Lectures 1-5 Flashcards
Describe a typical bacterial plasma membrane
Selectively permeable, contains cytoplasm, location of metabolic processes, detects environmental changes
What is the function of ribosomes in bacterial cells?
Protein synthesis
What is the function of the nucleoid in a bacterial cell?
Not a distinct structure, simply the location of genetic material within the cell
What is the periplasmic space and what type of bacterial cell has a larger one?
Contains hydrolytic enzymes and binding proteins for nutrient processing and uptake; gram negative cells have a larger periplasmic space because they have a thinner layer of peptidoglycan
What part of the bacterial cell protects from osmotic stress?
The cell wall, which also functions to maintain cell shape
Since bacterial cells replicate by binary fission, what are some possible sources of genetic variation?
- Mutation
- Horizontal gene transfer through conjugation
- Transduction
- Transformation
What are fimbriae?
Hair-like structures on bacterial cells that function in attachment to surfaces
How do flagella operate in bacterial cells?
They spin like a propellor (clockwise or counterclockwise) while anchored in the bacterial cell membrane
What color do gram positive cells stain?
Purple
What color do gram negative cells stain?
Pink or red
What is the substance that makes up bacterial cell walls?
Peptidoglycan
Which type of bacterial cell has a thicker layer of peptidoglycan and techoic acids in its cell wall?
Gram positive
Which type of bacterial cell has a thinner peptidoglycan cell wall and includes an outer membrane?
Gram negative
Which type of bacterial cell tends to be more resistant to antibiotics?
Gram negative
What are the functions of techoic acids in gram-positive cell walls?
- Maintain cell envelope
- Protect from environmental substances
- May bind to host cells
- techoic acids are negatively charged
- lipotechoic acid binds to membrane, wall techoic acid links stacks of NAGs and NAMs
What is the outer membrane of gram-negative cells composed of?
Lipids, lipoproteins, and LPS (which makes it more resistant to antibiotics)
What are some aspects of peptidoglycan structure?
- 2 alternating sugars: NAG and NAM
- Alternating D and L amino acids
- mesh-like polymer of identical subunits forming long strands
- chains joined by cross-links (covalent bonds for strength)
- strands have helical shape
What are the two sugar carriers involved in peptidoglycan synthesis?
UDP and bactoprenol pyrophosphate
What are plasmids and what purpose do they serve?
Extrachromosomal DNA that exist independent from chromosome and contain some nonessential genes; confer selective advantage to host (drug resistance?)
Where are NAM and NAG synthesized?
Cytoplasm
Protoplasts and Spheroplasts are osmotically sensitive because they lack a cell wall, what will happen if they are placed in an isotonic solution? A hypotonic solution?
In an isotonic solution they will survive, but in hypotonic solution they will lyse open
What are acid-fast cells? Describe their cell wall.
Resist decolorization with acid alcohol, so they have poor stain absorption followed by high stain retention.
Their cell wall is waxy which prevents most water soluble stains from crossing it, and causes cells to cluster together (sticky)
What is the function of the rough ER in a eukaryotic cell?
Transport of materials
What is the function of the smooth ER in eukaryotic cells?
Storage of calcium and lipids, site of lipid synthesis
Describe the ribosomes found in eukaryotic cells
Site of protein synthesis.
80S when bound to the RER or free in cytoplasm
70S in chloroplasts or mitochondria
What is the function of a eukaryotic lysosome?
Intracellular digestion using hydrolytic enzymes (“cuts things up”)
What is the function of a eukaryotic lysosome?
Intracellular digestion using hydrolytic enzymes (“cuts things up”
What is the function of eukaryotic mitochondria?
Energy production through TCA cycle, ETC, and oxidative phosphorylation
What occurs in the nucleolus?
Ribosome construction and ribosomal RNA synthesis
What is the function of the eukaryotic peroxisome?
Oxidation of fatty acids, destroys H2O2
What makes up the centrosome?
Protein fibers and centrioles
What are the 3 parts of a virion?
Nucleocapsid, protein coat, envelope (only some have)
What makes up the protein coat of virions and what is its purpose?
The capsid is made up of protein units called capsomeres
Function is to protect genetic material and aid in transfer
capsid is acquired during biosynthesis
Where is the virion envelope typically derived from?
The host cell’s plasma membrane, but it can also come from the host cell’s membrane bound organelles: Golgi or ER.
Overall composition is a combination of lipids, proteins, and carbs
acquired during maturation and release
What is the purpose of the spikes sometimes found on virion envelopes?
Spikes function in ATTACHMENT which allows for host-cell specificity
What makes up the nucleocapsid?
