Terms in this set (168)
What is made when a cell wants to make a specific protein?
differences from DNA
1. ribose sugar group
2. No thymine --> instead uracil
3. And RNA polymerase does NOT need a primer to start. Binds and recognizes a sequence in the DNA strand called a promoter
similarities to DNA
1. RNA polymerase can only make mRNA in the 5' to 3' direction.
2. Must use DNA as a template to create the proper sequence.
3 types of RNA
1. ribosomal (rRNA)
2. transfer (tRNA)
3. messenger (mRNA)
1. The negative strand is the template strand and is used to create a copy of the positive strand (which contains the gene).
2. RNA polymerase binds promoter with help from sigma factor (this recognizes promoter regions). Other transcription factors aid in ribosomal binding (yes, bacteria DO have transcription factors).
3. RNA polymerase melts open a stretch of DNA and reads the negative strand of DNA (it has to read in the 3' to 5' direction in order to synthesize mRNA in the 5' to 3' direction-just like with DNA).
4. Transcription ends when a terminator is encountered. The terminator occurs when the RNA forms a hairpin structure, which allows the RNA polymerase to dissociate from the DNA.
5. mRNA released
- genes can be located on either strand of DNA, so it is the promoter that indicates where the gene is
- the promoter is always upstream from the gene and the gene is in the 5' to 3' direction from the promoter
- a three nucleotide sequence that determines the amino acid needed in protein
- Start Codon sets the reading frame for translation
means that more than one codon can encode a specific amino acid
*However, each codon will always only specify ONE amino acid
- AUG (ATG in DNA), is always the first codon in a protein following a ribosomal binding site sequence
- If AUG is internal in protein, will also code for methionine
- three stop codons indicate the end of the coding sequence which terminates translation
- these do NOT code for an amino acid.
**process of decoding info carried on mRNA to synthesize a specific protein
a. All three RNAs come together: ribosome (rRNA)/mRNA/ tRNA
b. Initiating tRNA with fMet amino acid moves into P site on ribosome. This is the only amino acid that enters at the P site.
c. Next tRNA fills A site.
d. Peptide bond formation occurs and the 1st tRNA released via the E site.
e. Ribosome shifts and amino acids are added by reading codons until a stop codon is encountered.
1) Termination of protein synthesis at stop codon.
2) Translation machinery falls off.
f. Translation in Bacteria - can occur simultaneously with transcription.
major differences between prokaryotic and eukaryotic transcription/translation
4. Humans only make monocistronic mRNA whereas bacteria are capable of making polycistronic mRNA
major differences - processing
prokaryotes - mRNA not processed
eukaryotes - cap is added to 5' end of mRNA and poly A tail added to 3' end
major differences - introns
prokaryotes - no introns
eukaryotes - introns which are removed by splicing
major differences - translation
prokaryotes - translation of mRNA begins as being transcribed
eukaryotes - mRNA transcript transported out of nucleus to be translated in the cytoplasm
quorum sensing/ antigenic
A. Specific genes are activated only when critical mass is achieved
B. Antigenic/phase variation uses different transcripts which allows organisms to evade host responses.
*can "sense" and "talk" to each other
1. Operons consist of promoter, operator region, and set of regulated genes.
2. Control of transcription of the operon is regulated by DNA binding proteins known as repressors or activators.
a. Repressors stop transcription.
(a) An inducer blocks the ability of a repressor to bind to DNA.
(b) A co-repressor will block transcription by enhancing binding of DNA by a repressor.
b. Activators induce transcription. When an inducer binds to an activator, it causes the activator to bind to DNA and induces transcription.
