FINAL review Flashcards
5 kingdoms
prokaryotae- prokaryotic organisms (bacteria)
- protista- eukaryotic, unicellular (amoeba)
- fungi- eukaryotic- yeast and mold
- plants- all plants- conifers, flowering plants
- animals- all animals, insects, worms, vertebrates
domain
- based on RNA
- bacteria- peptidoglycan
- archaea- prokaryotic
- eukaryotes- protista, fungi, plant, animal
virus
- acellular
- no cytoplasm, no organelles, no plasma membrane
- either have RNA or DNA
- surrounded by a protein coat (capsid)
- some viruses have an envelope around capsid- proteins, carbohydrates, lipids
- envelope has spikes made up of protein or glycoprotein
- obligate intracellular parasites -> need host to reproduce
bacteriophage
- complex virus
- has a capsid
- DNA is within the capsid
- capsid and tail fibers are attached to the sheath
retrovirus
- RNA- genetic material
- has the enzyme reverse transcriptase
- reverse transcriptase- uses RNA as a template to make a complementary strand of DNA
- capsid and envelope
- ex. human immunodeficiency virus (HIV)
benefits of microbes
- protect us from disease by suppressing growth of pathogens (normal flora)
- pathogens do not get enough nutrients bc nutrients are being used up by the normal flora
- E. coli in large intestine makes vitamin K used for blood clotting (part of normal flora)
history of microbiology
- 1665- Robert hooke- plant materials (leaves and stems) little boxes called cells (not microbes)
- 1673-1723- anton van leeuwenhoek observe microbes under the microscope
Disproving spontaneous generation theory
- louis pasteur- father of microbiology
- 1861
- took a flask with a long neck and added broth -> bent the neck of the flask into an S shaped curve leaving the flask open (fresh air) -> heat broth -> microbes did not show up
- microbes got stuck in the curve of the neck like a filter
- successfully disproves the spontaneous generation theory
louis pasteur
- father of microbiology due to proving the spontaneous generation theory wrong
- microbes are ubiquitous
- foundation for the aseptic procedure used in the lab to prevent contamination
- fermentation -> yeast converted sugars to alcohol and CO2 in absence of O2
- pasteurization -> beverages such as milk are heated enough to kill microbes without destroying the flavor (doesnt kill ALL microbes) -> prevents diseases from spreading from food
Robert Koch
- proved germ theory of disease
- drew blood from animals that died of disease
- isolated rod shaped bacterium (isolate #1)
- grew that bacteria in lab and obtained pure culture of bacterium
- injected bacterium into healthy animals
- healthy animals soon became sick and died
- isolated rod shaped bacteria in these animals (isolate #2)
- isolate #2 came from experimental animals while #1 came from nature
- isolates were identical proving that is was the cause of the disease
- bacterium was identified to be bacillus anthracis (anthrax)
- steps are known as Kochs postulates - identifies the determinant of a disease
fungi
yeasts and molds
- eukaryotic
- unicellular/multicellular (most multi)
- ALL are heterotrophs
- cells walls are made of chitin
- sexually reproduce
- asexual spores
protozoa
- eukaryotic
- unicellular
- heterotrophs
- 2 stages:
- trophozoites- active, inside host
- cyst- dormant, outside host
algae
- eukaryotic
- multicellular
- ALL autotrophs- photosynthesize
robert whittaker
classifies organisms
- 5 kingdom system
- based on:
- cell type- prokaryotic/eukaryotic
- cellular organization- unicellular/multicellular
- nutritional requirements- photosynthetic/nonphotosynthetic
dark field microscope
- cells are not stained
- if you do not want the cells to be damaged use this
- field is dark but object is bright
phase contrast microscope
- no staining
- used to see internal structures: organelles, endospores (bright oval structure)
fluorescent microscope
- UV is light is used to illuminate the object
- cells are stained with fluorescent dyes
- Auramine O is used to stain Mycobacterium tuberculosis
- cells show up as glowing yellow objects against dark background
electron microscope
- transmission electron microscope (TEM)- internal
- scanning electron microscope (SEM)- surface
