Term Definition

3 kingdoms of life Bacteria, Archaea, Eucarya.

Common threads of life Growth, Metabolism, Motion, Reproduction, Response to stimuli.
Lucretius and Fracastoro Suggested invisible organisms cause disease.
Jansen Invents and develops first microscopes.
Hooke First description and depiction of microorganism.
Leeuwenhoek Discovered bacteria and protozoa.
Spontaneous Generation Formation of living organisms from inanimate matters.
Redi Fly larvae can only develop in meat that fly can reach.
Needham Boiled broth then sealed it. Microorganisms appeared.
Spallanzani Broth in flask then sealed and boiled. No microorganisms appeared.
Pasteur
Boiled broth in flask, curved neck of flask so air can enter but no dust, no
microorganisms appeared.
Tyndall Showed dust carried microorganisms.
Beliefs in the cause of diseases Supernatural forces, Poisonous Vapors, Imbalances between the four humors.
Bassi Showed microorganism (fungus) can cause disease in silkworms.
Berkeley Potato blight was caused by fungus.
Lister Sterilized instruments with heat, phenol to prevent infections.
Koch Demonstrated bacterium was causing anthrax.
Kochs Postulates
The microorganism is present in every case of the disease, but absent from
health organisms, the suspected microorganism must be isolated and grown in
pure culture, the same disease must result when the isolated microorganism is
inoculated into a healthy host, the same microorganism must be isolated again
from diseased host.
Agar and Petri Dish Used to develop microorganisms in the lab.
Jenner Immunized people from smallpox using cowpox virus.
Pasteur First attenuated vaccine from pure culture of pathogen attenuated.
Smith and Salmon Killed microbial cells effective as vaccines.
Behring
Humoral Immunity, antibodies produced in blood against toxin to be protective
against infection.
Metchnikoff
Cellular Immunity, Phagocytes engulfing disease-causing bacteria and provide
immunological protection.
Winogradsky
Oxidation of iron, sulfur, ammonia by soil bacteria for energy, transformation of
carbon dioxide to organic matter.
Beijerinck Isolated nitrogen-fixing bacteria and sulfate-reducing bacteria.
Taxonomy Artificial classification of organisms, based on visible similarities.
Phylogeny
Natural classification of organisms, reflects evolutionary relatedness between
organisms. Uses ubiquitous gene sequence to compare microorganisms.
Haeckels Proposal Plants, Animals, Microorganisms.
Chattons Proposal Eukaryotes and prokaryotes.
Whittakers Proposal Monera, Protista, Fungi, Plantae, Animalia.
Woeses Proposal Bacteria, Archaea, Eukaryotes equally distant, used 16S ribosomal RNA gene.
Endosymbiotic theory of evolution
Primitive eukaryotic cell engulfed an ancient prokaryote to create the first
eukaryotic cell.
Goals of Classification
Stability, Predictability, Build larger groups, Study a member, learn about the
group.
Linnaeuss scheme of classification Based on comparison of visible characteristics.
Hierarchical scheme of classification Kingdom, Phylum, Class, Order, Family, Genus, Species.
Name of bacterial species Lactococcus lactis (L. lactis), consists of genus name and epithet.
Use of bacterial species naming Appearance, Habitat, Characteristic property, Scientist name.
Characteristics used to separate bac
Biovars (Biochemical/Physiological differences), Morphovars (different
morphology shapes), Serovars (different antigenic properties)
Sj
Similarity coefficient, # similarities shared/# similarities compared, used to make
dendograms
Phage typing What bacteriophages can infect, bacteriophage has host range.
Genomic characteristics
G+C content (melting point + density), DNA hybridization (single strands allowed
to mix), sequencing genes give phylogenetic relationship.
Major differences between prokaryo
Eukaryotes have nucleus, organelles, size is 10x bigger, prokaryotic cells have
cell wall of peptidoglycan.
Shapes/Arrangements of cells Spherical Cells Cocci, Rodlike Bacilli, Spiral Spirilla, Other Irregular
Arrangements of Cocci
Streptococci (line of more than 2), tetrad (square), sarcinae (2 layers of
squares), staphylococci (big mass of layered cocci)
Arrangements of Bacilli Coccobacillus (circular bacilli), Streptobacillius (line of more than 2)
Bacterial Colony Morphologies
Form Punctiform, Circular, Filamentous, Irregular, Rhizoid, Spindle, Elevation
Flat, Raised, Convex, Pulvinate, Umbonate, Margin Entire, Undulate, Lobate,
Erose, Filamentous, Curled
Bacterial Cells vs Human Cells
Surface Area to Volume ratio of prokaryotes larger than eukaryotes, faster
growth.