point mutation/base substiution
single change in base pair
**most common type of mutation
no effect on the phenotype because of degeneracy of genetic code
**normally 3rd base in codon
-changes codon and wrong amino acid is inserted into peptide chain
**change in the phenotype as well as genotype
- causes the formation of a stop codon. **change in the phenotype as well as genotype
-addition or deletion of one or more basepairs to the genetic code
-a three nucleotide frameshift will result in the addition or deletion of one amino acid
**usually results in knockout mutation = shortened, non-functional protein
A. Chemical mutagens- generally causes altered base pairing by changing the hydrogen bond formation of affected bases
- changes base structure
- converts C to U
- add alkyl groups to nuclotides
- makes it so no Hydrogen bonding
- synthetic bases that improperly base pair
- used in place of normal nucleotides b/c resemble them
- only work in viral infected cells
- insert b/t pairs into DNA double helix and cause addition/deletion mutations
- increase frequency of frameshift mutations
- randomly insert into DNA causing inactivation of the gene
- causes thymine dimers --> covalent bonds b/t adjacent T molecules
- thymine dimers do not allow DNA polymerase to correctly read DNA coding sequence due to kinks in structure
- UV irradiation does not penetrate well
X-rays /gamma rays
-causes double stranded breaks in DNA backbone due to higher energy wave
- Ionizing radiation penetrates most material well
**harder to repair than thymine kink
- repair uses methylation to indicate parental strand of DNA and removal of incorrectly paired bases
- bacteria methylate adenines
- repairs oxidized bases by cutting out oxidized bases
- uses Photolyase and light to repair thymine dimers
**this is only in bacteria!!
- methylguanine methyltransferase repairs improperly methylated/alkylated guanines
- Dark repair
- uses enzymes to remove dimers
- Repair enzymes induced when TOO many thymine dimers have been created
- new polymerase is activated that repairs DNA by replicating DNA with many mutations due to the presence of many too many dimers
**NEVER DONE IN HUMANS B/C SO SLOPPY!
*guess at bases and hopes to get them right!
transformation (naturally occurring)
- naturally competent cells receive naked DNA, via a receptor on their cell surface.
1) Single stranded pieces get incorporated into bacterial chromosome by homologous recombination.
2) Mismatch repair or cell division determines if the newly acquired genetic material is expressed.
transformation (experimentally induced)
- Electroporation can induce a bacterium that is not competent to take up naked DNA - Plasmids or double stranded DNA (dsDNA) can be taken up
- Cells can be made chemically competent where large pores are induced in the plasma membrane
1) Bacteriophage injects phage DNA into a cell.
2) Phage DNA, capsid proteins, and phage structural proteins are made. The bacterial chromosome is destroyed.
3) Assembly of phage with phage DNA and a few that have mistakenly packaged bacterial chromosomal DNA instead of phage DNA.
4) Infection of new cell by newly synthesized phage- some containing bacterial chromosome fragments.
5) Cells infected by phage containing bacterial DNA can utilize information they receive. No new phage can be produced from these infections because viral genome is missing.
6) Undergoes homologous recombination with chromosome.
-only regions of chromosome near phage attachment sites can be moved
1) Lysogenic conversion occurs.
2) However, when phage genome is excised some of the bacterial chromosomal DNA is excised instead of the entire bacteriophage genome.
3) Transfer of bacterial chromosome to new bacteria occurs.
4) Phages may still be able to generate progeny phage depending on how much DNA from bacterial chromosome was excised.
1) The F (fertility) plasmid contains information for the transfer of the plasmid and synthesis of a sex pilus. A cell containing an F plasmid is called F+. A cell without an F plasmid is F-
2) F+ Donor attaches to F- recipient via the sex pilus. The F plasmid is replicated and transferred to F- cell via rolling replication. The plasmid is reformed in recipient cell. F- recipient is then an F+cell
3) Integration of F plasmid into bacterial chromosome--> Hfr cell. Sometimes when the F factor excises itself, it does so incorrectly, taking a fragment of the bacterial chromosome with it. This is then termed an F'
Hfr genetic transfer
- the integrated F plasmid is rarely completely transferred because replication includes the entire bacterial chromosome. Separation usually occurs before entire F plasmid is transferred. Therefore recipient cell receives DNA but usually remains F-.
1) Plasmid is a circular extrachromosomal piece of DNA that replicates independently of chromosome. Has own origin of replication.
2) R plasmid confers resistance to various antimicrobials agents such as antibiotics, or heavy metals. May or may not be conjugative.
- jumping genes --> have ability to insert ANYWHERE regardless of promoter, etc
1) Barbara McClintock
2) Insertion sequence (IS) (most basic form of moveable element) -Inverted repeats and the enzyme transposase. Transposase is the enzyme that allows transposon to "jump". Can inactivate the gene they jump into
3) Composite transposon-contains two IS that flank a resistance factor.
