Microbio

Describe RNAi and explain its applications.

RNAi (RNA Interface) and it is where small pieces of RNA can shut down protein translation by binding to the messenger RNAs that code for those proteins.

Describe shot-gun sequencing and explain the role of bioinformatics.

Shotgun sequencing is a way for determining the DNA sequence of an organism's genome. It involves breaking the genome into a collection of small DNA fragments that are sequenced individually; In bioinformatics is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of methods to understand its features, function, structure, or evolution.

Describe genomic and cDNA libraries and explain ow do you screen them.

A library is a convenient storage mechanism of genetic information. is representative of the organism's entire genome. cDNA library is representative of the organism's exonic regions, meaning that only the coding regions of the genome are recorded and stored in the library. You screen them once a particular DNA fragment is identified. If we know the partial sequence of a gene and want to determine its entire sequence, the probe should contain the known sequence so that the detected DNA fragment can contain the gene of interest.

Describe how to do an Ames test and explain what type of information can be gained.

Ames test it is a biological assay to assess the mutagenic potential of chemical compounds. It utilizes bacteria to test whether a given chemical can cause mutations in the DNA of the test organism. To do the test you put it on a plate and watch for growth.

Describe three different methods that can be used to insert DNA into cells.

The three different methods that DNA can be inserted into the cells are Conjugation (Conjugation is the transfer of DNA directly from one cell to another through cell-cell contact), Transformation (comes from dead bacteria lysing (splitting open) and releasing their genetic contents into the surrounding area.), and Transduction (the transfer of DNA from one cell to another by a virus)

Describe the three steps of translation.

The three steps of translation are initiation: The ribosome assembles around the target mRNA and the start codon 5' AUG is recognized. Elongation: The tRNA transfers an amino acid to the tRNA bound to the next codon, forming a peptide bond between the two amino acids. The ribosome then translocates to the next codon to continue the process, creating an amino acid chain in the direction from the N terminal to the C terminal. Termination: When a stop codon is recognized, the elongation of amino acid chain terminates. The ribosome then folds the polypeptide into its final structure.

Describe the regulation of the trp operon.

The trp operon is regulated by the trp repressor, When the repressor binds to the DNA of the operator, it keeps the operon from being transcribed by physically getting in the way of RNA polymerase, the transcription enzyme.

Describe the three steps of transcription.

Transcription takes place in three steps which are initiation (It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ''read'' the bases in one of the DNA strands.), elongation (the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs.), and termination (RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.).

Describe the composition and uses complex, reducing, selective, differential, and enrichment media.

Complex media is giving the bacteria everything they need to grow but not specific about the amounts so from batch to batch there is variation, reducing media gets rid of the oxygen making it possible for the bacteria to grow, selective media you are going to suppress organisms you do not want to grow, differential media allows you to distinguish them from one another, and enrichment media encourages growth of certain types of media and suppress other you are going to have a mix of bacteria.

Describe the four principles of effective disinfection and explain why they are important.

Concentration of disinfectant more is not always necessarily better if you have too much it interferes with itself and it don't have enough it not going to do anything., organic matter, pH, Time. These are important

Describe the CRISPR Cas9 system.

Crispr is a system that functions like our adaptive immune system once the bacterial cell knows that a bacteriophage has infected it it will send out an operon and it's going to degrade it before it has a chance to duplicate and takes a piece of that bacteriophage and memorizes it so it can attack quicklier if it comes back.

Describe how you clone a gene in bacteria and explain how you select for the clone.

DNA cloning is the process of making multiple, identical copies of a particular piece of DNA. You do this by cutting open the plasmid and pasting in the gene, then you Insert the plasmid into bacteria which then grow up lots of plasmid-carrying bacteria and use them as factories to make the protein. You select a clone by detecting its protein product expressed in the bacterial cell.

Describe DNA fingerprinting and explain how it can be used to identify microorganisms.

DNA fingerprinting is a method of isolating and identifying variable elements within a sequuence of DNA. It provides us an overall profile of the microbial community, and some can be used to identify subsets of the microorganisms present.

Describe DNA replication, in your answer include the functions of the proteins involved.

DNA replication is where you make two identical DNA's which happens in 4 steps one being the double stranded molecule being "unzipped" into two single strands. Step two is once the DNA strands have been separated, a short piece of RNA called a primer binds to the 3' end of the strand. Step three DNA polymerases is responsible for creating the new strand through a process called elongation, the lagging strand begins replication by binding with multiple primers DNA polymerase then adds pieces of DNA, called Okazaki fragments, to the strand between primers. Finally, the fourth step is Once both the continuous and discontinuous strands are formed, an enzyme called exonuclease removes all RNA primers from the original strands. These primers are then replaced with appropriate bases. DNA ligase joins Okazaki fragments together forming a single unified strand. The ends of the linear DNA present a problem as DNA polymerase can only add nucleotides in the 5′ to 3′ direction.

Describe the effect of halogens, heavy metals, antibiotics, aldehydes on microbes.

Halogens go off to the membrane and proteins so either alter membrane or stop synthesis of proteins. Chlorine Heavy metals such as ag hg cu zn because they release ions that interfere with the growth of the organisms Antibiotics: defense mechanism against other Aldehydes thye have functional groups that have proteins that make the act on them in way that lets them not derade

Describe the regulation of the lac operon in the presence of both glucose and lactose.

If both glucose and lactose are both present, lactose binds to the repressor and prevents it from binding to the operator region. The block of lac gene transcription is thus lifted, and a small amount of mRNA is produced. But since glucose is still available, the need for B-galactosidase and galactoside permease is limited.

Describe transformation, conjugation and transduction in bacteria.

