Microbiology Final

Why care about microorganisms?

disease, help with science, they everywhere

How do we account for the huge drop in death due to infectious disease in the US since 1900

• proper water and food handling

  • especially sewage treatment and drinking water treatment

• vaccines

• antibiotics

• sterile medical techniques

What are the top infectious diseases in terms of global mortality

1. 26% respiratory infections (pneumonia, influenza)

2. 18% AID’s

3. 17.5% diarrheal diseases (cholera, dysentery, typhoid)

4. 11% tuberculosis

5. 9% Malaria

6. 7% measles

7. 5% hepatitis B

8. 2.5% tetanus

9. 2.5% parasitic diseases

10. 1.5% misc

What disease is the #1 for childhood disease mortality

diarrheal

How much bacteria is in a typical gram of soil

10^9 (one billion)

What does the human body have more bacterial cells than

• skin

• mouth

• GI tract (10^12 (1 trillion) - 10^13 (10 trillion) cells/gram in large intestine)

• respiratory tract

• urogenital tract

What type of bacteria lives in geysers and hot springs

hyperthermophile bacteria

Why might there have been life on Mars?

ice found on the planet

What is the average range of size for microorganisms

between 100 μm and 10 nm

What are the most common bacterial shapes

• coccus (circular, studied in lab)

• bacillus (rod shaped, studied in lab)

• vibrio (rod shaped bur larger at one end smaller at the other)

• coccobacillus (round, not a perfect circle)

• spirillum (spiral)

• spirochete (tighter spiral)

What is the approximate diameter or a typical bacterial coccus

0.5 µm

Is a blood cell visible to the naked eye?

yes, when peering into a blue light

Where did Earth’s oxygen originate from

old star and microorganisms through photosynthesis in cyanobacteria

What primary structures distinguish EUKAYOTES from prokaryotes

• single or multicellular

  • can organize into tissues

• fungi, plants, protozoa, animals

• nucleus

• many membrane-bound organelles

What primary structures distinguish PROKARYOTES from eukaryotes

• single cells - chains or clusters

  • bacteria

  • archaea

• no true nucleus

• no membrane-bound organelles

What did the early evolution of eukaryotic cells look like

• likely evolved from prokaryotic organisms by intracellular symbiosis

• some organelles originated from prokaryotic cells

What happens during endosymbiosis (draw out later)

1. infoldings in the plasma membrane of an ancestral cell gave rise to endomembrane components, including a nucleus and endoplasmic reticulum

2. in a first endosymbiotic event, the ancestral eukaryote consumed aerobic bacteria that evolved into mitochondria

3. in a second endosymbiotic event, the early eukaryote consumed photosynthetic bacteria that evolved into chloroplasts

in endosymbiosis, what part(s) of the eukaryotic cell were once prokaryotes

mitochondria and chloroplasts

What is taxonomy

the classification, naming, aiding identification, ordered into groups (domain, phylum, class, order, family, genus, species - most to least inclusive)

*based on the judgement of scientists (constantly evaluated and revised)

How are species named with taxonomy

a binomial system (2 names) - genus and species (the names varied based on discovering scientist, shape, color, disease it causes)

In the scientific name, Escherichia coli, what does Escherichia refer to

the genus of the bacterium

What is phylogeny

natural, evolutionary relatedness between groups of living things (can use phylogeny to create a system of taxonomy)

Whose system of phylogeny is accurate Whittaker’s or Woese’s

Carl Woese’s system (containing 3 domains: bacteria, eukarya (or eukaryotes), archaea, and determined by DNA sequence)

Which level of classification was introduced in Woese’s classification system

domain

What are archaea

• prokaryotic cells

• unusual anatomy, physiology, and genetics

  • unique membrane lipids

• somewhat more similar to eukaryotes than other prokaryotes

• most are extremophiles

True or false, archaea are a type of bacteria

false

How to identify unknown organisms (microscopic and biochemical methods of identification)

run tests such as gram staining, culturing, and biochemical assays.

What is the MALDI-TOF identification of bacteria

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF)

What are nucleic acid-based methods of identification

the polymerase chain reaction (PCR), agarose gel electrophoresis (used in fingerprinting), the whole genome sequencing (WGS) process

What is the history of the first microscope (the simple lenses)

first spectacles, from Florence Italy 13th century, spread quickly

What was the first compound microscope

invented by Zecharia’s Janssen around the beginning of the 17th century, only had a magnification of 3x to 9x

Who probably recorded the first observation of bacteria

Van Leeuwenhoek who was a draper by profession, his microscope had magnifications to 200x and it was not a compound microscope

How does a simple lens work

refraction (bending of light rays, lens bends light and is made to focus it at a specific point, this results in image larger than size of original (e.g., overhead projector)