**don't need homologous recombination
- DNA that originated in another species
biosynthesis of DNA
1) DNA viruses can use normal cellular enzymes to create genome or bring in special DNA polymerases that can allow a virus to replicated DNA when cell is not dividing.
2) Life cycles may complex.
RNA Viruses usually replicate in the cytoplasm
1) Positive stranded RNA virus-its genome is like mRNA.
a. Genome can be directly read by cell's ribosomes to create enzymes, viral components.
b. Can encode a viral RNA dependent RNA polymerase. (Remember, similar to mRNA).
2) Negative stranded RNA-genome is in the negative orientation.
a. Needs to bring in a viral RNA dependent RNA polymerase (working enzyme) so that it can make viral mRNA to create viral proteins.
b. No enzyme in living organisms to create mRNA from mRNA...
c. Targets for anti-viral drugs?
- Some viruses create polycistronic messages that get translated into a polyprotein.
1) Requires the polyprotein to be cleaved into functional proteins.
2) Requires a virally encoded protease to be processed.
viral mutation and mutation rates - integration
- integration of viral/cellular genetic material can change cell morphology, insertional inactivation or change the way the cell divides
viral mutation and mutation rates - viral oncogenes
- gene whose activity is involved in turning a normal cell into a cancer cell.
a. Termed viral transformation (this is different from bacterial transformation).
b. Example: HeLa cells, transformed cells from Henrietta Lacks.
Viruses associated with cancer in humans are usually ? viruses?
- entirely resistant to disinfectants
protozoan cysts and oocysts
- more innately resistant to disinfectants, BUT killed by boiling for 5 minutes
- thick waxy cell calls can't be penetrated by gram stains
- can grow in tap water with little nutrition
- can grow in disinfectants b/c resistant
- resistant to alcohol and many disinfectants
- the time it takes to reduce a bacterial population by 90% under specific conditions
boiling water bath for 5 mins
destroys most microorganisms and viruses, but not effective means of sterilization
*requires minimus 30 mins to kill endospores
- reduces number of organisms, does not sterilize.
a. HTST (high temperature short time) 72OC for 15 sec
b. UHT (ultra high temperature)- 140-150OC for 2-3 sec.
- add pressure to wet heat (steam)
a. 15 minutes at 121oC, at 15 psi sterilizes most objects. Larger volumes of fluid will take more time to sterilize.
b. Need to allow steam into item being sterilized. Use sponges to block entry of airborne particulates for fluids, or just keep lids slightly unscrewed for bottles or beakers. Covering with aluminum foil works for materials inside beakers. Paper wrapping also works (similar to what Louis Pasteur did with his swan necked-flasks to keep bacteria out of his media)
(item must be heat resistant)
- denatures, but proteins can be more stable in dry heat
1) Flaming inoculating loop - incinerates!
2) Bake items at 160-170OC for 2-3 hours. (not including heating up and cooling down time!)
1) Membrane filters -mainly for fluids
2) HEPA (high efficiency particulate air) filters
- removes particles larger than 0.3um
ionizing (gamma radiation)
- sterilizes fairly rapidly
- protein, DNA damage, free radicals
- penetrates well
- can sterilize non-dividing organisms
**gram - most sensitive
- can sterilize heat sensitive items
i.e. medical equipment, surgical supplies
- due to lower energy waves, need longer time to sterilize
- does not penetrate
- damages DNA
- works best on actively multiplying organisms
- just heating water in cells
-(130,000psi) pasteurizes food by denaturing proteins and permeability of bacteria
issues with chemicals
may be toxic, lose activity in presence of organic material, be expensive, environmentally risky, have problems storing, or just not be compatible with what is being treated
a. Diluted solutions are more effective than pure alcohol, but evaporates rapidly.
- proteins more soluble and denature more easily when mixed with water
b. Antiseptic - coagulates enzymes, disrupts lipid membranes, little effect on endospores or naked viruses.
-toxic to humans
a. Formaldehyde-preservation of biological samples
b. Gluteraldehyde-sterilize medical instruments
- used for heat sensitive items!
ethylene oxide gas
-gas penetrates hard to reach places and fabrics
*Problems-toxic/explosive when mixed with CO2
- used for heat/moisture sensitive items!
