. Some eukaryotes are microbes. Viruses are non cellular. 3.

Which major groups of microorganisms are prokaryotic? eukaryotic?

Prokaryotic: Archaea and Bacteria Eukaryotic: Domain Eukarya. 4.

Which units of measurement apply best to bacteria? viruses? macroscopic eukaryotes?

Bacteria, Protozoa, fungi: micrometers µm Viruses: nanometers, nm Macroscopic eukaryotes: mm and if not visible with the eye then um (same as bacteria) 5.

Define: pathogen; symbiotic relationship; parasitism.

Pathogen: Any agent that can cause a disease. Ie. viruses, fungi, protozoans, helminths, bacterium, etc. Symbiotic relationship: When the microbe organism has relations with another organism that is mutually beneficial to both their survival. Parasitism: When a microbe organism is using another organism as a host for the microbes own benefit, in such a way that it causes harm to the other organism. 6. Which century saw the development of the scientific method? List the steps in the method. 17th century-1600s Hypothesis - an observation about nature that can be credited and disproved.

Test validity of hypothesis - conduct repeatable experiments and collect and analyze the data from these experiments. Conclusion - determine if data supports or refutes hypothesis Publish - Write and publish your findings for others to test and repeat experiment 7. Who is credited with the development of the first microscope? How did his discovery of what he called “animalcules” contribute almost two hundred years later to the development of the theory of biogenesis? Antonie van Leeuwenhoek - created the first microscope.300x mag. Described animalcules that he observed. "Father of bacteriology" Biogenesis - cells can only arise from preexisting living cells. Credited by Rudolf Virchow. 8. What is the taxonomic tree? How is it organized? Which is the most inclusive level of classification (the most diverse grouping of organisms) and which the least inclusive? A classification system for organisms as a visual representation of the relationships between species. It is organized based on shared characteristics, phenotypically and genotypically. Beginning with broad categories to narrow definitions. The most inclusive level is Domain, and least inclusive is Genus. Domain-Kingdom-Phylum-Class-Order-Family-Genus-Species 9.

Which taxonomic classifications are used in the scientific name of an organism?

The genus and species name. Genus and Species are the only two taxonomic classifications that are used in naming a species. With Genus being capitalized and species lowercase. 10. Define: domain. Name the three domains. Which cell types and organisms are found in each? The most inclusive classification. It is based on the cell type of the organisms. There are three domains: Eukarya - eukaryotes Prokarya - prokaryotes Arachaea - cells similar to prokaryotes but more closely related to eukaryotes

Ch. 3 Microscopy 1. Know units of measurement in the metric system for: a)

macroscopic specimens; give example: some protozoa,

b)

microscopic specimens made visible with a light microscope; give example

bacteria, archaea, algae, protozoa, and microscopic animals such as the dust mite.

c) microscopic specimens only visible with an electron microscope; give example viruses 2. First microscopes a)

Which century saw the development of the first microscopes? 17th

b) Anton van Leeuwenhoek described what he called “animalcules” using his 300X lens. Which microbes would he have been able to see at that power of magnification? -

protozoa, blood cells 3. Light microscopes and how they work a)

Differentiate types - brightfield vs. darkfield vs. fluorescent

Brightfield – light background; A microscope that uses visible light for illumination; the specimens are viewed against a white background. Darkfield- dark background; The specimen appears light on a dark background. Used for unstained specimens. The light is illuminated where it does not hit the objective lens and thus will not be apart of the image Fluorescent- Cell parts are labelled with fluorochromes; uses ultraviolet light instead of visible light plus fluorescent dyes to make structures glow

b)

Discuss: i. simple vs. compound: one lens for simple, compound more than one set of lenses (2 lenses) ii.

