Exam 1 Flashcards
Describe a virus
not a cell
cannot change or replicate without a host cell
contains nucleic acids (RNA/DNA) in a protein coat (capsid)
Describe bacteria
usually no internal membranes
nucleoid region with a single DNA molecule
one chromosome
Describe Archaea
Usually no internal membrane
nucleoid region with a single DNA molecule (one chromosome)
Describe Eukarya
Examples: Fungi, Protists, Algae
membrane enclosed nucleus with several DNA molecules (multiple chromosomes)
membrane-enclosed internal structures (mitochondria, chloroplasts)
Medical microbiology
pathogenic, virology, immunology
Environmental microbiology
ecology, bioremediation, wastewater and sewage treatment
Industrial microbiology
food (vinegar, cheese, yogurt, high fructose corn syrup)
fermentations (yeast - saccharomyces cerevisiae)
Agricultural microbiology
nitrogen fixation in legumes (Rhizobium)
rumen in cows, biological pest control
(Bacillus thuringiensis)
Biotechnology/genetic engineering
insert human genes into bacteria
ex: most insulin is now produced by microorganisms
What are the 5 kingdoms?
Plants
Animals
Fungi
Protists
Monera
How are species named?
Binomial naming structure
first part = genus
second part = species
What are the 3 domains?
Bacteria
Archaea
Eukarya
What is the order of the taxonomic scale?
(Domain)
Kingdom
Phylum
Class
Order
Family
Genus
Species
Are archaea more similar to bacteria or eukarya?
Archaea are more similar to eukarya at a cellular and genetic level
What is the difference between Heterotrophs and Autotrophs?
Heterotrophs = reduced, pre-formed, organic molecules from other organisms
Example: humans eat food to obtain energy
Autotrophs = CO2 or other principle biosynthetic carbon sources
Example: plants
What is the difference between chemoautotrophs and photoautotrophs?
Chemoautotrophs → energy source = oxidation of inorganic/organic chemicals
Example: nitrogen fixing bacteria/ bacteria oxidizing H2S, ammonia, methane, etc
Photoautotrophs → energy source = light
Example: plants use sunlight for carbon fixation (photosynthesis)
light-induced electron flow creates ATP by proton gradient and membrane ATPase
What is the difference between aerobes and anaerobes?
Aerobes - metabolism requires the presence of oxygen
Anaerobes - metabolism does not require the presence of oxygen
What is the difference between acidophiles and alkalophiles?
Acidophiles - prefer acidic conditions - pH below 7
Alkalophiles - prefer basic conditions- pH above 7
What is the difference between thermophiles and psychrophiles?
Thermophiles - high temperature optima
Hyperthermophiles - very high temperature optima - Found in unusually hot environments - Hot springs and deep sea thermal vents
Psychrophiles - low temperature optima
Found in unusually cold environments
Mesophiles - midrange temperature optima
Widespread in nature and most commonly studied microorganism
How many bacteria can be found per square inch of soil or drop of water?
Over a million
Do you have more bacterial cells or body cells?
More bacterial cells in your body than cells of your body
How does the total surface area of bacteria compare to the surface area of the Earth?
Total surface area of bacteria on Earth more than 4X surface area of Earth
What limits the distribution growth of microorganisms?
Probably only thing limiting distribution growth of microorganisms is water
What do microbial cells do?
- Metabolism: consume nutrient source for energy
- Grow and replicate: create new cell material to produce new cells
- Differentiate: form specialized cell structures/cell types for specific purposes
- Respond to signals: movement, cell-cell signaling
- Change genetically: vertical and horizontal gene transfer
What made Antonie van Leeuwenhoek famous?
1684 - discovered “animalcules”
When was the “Golden age of microbiology”?
1850-1930
What made Beadle and Tatum famous?
1941 - one gene- one enzyme hypothesis
What made Watson and Crick famous?
1953 - double helix structure of DNA
What made Carl Woese famous?