Nucleic acid; may be DNA or RNA that is single or double-stranded
Name the 5 steps common to the life cycle of all viruses
- Attachment - viruses attach to cell membrane (sometimes with spikes)
- Penetration/entry - endocytosis or fusion
- Uncoating - aided by viral or host enzymes
- Biosynthesis - production of nucleic acid and proteins
- Maturation and Release - nucleocapsid assembles and virus is released by budding or rupture (lysis)
What is the best supported explanation of how prions replicate?
Abnormal prion proteins convert normal prions to abnormal form through an unknown mechanism
What is the area of heaviest regulation during bacterial genome replication?
Initiation of transcription
In the DNA polymerase holoenzyme, what is the function of the beta clamp?
Holds the DNA
In the DNA polymerase holoenzyme, what is the function of the alpha area?
Alpha catalyzes DNA synthesis/phosphodiester bond formation
In the DNA polymerase holoenzyme, what is the function of the epsilon region?
Epsilon functions in proofreading/exonuclease activity
In the DNA polymerase holoenzyme, what is the function of the theta region?
Stabilizes epsilon
The 16S rRNA ribosomal subunit is contained within which bacterial ribosomal subunit?
30S, because the Shine Dalgarno sequence is contained in it which is important for initiation of translation
The 16S rRNA ribosomal subunit is contained within which bacterial ribosomal subunit?
30S, because the Shine Dalgarno sequence is contained in it which is important for initiation of translation
What directs the RNA polymerase to the promoter during transcription initiation?
Sigma factor
What effect does penicillin have on bacterial cells? Which type does it work on?
Penicillin is more effective on gram positive because it interferes with new peptidoglycan synthesis, it will not act on existing peptidoglycan.
Lysozyme acts on existing peptidoglycan by cleaving NAGs and NAMs, so this is effective on both gram positive and gram negative
What is the function of the gas vacuole in a bacterial cell?
Inclusion that provides buoyancy for floating in aquatic environments
Lysogeny
When the viral DNA is inserted into the bacterial DNA
Why are prions resistant to treatment?
They are already denatured
Which type of infection has a higher mortality rate?
Chronic
A plus strand RNA virus would be more likely to bring along what type of machinery?
RNA polymerase
What are some protective advantages of capsules?
Resistant to phagocytosis, protect from desiccation, exclude viruses and detergents, prevents antibody binding
A double stranded DNA virus would most likely bring along what type of machinery?
DNA polymerase
It would likely use host cell RNA polymerase
What does bactoprenol carry during peptidoglycan synthesis?
Bactoprenol attaches to NAM by a pyrophosphate group to move peptidoglycan units through the hydrophobic membrane
Endospore
Complex, dormant structure formed by some bacteria in order to resist a change in environmental conditions such as heat, radiation, chemicals, or desiccation.
- covered by thick layer of keratin
- good example of two different ways of regulating gene expression: alternative sigma factors and phosphorelay system
Chemotaxis
Move toward chemical attractants such as nutrients, away from harmful substances
The bacterial flagellum rotates like a propellor, in general what direction will it move with counterclockwise rotation?
Counterclockwise rotation causes forward motion (a run); Clockwise rotation disrupts the run causing cell to stop (tumble)
What type of bacterial cells do not form endospore said?
Gram negative
How do virulent phages reproduce?
They only have one reproductive choice, multiplies immediately upon entry and lyses bacterial host cell
How do temperate phages reproduce?
They have two reproductive options: to reproduce lyrically as virulent phages do, or remain in the host cell without destroying it (through lysogeny)
What type of cell wall is sensitive to tetracycline?
Gram-negative
Which of the 3 parts of the lipopolysaccharide (LPS) is the endotoxin and where is it located?
lipid A
Embedded in the outer membrane
What is the function of bactoprenol and what happens when it is blocked?
Transports the NAG-NAM pentapeptide repeat unit across the cell membrane
The pentapeptide cannot be transported across the membrane so peptidoglycan synthesis halts.
Bacterial mRNA has multiple genes coding for different polypeptides that make up the protein. Bacterial mRNA is___________
Polycistronic mRNA
Contains directions for more than one polypeptide
(eukaryotic mRNA is monocistronic)
What are the 4 antibiotics that interfere with peptidoglycan synthesis and how do they work?
Vancomycin: inhibits transpeptidation by binding to D-Ala-D-Ala
Cycloserine: blocks formation of D-Ala-D-Ala
Penicillin: inhibits the transpeptidation reaction.
Bacitracin: blocks the dephosphorylation of bactoprenol pyrophosphate.
What is unique about Archeal cell walls?
They are wall-less or they have a pseudopeptidoglycan ( pseudomurein) wall. Not made up of peptidoglycan.
What enzyme joins the okazaki fragments together? And how is that carried out?