path of light

- which lenses magnify? Ocular and objective together. (all) - determine total power of magnification: ocular X objective - parfocal – stays in focus once it is set at 4x, at other lenses just adjust

fine focus. iii. refractive index (Measure of how much substance slows velocity of light) and loss of light - effect on contrast at low power: At low power, there is less contrast because the light difference between the specimen and background is not great. - effect on resolution at high power and use of immersion oil: You will need to use more light because higher magnification requires more light, proper lighting is needed to see specimen details, and lens aperture decreases with higher magnification lenses. This is achieved by immersing both the objective lens and the specimen in a transparent oil of high refractive index, thereby increasing the numerical aperture of the objective lens. iv. viewing live specimens - wet mount- a glass slide holding a specimen suspended in a drop of liquid (as water) for microscopic examination v. viewing stained specimens - for identification and diagnosis The main reason you stain a specimen before putting it under the microscope is to get a better look at it, but staining does much more than simply highlight the outlines of cells. Some stains can penetrate cell walls and highlight cell components, and this can help scientists visualize metabolic processes. Stains also help distinguish between live cells and dead ones. Moreover, staining allows scientists count the number of cells of a particular type within a certain biomass. Twenty or more different types of stains exist, and each one has its purpose. 4. Define the three factors which affect the final image produced by a microscope a)

Resolution

resolution' is used to describe the ability of a microscope to distinguish detail. In other words, this is the minimum distance at which two distinct points of a specimen can still be seen - either by the observer or the microscope I.

discuss wavelength as it pertains to resolution: Shorter wavelengths --higher resolution

Shorter wavelengths yield higher resolution. The greatest resolving power in optical microscopy requires near-ultraviolet light, the shortest effective visible imaging wavelength. ii.

discuss refraction as it pertains to resolution:

In most instances, the imaging medium for microscopy is air, but high-magnification objectives often employ oil or a similar liquid between the objective front lens and the specimen to improve resolution. Refractive index, also called index of refraction, measure of the bending of a ray of light when passing from one medium into another. As the refractive index increases the speed of the light passing through a medium is slower. As light slows down the wavelength gets shorter and

yields better resolution. b) i.

Contrast

discuss stains as used in light microscopy vs. false coloration in electron microscopy

You can add false color afterwards to the picture but it will have no real relationship to the color of the organism. Stains in LM can serve as an identification method. c)

Magnification i.

what limits the degree of enlargement with any

microscope? The wavelength of light, limits the clarity of images. ii. what makes it possible to get greater magnification with electron microscopes? The electron wavelengths are a lot shorter so thus can have a clearer image at a higher magnification

5. Compare & contrast light microscopy (LM) vs. electron microscopy (EM) Light microscopy: Allows direct viewing Can view live specimens See natural colors Cheaper Some stains allow identification / diagnosis Con can't see past 1,500x Electron microscopy: Higher resolution at high magnification Provides internal and surface details Not useful for specific identification/diagnosis and expensive. Black and white image. Can't use live specimens, kills it in preparation and introduces artifacts. a) Electron microscopy - recognize differences - transmission (TEM) vs. scanning (SEM)

TEM: see internal detail, 2D image, 100,000x SEM: surface details, 3D, 10,000x b) be able to recognize which microscope was used to produce an image you are shown c) 6.

know the unique advantages and disadvantages of each

Stains in light microscopy - why are they used?

Cell staining is a technique that can be used to better visualize cells and cell components under a microscope. By using different stains, one can preferentially stain certain cell components, such as a nucleus or a cell wall, or the entire cell. Ch. 2 Chemistry of Life 1. Name the six major elements of life Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur a) define trace elements:

Micronutrients that are involved in enzyme function and maintenance or protein structure.

These include: zinc, nickel, and manganese 2.

