Microbiology exam 3

- study of function and transfer of genes

all genetic information in a cell

part of the genome, cluster of DNA, contains genes

segments of DNA

• deoxyribonucleic acid
• 3 nucleotide components: sugar (5 carbon deoxyribose), phosphate and nitrogenous base-
• hydrogen bonds between nitrogenous bases
• double helix, antiparallel, runs 5' → 3' and 3' → 5' (new always made 5' → 3

• A and T
• C and G

genetic makeup, represents only potential charecteristics

expression of genotype, the actual observable characteristic

continuous strand that is made in 5' → 3' direction

synthesized in pieces because there is no free 3' end

enzyme that unwinds the double helix

original DNA strand

where 2 strands are separated and new nucleotides are added

enzyme that adds new nucleotides and proofreads

small pieces of RNA where DNA polymerase can attach (only on lagging strand)

enzyme that joins fragments of DNA (glue) on the lagging strand

• DNA: deoxyribose, thymine, double stranded
• RNA: ribose, uracil, single-stranded

process of making mRNA from a DNA template

enzyme that makes a new strand of mRNA

site on DNA template where RNA polymerase binds (start)

site on DNA template that ends transcription (stop)

• 1. RNA polymerase binds to promoter site on DNA template
• 2. RNA polymerase synthesizes a complementary base strand of the DNA template working in a 5' → 3' direction.
• 3. transcription continues until a terminator is reached
• 4. RNA polymerase and a new mRNA are release from DNA template

process of protein synthesis

messenger RNA, carries info transcribed from DNA, specifies the amino acid sequence of the protein products

carries amino acids, contains anticodons which pair with the codons on mRNA

• site of translation, attaches to mRNA, small and large subunits
• 3 tRNA BINDING SITES: 
• A site (acceptor), holds tRNA carrying next amino acid
• P site (peptide), holds tRNA with growing peptide chain
• E site (exit), where tRNA leaves ribosome

ribosomal RNA, part of the ribosome

• 1. start codon, AUG signals mRNA to bind to small subunit of ribosome
• 2. initiator tRNA (with the amino acid methionine) attaches its anticodon (UAC) to mRNA in P SITE!!!!!!
• 3. large and small subunits join

• 1. mRNA is threaded through ribosome
• 2. 2nd tRNA (with amino acid) binds its anticodon with mRNA's codon in the A SITE! of the ribosome
• 3. peptide bond forms between amino acids
• 4. polypeptide chain is transferred to tRNA in A site and 1st moves to E site and is released
• 5. tRNA with growing polypeptide chain moves from A to P site.

• 1. elongation continues until a stop codon reaches the A site
• 2. ribosome splits apart and polypeptide chain is released 
• PROTEIN FOLDS AND BECOMES FUNCTIONAL! (active)

• set of three nucleotides bases on mRNA that encode for a specific amino acid
• 64 codons, 20 amino acids
• 61 sense, 3 nonsense

the nucleotides (3) on the mRNA code for a specific amino acid that together build up to create proteins.

code for amino acids

• stop codons
• UAA, UAG, UGA

• using feedback inhibition (inhibit enzyme reactions when unnecessary) regulated if only needed at certain times
• making enzymes is controlled by genetics, transcription and translation

• by a process that turns off transcription, repressor block RNA polymerase at the promoter
• caused by overproduction of end products

turned on (induced) by substrate of enzyme

• system of gene regulation
• includes genes promoter and operator

starts/ stops transcription of (lac) gene

where RNA polymerase initiates transcription

• lac operon ON: lactose → allolactose → binds to tell ribosomes get rid of repressor and to make beta-galactosidase
• lac operon OFF: repressor bound to operator, nothing happens

• a change in a base sequence of DNA, permanent and passed on
• ex. antibiotic resistance

a single base is replaced with another base

base substitution results in amino acid substitution

base substitution codes for a stop/nonsense codon

one or more bases are deleted or inserted

a substance that causes mutations

• chemicals (nitrates/nitrites, household cleaners)
• radiation (UV light, xrays. causes thymine dimers to form)

exchange of genes between 2 DNA molecules to form new combinations of genes

2 chromosomes break apart and rejoin, resulting in 2 original chromosomes having a combination of eachother

contributes to genetic diversity, genes for resistance to drugs develop, new nutritional and metabolic capacities develop, increases virulence

circular pieces of DNA, replicate separately from chromosomal DNA

• transformation
• conjugation
• transduction

process of genetic transfer when a cell lyses and naked DNA is transferred to another bacteria, donor combines with recipient DNA to form a new recombinant

can enhance pathogenicity (disease causability)

fertility, used in conjugation, carries genes for a sex pilus

resistance, transfers antibiotic resistance, can transfer resistance to heavy metals, synthesize factors such as toxins, enzymes and adhesion

