Unit 3 Micro test

Define Biochemical regulation

A process that prevents the synthesis of unneeded small molecules

True/False: organisms are rarely in starvation mode

False; They are usually in environments that a low on nutrients

Overtime the ribosomal subunits assemble around the mRNA and it moves from one codon to the next how many ATP's does it cost to move on?

1 ATP

What is the cost to attach each amino acid to its tRNA?

1 ATP

What is cAMP?

a signaling molecule

What is the size range of plasmids

1-1000 kbp

True/False: All plasmids are relatively the same size

False; They vary greatly in their size as well as physical properties

define negative supercoiling

this results from the underfunding of DNA (typical)

How is DNA packaged together? The structure that packages them together along with the DNA is referred to as:

with proteins; The nucleoid

State the reasons why biosynthesis reactions are expensive

- Putting pieces of molecules together usually requires energy in the form of ATP -Reduction reactions are often required using NADPH as an electron donor (each NADPH is roughly the equivalent of using 3 ATP) -The needed building blocks are often pulled out of the central metabolism preventing these carbons from bing oxidized to CO2 and as a result causing less energy to be released... loss in ATP

Describe the following biogeochemical cycles: Carbon Nitrogen Phosphorous And state whether there are other nutrients and other elements that can circulate give some examples.

-Carbon: photoautotrophic bacteria fix CO2; and heterotrophs release it Large geological reservoirs turn over slowly, however, carbons move quickly through living things -Nitrogen: Multiple redox states of N (such as NO2, NO, NH3+, etc.), Nitrogen moves through soil, water, and air Degradation of organic N from biomass releases ammonia, Ammonia (in fish poop) oxidized (by bacteria) to nitrite for energy, Nitrite is oxidized to nitrate for energy, and Nitrate N can be used by plants. -Phosphorous (think minerals and rocks) : Mostly as a phosphate, removed from rocks and then cycled throughout the ecosystem; one of the limiting nutrients in most environments - Various other nutrients and other elements: Sulfur, iron, and even mercury (can be cycled and can make things bad/ kill things off/ become fatal with the biogeochemical cycle)

While some components of viruses are essential, some are not necessary but they can be present list and describe these components

-Envelope: Piece of organelle membrane or cell membrane covering capsid, This usually contains viral proteins, this make the virus susceptible to some disinfectants -Spikes (peplomers) extend from the envelope~ These are proteins used for attachment and escape -accessory enzymes~ reverse transcriptase (an enzyme that catalyzes the formation of DNA from an RNA template in reverse transcription) -Matrix proteins~link core to viral envelope

explain how biofilms can be problems in both the industrial setting and medical setting

-Industrially: can plug pipes, stimulate corrosion, and impair the heat exchanges This can cause biocides to be less effective because only the surface layers are killed. Ex. waste in a pipe eventually a thick biofilm will form and clog the pipe -Medically: Infections can lead to the colonization of artificial structures. It is very difficult for antibiotics to completely ride the infection Ex. Heart valves can seed infections elsewhere in the body and cause the build up in blood vessels like the pipes.

* look up in more detail Name and describe the three main stages of translation:

-Initiation: This occurs while transcription is in process. It requires 30S subunit, mRNA, first tRNA, GTP, and proteins. First the tRNA carries N-formyl-methionine, and binds to AUG and then the 50S subunits joins to make 70S ribosome -Elongation: A-tRNA binds to the A site forming a peptide chain which leads to the synthesis of a new amino acid; The energy driven ribosome moves allowing the tRNA-peptide into the P site and the A site become empty awaiting new tRNA. -Termination: stop codon: no tRNA binds; protein release factor finds empty A site and ends the process. 30-40 different rRNAs The Amino acid attaches to the 3' end and the anti-codon base pairs with the codon on the mRNA The Amino acid and the anticodon must mach each other for proper decoding.