- beam of electron is used in place of light
- cells are stained
basic dyes
- bacteria are negatively charged
- basic dyes are positive -> stain bacteria
- ionic bond is formed between cell and stain
- dyes are salts
- color
- methylene blue chloride
acidic dye
- negative charge
- stain background
- sodium eosinate
- nigrosin
gram staining
- first add crystal violet as a primary stain to bacterial specimen -> this stains both + and - cells purple or blue
- iodine, a mordant (strengthens the ionic bond btwn the bacterial cell and crystal violet), makes dye less soluble so it adheres to cell walls -> both + or - remain purple or blue
- acetone-alcohol (decolorizer) washed stain away from gram neg -> gram - cells become colorless while gram + remain purple or blue (differentiation step)
- Safranin (basic counterstain) allows dye adherance to gram-negative cells -> gram - cells turn pink while gram + remain purple or blue
- gram neg -> pink
- gram pos -> purple
acid fast staining
- differential staining
- two genera are acid fast:
- myobacterium and nocardia
- they have waxy substance known as mycolic acid (complex lipid) in their cell walls
- acid fast staining is used to identify these two bacterium (used for tuberculosis)
- carbolfuchsin- primary stain
- acid-alcohol- decolorizer
- methylene blue- counterstain
- acid-fast= red
- nonacid-fast=blue
- both start out red due to primary stain -> decolorizer -> nonacid-fast loses color -> counterstain -> nonacid-fast turns blue -> acid-fast stays red
gram neg vs pos
- gram positive is thick (peptidoglycan)
- gram neg is thinner (only one or two layers of peptidoglycan
capsule staining
- capsule is a gelatinous substance found around the cell wall
- cannot be stained
- not all bacteria has capsule
- stain the background using nigrosin
- stain the cell body with crystal violet
- background is black
- capsule shows up as a clear ring around the stained cell
- capsule is not being stained
endospores
- 2 genera of bacteria that make endospores are bacillus and clostridium
- endospores are resistant to hostile environmental conditions (heat, UV light, disinfectant, desiccation)
- dormant stage of the cell allows to avoid harsh environment and death
- endospores are formed within the vegetative cell (active cell)
- once formation is complete, endospores are released into environment
- vegetative cells make endospores when the environment lacks nutrients
endospore staining
- malachite green- primary stain
- water- decolorizer
- safranin- counterstain
- endospores=green
- vegetative cells=pink
- both vegetative and endospores pick up primary stain -> both turn green -> water decolorizes vegetative cells -> vegetative cells pick up counterstain (safranin) and turn pink -> endospores remain green
nucleosomes
- segments of DNA are wrapped around histone proteins
- these are packages
- move through the nuclear pores
- DNA + histone = nucleosome
ribosomes
- free in the cytoplasm
- show up as dots in a micrograph
- attached to rough ER
- made up of 2 subunits
- each subunit is made up of proteins and ribosomal RNA
- eukaryotic cells has 80s ribosome
- larger and denser than prokaryotic ribosomes (which is 70s)
- prokaryotes and eukaryotes
helminths
- worms
- multicellular
- eukaryotic
- animal kingdom
- do not have a well developed nervous system or digestive system
- they do have a complex reproductive system
- platyhelminthes (flatworms) and nematodes (round worms)
platyhelminthes
- trematodes (flukes)
- cestodes (tapeworms)- segmented, scolex
- hermaphroditic
taenia solium
- tapeworm
- eggs and larvae are infectious
- neurocysticercosis
nematodes
- roundworms
- dioecious- male and female
giardia lamblia
- flagella
- 2 nuclei
- contaminated food and water
- weight loss
- wilderness water
balantidium coli
- cilia
- paramecium
- 2 nuclei
- macronucleus- protein synthesis
- micronucleus- transmit genetic information
hemoflagellates
- long, slender
- flagellum
- 1 nucleus
- no cyst phase -> only trohphozite
- ex. trypanoasoma gambiense (africian sleeping sickness)
- ex. trypanosoma cruzi (chagas disease)
yeast
- unicellular
- oval or circular in shape
- many reproduce by budding
- sometimes the buds fail to separate from the parent -> pseudohyphae are formed