-can be inactvated by organic compounds or impurities present on surface.
a. Chlorine- effective against almost all bacteria, viruses, fungi, and endospores. Common source of chlorine- sodium hypochlorite (bleach).*
b. Iodine- used as a tincture (in alcohol) or as an iodophore. Can be used as a *
disinfectant or antiseptic
-unstable form of oxygen used as an alternative to chlorine for disinfecting drinking/waste water
- unstable and breaks down very rapidly.
- can be broken down by catalyase created by microbes (as well as human cells) can be used BEST as a disinfectant and not an antiseptic
- leaves no residue and can be used to sterilize food containers
- more potent than H2O2
- can be used in the presence of organic compounds, leaves no residue and can be used on a wide range of materials
- act on cytoplasmic membrane and denatures proteins. Do not reliably inactivate all viruses. However, they can leave an active antimicrobials residue. Non-toxic.
a. Hexachlorophene -works best against S. aureus however, may be neurotoxic.
b. Triclosan-where isn't it?
**one of earliest disinfectants!
- detergents which act to primarily disrupt cell membrane.
a. Anionic detergents -common soaps and detergents reduce surface tension of liquids- Aids in removal of dirt and organic matter and facilitates mechanical removal of organisms
b. Little antimicrobial effect
- aka Quats
a. Like commons soaps and detergents reduce surface tension of liquids.
b. Quats are cationic (positively charged) and attracted to the negative charge of cell surface and reacts with membrane
i Destroys vegetative bacteria and enveloped viruses
ii Not effective on endospores, mycobacteria and naked viruses
iii Aids in removal of dirt and organic matter and facilitates mechanical removal of organisms
- inhibits growth of many pathogens and spoilage microorganisms by slowing or stopping critical enzyme reactions but NOT psychophilic or psychotrophic organisms!
- decrease availability of water, limiting growth of most microbes b/c they NEED water to survive!
- draws water out of cells and dehydrates them
- freeze-drying - first frozen, then dried in vacuum
pH - acetic acid
first antimicrobial agent
- discovered the first antibiotic (penicillin) in 1928
- naturally occurring substance produced by fungus or other microbes
Chain and Florey
- followed through on Fleming's findings to isolate and produce penicillin
- causing greater harm to microbes than to human host
- lowest dose toxic to patient divided by the dose typically used to therapy
*high therapeutic index = less toxic!
- slow growth enough for immune system to come and wipe out
- kill organism
- affect on wide range
- acute life-threatening situations
- disrupts normal microbiota
- limited range
- pathogen must be identified
- less disruption to microbiota
- interfere with each other
- enhance each other
- give the same effects as they would alone
If a drug is unstable at low pH, how is it administered?
IV or butt shot
adverse effects of drugs
- allergic responses
- destruction of normal microbes
innate or intrinsic resistance
- organism cannot be acted upon because of inherent resistance
**gram - more resistant to antibiotics b/c lipid bilayer of outer membrane prevents drugs from entering
beta lactam drugs
- CELL WALL SYNTHESIS
- active against growing/dividing microorganisms
- they bind and inactivate the transpeptidases used to create the peptidoglycan wall (transpeptidases are also called penicillin binding proteins)
- all have a beta lactam ring structure
- Penicillin G& V-(narrow spectrum)- work only against gram positive organisms
- resistant penicillins
- methicillin, dicloxicillin
broad spectrum penicillin
-Semisynthetic penicillins- Ampicillin, amoxicillin
- works against gram negatives as well as gram positives
extended spectrum penicillins
- more effective against gram negatives, but still can be rendered useless by beta-lactamases
- Ticarcillin and piperacillin
penicillins + beta-lactamase inhibitor
- Augmentin (amoxicillin and clavulanic acid)
- CELL WALL SYNTHESIS
- have four generations of cephalosporins
- Cephalosporins of higher generation are normally broader spectrum against gram negatives (but lose their ability to target gram positives)
- Each generation of cephalosporin is more resistant to the action of beta-lactamases (however, beta-lactamases DO act on these drugs at low frequencies due to the presence of the beta-lactam ring)
carbapenems and monobactams
-CELL WALL SYNTHESIS
- very resistant to beta-lactamases
- Carbapenems work against gram positive and negatives, monobactams work best against enterbacteria (gram negatives).