Describe the process of gene expression from gene to protein:

-Regulation- determines whether the gene is used or not -Transcription- Making mRNA with genetic info -Translation- converting mRNA information into a string of covalently attached amino acids: polypeptides; converting information found in a pattern of nucleotides into a pattern of amino acids that requires ribosomes (made of rRNA and proteins with large and small subunits), tRNA

Name and define the five conformations of Plasmids

1. Nicked open-circular DNA- has one strand cut 2. Relaxed circular DNA- is fully intact with both strands uncut (the supercoils have been removed because it has been enzymatically relaxed) 3.Supercoiled (or covalently closed-circular) DNA is fully intact with both strands uncut and with an integral twist resulting in a compact form 4. Linear DNA has free ends 5. Supercoiled denatured DNA- has unpaired regions that make it slightly less compact than the supercoiled DNA Look at rubberband analogy

List the three main mechanisms by which Plasmids can be transferred from one bacterium to another and define each

1.Transformation- the taking up of "naked" DNA from a solution. 2.Transduction- The transfer of DNA from one cell to another by a virus; bacterial DNA from one cell to another 3.Conjugation- The direct cell to cell transfer of DNA; the plasmid may be transferred from one bacterium to another via sex pili encoded by some of the tra genes; may be the most important because it allows the transfer of genes from two unrelated organisms; very wide spread; requires direct cell cell contact; the donor attaches to the other bacterium; pills contracts bringing the cells into contact with each other to allow the DNA to transfer from one to another.

what is the average molecular weight of an amino acid? If you have a protein that consists of 500 amino acids, how many bases code for an amino acid? How many bases long is the mRNA for this protein?

100g/mol; each amino acid codon for each amino acid is 3 bases long and so the actual genetic information for one protein in the mRNA is 1500 bases in size

Translation has an additional cost to the original energy used for translation and this energy cost is ...

2 ATP per codon translated

What is the cost each time a base is added to mRNA? And what is the coroughlyst of making an mRNA that codes for one protein.

2 phosphate groups which is the equivalent of losing 2 phosphates from an ATP, so the cost to assemble this one mRNA molecule is 3000 ATP (this does not include the cost os assembling the nucleotide themselves from simpler molecules)

Name and define some characteristics needed on a naturally occurring plasmid to convert it to an artificial plasmid that can be used as a vector in genetic engineering. The gene to be replicated is normally inserted into a plasmid that has these qualities.

A gene that confers (gives) resistance to particular antibiotics (ampicillin most frequently used for bacterial strains) , an origin of replication to allow the bacterial cells to replicate the plasmid DNA and a suitable site for cloning.

The Open reading frame (ORF) is...

A section of DNA that when viewed as a mRNA has an AUG codon, multiple bases in groups of 3 and a stop codon; it has the potential to be translated ; on either sides of this open reading frame is DNA that is transcribed but not translated known as the untranslated regions (UTR); This is the actual coding information/ the actual information for making the protein

Define Transposons

A small segment of DNA that is capable of replicating and inserting copies of DNA at random sites in the same or a different chromosome

Define Bacteriophage

A virus that parasitizes (infest or exploit- make full use of) bacterium by infecting it and reproducing inside of it; The phage attaches to a surface and injects its DNA

DNA and RNA or any kind of base paring is always done in an ______________________ fashion

Anti-parallel

What types of things are bacteria sensing in their environments?

Availability of nutrients in general concentration of specific nutrients - specifically glucose oxygen, temperature, osmolarity, and associated stress Population size of their own species Whether they are floating or attatched

describe the starvation responses

Bacteria is frequently on the verge of starvation because in natural environments there is not a ton of nutrients because although they are coming in as soon as they come in they are being immediately used up! The bacteria responds by: lowing the metabolic rates, making themselves smaller by increasing the surface area to volume ratio; Induction of low Km uptake systems (going 1/2 as fast as you can go you want this to be low) Release of extracellular enzymes, scavenging molecules , Production of resting cells, and spores

Why are yeast important on this test?

Because they are organisms that naturally harbor plasmids

Define Positive control

Binding of protein to DNA promotes transcription; you get more transcription

Define Negative control

Binding of protein to the DNA that prevents transcription; We see this a lot in bacteria

What is the C:N ratio in amino acids?

C:N; is 2.4:1 ratio almost twice as much nitrogen as the organisms needs.They have more Nitrogen in amino acids than you dietarily need; Meaning you take what you need and you get rid of the excess by putting the nitrogens in forms such as NH4 + which can be used as an energy source.