Epulopiscium Fishelsoni Guest at fishs banquet, found in gut of brown surgeon fish, large
Thiomargarita Namibiensis Sulfur pearl of Namibia, found in ocean sediments, larger than E. fishelsoni.
Nanochlorum eukaryotum
Green alga, smaller than a human cell but is a true eukaryote nucleus,
mitochondrion, chroloplast.
Bacterial Envelopes
Gram-negative outer membrane, cell wall, cytoplasmic membrane, Gram-
positive cell wall, cytoplasmic membrane, Mycoplasma cytoplasmic
membrane.
Cytoplasmic membrane
Contains cytoplasm, regulates what comes in and out, made up of a fluid
phospholipid bilayer, contains proteins (transmembrane and peripheral
membrane proteins).
Phospholipid Structure
Structurally asymmetric, charged polar heads, nonpolar hydrophobic long lipid
tails.
Peptidoglycan Cell Wall
Gives cell shape and rigidity, osmotic pressure, peptidoglycan composition. Very
thick around gram-positive, thin around gram-negative.
Peptidoglycan Cell Wall Anchoring
Gram-positive has teichoic acid (structure) and lipoteichoic acid (anchorage).
Gram-negative has cell wall anchored by lipoproteins.
Outer membrane
Gram-negative, acts as protective barrier and regulates molecules coming
through, made up of a fluid phospholipid bilayer (inner layer phospholipids,
outer layer LPS, endotoxin, phospholipids). Anchored to cell wall by
lipoproteins.
Capsule/Slime layer
Protection, reservoir of stored food, site for waste disposal, helps keep shape
and rigidity, prevents infection, aids in cell adhesion and motility.
Flagella Movement of bacterial cells, made up of protein polymer
Pili/Fimbriae Thinner than flagella, adherence to surfaces, sex pili for mating.
Arrangements of bacterial flagella
Monotrichous single flagellum, Amphitrichous single flagellum at each pole,
Lophotrichous two or more flagella at pole/poles, Peritrichous flagella all
over surface.
Taxis with flagella Bacterial movement. Counterclockwise forward, Clockwise tumbling
Chemotaxis Directional movement towards specific chemical.
Cytoplasm
Site of metabolism, 90% water, nucleoid (irregular mass of DNA), ribosomes,
inclusion bodies (storage, gaz, magnetosomes).
Endospores
Most resistant biological structures, no metabolism, state of survival induced by
unfavourable growth conditions.
Sporulation
Divides into 2 unequal parts. Larger part engulfs smaller part becomes
forespore. Forespore matures to become an endospore synthesis of protective
thick wall, dehydrated, lysis of cell to release endospore.
Germination
Endospore to vegetative cell; water enters, endospore swells and ruptures coat,
germ tube grows.
Binary fission Divide near midpoint to form two daughter cells.
Budding Forms bubble-like structure that comes out and separates from parent cell.
Fragmentation Filamentous growth, extends from main outwards like branches.
Asynchronous cultures Timing of cell division is random.
Synchronous cultures Timing of cell division is fixed.
Generation time
Period for cell to enlarge, divide, and produce 2 daughter cells. All cells in
population have same generation time.
Lag phase Time for cells to adjust to new/fresh medium and start dividing.
Exponential/Log phase
Period where nutrients are not in limiting amounts and cells divide at maximum
speed.
Stationary phase
Culture switches from log phase to stationary phase when nutrient
concentration is limiting and toxic waste accumulates so cells divide slower.
Death phase
Nutrients completely consumed, cells stopped growing and starting to die, but
not all cells die.
Reasons for long Lag phase
Inoculum taken from old culture, from rich medium to poorer one, from
chemically different medium, from refrigerated cells, in cold medium.
Chemostat
Provides constant flow of nutrients, concentration of one of the nutrients is
limited to reduce growth rate, some growing culture should be removed at the
same rate of growth rate = loss rate so always the same amounts of cells
growing.