- CELL WALL SYNTHESIS
- acts on the bactophrenol that transports peptidoglycan monomers out of the cell
- CELL WALL SYNTHESIS
- binds to the tetrapeptide sidchain, not to penicillin binding proteins
- PROTEIN SYNTHESIS
- Changes shape of ribosome causeing misreading of the mRNA (irreversible-cidal)
- Actively transported into cell by respiratory processes, therefore are not effective against anaerobes, enterococci, and obligate fermenters (streptococci)
- PROTEIN SYNTHESIS
- Block attachment of tRNAs reversibly (static)
*Problems: cause discoloration in teeth of children
- PROTEIN SYNTHESIS
- Erythromycin, clarithromycin, azithromycin-prevents protein synthesis (static)
- Works best against gram positives
- PROTEIN SYNTHESIS
- inhibits peptide bond formation (static to cidal depending on concentration)
- Can cause aplastic anemia
- Has a low therapeutic index.
- PROTEIN SYNTHESIS
- clindamycin inhibit protein synthesis (static)
- Good against wide variety of gram pos. and gram neg. organisms, however Clostridium difficile is resistant, emerging threat
- PROTEIN SYNTHESIS
- synergistic combination of two drugs that can together be bactericidal
- they act on TWO sites of the 50S subunit
- individually they are static
- NUCLEIC ACID SYNTHESIS
- ciprofloxacin inhibit topoisomerases (DNA gyrase) and acts to inhibit DNA synthesis (cidal)
- NUCLEIC ACID SYNTHESIS
- binds RNA polymerase and inhibits mRNA synthesis (cidal)
- resistance develops rapidly
- FOLIC ACID, NUCLEOTIDE SYNTHESIS
- sulfa drugs
- FOLIC ACID, NUCLEOTIDE SYNTHESIS
- PLASMA MEMBRANE
- topical only
emhambutol, isonazid, pyrazinamide
- acts specifically on the synthesis of the cell wall of the organism that cause tuberculosis, Mycobacterium tuberculosis.
minimum inhibitory concentration (MIC)
- lowest concentration of a specific antimicrobial drug needed to prevent visible growth of a given organism in vitro, without killing
- determined using serial dilutions of one antimicrobial drug
minimum bactericidal concentration (MBC)
- lowest concentration of an antimicrobial that kills 99.9% of a given organism
- this assay is performed in combination with the MIC assay
---> the actual organisms used in the MIC test, which survived the MIC of the drug, are exposed to increasing concentrations of the same drug
---> the lowest concentration of antibiotic that then kills all bacteria will be the MBC
- used to determine susceptibility of given bacterial strain to a battery of antimicrobial drugs
- clear zone = bacteria is susceptible to drug!
- modification of K-B method
- multiple strips containing a gradient of concentrations of antimicrobial drug placed on surface of agar that has been inoculated with organisms
- produces teardrop shape clearing
- can help asses MIC
- result of use of antibiotics to select organism that have mutated or acquired resistance factors that allow them to survive
- chances of mutation low
- can accumulate over time with selection pressure
ex. one base pair change can make streptomycin resistant
transfer of genetic information
- conjugation --> R plasmids that carry several different resistance genes
- some bacteria produce enzymes that chemically modify a specific drug, interfering with its function
alteration in target molecule
- antibiotics recognize and bind to specific target molecules in a bacterium, interfering with its function
- BUT minor structural changes in target can prevent antibiotics form binding
decreased uptake of drug
- changes in porin proteins can prevent certain drugs from entering the cell, so organism avoids effect of antibiotics
increased elimination of drug
- when cell makes more efflux pumps, can expel antibiotic faster so not effective
A. No naturally occurring antiviral drugs.
B. Use host's metabolic machinery to replicate, giving very few targets for antiviral therapy.
C. Mainly target three areas (what can we target on viruses?). Additionally, they are specific for a unique virus or genus of viruses and NOT used for all viruses.
antiviral drugs - viral uncoating
- Amantadine, Rimantadine
- only used against Influenza A.
antiviral drugs - nucleid acid synthesis
- herpesvirus family members and HIV
- Nucleoside analogs, Non-nucleoside polymerase inhibitors, non-nucleoside reverse transcriptase inhibitors
antiviral drugs - assembly and release of particles
- Protease inhibitors (HIV), neuraminidase inhibitors (influenza/ Tamiflu, Renlenza)
antifungal drugs - plasma membrane synthesis
- polyenes, azoles, allylamines
antifungal drugs - cell wall synthesis
antifungal drugs - cell division
- ring worm or jock itch
antifungal drugs - nucleic acid synthesis
- yeast infection
- microbe establishing itself and multiplying on body surface
1) Primary versus secondary infections.