Define complementary pathways in microbial metabolism

Carbon: aerobes oxidize to CO2 which autotrophs use the fermenters produce organic acids that are usable by aerobes- They do not have to start with glucose

Define Dissimilation

Chemicals need as electron sources or sinks; because there is always a need for energy; When molecules are not taken up for biomass; They take the electrons and throw them away. These are pretty much limitless reactions because you don't want the reactions that make energy to stop. Taking hydrogen sulfide and making sulfate. These reactions happen as much as possible they happen at a large extent. These have a more effect globally because they occur more often. Goal is to release energy; Ex. electron sink reactions and energy source reactions

Define Biofilms

Communities of microbes attached to a surface This surface may be a nutrients source or neutral Organic molecules absorb to surfaces Cells use fimbraiae and slime to adhere The community is embedded in extracellular polysaccharides Multiple species are within this communities with different niches represented These communities are part of a food web they provide nutrients for protozoa Cels show different patterns of behavior than floating this changes in gene regulation (such as loss of flagella/ change in characteristics because they are now sesile not mobile) Cells move within the biofilm; The cells and pieces of the biofilm can leave and colonize in new areas. Once they become sesile they can regrow their flagella and become mobile again

List the ways that regulation is controlled

Control of transcription through the bindings of proteins to the DNA; Normally in bacterial cells the genes are turned on, however, in eukaryotes the genes are usually turned off until they are needed.

Define Central dogma

DNA must be replicated to continue the species. Transcription and translation use genetic information to make proteins

Define modulon

Different operons/regulons affected by the same environmental signal- the umbrella over operons and regulons Something major is occuring in the cell saying we need to do multiple things transcribe multiple genes at a time ex. Nutrient and energy supply: change in an available carbon specifically glucose, N or P limitation (without these you can't make nucleotides or carry out glycolysis)

Define Regulon

Dispersed genes or operons controlled by same signals; They are not physically adjacent to each other; The same protein controls them all still; related proteins, dispersed

True/False: Plasmids cannot be transferred from one bacterium to another

False

True/False: Viruses have a cytoplasm

False

True/False: The energy cost per amino acid is relatively constant

False, The cost per amino acid made vary wildly

True/False: The prevention of positive regulation is the same as inhibiting

False, While inhibiting is turning the gene off, the prevention of positive regulation is keeping the gene off that is already off. ex. glucose for the lac operon

True/False: A bacterium can acquire any plasmids handed to it with no effects or destruction of one of the plasmids

False, different plasmids can only exist in a single bacterial cell if they are compatible

True/False: The sporification process can be stopped easily at any point.

False, once you get to a certain point you cannot go back

True/False: microbes in your intestine are mostly strict aerobes

False: They are anaerobes

True/False: In bacteria the DNA is packaged by histone proteins just like in eukaryote DNA

False; Although it is still packaged by proteins they are not histone proteins

True/False: Large linear fragments migrate at various rates

False; Large linear fragments migrate at a certain fixed rate regardless of length

True/False: like Eukaryotes Prokaryotes have a lot of non-coding DNA sections:

False; Prokaryotes have a much higher proportion of genes; a lot less DNA "junk"; This is because they cannot afford to keep all the junk due to their energy supply

True/False: Most lab and culture media are Cholesterol-based.

False; Protein-based

True/False: Proteins do not cost a lot of energy to make so if the bacteria don't need them they are made anyways for storage purpose

False; Proteins take a lot of energy to make so if we do not need the proteins we do not make them.

True/False: RNA polymerases needs a primer

False; RNA polymerase needs a templates but NOT a primer; Primers are required for DNA synthesis not RNA synthesis. The template= section of the DNA being copied

True/False: Viruses are cells

False; They are particulate living entities - non-soluble but non-cellular

True/False: of the two strands of DNA; One is known as the sense strand and the other is known as the antisense strand

False; sense and antisense can alternate it just depends on what can be copied the quickest at the time; This is because you always go 5' to 3'

True/false: if you can stop the cell signaling of the bacteria you stop the bacteria from growing

False; you're stopping the production of harmful proteins

List the five main classes that classify plasmids by their function and state whether or not plasmids can belong to more than one of these functional groups.

Fertility (F)-Plasmids Resistance (R) plasmids Col plasmids Degradative plasmids Virulence plasmids Plasmids can belong to more than one of these functional groups.

How do you make any type RNA?

From genes in the DNA

Define Operon

Genes are physically adjacent and regulated together; controlled by a single protein

What happens within the spores?