In transformation, a bacterium takes in DNA from its environment, often DNA that's been shed by other bacteria, If the DNA is in the form plasmid, it can be copied in the receiving cell and passed on. In transduction, viruses that infect bacteria move short pieces of chromosomal DNA from one bacterium to another by accident. In conjugation, DNA is transferred from one bacterium to another. After the donor cell pulls itself close to the recipient using a structure called a pilus, DNA is transferred between cells.

Describe the three physical methods used to control microbial growth.

Ionizinig radiation right a Membrane permeability, damage to proteins target enzymes we use a drug that would effect them and not us , and damage to nucleic acids it would dmage it furthering it from diiding.

Discuss the oxygen requirements for obligate aerobes, facultative anaerobes, anaerobes, aerotolerant anaerobes, and microaerophiles.

Obligate aerobes need oxygen to survive so if there is not enough oxygen around it will not grow, Facultative anaerobes can grow if oxygen is present but also possible to grow with limited amounts of oxygen, Obligate Anaerobes oxygen is toxic to them so they will not grow when oxygen is present, Aerotolerant anaerobes tolerate different concentration of oxygen but prefer concentration amount that is less than the atmosphere.

Describe the effect of alcohols, bisphenols, biguanides, phenol and phenolics on microbes

Pheno and oehnolitics go after the plasma membrane as well as bisphenols but depends on the composition of the plasma membrane on whether they will be effective or not. Biguanides go after the permeability of the plasma membrane. Alcohols cause proteins to denature but only work if there is a suffiecen t amount of water present

Describe the structure and function of plasmids.

Plasmids are used in genetic engineering to amplify, or produce many copies of, certain genes. They are made up of circular double chains of DNA.

Describe how plate count, filtration, most probable number, direct microscopic counts and turbidity are used to determine the number of microorganisms.

Plate count is set up a serial dilution where you take the organism and dilute it out and plate it and you are spreading out the bacteria down to a range, we can count so 30-300 colonies on a plate. Filtration is when you take a known volume of water and run through a filter and it captures the bacteria then you put it on a petri dish and it should grow up as a single colony and do the math knowing the number of bacteria that are there and the amount of water used. Most probable number is take tubes an inoculate and look for either growth r no growth and depending on how many tubes have growth and how many don't and it gives you an estimate about how many microorganisms were present in the ample, microscopic counts you take a known volume of fluid and put it on a microscope slide with a grid on it and you set up rule to count and then you count 7 grids and you calculate an average, And in turbidity you have a light source so the more bacteria the less light comes through and vice versa.

Describe PCR.

Polymerase chain reaction is a method widely used to rapidly make millions to billions of copies of a specific DNA sample. Happens in four steps Initialization, Denaturation, Annealing, and Elongation or Extension.

Describe southern blotting and explain how it can be used to identify microorganisms.

Southern blotting is a technique used to detect a specific DNA sequence it involves separating DNA fragments based on size through electrophoresis, transferring them to a membrane, hybridization with a labeled sequence, washing, and finally detection of labeled DNA.

Describe the regulation of the lac operon.

The activity of the promoter that controls the expression of the lac operon is regulated by two different proteins. One of the proteins prevents the RNA polymerase from transcribing (negative control), the other enhances the binding of RNA polymerase to the promoter (positive control).

Describe the five different types of mutations that can occur and the potential effects to the organism.

The five different types of mutations are missense mutation (when a single nucleotide gets changed in your DNA changing the amino acids), nonsense mutation (you've mutated the codone form an amino acid to a stop), silent mutation (happen in the wobble position so it changes the DNA but not the amino acid), insertions (you add one nucleotide), and deletions (you remove one complete nucleotide.), this affects all the amino acids after it.

Describe the four conditions that play a role in the effective treatment of a microorganism and explain why they are important.

The four condition that play a role in microbial death are number of microbes, time of exposure the longer the better and the shorter it's not going to be as effective, environment, and microbial characteristics such as what does it use what does it do so we know properly what will kill it and what wont such as if it's a thermophile what would normally be high might be ok for that organism..

Describe the four phases of bacterial growth and explain what is happening metabolically during each phase.

The four phases of bacterial growth are lag phase (is the transfer of the bacteria to fresh media that has plenty of resources to divide), log phase (is where they divide every 20 minutes until they don't have any more resources.), stationary phase (they are not dividing because of they ran out of resources but they also have not begun to die.) and death phase is when they being to die.

Describe the physical and chemical requirements for microbial growth.

The physical requirements are temperature (the optimal temperature is needed so it does not denature), pH (changes the ion concentration which will mess with the proteins which impacts metabolic function), and osmotic pressure (maintains water balance if you are losing to much water or gaining to much water it can also affect your metabolic process too much water and you could burst open. Now the chemical requirements are carbon (needed because it is base for all the macromolecules), nitrogen, sulfur, and phosphorous these are a part of the carbon skeleton, Trace elements (we only need small number of certain elements), oxygen (depends on their metabolic capabilities), organic growth factors (need vitamins, enzymes that help maintain functionality).

Describe how the disc diffusion method can be used to determine the effectiveness of a chemical against a microorganism.

he disk diffusion method what you do here is take bacteria one type and spread it all over the plate and what you want to end up with is along a bacterial growth so here when I'm trying to get isolated colonies or trying to get separation we just want to watch it bacteria growing on the plate then what you do is you take this and you soak them either in different concentrations of a chemical or different chemicals and you put those on the plate and you allow them to grow so you can look at this for chemicals or you can do this antibiotics they're going to do both of those experiments this semester as well we're going to take some chemicals when it takes some anabolics are in spread bacteria on a plate and we're going to look at which bacteria are susceptible to which chemicals and winter susceptible to certain standards