- primary is initial infection
- secondary is additional infection as a result from primary infection
2) Primary vs secondary response
primary vs opportunistic pathogen
A. Primary pathogen - When we have them, Will always cause infection/disease
1) i.e. the flu
B. Opportunistic pathogen - Commensal organism that is allowed into protected sites.
1) i.e. Staph epidermidis (catheters can transmit this if not properly used and sterilized; increased resistance in hospitals now)
- degree of pathogenicity of an organism
- makes more harmful and more of a primary pathogen instead of opportunistic
- traits of microorganism that specifically allow it to cause disease
- number of microbes in a dose that will kill 50% of inoculated test animals
- lethal dose
- number of microbes in a dose that will produce a demonstrable infection in 50% of inoculated test animals.
- the lower the ID 50 number is, the more infectious it is b/c it takes a lesser amount of the virus to cause the infection
- infectious dose
- time between introduction of organism to onset of symptoms, no clue you have been infected
- initial feelings of malaise
- period of invasion
- Individual experiences classic signs and symptoms of disease
a. Sign: measurable, observed
b. Symptom: subjective, felt
- period of recuperation and recovery
persistence of infection - acute
- illness is short term b/c pathogen is eliminated by the host defenses
- person is usually immune to reinfection
persistence of infection - chronic
- illness persists over a long time period
1) i.e. mononucleosis: can have symptoms for 3 weeks, but then still shed the virus for up to 18 months after
persistence of infection - latent
- illness may recur if immunity weakens
1) i.e. chicken pox: can reactivate later in life as a result of stress, age, etc.
2) another example is herpes viruruses
A. The microorganism must be present in every case of the disease.
B. The organism must be grown in pure culture
C. The same disease must be produced when a pure culture of the organism is introduced into susceptible hosts.
D. The organism must be recovered from the experimentally infected hosts.
mechanisms of pathogenesis
A. Production of toxins that are ingested.
B. Colonization of mucous membranes of host, followed by toxin production.
C. Invasion of host tissues.
D. Invasion of host tissues followed by toxin production.
- number of cases of a disease in a specific time
- total number of cases (old and new) that has occurred in a given population
- incidence of illness in regard to specific disease
- death rate in regard to specific disease/population
2) Symptomatic/asymptomatic infections
B. Animal reservoirs
1) Animal reservoirs for disease that can infect humans and animals (rabies)
2) Zoonosis-accidental infection of human by animal pathogens (Lyme disease)
a. easiest way to get infected with cold
2) Indirect-fomites or inanimate objects which can transfer disease.
3) Droplet transmission
C. Incubation period
- genetic component to autoimmune progression and higher risk for disease in women
1) Age-especially the very young (<1 year) and anyone over the age of 50.
2) Stress-especially college age students.
4) Organ transplant recipients
5) Pregnant women
6) Genetic factors
7) Excess in Drinking/Drugs
- protecting individuals who are not vaccinated (too young, too old, religious beliefs, cultural beliefs) by restricting the reservoir the pathogen
**NC nursing rules and guidelines require that every nurse must be properly vaccinated so that don't spread to patients b/c more likely to be vector or reservoir
b. Double-blind - physician as well as patient does not know who is on actual medication and who is not (placebo)
- you can eradicate these diseases
1. i.e. smallpox is eradicated b/c everyone got vaccinated and the virus couldn't infect any humans, so it died
- you CANNOT eradicate these diseases impossible!!!
1. i.e. tetanus, botulism, anthrax are out in the environment and can't be controlled
ability to create pathogens
- new organisms evolve into pathogens.
i. i.e. turtles and salamanders are now dying off exponentially from diseases jumping from humans to salamanders that are not transferring the disease to turtles
- infections and disease not present before hospitalization.
i. Responsible for about 20,000 deaths in the U.S. per year.
1. Approximately 10% of American hospital patients (about 2 million every year) acquire a clinically significant nosocomial infection
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