Genes get activated during the sporification process and that creates a sigma factor that leads for another gene to get transcribed... The sigma factors allow for a thick cell wall to be produced?!! I don't know if sigma factors are supposed to mentioned here or if the right conclusion was made

Define repression

Genes that are normally in use are shut off when no longer needed, ties into metabolism ex. genes that make amino acids to make more proteins; you need to shut these off to conserve energy if you have a lot of proteins present; mostly when They are doing biosynthesis and they don't need this any more so they are going to turn these genes off

explain why genetic recombination is important and explain how it occurs in both eukaryotes and prokaryotes

Genetic recombination produces diversity in the population, necessary for evolution/survival. This is important because of changes that occur in environments conditions, and due to this genetic diversity some genotypes will be favorable and these species with the favorable genotypes will be better adapted to their environment will have a better chance at reproduction and continuance Eukaryotes: Sexual reproduction that allows combinations of genomes; specifically gamete production and crossing over through meiosis which allows for many genetic combinations each generation teachers new diversity Bacteria: they do not have sex or meiosis just binary fission resulting in daughter cells being clones of patrons the genetic recombination is separated from reproduction; Horizontal transfer is what provides the genetic diversity for bacteria.

What is the typical structure of an amino acid?

Has a carboxyl group and an amino group

List the ways in which episomes replicates

Herpesviruses- replicated in a rolling circle mechanism similar to bacterial phage viruses Others- replicates through a bidirectional replication mechanism (the Theta type plasmids) In either case episomes remain physically separate from host cell chromosomes In cancers these episomes passively replicate together with host chromosomes when the cell divides. These initiate lytic replication to generate multiple virus particles and they in feral activate cellular innate immunity defense mechanisms that kill the host cell.

What tells the RNA polymerase that it is done transcribing the DNA?

In some bacteria "Rho" binds to the DNA-RNA hybrid (when DNA and RNA are base-paired to each other) and destabilizes it thus ending transcription. Or the hairpin loop- it destabilizes the interactions between the DNA and the m RNA and the polymerase because the U-A pairs are very weak and the complex falls apart. Something weakens the bond and it falls off not being able to get back on after it leaves. Remember transcription is not codon dependent meaning that it does not start at the start codon or stop at the stop codon.

Explain what you need to know about corynebacterium diphtheriae

It is a gram positive pathogen that is dangerous because of its toxin. Virulent stains produce diphtheria toxin. This toxin is coded for by a prophage (corynephage) Integrase for inserting DNA- proteins for viral capsid and tail fibers are all present as well as toxin gene Association is fairly stable

What is the purpose of the Active cyclic AMP receptor protein (CRP)? AKA CAP (another word)

It is a protein that needs to bind to DNA to turn on the lactose operon (and other operons); This binding/ or activation of the protein is prevented by the presence of glucose; it is activated by the binding of cAMP(must have cAMP to be in its active form)

explain how E. coli O157: H7 is important on this test

It is responsible for very dangerous food poisoning Hemolytic Uremia syndrome= blood in urine because the kidney is being killed Shiga toxins- genes associated with a prophage two types: STX1 and 2 p0157 plasmid- gene for a protective catalase (breaks down peroxide and protects the organism from peroxide and other various proteins) and virulence proteins Former F plasmid? Insertion sequences may still be active. Dangerous because of toxic genes are acquired

define miniprep as a method to isolate plasmid DNA from bacteria

It is used to quickly find out whether the plasmid is correct in any of several bacterial clones. The yield is a small amount of impute plasmid DNA which is sufficient for analysis by restriction digest and for some cloning techniques

Explain how biochemical regulation works.

Key enzymes in metabolic pathways normally work so that the enzyme performing the first reaction is shut down by an abundance of the product of the pathway (not the product of that particular enzyme) this process is known as the end product inhibition or feedback inhibition. For this to work the enzyme needs to possess another site in addition to the active site (Where the substrate binds) this site is called an allosteric site (usually meaning other space)

Describe the less common lysogenic cycle (AKA lysogen) of bacteriophages

Lysogeny is an effective way to multiply the viral DNA, This occurs because some viruses do not readily lyse cells This is when the viral DNA inserts/incorporates into the bacterial chromosome becoming a prophage The bacterial replication also replicates the viral DNA The Prophage may bring new genes for use by the bacterium Damage to bacterial DNA prompts virus to begin lytic cycle, DNA excises (is cut out) , virus multiplies This arrangement can be stable long term

Do viruses reproduce asexually or sexually?

Neither, they only assemble

When the stop codon is in the A site of the Ribosome does tRNA bind?

No

If both glucose and lactose are present will the organism automatically start using lactose for energy by activating the lac operon?