DNA ligase
Forms a phosphodiester bond between the 3’ OH group of the growing strand and the 5’ phosphate of the Okazaki fragment
A turbid culture would indicate what?
More host cells are present, viruses have not been actively reproducing
Infectious dose
The smallest amount of virus needed to cause infection of 50% of exposed host cells or organisms
Do bacterial cells have similar cytoskeletal elements as eukaryotes?
Yes! Tubulin and actin homologs
What is the function of the S layer
Protects
What is the evidence supporting endosymbiosis in eukaryotic mitochondria?
70S ribosomes, circular DNA, double membrane, and division by binary fission
Bacteria lack cholesterol in their cell membranes, what do they contain to stabilize the membrane?
Hopanoids - sterol like molecules used for stabilization of bacterial cell membranes
Magnetosomes
Inclusion bodies found in aquatic bacteria that function as magnetite particles (iron) for orientation in Earth’s magnetic field
What are the three parts that make up LPS and what are their characteristics/functions?
Lipid A: embedded in outer membrane; releases endotoxins (could be in response to antibiotics)
Core Polysaccharide: extends out from the cell
O side chain (O antigen): extends out from the cell; acts as a disguise so host does not recognize as a foreign pathogen
Hypotonic solution
Solute concentration is greater inside the cell than outside, water will move in causing cell lysis
What makes gram negative cells’ outer membrane more permeable?
Porins (remember OmpF and OmpC)
Hypertonic solution
Solute concentration inside the cell is less than outside the cell, water will move out causing plasmolysis
What do gram positive cells secrete to aid in the degradation of nutrients?
Exoenzymes
What are the subunits of the bacterial ribosome?
16S small subunit
23S and 5S large subunit
Total of 70S
How are non-enveloped virions released from the host cell?
They lyse the host cell; viral proteins may attack the peptidoglycan or membrane
How are enveloped virions released from host cell?
Budding; viral proteins are placed into the host membrane (this is key!), nucleocapsid may bind to these viral proteins, virus may use host actin tails (part of cytoskeleton) to propel through host membrane
What are the four different characteristics used for classification of viruses?
Nucleic acid type
Presence or absence of envelope
Capsid symmetry
Dimensions of virion and capsid
Virulent phage
Has only one reproductive choice: must multiply upon entry and lyse bacterial host cell
What is the role of sigma factors during transcription in bacteria?
Sigma factors recognize specific promoter regions (pribnow) and form holoenzyme which is key for initiation of transcription
Temperate phage
Has two reproductive options: reproduce lytically as virulent phages do, or remain within the host cell without destroying it (many do this by becoming prophage - through lysogeny relationship)
What are some possible mechanisms by which viruses such as HPV cause cancer?
Viral proteins bind host cell tumor suppressor proteins
Carry oncogene into cell and insert it into host genome
Altered cell regulation
Insertion of promoter or enhancer next to cellular oncogene
What type of bonds are found in bacterial and eukaryotic lipids?
Ester bonds (2 hydrocarbons attached to glycerol)
What type of bonds are found in archaeal lipids
Ether bonds (branched molecules, tetraethers)
What would happen if we did not have IF-3 during initiation of protein synthesis?
The 30S subunit would bind to the 50S subunit at the wrong time, prematurely forming the initiation complex
Type IV secretion system
Secretes proteins, DNA from donor to recipient bacterium during conjugation, found in both gram positive and gram negative cells, requires energy
Bacteria lack cholesterol in their cell membranes, what do they contain to stabilize the membrane?
Hopanoids - sterol like molecules used for stabilization of bacterial cell membranes
What homologs of eukaryotic cytoskeletal elements have been found in bacteria?
All 3! Tubulin, Actin, and Intermediate Filaments
Magnetosomes
Inclusion bodies found in aquatic bacteria that function as magnetite particles (iron) for orientation in Earth’s magnetic field
What are the three parts that make up LPS and what are their characteristics/functions?
Lipid A: embedded in outer membrane; releases endotoxins (could be in response to antibiotics)
Core Polysaccharide: extends out from the cell
O side chain (O antigen): extends out from the cell; acts as a disguise so host does not recognize as a foreign pathogen
What are some functions of LPS
Contributes to negative charge Stabilizes outer membrane Attachment and biofilm formation Permeability barrier Protection from host defenses (O side chain) Endotoxin (Lipid A)
What do gram positive cells secrete to aid in the degradation of nutrients?
Exoenzymes
What are the subunits of the bacterial ribosome?
16S small subunit
23S and 5S large subunit
Total of 70S
Do virions contain enzymes?
YES, some are associated with the envelope, but most are within the capsid
Sense strand RNA virus
Made up of mRNA’s so the genome can be directly translated, still need to make + and - strands
No need to make DNA ever!