• sex pilus: connection between 2 cells
• donor has F+ plasmid
• recipient has no plasmid, F-

• 1. sex pilus grows out of F+ call and attaches to F- cell 
• 2. copy of F+ is transferred to F--results in two F+

process of genetic transfer in which DNA is passed from one bacterium to another by a bacteriophage (virus)

• segments of DNA tht move from 1 region to another, "jumping genes"
• advantages: genetic diversity, change in morphology and pigmentation traits, replaces damaged DNA
• disadavantages: mutations, cell dysfunction

techniques in microbiology that manipulate DNA

use of microbes to produce food antibiotics, vitamins, and enzymes

enzymes from bacteria, recognize foreign DNA and can break bonds when adjacent nucleotides, used in recombinant DNA technology

technique that produces readable patterns of DNA fragments, uses a soft agar gel and electrical current to separate fragments based on SIZE

used to determine the exact genetic code (order of bases), Sanger method

makes multiple copies of a piece of DNA enzymatically (Taq polymerase from T. aquaticus)

DNA profiling, forensic tool, uses restriction enzymes to cut DNA at specific parts and separate with gel electrophoresis

idea of classifying organisms

• 2 are prokaryotic cells- archea and bacteria
• Eukarya is other domain

Eukara

Chroloplasts in past were prokaryotic cell. Then they were endocitosed and evolved into organelle. Same is true with mitochondria.

Eukara

• 1. hypothermophiles (like to grow in hot environment)
• 2. extreme halophiles- like to grow in salty enviroment
• 3. methanogens- like to produce methanin

peptodiglycan

pseudomurin

cellulose

Kieten

• each species retains some characteristic from ancestor(idea behind taxonomy)
• look at: anatomy, fossils, and rRNA

Binomial Nomenclature (genus + specific epithet)

They are not made of cells. This system divides organisms into eukaryotic and prokaryotic cells.... Can't put them in either.

Fermacutes, Atino bacteria

Kingdom, Phylum, Class, Order, Family, Genus, Species

Grown in laboratory media

• population of cells derived from a single cell
• Ex: streak out plate and get a colony... all came from one cell.

• genetically different cells within a clone
• Ex: streak out plate and get a mutation... it starts to reproduce within colony

-ales

-aceae

pseudomonales and psedomonaceae.

how much G + C they had (high G + C) (low G + C)

• 1. animalia 
• 2. plantae:
• 3. fungi:
• 4. protista:

• multi-cellular, no cell wall, chemoheterotrophic (organic carbon, energy source)
• ex: worms

multicellular, cellulose cell wall, usually photoautotrophic

Chemoheterotrophic (just like you and i), unicellular or multicellular, cell walls of chitin, have sexual and asexual reproduction

Most people don't consider this a kingdom anymoreA catchall kingdom of eukaryotic organisms that so not fit in any other kingdoms(Grouped into clades based on rRNA)

yeast and molds.

-ales

-viridae

Viridae

Virus

• Common, everyday name.
• Example: HIV

• end in number.
• ex: HIV 1 or HIV 2

• Classification- looking at how they are related to one another
• Identification- looking more at what we do in the lab and see how we can identify them

• 1. Morphological characteristics- cocci, balicilli, presence and endospores, capsules, flagella
• 2. Differential staining (gram stain, acid fast)
• 3. Biochemical tests- determines presence of bacterial enzymes (catalase)

Gram stain

Give you information about cell wall.

always used for identification of bacteria, series of yes or no question... "Is it gram positive" Y or N... not "gram positive"

you don't have to inoculate anything, scoring with 5 digit number... look up number in book. (no critical thinking)

• 3 tests based on same principle: antibody (proteins)- antigen binding
• **bc the bonding of antibodies and antigens is so specific... great for IDing

• 1. Slide agglutination test: bacteria clumps together if positive test
• 2. ELIZA test- attach an enzyme to antibody... if antibody binds to antigen we can tell by adding a substrate and see if it attaches to the enzyme or not
• 3. Western blot- put proteins on gel and they'll be separated by size using gelophoreeses... transfer it to filter paper. antibodies will stick.