Parameters affecting microbial grow
Temperature (hyperthermophiles, thermophiles, mesophiles, psychrotrophs,
psychrophiles), pH (neutrophils, acidophiles, alkalophiles), gaseous environment
(aerobes, anaerobes, facultatives, capnophiles).
Toxic molecules from oxygen Superoxide Radical, Hydrogen Peroxide, Hydroxyl Radical.
Protective enzymes against oxygen Superoxide dismutase, Catalase, Peroxidase.
Anaerobic jar Oxygen removed by combining with hydrogen to make water.
Growth on solid media
Cells in center death/stationary phase, Cells on edge exponential phase
(growing), Cells at surface aerobic conditions, Cells under surface anaerobic
conditions.
Cell count technique
Take diluted sample, spread colonies, then count colonies. Colonies are
multiplied by dilution to get cells/mL.
Mathematics of cell growth Cells number: N = N0 X 2^n, where then n = 3.3(log(N) log(N0))
Gene DNA segment that codes for protein.
Genome All the genes in cell/virus.
Genotype Specific set of genes of an organism.
Phenotype Observable characteristics.
Prokaryote are _ , has genes Haploid (1N).
Eukaryote are _ , has genes Diploid (2N) .
Griffiths Transformation Experimen DNA/Proteins caused disease? DNA.
Averys Experiment DNA contains genetic information.
Hershey-Chase Experiment DNA carries genetic information for T2.
Central Dogma
DNA goes through replication, transcription to RNA, which then goes translation
to protein.
Nucleoside Sugar ring, base.
Nucleotide Sugar ring, base, phosphate.
Organization of DNA in Eukaryotes
Inside nucleus, genome of 10^9 bp, linear chromosomes, compact and
organized (chromatin), small basic proteins (histones), no plasmids.
Organization of DNA in Prokaryotes
No nucleus, anchored to cell membrane, genome of 10^6 bp, one circular
chromosome, supercoiled, small basic proteins (nonhistone), has plasmids.
Nucleosome
Histone H1 binds to linker regions (14-100 bp) promoting chromatin structure
which is made up of nucleosomes (histone octamer and 146 bp).
DNA Replication
Helicase unwinds DNA helix, uses strand as template for DNA polymerization
(DNA polymerase III, 750-1000 bp/sec). Opens replication fork, one parent
strand is formed with one replica (semi-conservative), synthesized 5 to 3, with
3 to 5 exonuclease activity (in DNA polymerases, proof-reading).
Replication of bacterial DNA
Replication forks happen and as it goes around the circle, another circle forms
which is at the opposite side, end result are 2 loops.
Rolling-Circle Replication
From nick, DNA replication occurs along the circle as the previous strand is
rolled out into a line.
SSBs Single-stranded DNA binding proteins keeps two strands of DNA separated.
DNA gyrase (Topoisomerases) Release tension created by helicases unwinding DNA.
DnaA helicase Binds to oriC locus.
DnaB helicase Replaces DnaA, replication fork unwind at 75-100 rev/sec.
Primase (RNA Polymerase) Short RNA at lagging strand complementary to DNA.
DNA Polymerase III (Lagging Strand) Uses RNA as primer and synthesizes 5 to 3.
Okazaki fragments Strands of non-connected DNA on lagging strand.
DNA ligase Fills gap between fragments
Gene (Cistron) Nucleotide sequence that codes for mRNA, tRNA or rRNA.
Bacterial genes Have 4 parts: promoter, leader, coding region, trailer. Mostly continuous.
Eukaryotic genes Mostly interrupted by introns.
Codon 3 consecutive nucleotides that specify an amino acid.
Genetic Code
Degenerate, more than 1 codon for each amino acid. 61 sense codons, 3 stop
codons, Trp and Met only have 1 codon.
Wobble Pairing Anticodons with I, bonds G to U, I to C, I to A, I to U.
Mutations of DNA
Spontaneous (happens by DNA Replication), Point Mutations (silent doesnt
change codon, missense changes codon, nonsense creates stop codon,
frameshift deletions and insertions).
Forward Mutation Wild type allele into a new allele.
Reversion Mutation Changes a mutant allele into a wild type allele.
Suppressor Mutation Second change in the same gene that compensates for forward mutation.
DNA Repair Proofreading of DNA polymerases
Nucleoside Excision Repair
UvrAB looks for thymine dimer. UvrA released, UvrC binds. UvrC cuts both sides
of thymine dimer. UvrD (helicase) removes damaged region. UvrC and UvrC
released. DNA polymerase fills in gap, DNA ligase seals gap.