- Candida albicans make pseudohyphae (part of the normal flora of intestinal tract of humans)
mold
- multicellular
- filamentous
- filaments are called hyphae
- fragments of hypha can grow into a fungus
osmotic lysis
-antibiotics that target cell walls cause osmotic lysis -> kills
mycology
-study of yeast, molds, mushrooms
cutaneous mycosis
- affects the hair, nail, skin
- ringworm, tineas
- caused by the fungi- dermatophytes
- produce keratinase- breaks down keratin
- tinea pedia- atheletes foot:
- caused by trichophyton rubrum- itching, scaling skin
- spread by direct contact, shower room floors
simple diffusion
- O2
- water
pili
-filamentous
candida albicans
- yeast
- make pseudohyphae (part of the normal flora of intestinal tract of humans)
- opportunistic mycosis
- thrush
- normal flora
definitive/intermediate host
- definitive host- adult -> sexual reproduction
- intermediate host- immature worm (larvae) -> asexual reproduction
prokaryotes
-have no cilia
lactose
- disaccharide
- milk sugar
- made up of glucose and galactose
maltose
- disaccharide
- made up of two glucoses
- breakdown product of starch
cellular respiration
- glucose is catabolized
- oxidation reduction rxn
- loss of electron or hydrogen atom- oxidation
- gain of electron of hydrogen atom- reduction
- leo says ger
- these rxns are coupled
- organic molecules are oxidized
- NAD+- coenzyme/electron carrier picks up the H+ (reduced) -> NADH
- doesnt need O2
anaerobic respiration
- similar to aerobic respiration (all the same stages)
- final e- acceptor is an inorganic substance other than O2
- pseudomonas aeruginosa uses nitrate ion as the final e- acceptor
- doesnt produce as much ATP
- more than 2 and less than 38
- depends on species
lactic acid fermentation
- only glycolysis takes place
- glucose is broken down to 2 pyruvic acid
- 2 NADH
- 2 ATP
- once pyruvic acid is made it is converted to lactic acid
- NADH is oxidized to NAD+
- pyruvic acid gets reduced to lactic acid
- regenerates NAD+
- NAD+ participates in glycolysis again to get 2 more ATP
- pyruvic acid is the organic molecule final e- acceptor
- lactobacillus does this (aerotolerant anaerobe- even in presence of O2 it doesnt use it)
alcohol fermentation
- glylocysis
- 2 ATP
- 2 pyruvic acid
- 2 NADH
- pyruvic acid is converted to acetaldehyde
- CO2 comes out
- NADH is oxidized to NAD+
- acetaldehyde is reduced to ethanol
- final e- acceptor is acetaldehyde
- ex. saccharomyces- yeast (Facultative anaerobe- grows in presence or absence of O2 but grows better with O2) -> that means we must make sure there is no O2 to make alcohol
- if there is O2 it will carryout aerobic respiration and make water
light dependent photosynthesis
- chlorophyll
- cell light hits cholophyll molecules
- e- absorb light -> energized
- e- jump out of chlorophyll molecule
- e- go through electron transport chain in chloroplast
- similar to aerobic respiration ETC
- chemiosmosis -> makes ATP by photophosphorylation
- energized e- ends up with NADP+ -> NADPH
- e- that come out of chlorophyll molecule are replaced by e- from water -> breaks down water into O2 and H -> releases O2
- no CO2 used
- ATP is made
gene
segment of DNA that codes for a functional product
- functional product- protein
- most genes code for proteins
- .1% of genes have instructions to make tRNA and rRNA
- genes are passed on from one cell to another- one generation to another
- DNA has to be replicated
promoter
where gene begins
- control regions
- unique nitrogen base sequence
- made up of DNA
RNA polymerase
- transcription- DNA is copied onto mRNA
- makes mRNA
- enzyme
- major role in transcription
- attaches itself to the gene near the promoter
- segment of gene separates
- one strand is template strand (instructions)
- attaches RNA nucleotides together -> chain
- free RNA nucleotides are floating around where ever transcription is taking place
- once nitrogen base are exposed on template strand complementary base pairing takes place between nitrogen base on the free RNA nucleotide and the nitrogen bases on the template strand
- uracil on the free RNA pairs with the adenine on the template strand
- RNA polymerase attaches the pairs