Antisense Strand RNA Virus
Must make Sense strands (+ strand) first in order to be translated
No need to make DNA ever!
Sense strand RNA virus
Made up of mRNA’s so the genome can be directly translated, still need to make + and - strands
What are 3 possible methods for viral entry and uncoating?
Fusion of the viral envelope with host membrane; nucleocapsid enters
Endocytosis in vehicle; endosome aids in viral uncoating
Injection of nucleic acid
How are non-enveloped virions released from the host cell?
They lyse the host cell; viral proteins may attack the peptidoglycan or membrane
What are the four different characteristics used for classification of viruses?
Nucleic acid type
Presence or absence of envelope
Capsid symmetry
Dimensions of virion and capsid
An alternative viral classification system was created by David Baltimore, what is his system based on?
The viral genome and method of biosynthesis; encompasses 7 life cycle groups based on: dsDNA, ssDNA, dsRNA, ssRNA (+ or -), and retrovirus
Virulent phage
Has only one reproductive choice: must multiply upon entry and lyse bacterial host cell
Temperate phage
Has two reproductive options: reproduce lytically as virulent phages do, or remain within the host cell without destroying it (many do this by becoming prophage - through lysogeny relationship)
What is the promoter in bacterial DNA transcription?
Pribnow box - contains consensus sequence
Pribnow is located in promotor region so it does NOT get transcribed
What is the role of 16S rRNA?
Ribosomal binding site (RBS), binds to Shine Dalgarno site on mRNA for protein synthesis initiation (LEADER sequence)
Binds protein needed for initiation of translation and amino acyl-t-RNA
What are the advantages of temperate phages that undergo lysogeny?
Phage remains viable but may not replicate, multiplicity of infection ensures survival of host cell
What are some possible mechanisms by which viruses such as HPV cause cancer?
Viral proteins bind host cell tumor suppressor proteins
Carry oncogene into cell and insert it into host genome
Altered cell regulation
Insertion of promoter or enhancer next to cellular oncogene
Holoenzyme
Core enzyme + sigma factor (only the holoenzyme can begin transcription)
What is the role of 23S rRNA?
Ribozyme catalyzes peptide bond formation
Type IV secretion system
Secretes proteins, DNA from donor to recipient bacterium during conjugation, found in both gram positive and gram negative cells, requires energy
What would happen if there was an error in the DNA coding for the enzyme Helicase?
The DNA would not unwind at the ORI which would halt the entire process of transcription
What would happen to the cell if there was a mutation in the SSBP (Single Stranded Binding Protein)?
There would be nothing holding the two unwound strands of DNA apart which would make DNA pol or RNA pol slow down or stop the process of replication or transcription.
What would happen to the cell if there was a mutation in its topoisomerase gene?
Topoisomerase helps prevent supercooling as the DNA is unwound. If there is a mutation then it would not be able to make the nicks in the DNA to prevent supercooling. The result would be supercoiling of the DNA which will halt or disrupt DNA replication or transcription
What would happen to the cell if there was a mutation in it’s Primase gene?
Primase adds the RNA primer so DNA pol has a place to bind. If there is a mutation then the Primase will not be able to place a RNA primer on the DNA strand and the DNA will not be replicated. This will most likely result in cell death.
What would happen to the cell if there was a mutation in epsilon ( one of the three parts of the core enzyme in DNA pol III)?
The core enzyme would lose the ability to proofread so any mistakes that are made cannot be fixed via DNA pol III. Other mechanisms of DNA repair would have to be used (if possible)
What would happen to the cell if there was a mutation in the Alpha gene. (One of the three parts of the core enzyme in DNA pol III)
Alpha is important in the synthesis of the DNA and bond formation. If there is a mutation then synthesis will not occur and the cell will not replicate and most likely will die
What is the main difference in bacterial transcription and translation from eukaryotic?
Bacterial transcription and translation is coupled.
What is key in the initiation stage of transcription?
Sigma factor binding to the promoter to attract the holoenzyme.
During elongation of transcription is it necessary for there too be a primer for RNA pol to begin transcribing the DNA strand?
No. RNA pol doesn’t need a primer to begin transcription. Once RNA pol recognizes the consensus sequence it begins transcribing the DNA into mRNA.
How does the cell know glucose is there? What happens when glucose is not present but lactose is?
The ratio of AMP. AMP increases as glucose decreases which results in the formation of cAMP which binds to CAP.
the presence of allolactose bound to the repressor and CAP w/ cAMP bound to the CAP site results in the transcription of the lac operon.
What is an example of a second messenger molecule?
A second messenger molecule is cAMP
At what point on the promoter does sigma factor bind to give initiation?
-10 or the Pribnow box.
What is an example of a co repressor
Tryptophan
What is an example of a modulon?