Describe the basic structure of atoms a)

valence shell electrons; octet rule

Valence Shell: The number of electrons an atom can take on or lose in their outermost shell. Octet- a rule that states that every atom wants to have 8 electrons on its outermost electron shell b)

isotopes - medical significance of radioisotopes

Isotope: an atom of an element that is the same except with slightly more mass; either in protons, neutron, electrons, etc. making it radioactive. Radioisotopes are important for medicine in that these isotopes emit detectable signs that can be used to trace the position of atoms in treatment and/or diagnosis. 3. a)

Differentiate between the three types of chemical bonds discuss relative stability and significance of each in biology

Covalent: Electron Sharing bond; two atoms stick together to share their electrons - both valence shells are happy. Also forms carbon backbones/chains. Strongest bond. Hydrogen: Attraction between polar molecules; strong affinities between opposite charges seen with water.

Ionic Bond: Electron Transfer bond; atom either gains or loses electron to another atom. Weakest dissociates in water. 4.

Define: a) Electrolyte: a compound that ionizes in a solution - disassociates into ions - and is able to conduct an electrical current. b)

solvent; solute

Solvent: A dissolving medium

Solute: The substance that is uniformly dispersed in a dissolving medium - solvent. c)

pH scale; acidic; basic or alkaline; significance of pH7

pH scale - A way to measure the concentration of Hydrogen ions in a solution. It can then be used to rate the acidity and alkalinity of a solution. Acid: a solution with a pH below 7, suggesting it has a high concentration of hydrogen ions, less -OH (hydroxide ions) Basic/alkalinity: A solution with a pH greater than 7, suggesting lower concentrations of hydrogen ions, and more hydroxide ions. Significance of pH7: the pH of pure water, when the solution is neither acid or basic, but neutral. Organism are best grown at this pH. 5.

Water - discuss its significance to biological reactions a) ~70% of the cell by weight- Because it is a universal solvent, it can carry nutrients to cells and carry waste away from it b)

discuss the polarity of the water molecule as the “universal solvent”

There is an uneven distribution of electron density which allows it to dissolve other polar substances easily as the positive ends of a molecule are attracted to the negative ends of the water molecules. It is a polar molecule that is composed of Hydrogen bonds, relatively weak bonds between the hydrogen atoms of one water molecule and the oxygen atom of another water molecule. These traits allow it to easily dissociate its hydrogen bonds and form new bonds with charged or other polar molecules. Polarity: a way to describe a molecule with asymmetric charges, having a positive and negative polar end. c)

dehydration synthesis vs. hydrolysis

i. process of removing water in a reaction to form larger molecules ii. process of adding water to a reaction to break the bonds. 6.

Name the four families of biological molecules.

Carbohydrates: monosaccharides/polysaccharides. Glyosidic bonds. Functions: structure, support, energy storage. Proteins: peptide bonds between amino acids. Functions: membranes, enzymes, hormones, antibodies Lipids : glycerol + fatty acid (monoglyceride/diglyceride/triglyceride). Ester linkage. Simple lipids are esters of fatty acid with various alcohols. Compound lipids are esters of fatty acid with alcohol and additional groups. Functions: form membranes, energy storage. Phospholipids are complex lipids. Nucleic Acids: sugar phosphate bonds. function for information storage. DNA is phosphate group with deoxyribose and base. RNA is uracil, ribose, and phosphate group, ATP is adeno ribose and triphosphate For each: a) names

7.

recognize the general structural formulae for the monomers, and their

b)

name the chemical bond type between monomers which forms polymers

c)

recognize the generalized structures of common polymers

d)

describe the major functions of each in the cell

Phospholipid bilayer; membranes; discuss a)

nonpolar vs, polar; hydrophobic vs. hydrophilic

Phospholipids orient in water to form a lipid bilayer, as seen in membranes. They have a hydrophilic phosphate heads (polar & water loving) and hydrophobic tail (nonpolar & hate) so they orient where it creates a barrier between the cytoplasm and extracellular space. The hydrophilic regions form hydrogen bonds with water, other side removes itself from water. 8.