No, They will use the glucose first until it starts depleting then the lac operon will be induced later when the lactose needs to be broken down. the bacteria grows slower when using lactose

Are all plasmids either non-conjugative or conjugative?

No, there is an intermediate class of plasmids that are mobilizable and carry only a subset of the genes required for transfer. They can parasitize a conjugative plasmid, transferring at a high frequency only in its presence.

Define vegetative cell

Normal cell not really growing or dividing

How do bacteria respond?

Numerous types of changes resulting from changes in gene expression- what genes are turned on or off Behavioral changes such as direction of swimming Stringent response- when you run out of amino acids Cellular differentiation- when cell's shape changes in starvation and causes spore formation- requires lots of genes Stress response- oxidative stress/ heat shock Aggregation/ cell-cell interactions- communication and quorum sensing

Define obligate intracellular parasites

Obligate intracellular parasites cannot reproduce outside their host cell, meaning that the parasite's reproduction is entirely reliant on intracellular resources.

What structure are Promoters and Operators located in?

Operon Structure

Various stresses such as what can affect the bacteria

Osmotic pressure, and heat

List the barriers that keep viruses limited to certain types of host cells

Species barriers: rabies is not specific but most are tissue type: rabies only affect nerve and salivary tissue Cell type: HIV infection mostly restricted to helper T cells, a kind of lymphocyte different characteristics of the host cell such as can the virus attach to the cell surface.

Define Promoter

The site on DNA recognized by RNA polymerase as the place to begin transcription; Where the RNA polymerase binds (What carries out transcription) - particular sequence that the polymerase recognizes.

What are the most commonly used bacterial cloning vectors? List characteristics of these cloning vectors as well as the process

Plasmids; contain a site that allows DNA fragments to be inserted (ex. a multiple cloning site or polylinker which has several commonly used restriction sites to which DNA fragments may be ligated (glued). 1. the gene of interest is introduced into the bacteria by transformation- these plasmids contain a selectable marker usually and antibiotic resistance gene 2. the cells are exposed to a selective media and only cells containing the plasmid may survive. ex placing the cells in an antibiotic solution that will not react or kill off cells with the selectable marker. Antibiotics act as the filter

Give examples where nutrients in the environment come from.

Polysaccharides and proteins are the most abundant nutrient in the environment The Terrestrial primary producers (lost of plants taking CO2 and producing organic material): Plants They provide storage products- Starch= Storage polymers of glucose and these are readily broken down enzymatically They also provide: Structural products- Celluloses, hemi-celluloses etc. These are harder to break down and different time scales- take a much longer time to break down

Define Genetic Regulation

Prevents the synthesis of the enzymes that make the small molecules Results in additional energy savings

Because living things are made of a ton of proteins, They must have an abundant amount of _________________ which break down the proteins.

Proteases- used to take advantage of all the proteins that are available

What is located upstream from the gene and what do they do?

Regulatory sequences that control whether transcription occurs

Define replicon and state its function within the plasmid;

Replicon= stretch of DNA that can act as an origin of replication or AKA self replicating unit.Replicon= Unit of DNA capable or replicating autonomously within a suitable host; .This allows plasmids to replicate independently/ autonomously

What are frequently used to analyze purified plasmids?

Restriction Digests where the enzymes specifically read the DNA at certain places to show sequences.

What is the monomers that make up the polymer RNA?

Ribonucleoside triphosphates: ATP, UTP, GTP, and CTP

What are the monomer units that assemble the RNA polymer?

Ribonucleoside triphosphates: such as ATP, UTP, GTP, and CTP; These supply power for the reaction; only one phosphate there 2 are popped off in the formation of the polymer. cost of about 2 ATP every time

Define genomic islands

Sections of DNA that are "separate" from genome They have been acquired in evolutionary history, recently or a long time ago they are not found in all members of a species They contain one or more genes that assist the bacterium in pathogenicity, adaption to an environment, etc. They are or once were mobile, they are often bordered by (flanked by) direct repeats Pathogenicity islands are involved in infections When the average G and C percentage changes abruptly it gives us an indication of some insertion event An individual will pick up the genes and multiply then it will produce two daugher cells "clones" with the same gene info

Define and describe Quorum Sensing.