How does the compound lens system work

total magnification = the product of the magnification of each lens, compound scopes usually use combo of 10x ocular lens plus a choice of other, objective lenses

Why can’t we see smaller and smaller objects by simply adding more and more (or stronger) lenses

to a point, magnification can increase, but beyond a certain point, image is no longer clear, because the resolution (ability of a lens to distinguish or separate small objects that are close together) puts practical limits on magnification

What os the theoretical limiting factors of resolution

• “resolving power” also known as “d”, the resolution distance (or just “resolution”), we want this number to be SMALL

• “wavelength” can be any illumination source

• the numerical aperture is “a measure of light passing from the object and into the objective to maximize optical claritry and resolution”

How can we decrease “d”

make the numerator smaller, by making the denominator larger (with a better lens, increase the refractive index f what is between the lens and the subject

What is fluorescence microscopy

fluorescent staining of a fresh sample of cheek scrapings from the oral cavity (used to visualize specific microorganisms and/or specific structures or genes in them)

What are types of light microscopy

brightfield, darkfield*, phase contrast*, differential interference contrast (DIC) microscopes*, fluorescent (uses colored fluorochromes to create contrast), confocal (uses a laser to scan multiple planes successively)

*these three enhance contrast without staining

What are examples of macromolecules (big molecules)

• lipids

• proteins

• carbohydrates

• nucleic acids

What is the most abundant biological molecule

water, the aqueous environment plays a large role in determining how macromolecules assemble to form structures in the cell

What happens during the formation of a hydrogen bond

a hydrogen atom is shared between two molecules

What happens in the aqueous environment

water interacts with itself and with other polar molecules and ions (such polar molecules are therefore called hydrophilic molecules)

what are examples of polymers

proteins and starches

what are organic chemicals

compounds containing both carbon and hydrogen atom

Why is carbon important

it is a FUNDAMENTAL ELEMENT OF LIFE, contains 4 electrons in its outer orbital, can form single or double or triple covalent bonds, can form linear or branched or ringed molecules

What are the four families of macromolecules

carbohydrates (monosaccharides, disaccharides, polysaccharides), lipids (triglycerides (fats and oils), phospholipids), proteins (amino acids), nucleic acids (DNA and RNA) —> except for lipids, all are formed by polymerization, where subunits called monomers are bound into chains called polymers

What kind of macromolecule is cholesterol

lipid

what is the function of carbohydrates

energy storage, food, structural role in plants, fungal cell walls, exoskeletons of insects

What is the function of lipids

energy storage, membrane structure, insulation, hormones, pigments

What is the function of nucleic acids

storage and transfer of genetic information

What is the function of proteins

enzymes, structure, receptors, transport, structural role in cytoskeleton of a cell and the extracellular matrix

What are triglycerides

fats and oils

• a saturated fatty acid forms a triglyceride whose straight chains pack together to form (solid) fats

• an unsaturated fatty acid forms a triglyceride whose bent chains produce oils

What are phospholipids

amphipathic molecules

• can arrange themselves in various ways

  • liposomes, micelles, lipid bilayer

Which macromolecule has the most complex structure

proteins

• predominant macromolecule in cells

• functions: support, enzymes, transport, defense, movement

• monomer: amino acids

• structure: polymer “peptide”, subunits linked by peptide bonds

What are the protein structure four levels of organization

primary protein structure - sequence of a chain of amino acids (the primary structure of a protein is the sequence of amino acids)

secondary protein structure - local folding of the polypeptide chain into helices or sheets (the secondary structure of a protein may be an alpha-helix or a beta-pleated sheet, or both)

tertiary protein structure - three-dimensional folding pattern of a protein due to side chain interactions

quaternary protein structure - protein consisting of more than one amino acid chain (the quaternary structure exists only in proteins that consist of more than one polypeptide chain)

What is the cell envelope made up of (moving inward)

• glycocalyx (not on all bacteria)

• outer membrane (not on all bacteria)

• cell wall

• cytoplasmic (or “plasma” or “cell” membrane)

What is glycocalyx

polysaccharide (sometimes combined with protein) layer outside the cell

What are the two types of glycocalyx

1. slime layer - loose, protects from loss of water and some nutrients

2. capsule - bound more tightly, thick, gummy

   *neither are necessary for survival

What does bordetella pertussis cause

whooping cough

What is a biofilm

microbial colonies encased in an adhesive, usually polysaccharide material, and attached to a surface that provides protection and stability, allowing for increased resistance to environmental stresses and antibiotics.

how does dental plaque form

biofilms (streptococcus mutans - convert sucrose —> glucose (& fructose) —> dextran (polysaccharide glycocalyx) —> dental plaque)