CAP
What is the role of molecular chaperones?
Aid in protein folding
During protein splicing, which part of the polypeptide will remain in the protein?
Exteins (think Exteins get to “exit” as complete proteins)
Introns will be spliced OUT!
Type IV secretion system
Protein secretion pathway that secretes DNA from donor to recipient bacterium during conjugation
Found in both Gram positive and Gram negative cells
Constitutive genes
“Always on”
Includes housekeeping genes because these are required for basic cellular function
Inducible genes (provide example)
“Off but can be turned on”
Example: Lac operon
What will happen to cAMP if glucose is not available?
cAMP will bind CAP (which is an example of a modulon), activating it which then acts as a promoter of transcription on the lac operon
Repressible genes (provide example)
“On but can be turned off”
Example: Trp operon
Repressor protein
Type of regulatory protein that inhibits transcription by attaching to the operator and blocking RNA polymerase or preventing its movement
Note that if an inducer is present, the repressor protein is prevented from binding and transcription occurs
Activator protein
Type of regulatory protein that promotes transcription by binding to the activator sites which facilitates RNA polymerase binding
Regarding the Trp Operon, what will occur when tryptophan levels are low? What about high?
When tryptophan is low, Trp repressor is inactive, transcription will occur so that more Trp is made
When tryptophan is high, Trp acts as a corepressor binding to the Trp repressor protein (activating it) which then binds to the operator and blocks transcription so that no more Trp is made
Does transcription control of arabinose operon act positively or negatively?
Both!
When arabinose is present, it binds AraC and breaks DNA loop, in this case it is an activator
When arabinose is not present, two AraC proteins interact, causing DNA to bend, transcription is inhibited, in this case it is an inhibitor
What is the function of riboswitches in gram negative bacteria?
Regulation of translation
During conjugation between F+ and F- cells, what is the resulting cell?
F+ is the conjugant
What is an example of a riboswitch?
MicF - inhibits ompF mRNA translation which will prevent the diffusion of solutes
What is the resulting cell from F’ conjugation?
F’ is the conjugant
Of OmpF and OmpC, which porin is bigger?
OmpF
Transduction
Type of horizontal gene transfer involving transfer of bacterial genes by virus; occurs during the lytic cycle of virulent phage
If errors occur during lysogeny, may need transduction of host genes to correct them (specialized transduction)
During bacterial conjugation, can genetic material move back and forth between cells?
NO, conjugation is always unidirectional
What is the resulting cell from F’ conjugation?
F’
What are the end products of the EM pathway and where does it occur?
2 pyruvate
2 ATP
2 NADH
Cytoplasm
What are the end products of the ED pathway and where does it occur?
1 ATP
1 NADPH
1 NADH
Cytoplasm
What are the end products of the pentose phosphate pathway and where does it occur?
6 CO2
12 NADPH
Cytoplasm
What are the end products of the TCA cycle and where does it occur?
2 CO2, 3 NADH, 1 FADH2, 1 GTP
IF you start with glucose these will double
Cytoplasm
Where does the ETC take place in bacterial cells?
Cell membrane
Why do you get less ATP from fermentation than you would get from aerobic cell respiration?
With fermentation you only get substrate level phosphorylation, whereas aerobic respiration allows for oxidative phosphorylation which is a big producer of ATP
the ETC may be shorter in bacterial cells, what effect does this have on overall cell metabolism?
There will be less electron carriers, so there will be less protons pumped across, and there will be a lower P/O ratio - meaning less ATP is produced
What is the ATP yield of anaerobic respiration
2 ATP
Can only undergo substrate level phosphorylation
Facultative anaerobe
Can undergo both aerobic and anaerobic respiration, but more growth is typically seen in oxygenated media because more ATP can be made there
Obligate anaerobe
Can only undergo anaerobic respiration, O2 is often toxic to them
Aerotolerant anaerobe
Can undergo both aerobic and anaerobic respiration
There is no advantage/disadvantage to either so there will be an even distribution of growth in media
Microaerophile
Needs less than atmospheric O2 levels, so will be in the middle of a test tube
4 unifying themes of fermentation:
- NADH is oxidized to NAD+
- Oxygen is not needed
- Electron acceptor is often pyruvate
- ETC cannot operate, so PMF is generated by ATP synthase operating in the reverse (pumping protons out of the cell)
Homolactic fermentation
Type of lactic acid fermentation that uses EM pathway and directly reduces all pyruvate to lactate
Heterolactic fermentation
Type of lactic acid fermentation that forms substantial amounts of other products during fermentation process (CO2, ethanol, etc.)
What is occurring during phase 1 (lag phase) of the microbial growth curve?