• Always uses lytic phage. 
• Primarily used for tracing outbreaks, see where original source was... look at patternsPlate bacteria out, Put it on grid, if phage infect bacteria... it is gonna replicate cause cell too lyse and create clearing called a plaque

• Virus that invades bacteria
• Part of Transduction

use glass slide and spot DNA on slides. one slide can have 10,000 different sequences of DNADNA on slide is SINGLE stranded! (its hybridization)take DNA sample from patient, put florescent label on it.. which dot lights up

• Southern blotting
• Probes
• DNA chips
• FISH

drug to knock out expression of specific gene

used for identification

used to try and see what organisms are related.. classification

similarity in rRNA

Eukaryotic, unicellular, classified by motility, some parasitic, heterotrophic (get food from outside of body by vacuoles/cell membrane absorbtion)

Moisture, water and soil, some can live in extreme environments

Motile feedingstage, requires water and food

Dormant stage, conditions unfavorable

Division of 1 cell into 2 identical cells

Protrusion off of parent cell

Nucleus undergoes multiple divisions before the cell divides (plasmodium)

Genetic exchange between 2 mating pairs that requires cell to cell contact

Domain: eukarya, kingdom: protista, subkingdom: protozoa

Move by pseudopods, example amoeba

Flagellated, example euglena or trypanosoma

Move by cilia, example stentor or paramecuim

nonmotile, most parasitic, example plasmodium causes malaria or toxoplasma can harm babies transmitted by cat poop

Eukaryotic, uni or multi cellular, classified by color/pigment, contain chloroplasts, photoautotrophic (make food from the sun)

Body, performs photosynthesis

Root-like anchors

Stem-like

Leaf-like

Aquatic, soil, rocks, cool water often near surface

Asexually by binary fission, sexual not very frequent

• Domain: eukarya
• kingdom: protista
• subkingdom: algae

Brown algae, kelp, big, can get to 50 meters, found in coastal waters, used in ice cream/ toothpaste/ soap/ lotion

Red algae, deeper in ocean, used to make agar

Green algae, contain chlorophyll, most microscopic, example volvox or spirogyra

Most numerous unicellular algae, important in food chain, have shells

Plankton, cause red tide, photosynthetic, have shells

Blue-green, domain bacteria, prokaryotic, example oscillatoria and anabaena

Study of fungi

Eukaryotic, multicellular (except yeast), classified by spores, some parasitic, macrofungi (mushrooms), microfungi (molds & yeast), cell walls made of chitin

Heterotrophs, absorb or decompose animal and plant debris

Low moisture, pH 5, can grow in high salt and sugar concentations

Filaments of cells, develop from spores, grow by elongating at tips, each part can form a new mold

Group of hyphae

Cross-walls in hyphae

No crosswalls

Fragmentation of hyphae, produced in chains

Fragmentation of hyphae, produced in sacs

Union of 2 nuclei of 2 morphologically similar cells, (+) and (-) come together

Union of 2 nuclei of 2 morohologically similar or not similar cells, produced in ascus (sac-like structure)

Union of 2 mating strains that bud off of parent cells, produced in club shaped structure

• Domain: eukarya
• kingdom: fungi

Nonseptate hyphae, asexual sporangiospores, sexual zygospores, example rhizopus or phycomyces

Septate hyphae, asexual conidiospores, sexual ascospores, example aspergillus or penicillium or yeast

Septate hyphae, sexual basidospores, asexual conidiospores, example club fungi or mushrooms or puff balls

unicellular, nonfilimentous, spherical or oval, can grow with or without oxygen, can ferment carbs to create carbon dioxide and alcohol, make bread/ beer/ wine (cereviseae), yeast infections (candida albicans)

Budding example cereviseae and fission (2 new cells) example longname octosporous

Food chain, mushroms for food, bread/ beer/ wine, drugs (penicillin), anticancer drugs