What is the cell wall

the fundamental unit of the cell wall is a carbohydrate polymer (in other words, a polysaccharide) called peptidoglycan (peptides + carbohydrates)

What are the two monomers (building blocks) or peptidoglycan

N-acetylglucoasamine (NAG or just ‘G’)

N-acetylmuramic acid (NAM or just ‘M’)

What is peptidoglycan

the cross-links in peptidoglycan are chains of amino acids

What does a lysozyme do

breaks bond between NAG and NAM monomers in peptidoglycan

How were lysosomes discovered

by Alexander Fleming in early part of this century - found in tears, saliva, nasal and sinus fluids

Is penicillin only effective against growing bacteria

yes

what is the difference between gram positive and gram negative bacteria

gram positive - thick peptidoglycan, membrane

gram negative - thin peptidoglycan, membrane, periplasm, lipopolysaccharide

what are lipopolysaccharides (LPS)

• large, complex molecules composed of polysaccharides linked to lipid molecules

• lipid portion is buried in the membrane, while polysaccharide portion lies on the surface of the cell

• composed of the polysaccharides varies among bacterial species and even among individuals within a species

What is an endotoxin

LPS (lipopolysaccharides) acts as a toxin in animal hosts. lipid portion is toxic, including fever, shock, blood coagulation, weakness, and inflammation, releases when cells lyse

What is a porin

the outer membrane of gram-negative bacteria restricts passage of many molecules into cell (including penicillin) but has a large number of protein channels which allow some molecules in

true or false, lipopolysaccharides (LPS) can make you sick

true

What does a typical gram-negative bacterium have that a typical gram-positive doesn’t

outer membrane

what are characteristics of gram-positive bacteria

number of layers - one

chemical composition - peptidoglycan, teichoic acid, lipoteichoic acid, mycolic acids and polysaccharides in some cells

overall thickness - thicker (10-80 nm)

outer membrane - no

periplasmic space - narrow

permeability to molecules - more penetrable

What are characteristics of gram-negative bacteria

number of layers - two

chemical composition - lipopolysaccharide (LPS), lipoprotein, peptidoglycan, porin proteins

overall thickness - thinner (8-11 nm)

outer membrane - yes

periplasmic space - extensive

permeability to molecules - less penetrable

true or false, prokaryotes have chromosomes

true

true or false, bacteria in have DNA in other places besides chromosomes

true

What is within the cytoplasm

• genetic material in prokaryotes

  • chromosome

  • plasmids

• ribosomes

• storage bodies and inclusions

What is genetic material

bacteria generally have a single large chromosome, it is not bounded by a membrane

What are plasmids used as

vectors for transferring DNA into genetic energy

What are plasmids

• contain genes which are not necessary for the organism’s survival but which may be useful to it (eg antibiotic reisitance genes, genes for enzymes which degrade pollutants for consumption by the cell, etc)

• can be transferred ‘horizontally’ (from mature cell to mature cell)

What happens to plasmids in a bacterial host cell

a cell may contain no plasmids, one plasmid, or many copies of a plasmid, a single host may contain a number of different plasmids

What are ribosomes

• used for constructing proteins from messenger RNA (mRNA)

• in two parts and made up of proteins and ribosomal RNA (rRNA)

bacterial endospores are made primarily for

survival

What are bacterial endospores

• formed for survival, not reproduction (unlike most fungal and plant spores)

• toughest, most resistant life form of all, partially due to the presence of dipicolinic acid in the spore coat

• formed within cell (endo = inside) unlike fungal spores

what is the significance of endospores

two major genera have them: bacillus and clostridium (persistence and resistance of endospores contribute to the pathogenicity of these species

• bacillus anthracis - causal agent of anthrax

• clostridium tetani - casual agent of tetanus

• c. perfringens - casual agent of gas gangrene

• c. botulinum - casual agent of botulism

What is bacterial motility

tumbling and running of bacteria (movement)

in response to an attractant, a bacterium will increase the duration of its , relative to its _

runs, tumbles

What are eukaryotic motility structures (flagella)

found singly of in pairs at the end of some protozoa and algae

• are much longer than bacterial flagella

• move in whip-like manner rather than rotation of prokaryotic flagella

similar in composition but differ in size and function from cilia

What are eukaryotic motility structures (cilia)

• only found in ciliates, a type of protozoan

• shorter, more numerous than flagella (of eukaryotes)

similar in composition but differ in size and function from flagella

What did Robert Koch do

first to prove the ‘germ theory’ of disease

What are the potential methodological difficulties with the ‘germ theory’

• personal safety

• difficulties of detection

  • visibility

  • culturability

  • unknown life cycle