Cell is synthesizing new components (to replenish materials or adapt to new medium or conditions)
This phase can be very short or absent in some cases. It is when the cell senses that temperature and other conditions are just right to go into metabolically active state
Lactic acid fermentation
One of the most common fermentation pathways; involves the reduction of pyruvate to lactate
Examples: cheese, yogurt, sausage
What is occurring during the stationary phase of the microbial growth curve?
Closed population growth eventually ceases, total number of viable cells remains constant. Nutrients start to become limited.
(Amount of cells dividing = amount of cells dying)
Alcoholic fermentation
Pyruvate –> acetaldehyde –> ethanol
Examples: beer and wine
How is the genetic material separated during binary fission?
The origins of replication adhere to opposite poles of the cell
When will OmpC be the dominant porin protein?
In high osmolarity intestinal tract - aka when osmotic pressure is sensed (lower levels of diffusion), sensor kinase EnZ is activated by autophosphorylation which will phosphorylate OmpR (response regulator) and alter transcription so that OmpC is transcribed and OmpF is downregulated
What does a DNA binding protein do?
Binds DNA and alters transcription as an activator or repressor
(Response-regulator protein activated by sensor kinase)
When will OmpF be the dominant porin protein?
In dilute environments (allows for more diffusion of solutes)
What prevents a continuous tumble during chemotaxis?
CheZ
During chemotaxis, what will occur as the concentration of attractant decreases?
As concentration decreases, there will be fewer ligands bound than MCPs methylated, triggering a tumble
(CheA is activated/autophosphorylated and CheB is actively removing methylation which will then allow for continuation into a run)
What is the importance of sigma factors in sporulation?
Spatial and temporal regulation during spore formation occurs due to differences in sigma factors between the spore and mother cell
Spontaneous mutations
Only arise without exposure to external agents
Rare due to proofreading and DNA repair
Induced mutations
Caused by agents that directly damage DNA, either chemically or physically
(examples: nitrous oxide, UV light, X-rays)
Conditional mutations
Expressed only under certain environmental conditions
Autotrophic mutant
Unable to make an essential macromolecule such as an amino acid or nucleotide; has a conditional phenotype!
(Ex: Needs histidine to properly grow)
What is the purpose of DNA methylation in mismatch DNA repair?
Distinguishes old DNA strands from new DNA strands (old DNA will be methylated and the repair system will cut out the mismatch from the unmethylated strand)
What is the key protein in recombinational DNA repair and what is its significance?
RecA protein; catalyzes the recombination events
For example, if you want to explain mutations in the lab, you need to inactivate the RecA protein
Most common is homologous recombination
Effectiveness of anti microbial drugs can be expressed in two ways. What are those?
MIC (minimal inhibitory concentration)
MLC (minimal lethal concentration)
What is minimal inhibitory concentration (MIC)?
The lowest concentration of drug that inhibits growth of a pathogen
Explain the mechanism of action for phenols to control microorganisms
Act by denaturing proteins and disrupting cell membranes
They are lipid soluble
What is minimal lethal concentration (MLC)?
Lowest concentration of drug that kills pathogen
Explain the mechanism of action for halogens- Iodine and chlorine to control microorganisms
Halogens such as Iodine are a skin antiseptic. Act by oxidizing cell constituents and iodinates proteins making. (oxidizing agents)
At high concentrations kills spores
Chlorine oxidizes cell constituents, destroys vegetative bacteria and fungi. Also kills spores
Describe Binary Fission
Occurs in bacteria and archea. All must replicate and segregate the genome prior to division. The genome is replicated and partitioned at each pole. Then cytokinesis occurs splitting the one cell into two.
There is no genetic variation.
Distinguish between -cidal and -static agents
Cidal agents kills pathogens and many nonpathogens but not necessarily endospore a
Static agents inhibit growth. When the static agent is removed or the cells are transferred the cells will grow again.
Explain the mechanism of action for alcohols to control microorganisms
Denature proteins and possibly dissolve membrane lipids
Inactive some viruses
Most common are ethanol and propanol
Needs water to be present inorder to function
Explain the mechanism of action for heavy metals to control microorganisms
Heavy metals combine with and inactivate proteins; may also precipitate proteins (make them fall out of solution).
Ex: ions of Hg, Ag, arsenic, Zn, and Cu
Effective but usually toxic
Mechanisms of action of sulfamethoxazole
It’s an example of a sulfonamide that causes the cell to be static and acts by blocking folic acid synthesis by competing with PABA
Explain the mechanism of action for aldehydes to control microorganisms
Aldehydes cause things to cross link. They combine with and inactive nucleic acids and proteins.
Can kill spores, highly reactive.