- moves segment by segment
- polymerase is released from the gene at the terminator
- mRNA has a specific nitrogen base sequence
codon
- 3 nitrogen base sequences next to each other on the mRNA
- codes for an amino acid
- different codons can code for the same amino acid -> degeneracy of the genetic code
- associated with mRNA
- ex. UAG
degeneracy of the genetic code
- helps cell survive under certain conditions
- different codons can code for the same amino acid
- silent mutation
tRNA
- one end has anticodon
- other end picks up amino acid from the cytosol
- transfers amino acids from the cytosol to the ribosome
- specific group of tRNA for each amino acid
- specificity is based on the anticodon it has
- reads the message
- ex. tRNA is specific for alanine -> cant pick up any other amino acid -> specific anticodon for alanine
ribosome
- holds mRNA so tRNA can read the message and bring the appropriate amino acid to the ribosome
- has the enzyme that attaches amino acids together (peptide bonds)
translation
- attachment of ribosome (large and small subunit) to the mRNA near the start codon
- tRNA recognizes the codon
- tRNA brings MET to the ribosome
- complementary base pairing occurs on the codon on the mRNA and the anticodon on the tRNA
- tRNA molecules are held in place and the amino acids are next to each other
- enzyme attaches the amino acids together -> dipeptide
- dipeptide gets transferred on to tRNA and it moves on to next segment
- forms a polypeptide
- ribosome reaches stop codon -> end of translation
- polypeptide is released
- tRNA subunits come apart
- mRNA and tRNA is released from ribosome
- mRNA is translated again to make another copy of the polypeptide chain
genetic transfer
- 2 DNA in the same cell
- piece of DNA is transferred from a donor to a recipient
- bacteria has one DNA molecule
- if genetic transfer takes place the bacteria can have 2 DNA molecules
- 3 methods of transfer:
- transformation
- conjugation
- transduction
genetic transfer: transformation
- DNA from a donor cell is transferred to recipient
- naked DNA transfer
- donor cell is dead
- when bacterial cell dies the DNA is released into the environment
- DNA gets fragmented into pieces
- recipient cell comes in contact
- DNA penetrates cell wall of recipient -> 2 DNA molecules
- own chromosome and donor DNA present
- when the own chromosome and donor DNA come in contact -> crossing over
- donor DNA aligns with complementary bases
- *can make the recipient cell more pathogenic -> picks up genes that can code for capsules
- becomes a capsulated bacteria- more pathogenic bc capsule protects bacteria from phagocytosis
genetic transfer: conjugation
- subspecies of the same cell
- F+- has the pilus (filamentous structure found on the surface) and small circular DNA (F plasmid/factor)
- F+ cell has plasmid and chromosome (they are separate)
- F– does not have pilus
- F+ uses it pilus and attached to F- and conjugates
- F plasmid- has genes for the pilus
- plasmid gets replicated and copy gets transferred to the F- cell through the pilus
- F- becomes F+ -> makes two F+ cells
- F+ has 2 DNA molecules (chromosome and plasmid)
- f plasmid gets inserted into chromosome -> becomes an Hfr cell (high frequency of recombination cell)
- Hfr cell- very good at conjugation
- Hfr cell- makes the pilus
- Hfr and F- cell conjugation:
- during conjugation the DNA gets replicated and starts in the middle of the f plasmid
- piece of f plasmid and piece of chromosome get replicated and transferred into the F- cell
- F- cell never gets the entire chromosome or plasmid bc it is much larger than the cell and they dont stay conjugated for long enough
- F- gets only a piece of donor DNA and plasmid -> inserts into chromosome and becomes recombinant -> doesnt become F+ cell and does not make pilus
- can make an F- cell resistant after it picks up DNA from another Hfr cell -> shares resistance
genetic transfer: transduction
- DNA of donor cell is transferred with recipient cell
- bacteriophage is a virus (acellular) that infects bacteria
- bacteriophage picks up donor DNA and releases it into recipient cell
- bacteriophage gets into host cell to reproduce itself