Sensing whether or not your population is at threshold levels Examples: Pathogenesis- Bacteria monitor their own population size. Pathogenesis do not produce important molecules too soon to tip off the immune system- they do not produce proteins quickly they wait until they have the proper numbers to actually have an effect on the population Light production- Light takes energy; lots of it; The issue here is that one single bacterium cannot make a lot of light; So you must have enough individuals to contribute/ add tougher to make a light that can be seen. Don't wanna spend ATP in vain Bacteria form spores when in high numbers, avoid competition between each other; All of them are clones of each other they are fighting each other and fighting for nutrient; This allows them to sense that there are a lot of them there and so they become spores to avoid killing each other off System requirements: A signaling molecule that increases in concentration as the population increases; A Low molecular weight substance They must also have a receptor so that they can get the information from the other cells. Ideas for antibiotics where if you can stop the signaling you could possibly stop the infection before it becomes bad

List some primary differences in the way that small plasmids replicate and larger plasmids replicate

Some small plasmids make use of the host replicative enzymes to make copies of themselves. Larger plasmids may carry genes specific for the replication of those plasmids.

define stringent response

Stringent response- bacterial response to rapid drop in nutrients such as a drop in amino acids this is triggered when an empty tRNA binds to ribosome. RelA component (realizes that the t RNA comes up empty) generates alarmones- These are signaling molecules that lets the rest of the cell know there is a problem. ex. ppGpp is a global controller signaler that turns on and off a lot of genes ppGpp turns on/off several genes Multiple effects to stop growth: stops proteins synthesis, cell division, synthesis of new DNA, lipid synthesis these all stop so that all the resources can be diverted into amino acid synthesis. After the amino acids are back then the bacterium resumes growth at appropriate rate.

What does it mean for genes to be in operons? Are operons present in Eukaryotes?

That they are located together, regulated together, and are transcribed together. An efficient way to make a protein. One segment of mRNA codes for more than one protein usually. This makes the process more efficient. these genes are physically grouped together and have the same regulatory control for the whole group Eukaryotes do not have operons.

What part of the tRNA binds with the codon on the mRNA?

The Anticodon

DNA is negatively super coiled in the bacteria Chromosome structure. Describe what this means

The DNA is slightly under wound by the enzyme Topoisomerase (the enzyme responsible for determining the shape of the DNA). This negative under wounding makes separation of strands easier during transcription. This super coiling creates twisted loops. This supercoiling regulates the access to the DNA.

define Sense

The Strand of the DNA that looks like the mRNA (the only difference is that T and U)

What happens when the bacteria is low on glucose and lactose is present?

The adenylate cyclase is activated, and cAMP is abundant, The cAMP binds to the CRP and the complex binds to the DNA and promotes transcription of the lac operon. Eventually resulting in the proteins:lacZ, lacY, and lacA

Define heat shock proteins

The are proteins that help to protect and repair other critical proteins in the cell. Heat and other environmental stresses turn on genes for these protective proteins.

Define Virion

The complete infective part of a virus outside of a host cell (core DNA or RNA and capsid)

Define degradative plasmids

The enable the digestion of unusual substances ex. toluene and salicylic acid

define mobilome

The entire set of mobile genetic elements; analogous to genome and proteome, "element": some piece of DNA that can behave as a unit Can be extrachromosomal (such as a plasmid) or part of the chromosome; some elements can transition between being part of the chromosome and being extrachromosomal These can exist as transposons, phages, and individual genes, larger elements are made of these smaller elements, and they can be passed between cells by different mechanisms.

Describe the cooperation of faculatative anaerobes and strict anaerobes within pond water

The facultative anaerobes consume oxygen, maintaining an anaerobic environment for anaerobes.

Define induction

The genes are turned off until they are needed, ties into metabolism; ex. genes that break down lactose only needed when lactose is present; normally in catabolic enzyme genes (what break things down), mostly involving negative regulation, genes normally off are turned on; The negative control being removed by the binding of an inducer to a repressor which acts as a small molecule binding to a protein (because that is what it is) this causes the repressor to shift shapes and leave the DNA strand; Inducer= what the proteins break down; it induces its own break down; most of the time... sometimes this isn't the case such as the lac operon.