1977 - used rRNA to form the Three Domain hypothesis
What made Craig Venter famous?
1995 - completed first complete genome sequence of an organism
Haemophilus influenzae
What made Ferdinand Cohn famous?
- German Botanist in mid 1800’s
- First to classify algae as plants, regarded bacteria as members of plant kingdom
- Classified bacteria based on their shape
- Studied Bacillus and discovered they can form heat-resistant cell structures (endospores)
What made Louis Pasteur famous?
- French chemist in the late 1800’s
- Refuted the spontaneous generation of germ theory
- Showed that fermentation is caused by microorganisms and that heating liquids can stop this (led to pasteurization)
- Pioneered ideas of vaccination and immunity
developed first vaccine for rabies
What made Robert Koch famous?
- German physician in late 1800’s
- First to isolate Bacillus anthracis and Mycobacterium tuberculosis
- First to link a specific bacterium (B. anthracis) to a specific disease (anthrax), and
developed “Koch’s Postulates” as criteria for this
What are the Koch’s Postulates?
- The specific bacterium must be present in diseased animals and not in
healthy animals - The bacterium must be isolated and obtained in pure culture
- The pure culture is used to inoculate a healthy animal, and this animal must
become sick with the disease - The same bacterium is isolated again from the new infected animal
What made Paul Ehrlich famous?
- German scientist in early 1900’s
- Developed first antimicrobial chemical (Salvarsan) to treat syphilis
- Developed the idea of chemotherapy
Alexander Fleming - Scottish pharmacologist in early 1900’s
- Discovered the first antibiotic (penicillin) in 1928 when he noticed mold
contaminating plates of Staphylococcus, which seemed to kill the bacteria - Discovery ignored until large scale production of penicillin in the 1940’s
What was the first antibiotic ever discovered?
penicillin
What was the first disease discovered to be caused by a bacertium?
Anthrax
What made Walter Reed famous?
- US army physician around 1900
- First to show insect vectors can spread human disease by showing that Yellow
Fever virus is transmitted by certain mosquitoes
What is the significance of Yellow Fever?
- Yellow Fever was important historically in the Americas
- 1802 Haitian Revolution – half of Napoleon’s army wiped out by Yellow
Fever - 1878 Memphis – worst Yellow Fever epidemic in US history (5,000 deaths)
- 1905 New Orleans – epidemic ended by controlling mosquitos (452 deaths)
- Yellow Fever delayed construction of Panama
- caused by mosquitos
What happens to an atom that is reduced?
Reduction is gain
atom gains electrons and becomes more negative
What happens to an atom that is oxidized?
Oxidation is loss
atom loses electrons and becomes more positive
What are ionic bonds?
bonds based on charge interactions
example: NaCl
some biological elements often exist in charged states (example: OH-)
What are the four major classes of biological molecules?
Lipids
Proteins
Nucleic Acids
Carbohydrates
What are the four kinds of monomers for biological molecules?
Fatty acids
amino acids
nucleotides
monosaccharides
What are the four kinds of polymers for biological molecules?
Lipids
Peptides/Proteins
Nucleic Acids
polysaccharides
What is the difference between an unsaturated and saturated fatty acid?
Unsaturated has one or more double bonds
*adds a kink to the structure
saturated fatty acids have the maximum amount of double bonds
What is the difference between an ether and ester linkage?
ester = very common, contains carbonyl
ether = lacks carbonyl, uncommon in most organisms, found primarily in Archaea
What are common head groups of fatty acids?
Glycerol
Ethanolamine
Choline
What are the different levels of protein organization?
primary = sequence of amino acids
secondary = folding of subdomains within the protein chain based on hydrogen bonds
tertiary = structure of a protein composed of secondary structure subdomains
Quaternary structure = structure of a protein composed of secondary structure subdomains
What are two common carbohydrates found in organisms/cells?
hexose (6C) and pentose (5C)
mainly used for metabolism
structural component of nucleic acids and bacterial cell wall
What can carbohydrates be used to make?
glycoproteins (modification to proteins)
glycolipids (modification to lipids)
produce specialized cell structures
What are different nucleic acids found within cells?