Mechanisms of action for penicillins
Inhibit peptidoglycan synthesis by blocking the enzyme that catalyzes transeptidation (formation of cross links in peptidoglycan
Prevents the synthesis of complete cell wall leading to lysis of cell
Many people are allergic to it
Other actions include:
binding to periplasmic proteins
activates bacterial auto lysine and more in hydrolases
Stimulate holing to form hole or lesions in the plasma membrane
Mechanisms of actions for Streptomycin
An antibiotic active against tuberculosis
Acts by inhibiting protein synthesis by changing the shape of 30S portion causing code on mRNA to be read incorrectly
Discovered by Waksman
Mechanism of action of tetracycline
Combine with 30S ribosomal subunit to inhibit the binding of aminoacyl-tRNA molecules to the A site of the ribosome
Interfere with the attachment of tRNA to the mRNA-ribosome complex
Mechanism of action of trimethoprim
A structural analog of a portion of dihydrofolic acid, competitively inhibits the synthesis of tetrahydrofolic acid.
Interferes with folic acid production
Can be combined with sulfa drugs to increase efficacy of treatment
Combination blocks the two steps in folic acid synthesis
Mechanism of action of Isoniazid
Thought to inhibit lipid synthesis
Putative enough-reeducate inhibitor
It’s a metabolic antagonist
Mechanism of action for chloramphenicol
Binds to the 23S rRNA on 50S ribosomal subunit and inhibits peptidyl transferase reaction
So inhibits the peptide bond formation
Toxic with numerous side effects
An example of inhibition of protein synthesis
Mechanism of action of Cephalosporins
Structurally and functionally similar to penicillins just fewer allergic reactions
So used in most patients that are allergic to penicillin
An example of inhibition of cell wall synthesis
Mechanism of action for ciprofloxin
Functions by inhibiting DNA gyrase and a type II and IV topoisomerase necessary to separate bacterial DNA, thereby inhibiting cell division
Broad spectrum antibiotic of the fluoroquinone class.
Active against gram - and gram + bacteria.
Nucleic acid synthesis inhibition
Mechanisms of action of Nalidixic acid
The first synthesized quinolone
Act by inhibiting bacterial DNA-gyrase and topoisomerase II
Mechanisms of action of Vancomycin
Important for treatment of antibiotic resistant staphylococcal and enterococcal infections
It inhibits cell wall synthesis.
Glycopeptide antibiotic
“Drug of last resort”
Mechanism of action of erythromycin
Binds to 23S rRNA of 50S ribosomal subunit to inhibit peptide chain elongation
Used for patients allergic to penicillin
What are the 5 antibacterial drug mechanisms?
1) inhibition of cell wall synthesis
2) inhibition of protein synthesis
3) inhibition of nucleic acid replication and transcription
4) Injury to plasma membrane
5) inhibition of synthesis of essential metabolites
What are the antibiotics that fit under the inhibition of cell wall synthesis mechanism. (One of the 5 mechanisms of anti microbial drugs)
Penicillins
Cephalosporins
Bacitracin
Vancomycin
What are the antibiotics that fit into the category of inhibition of synthesis of essential metabolites such as folic acid(one of the 5 main mechanisms of anti microbial drugs)?
Sulfanilamide
Trimethoprim
Ionazid acts on lipid synthesis in acid fast cells
What are the antibiotics that fit under the inhibition of protein synthesis mechanism of anti microbial drugs (one of the 5 main mechanisms of anti microbial drugs)
Chloramphenicol
Erythromycin
Tetracyclines
Streptomycin
What steps in peptidoglycan synthesis occur inside the cell?
The precursors to synthesis are ALL inside the cell;
- linking together of NAG and NAM with UDP
- Formation of lipid 1 and lipid 2
- Bactoprenol carries NAG-NAM pentapeptide across lipid bilayer to outside
What steps in peptidoglycan synthesis occur outside the cell?
- Cross links are formed by transpeptidation
- NAG-NAM pentapeptide is attached to the growing end of a peptidoglycan chain
What do biofilms do?
contributes to antibiotic resistance, resists a lot of disinfectants
Describe spirochete motility
- multiple flagella form axial fibril which winds around the cell
- flagella remain in periplasmic space inside outer sheath
- allows for movement through viscous fluids using corkscrew movements
What two types of motility are good for movement on solid surfaces?
twitching and gliding (pseudopodia)
how are viruses classified?
by morphology: helical, polyhedral, enveloped, complex
Which site on the ribosome is the amino-acyl site where tRNA enters during translation?
A site
Which site on the ribosome contains the transfer RNA with growing peptide chain?
P site
when 23S catalyzes peptide bond it will transfer to E site
Which site on the ribosome is the exit site during translation?