Define horizontal gene transfer

The host to host transfer of genetic material by mechanisms such as transformation, transduction, and conjugation; genes are passed to others that are not their offspring or part of their family tree. These include: Genes for infecting a host, Genes for metabolizing compounds, and Genes for antibiotic resistance Genetic elements that can be exchanged horizontally with others = collectively called the mobilome This is what provides the genetic diversity in bacteria This can occur by use of plasmids, prophages, islands, random DNA, and transposons which can all be transferred by transformation, transduction, genomic transfer agents, and conjugation.

define ecology

The interactions around living things and their evironments

Define Operator

The location where regulatory proteins bind; some inhibiting proteins bind here preventing transcription and others can bind that promote transcription.

Describe the life cycle of a virus

The manner of infection and reproduction depends on whether the host is prokaryotic or eukaryotic: 1. Adsorption= following contact molecules on surface of viruses bind to particular molecules on host cell 2. Penetration= the nucleic acid must get access to the machinery of the cell to replicate In Eukaryotes this happens by endocytosis and in prokaryotes this occurs by injection 3.Synthesis/replication= once inside the cell the nucleic acid issues orders that lead to replication of the nucleic acid and transcription (usually) as well as translation, this produces the necessary proteins such as lapsed proteins and spikes etc. 4. Assembly= a spontaneous process where the capsid proteins and nucleic acid combine to make virion this is a cheap but highly inefficient process 5. Release= successful parasite must spread to others; viruses cause lysis of cell or push through the cell membrane and the virions may acquire an envelope Many eukaryotic viruses are released by budding including HIV and influenza

explain why staphylococcus aureus is important on this test

The specific organisms that contain the SCC mec- which is the strand of DNA that is a genomic island containing resistance genes (staphylococcal cassette chromosome)- encodes mega complex This includes genes for regulator proteins and for PBP2, a penicillin (oxacillin and methicillin) resistant transpeptidase (an alternative to peptidoglycan that is resistant to penicillin) It also encodes car genes that codes for recombinases that are responsible for precise excision of element, probably need for transfer. It is composed of plasmids, IS, and transposons There are at least 6 different types; erythromycin resistance This makes it hard for someone infected with this bacteria to get rid of them

Define Antisense

The strand of the DNA that is copied complimentarily to mRNA

What is mRNA used for?

The synthesis of proteins

Define Translation

The synthesis of proteins by ribosomes using information in an mRNA, The genetic code specifies the information; The tRNA converts info from code of nucleotides to amino acids; Ribosomes act as work bench and enzymes

Contrast the mRNA in bacteria with that of eukaryotes

There are no introns (Arachaea have these), no 5' cap or poly- A tail ( it does not need this protection when exiting the nucleus because there is no nucleus), There is an immediate initiation of translation while transcription is sill in progress (in bacteria/ prokaryotes)

What is the result of the inhibitor binding to the allosteric site?

There is a shape change in the protein that distorted the active site and prevents the conversion of the substrate to the first product in the pathway. This then stops the chain reactions from occurring. This is because the product from this first enzyme was the substrate for the next enzyme and without a substrate the reaction or the enzyme substrate complex cannot be formed and no product can be produced.

What happens with the concentration of the product drops and the first enzyme of the metabolic pathway has been "turned off" due to an inhibitor in its allosteric site?

There will be less binding of that molecule to the allosteric site of the first enzyme resulting in increased activity of the enzymes with the final result being a return of sufficient need product to meet the cell's needs.

Extracellular molecules

These are important because polymers are too large to enter the cells these include: proteins, starch, cellulose which are all valuable nutrients Enzymes produced and released from the cell- These break down the polymers into Low molecular weight molecules that can be taken up and the nutrients can be absorbed this is a good way to reduce energy spent on making nutrients because the nutrients gathered exceed the energy cost. Ex. of low molecular weight aids (movers) -Siderophores= hemolysins collect iron/ binds and transports Antibiotics may slow the growth of competition when nutrients are in short supply (They get sent out)

Define isogenic human disease models

They are a family of cells that are selected or engineered to accurately model the genetics of a specific patient population, in vitro. They are provided with a genetically matched 'normal cell' to provide an isogenic system to research disease biology and novel therapeutic agents.

Define catabolic plasmid

They are giant bacterial plasmids that encode vast arrays of catabolic gene clusters.