DNA = information storage molecule
RNA = protein synthesis template
ATP/GTP = energy currency
What is a nucleoside vs nucleotide?
both have nitrogenous base and sugar
nucleoside lacks phosphate group
What is mRNA?
messenger RNA
coding information for proteins
What is tRNA?
transfer RNA
adapter that translates mRNA sequence into protein sequence
What is rRNA?
ribosomal RNA
structural components of the ribosome
enzyme that forms peptide bonds during protein creation
What is sRNA?
small regulatory RNA
small antisense RNA fragments that silence mRNA transcripts
What nucleotides can be used as energy currency?
RNA forms of ATP, GTP, and sometimes CTP are used as energy sources for anabolic reactions
deoxynucleotide (DNA) counterparts are not
What is used to speed up reactions?
enzymes act as catalysts
What leads to variation in genetic information?
imperfect replication
variation is the substrate for natural selection/ evolution
How old is the Earth?
4.6 billion years old
How old are microbes?
microbial mats (stromatolites) are 3.8 billion years old
How old are Eukaryotic microfossils?
1.8 billion years old
How old are multicellular eukaryotic fossils?
700 million years old
How old are Homonid fossils?
6 million years old
How old is the homo species?
100,000 years old
How much longer have microorganisms been around compared to multicellular organisms?
microbes have been around 5x longer than multicellular organisms
What was it like on young planet Earth?
no oxygen
no ozone
temperature > 100ºC (water was all vapor)
atmosphere: methane (CH4), carbon dioxide (CO2), nitrogen gas (N2), hydrogen sulfide (H2S), ammonia (NH3)
What was the Miller-Ulrey Experiment?
Stanley Miller, under Harold Urey, University of Chicago, 1953 * Mixed water vapor, CH4, NH3, and H2
* Electric spark passed between electrodes in flask
* After 2 weeks 10-15% of carbon was in organic molecules
o 11 of 20 canonical amino acids
o Modern analysis of sealed sample vials found more than 20 amino acids
o Reactions with other pre-biotic gases yielded even more diverse molecules
* Major reactant generated from conditions is HCN
o HCN + formaldehyde = glycine
o HCN + ammonia = amino acids, adenine
* Variants of experiment have yielded all amino acids, hydroxy acids, purines, pyrimidines and sugars
No O2 to oxidize, biological molecules were stable
What is the RNA world hypothesis?
- RNA nucleotides could polymerize – this creates genetic information
- RNA can also fold into catalytically active structures
o Ribozymes – Thomas Cech, Sidney Altman, Nobel Prize 1989
o Self-splicing introns, RNase P (maturation of tRNA), 23S rRNA - Theoretically, a RNA could replicate itself
o More likely, another copy of itself
o Replicate itself based on genetic information
o Using biological catalyst
o It is alive - In 2009, Tracey Lincoln and Gerald Joyce created self-replicating RNA
o Two RNA molecules, each replicates the other
o Uses ribonucleotides and nothing else - RNA replication is error-prone
- Replication errors would create mutant varieties of self-replicating RNAs
- Natural Selection/Evolution can begin
o Speed of replication
o Replication fidelity
What led to the development of cells?
- Lipids spontaneously form vesicles at normal temperatures
- Plausible as Earth cools vesicles spontaneously form around RNA
- Multiple RNA could be in same cell
- Some could code for protein
- Some could make protein from RNA sequence
What is the difference between DNA and RNA?
DNA is missing the hydroxyl group on the 2’ carbon
DNA is much more stable than RNA and less prone to replication errors
presence of DNA allows for the establishment of the Central Dogma
What is the central dogma?
DNA –> RNA –> Protein
How did early cells get energy?