Proteins - the most prevalent and diverse of biological molecules a) describe the levels of folding & the major bonds which contribute to folding at each level b)

significance of shape to function of proteins

c)

causes of denaturation

i. primary structure - polypeptide chain ii. secondary structure - hydrogen bonds create regular helices or pleats iii. tertiary structure - disulfide bridges, ionic bonds, and hydrogen bonds b/w R groups iv. quaternary structure - 2 or more polypeptide chains v. shape is critical to function. Folding creates unique shapes and potential for specificity.

vi. Low pH, high heat, high salt Chapter 4 - Cell Structures Prokaryotic vs. Eukaryotic cells - two fundamental cell types All cells that are not prokaryotic are eukaryotic. All organisms that are not in the Domains Bacteria or Archaea are in the Domain Eukarya. Eukaryotes include algae, protozoa, fungi, plants and animals. There is growing evidence that supports the theory that eukaryotic cells evolved from simpler prokaryotic cells about 2.5 billion years ago.

1. Compare basic similarities of the two cell-types a)

watery cytoplasm

b)

plasma membrane - a phospholipid bilayer

c)

ability to utilize an energy source

d)

DNA encoding inheritable traits

e)

ability to duplicate and divide

i. Prokaryotes: Cytoplasm - water and solute Has fluid mosaic model - proteins move freely within membranes. Has anchor for filamentous appendages (cilia/flagella). Energy production. Nucleoid - DNA is double helix, circular, supercoiled, Plasmids - extrachromosomal DNA Uses a pilus for DNA transfer and gliding motility. Made of pilin tube

2.

Contrast important differences between the cell-types a)

size

b)

simple or complex organization

c)

presence or absence of membrane-bound nucleus and other membranous organelles

d)

type of ribosome

e)

location in cell where ATP synthesis takes place

f)

structure of flagella and source of energy for movement

i. Prokaryotes are smaller than eukaryotes.

i. prokaryotes does not have membrane bound nucleus or organelles i. prokaryotes have 70S ribosome, eukaryotes 80S ribosome i. prokaryotes take place in the membrane, eukaryotes in the mitochondria i. prokaryote flagella: composed of flagellin which is attached to a protein hook, and basal body that are anchored in the membrane and cell wall. Powered by proton motive force and rotates. ii. Eukaryote flagella: powered by ATP. Composed of microtubules of tubulin protein and is an extension of the cytoskeleton, covered by the plasma membrane. Has wave like movement. Prokaryotic Cells - Domain Bacteria (covered here) & Domain Archaea (covered in Ch. 10) 1.

Major features a)

single-celled

b)

size range; size relative to Eukaryotes

c)

identify morphologies - know terms

d)

identify multi-cellular arrangements - know terms

Major structures - identify structures & describe functions: 2.

Plasma membrane - universal i.

phospholipid bilayer - describe chemical structure

Large molecules are impermeable, smaller molecules are permeable, ions penetrate slowly ii.

b)

how does it work as a selective barrier?

iii.

to what is it permeable? impermeable?

iv.

roles of membrane proteins

v.

describe the fluid mosaic model

membrane transport mechanisms:

Proteine - function as enzymes that catalyze reactions, for support, as mediators of changes in membrane shape during movement. Some proteins are channels that allow substances to enter and exit the cell i.

passive vs. active transport

ii.

define osmosis

iii. effect of osmotic pressure on cell under three environmental conditions iv.

which condition leads to: osmotic lysis? Plasmolysis?

Hypotonic can cause osmotic lysis. Hypertonic cause plasmolysis. 3.

Cell wall a) how does it prevent osmotic lysis? The cell wall is strong and can contain the swelling b)

peptidoglycan - composition; action of penicillin? Lysozyme?

i. Structure: woven sac in shape of cell by repeating disaccharides and woven with peptide cross bridge. Has several components. ii. All animals have vesicles of lysozyme and penicillin to break down peptidoglycan- killing the bacteria.

c)

atypical i.

Mycoplasma - wall-less bacterial genus

ii.

Mycobacteria - atypical cell walls - require special stain

iii.

Domain Archaea - chem...