- bacteriophage attached to donor cell
- phage DNA gets released into host
- phage DNA gets replicated
- donor chromosome gets fragmented
- assembly of phage takes place ->
- by mistake sometimes fragments of bacterial DNA gets enclosed into the protein code of the phage
- transducing phages- have bacterial DNA in them instead of phage DNA
- donor cell breaks down and dies
- phages are released including transducing phages
- transducing phage comes in contact with bacteria and releases donor DNA into bacteria (receiving cell)
- donor DNA gets inserted into the chromosome of the recipient cell -> recombinant
- sometimes transducing phages pick up toxic genes and spreads it
operon
- many genes are controlled by the same control region (promoter)
- has many genes
- controlled by the same control region (promoter)
- regulation
- genes of the same operon share a promoter
lactose operon
- repressor protein hop onto the operator protein and block RNA polymerase
- when RNA polymerase attached to promoter it cannot get to structural genes bc of the repressor blockage
- only when the RNA polymerase is able to pass over the structural genes will the mRNA of the structural genes will be made
- no mRNA -> no translation -> no proteins
- inactivates lactose operon
- if lactose is in environment it will bind to repressor protein -> inactive repressor protein
- pulls the repressor protein from the lactose operator -> no more blockage
- RNA polymerase is able to make mRNA for the structural genes
- lactose activates the lactose operator by inactivating the suppressor
repressor protein
- on the operator
- if something is bound it is pulled form the operator -> inactive
- if nothing is bound it block RNA polymerase from making mRNA of the structural genes
inducible gene
- beta galactosidase gene
- helps the cell to save its energy and chemical resources such as amino acids
- cell is not making something that it does not need
- enzyme is made in presence of substrate
dissimilation plasmids
- have genes that code for enzymes that break down petroleum
- found in pseudomonas
- used in bioremediation- use of microbes to clean up chemical pollutants
- clean oil
bacteriocin plasmids
- code for toxins
- toxic to certain species of bacteria
- ex. lactococcus lactis has a bacteriocin plasmid
- codes for toxin -> nisin
- nisin prevents the germination of clostridium endospore
- helps lactococcus lactis -> prevents growth of other bacteria so it has more nutrients for itself
- preserve cheese
- does not cause food poisoning
transposons
- small segment of DNA
- transposed (move) one region of DNA to another
- jumping genes
- can cause problems by messing up sequences
- doesnt move often tho
- found in all organisms
- simple transposons (insertion sequences)- has a gene that codes for an enzyme -> transposase
- transposase- helps simple transposon to move from one part of the DNA to another -> cutting and sealing
- translated from insertion
- unique nitrogen base sequence on each side
complex transposons
- unique nitrogen base sequence on each side
- made up of 2 insertion sequences
- in between there is a gene that codes for antibiotic resistance
- found in bacteria
- often found in r-plasmid
- can move from the plasmid to the chromosome
- can be transferred through conjugation
genetic engineering mechanisms
- use plasmid (small circular DNA found in some bacterial cells) as a vector and insert a gene of interest (human insulin) into the plasmid
- plasmid becomes a recombinant plasmid
- recombinant plasmid is introduced into a bacterial cell (E. coli) -> becomes the recombinant cell/transformed bacteria
- E. coli transcribes and translates the gene and makes the human insulin
- once recombinant cell is made it can be grown in a nutrient broth like any other e. coli cell -> descendants of the recombinant will also be recombinant
- easy to make a lot human insulin
tools used in genetic engineering: restriction enzymes
- restriction enzymes come from bacteria
- used to breakdown phage DNA in the bacteria
- extract the restriction enzyme from bacteria and use it for genetic engineering
- EcoR1, BamHI -> recognize specific sequences
- restriction enzymes make staggered cuts in the DNA