Likely from substrate level phosphorylation
membrane allows for electrochemical gradients and respiration
since there was no O2, anaerobic respiration occured
What is the difference between Heterotrophs and lithotrophs?
o Heterotrophs – organic molecules present
* No photosynthesis, primary production via Miller-Urey type reactions
* organic electron donors, electron flow creates ATP by proton gradient and membrane ATPase
o Lithotrophs – inorganic nutrients in abundance
* Could use FeS, H2S and S to make ATP, fix CO2
* Performed by some thermophilic Archaea today
* inorganic electron donors, electron flow creates ATP by proton gradient and membrane ATPase
When did anoxygenic photosynthesis appear?
about 3.8 billion years ago
What happened to oxygen when it first appeared on Earth?
Bound up by limestone, iron, or other minerals
Found as Banded Iron Formation (2.3-2.5 billion years ago)
o Once exposed minerals fully oxidized, then O2 accumulates in air
When did oxygen photosynthesis appear?
about 2.4 - 3.2 billion years ago
What was the Oxygen Carastrophe?
Huronian Glaciation
* O2 reacted with CH4 (potent Greenhouse gas) in atmosphere to make CO2
* Sun weaker at time, Earth required stronger Greenhouse Effect to keep warm
* “Snowball Earth” – surface of Earth completely frozen
* Lasted 300-400 million years
Largest mass extinction of all time
* O2 very reactive and toxic
* Killed the vast majority of life on Earth at the time
o Survivors developed O2 resistance, some O2-dependent metabolism
* Glaciation probably didn’t help
What made Earth more habitable?
- UV rays react with O2 in atmosphere to create O3 (ozone)
- Ozone layer blocks majority of UV light from reaching Earth surface
- Allows microbes to colonize ocean surface waters, then land
- Leads to probably the largest explosion in biological diversity
What implies that all life on Earth is related?
o All cells use same energy currency
o All respiration enzymes are evolutionarily related
o All ATPases are evolutionarily related, use proton gradients
What is the Endosymbiotic Theory?
One prokaryote engulfed another to lead to the development of mitochondria and chloroplasts
cyanobacteria –> chloroplasts
rickettsia –> mitochondria
host cell was likely archaea
What implies that endosymbiosis occurred multiple different times?
Some protists have chloroplasts that are not related to chloroplasts from majority of photosynthetic eukaryotes
What is a protist?
A protist is any eukaryotic organism that is not an animal, plant, or fungus.
What is the difference between catabolism and anabolism?
catabolism - breaking down chemicals to produce energy and waste products
anabolism - creating cell components using energy
What are the energy source prefixes?
light = photo
organic and/or inorganic chemicals = chemo
organic chemicals = organo
inorganic chemicals = litho
What are the different carbon source prefixes?
CO2 = auto
organic chemicals = hetero
CO2 and organic chemicals = mixo
Why don’t exergonic reactions occur spontaneously (often)?
- Activation energy is required to start the reaction
o Wood will burn, but requires ignition - Catalysts lower activation, increasing reaction rate
- Enzymes are biological catalysts
What are enzymes?
- Proteins
- Folding determines very specific binding properties
- Many require cofactors
o Provide energy
o Determine activity
o Provide chemical modifications - Perform both exergonic and endergonic reactions
- React with substrate(s) to form enzyme-substrate complex, which is more reactive
- Products more specific than chemical catalysts
What is the difference between substrate level phosphorylation and oxidative phosphorylation?
Oxidative phosphorylation uses the proton motor force to make a proton gradient to generate energy and the final electron receptor is oxygen
substrate level phosphorylation is when a phosphate group is transferred directly from one compound to another for energy transfer
What are the products if the citric acid cycle (TCA/Krebs)?
3 NADH
1 FADH
1 GTP (ATP)
What is a species?
the basic category of biological classification,
composed of related individuals that resemble one another, are able to breed among themselves, but are not able to breed with members of another species.