Base Excision Repair
DNA glycosylase recognizes non proper base pair matching, cleaves bond
between base and sugar. AP endonuclease cleaves DNA backbone on 5 side of
missing base. DNA polymerase uses 5 to 3 exonuclease to remove damaged
region and then adds normal DNA. DNA ligase seals region.
Mismatch Repair
MutH, MutL, MutS goes along strand. MutH cuts the strand, exonuclease digests
strand beyond base mismatch. DNA polymerase fills the gaps, DNA ligase seal
the ends.
Error Free Systems
Direct removal of lesions (thymine dimers photoreactivation/photolyase,
methyls methylguanine methyltransferase, alkyls alkyltransferase).
Recombinational Repair
By recombination, region from another strand replaces the gap in another
strand, then the region which is now missing is filled with DNA polymerase and
ligase. Uses recA protein.
Postreplication Repair Mismatch repair, scans newly replicated DNA.
3 types of RNA
mRNA (proteins), tRNA (carries amino acids to ribosome), rRNA (16S, 23S, part
of ribosome)
RNA synthesis
5 to 3, adds 40 nt/sec at 37 C, moves along DNA forming 12-20 bp transcription
bubble. Transcription starts at promoters and stops at terminators.
Prokaryotic Terminators
Two types, Rho dependent needs rho factor, no poly-U tract, no hairpins
sometimes. Rho independent no need for rho, 6 uridines after hairpin
structure.
Eukaryotic mRNA
Monocistronic (1 gene), Cap structure at 5 end, PolyA tail at 3 end, lots of
introns, transcription (nucleus) and translation (cytoplasm)
Prokaryotic mRNA
Multicistronic (operon), no cap at 5 end, no poly-adenylation at 3 end, no
introns, transcription and translation coupled.
Protein Synthesis
mRNA translated into amino acid chain (protein). Ribosome at site of translation
(900 residues/min, 15 amino acids/sec), 80 nt apart. tRNAs bring amino acids to
ribosome, tRNAs read mRNA codons. Ribosomes synthesize proteins from N-
terminus (NH2) to the C-terminus (COOH)
Translation Steps
Initiation, Elongation, Termination. Ribosome goes along mRNA from Shine-
Dalgamo sequence, each amino acid is attached to tRNA that comes to
ribosome to drop off their amino acid after matching with respective codon.
tRNA Structure
73 to 93 nt, cloverleaf secondary structure, anticodon triplet complementary
to codon triplet on mRNA, amino acids attached to tRNA at 3 end.
Regulation of mRNA Synthesis
Negative Control Induction, gene is turned on when enzyme needed by having
an inducer molecule either turn off or on the repressor by attaching to it.
Repression too much of end product leads to corepressor which activates the
repressor. Positive Control only turned on in presence of controlling factor,
meaning it only transcribes if the factor is present.
Tryptophan Operon Leader
Initiation and continuation of transcription controlled by levels of tryptophan.
Low level of tryptophan leads to ribosome to stop, high level of tryptophan
leads to ribosome to continue.
DNA recombination in bacteria
Homologous recombination (Crossing-over), nonreciprocal recombination, site-
specific recombination (viruses), replicative recombination (mobile genetic
elements)
Crossing-Over
Helicase and nuclease unwinds DNA, RecA-like proteins help it stay in shape, the
strands then migrate to resolve in spliced and patched DNA strands.
Nonreciprocal Recombination
Strands are separated, segment of donor strand is separated, the same region
on the host strand is removed and replaced, and the gaps are filled and ligated.
Bacterial Plasmids
Circular double-stranded DNA, number of copy per cell varies, exists
independently from host chromosome, and has few genes that could be
integrated into host chromosome.
Different types of plasmids and fact
Fertility factor, Resistance factors, Col plasmids, Virulence plasmids, Metabolic
plasmids.
Bacterial Gene Transfer
Conjugation (sex pilus), DNA transformation (naked linear DNA/plasmids taken
from cell environment), Transduction (bacteriophages)
Fertility Factor
Conjugative plasmid, genes for cell attachment and plasmid transfer, F+ (donor)
F- (recipient) cell, plasmid is episome (can replicate freely in cytoplasm), has
own origin of replication (oriV).