- they fragment DNA
- ends of the fragment are single stranded
- destroy phage DNA
introducing the recombinant plasmid into the cell
- take a bunch of recombinants and put them into a tube with host cell (e. coli)
- some of the e. coli will come in contact with the recombinant plasmid and pick it up and some will not
- incubation
- there will be two populations of e.coli (one with recombinant and one without)
- they select the recombinant cell by plating the mixture on the medium with the ampicillin antibiotic -> incubate
- the colonies that show up on the plate are the ones with the recombinant plasmids bc they have the selection markers (antibiotic resistant genes) in their plasmid
cDNA
`-complementary DNA
- cDNA does not exist in nature
- cDNA- synthetic gene that only has exons
- mRNA is used to make cDNA (by scientists- not in nature)
- DNA nucleotides and reverse transcriptase enzymes are added to the tube with mRNA
- reverse transcriptase uses mRNA as a template to make a complementary strand of DNA
- DNA polymerase is then added to the tube and uses the DNA strand as a sample to make the second strand -> makes cDNA
- cDNA only has exons
- if we want to introduce eukaryotic gene into a prokaryotic cell we use cDNA
- if we place natural eukaryotic gene into bacterial cell it wont be able to remove the introns
- functional protein will not be produced by the prokaryotic cell
- no translation
eukaryotic: introns and exons
- introns- noncoding regions
- exons- coding regions
- prokaryotic genes only gave exons
- when the eukaryotic gene is transcribed the RNA also has exons and introns
- eukaryotic cells have certain enzymes that remove introns and stitch the exons to make the mRNA
southern blotting
- used in genetic screening
- take blood and DNA
- fragment DNA using restriction enzyme (made from bacteria)
- DNA fragments are separated by gel electrophoresis by size
- the DNA bands show up
- smaller pieces move faster in the gel (more further down the smaller)
- DNA bands are transferred onto nitrocellulose filter/membrane
- nitrocellulose filter holds onto molecules like DNA
- place the nitrocellulose filter and attached DNA into a zip lock bag
- a solution containing many copies of the radioactively labeled probe (complementary to gene of interest) is added
- incubate
- probe will hybridize/comes together with gene of interest through complementary base pairing
- remove and rinse nitrocellulose filter
- expose to x-ray film
- where ever there there is radioactive activity it will blacken -> tells us where the probe and therefore the gene of interest is
- a black band shows up for carrier
- a black band show up larger and wider for someone with the disease (bc twice as many copies of the gene of interest)
probe
-single strand of DNA that is complementary to the DNA of interest
PCR
-polymerase chain reaction
product of transcription
- not new DNA
- tRNA
- make mRNA
chemoautotroph
-uses glucose for carbon and energy
lipase
- decrease pH
- cleave triglycerides
cyanobacteria
-photoautotroph
facultative halophils
-grow with or without salt
clostridium tetani
- causes tetanus
- infects deep puncture wounds
- endospores becomes vegetative cells in the puncture wounds (found in soil)
- vegetative cells produces neurotoxin *
- vegetative cells stay in the wound but the neurotoxin goes in the blood and nervous system
- causes spastic paralysis -> stiffness of the muscles
- lockjaw
- DTP vaccine- made up of tetanus toxoid (inactive)
- antitoxin- made up of antibodies specific for tetanus toxin
- antibodies are known as tetanus immune globulins (TIG)
lysogenized strain
- phage DNA is inserted in the chromosome of the bacteria -> phage DNA has gene to make toxin
- scarlet fever
- corynebacterium diphtheriae
- streptococcus pyogenes- scarlet fever -> strawberry tongue
mycoplasm
-no cell wall
viroid
-infectious DNA without capsid
pseudomonas aeruginosa
- gram negative
- rod shaped
- opportunist -> causes problems when someones immune system is weak
- *makes a water soluble pigment (blue-green)
- causes skin infection if the skin is damaged (burn victims are vulnerable)
- burn and wound infections
- gentamicin, polymyxin
spirochetes
-axial filaments