E site
retroviruses require what?
reverse transcriptase to create DNA from RNA which then incorporates into host DNA in the nucleus
Prions
unfolded or misfolded infectious proteins that are very difficult to kill
cause disease in humans and animals such as CJD and kuru
Does the shine dalgarno sequence get
transcribed?
Yes, the leader sequence gets transcribed but it does not get translated
Does Rho indicate prokaryotic or eukaryotic transcription?
prokaryotic
What is a polysome or polyribosome?
Refers to the fact that multiple ribosomes are bound to prokaryotic mRNA at once
Remember that in bacteria translation and transcription are synchronized
Put these steps in order: IF2 interacts with charged tRNA, IF3 binds to 30S subunit, 50S binds to 30S to initiate transcription, IF1 aids in release of IF3
- IF3 binds to 30S subunit
- IF2 interacts with charged tRNA so that we’re all set
- IF1 aids in release of IF3
- 50S binds to 30S to initiate transcription
How does the ribosome know when to stop translation?
when it encounters a stop codon, which does not code for any amino acids
What is an example of catabolite repression?
CAP (glucose sensing)
What is the general definition of a riboswitch?
A sensor RNA that can alter transcription (if it continues or terminates) or translation
What is the function of CheB during chemotaxis?
removes methylation
What is the function of CheY during chemotaxis?
interacts with the flagellar switch
What is the function of CheR during chemotaxis?
adds methylation
During chemotaxis, what will occur when ligand concentration decreases?
CheA autophosphorylates activating CheY which will trigger a tumble. At the same time CheB is removing methyls so that we will start to run again
What senses nutrient deprivation just prior to sporulation?
Kinase A – which then stimulates phosphorelay and that’s what activates cleavage of sigma factors which were previously inactive (spatial regulation)
silent mutation
do not alter phenotype
missense mutation
single nucleotide change that alters phenotype
frameshift mutation
insertion or deletion by a factor other than 3
Ames test
carcinogenicity test that is positive if reversion rate in presence of suspected carcinogen is greater than the reversion rate in absence of suspected carcinogen
what is transformation?
taking up naked DNA as a way to gain genetic variation
conjugant
recipient of transfer
transformant
cell that transfers genetic material
What does Hfr stand for?
high frequency of recombination meaning that there are lots of recombinants
What is the significance of the pentose phosphate pathway?
generation of intermediates like G3P that can regenerate glucose 6 phosphate which can be broken down into CO2
Why is fermentation important?
It regenerates NAD by oxidizing NADH
UV light as a disinfectant
causes dimerization (thiamine dimers, pyrimidine dimers)
Kirby bauer test
standardized disk diffusion test to determine if effective concentration of drug in body can be reached; does not tell you much about MBC or MIC
E-test
similar to Kirby Bauer but uses strip rather than disk, the strips contain gradient of antibiotic. Intersection of elliptical zone of inhibition indicates the MIC
LPS is found in the outer membrane of gram negative cells and is known as: A. Exotoxins B. Teichoic acid C. Murein D. Endotoxin
D. Endotoxin
Which of the following is not a mechanism by which viruses cause cancer?
A. They carry cancer causing genes into the cell
B. Encode cancer causing genes
C. They produce defective interfering particles
C. They produce defective interfering particles
mRNAs that direct synthesis of more than one polypeptide are known as: A. Inteins B. Monocistronic C. Polycistronic D. Exteins
C. Polycistronic
During replication the two strands on the DNA molecule are unwound by: A. Ligase B. Helicase C. Primase D. Polymerase
B. Helicase
The region at which RNA polymerase binds is the \_\_\_\_\_ region A. Leader B. Promoter C. Coding D. Trailer
B. Promoter
Which of the following is not a method of genetic variation used in bacteria? A. Mutation B. Opsonization C. Transduction D. Transformation
B. Opsonization
The site on which a repressor protein binds is the: A. Operon B. Promoter C. Operator D. Regulator
C. Operator
Which of the following is not a regulatory mechanism used to control the Trp operon in E. Coli? A. Catabolite repression B. Repression C. Attenuation D. None of the above
A. Catabolite repression
Removal of the methyl group from methyl accepting chemotaxis proteins by CheB results in the continuation of a run (true or false)
True
Conjugation differs from reproduction because conjugation
A. Replicates DNA
B. Transfers DNA vertically to new cells
C. Transfers DNA horizontally to cells in same generation
D. Copies RNA to make DNA
C. Transfers horizontally to cells in same generation
A \_\_\_\_\_ strain is one in which an F plasmid is integrated into the host chromosome and as a result its genes are often donated to the recipient during conjugation A. F' B. F+ C. F' D. Hfr
D. Hfr
What is the fate of pyruvic acid in an organism that uses aerobic respiration?
It is converted to acetyl coA
A strictly fermentative bacteria produces energy by:
Glycolysis only