Define Virus

They are intimate parasites that are not made of cells (meaning they are in violation of cell theory) They do not grow but they self assemble; They do not metabolize but they steal energy; they cannot reproduce without a host cell; can evolve over time; some can respond to environmental stimuli they have a complex organized structure; It is debatable if they are alive or not

Define Riboswitches and list their main functions

They are switches and ribo= RNA; 5' UTR (untranslated region) region= aptamer= stretch of nucleic acid that binds to a specific protein ; The secondary structure binds to a small molecule and affects the rest of the mRNA; Could form premature transcription termination, block ribosome binding site, cause mRNA to self-destruct- all three are controlling transcription/ controlling gene expression. These are structures that form within the RNA

Describe what artificial plasmids are used for

They are used as vectors (conveying DNA or genetic information from one organism to another) in molecular cloning by serving to drive the replication of recombinant DNA sequences within host organisms

Define non-conjugative plasmids

They can be transferred only with the assistance of conjugative plasmids.

Describe the structure of a ribosome and list its function.

They consist of 3 types of rRNA and dozens of proteins They exist as two subunits (the small and the large) that combine together The rRNA acts as an enzyme to connect amino acids

Define conjugative plasmids

They contain a set of transfer or tra genes with promote sexual conduction between different cells. This is present in R and F plasmids

Define resistance (R) plasmids

They contain genes that provide resistance against antibiotics, poisons, or heavy metals

Define Fertility (F) -plasmids

They contain tra genes ( they are conjugative plasmids) They are capable of conjugation and result in the expression of sex pili/ plus; The parts of an F-plasmid: transfer genes (tra genes), origin of transfer, replication genes, and origin of replication (important part of any DNA type)

While some plasmids are numerous throughout the cell and can be divided evenly into daughter cells during binary fission; some plasmids are known as single-copy plasmids. What must the single-copy plasmids have in order to insure that a copy is distributed to both daughter cells?

They must have systems that attempt to actively distribute a copy to both daughter cells such as parABS system and parMRC system. These are often referred to as the partition system or partition function of a plasmid

Define Virulence plasmids

They turn the bacterium into a pathogen

Most bacteria genomes are single, covalently closed, circular DNA molecules describe what this means.

This means that the DNA originates from a linear form and is ligated (glued) by DNA ligase to form a covalently closed ring. Alternative definition: a circular molecule of double-stranded dna which is supercoiled, or coiled up on itself due to internal tensions, because there are no breaks in the phosphate backbone (upon which the nucleotide bases are mounted) to relieve the tensions and allow it to form an open circle. Think about a really big plasmid- this helps describe the DNA structure. Negatively supercoiled- helps it to pack more tightly; it is an underwinding- double strand/ one strand is cut and then twisted the other way and then reattached, creating torsional stress. This doesn't happen naturally- has to be carried out by the enzyme topoisomerase- this does not change the chemical make up of the DNA but it does change the shape. This might make it easier to get the strands unwound for transcription.

What carries out supercoiling of the DNA?

Topoisomerases

True/ False: Something that dissociates the newly constructed mRNA from the DNA is going to act to stop transcription.

True

True/False: Bacterial genomes have about a dozen or so "transposable elements" meaning that they can move from one place to another; a bacterial genome has a dozen or so jumping genes which are pieces of DNA that copy themselves the DNA either cuts out, inserts elsewhere or copies itself and the copy inserts elsewhere. Some are simple insertion sequences which code for transposes and repressors and some are composite transposons where their insertion sequences flank other DNA which typically are antibiotic resistance genes.

True

True/False: Cells can go from being a spore to being a vegetative cell and vise versa multiple times.

True

True/False: Double stranded DNA and even transient DNA-RNA hybrids are antiparallel

True

True/False: Fermenting organisms will partially oxidize the sugars but aerobes can take these acids and oxidize them all the way down to CO2

True

True/False: In order to get the lactose operon released There needs to be both a positive and negative regulation.

True

True/False: Microbs have a huge impact globally even though they are extremely small

True

True/False: Most organisms have a 5:1 carbon:Nitrogen ratio

True

True/False: Promotors and operators are regulatory sequences

True

True/False: Proteins are a major energy cost because if cells are not provided with amino acids they must make them from whatever organic materials are available

True

True/False: The insertion of genetic elements often causes direct repeats to be generated. The past insertion of DNA can be recognized by the direct repeats that result.

True

True/False: The number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances

True

True/False: The presence of abundant or enough glucose prevents positive regulation of the lac operon

True

True/False: The rate of migration for small linear fragments is directly proportional to the voltage applied at low voltages. At higher voltages, larger fragments migrate at continuously increasing yet different rates. Thus, the resolution of a gel decreases with increased voltage

True

True/False: Viruses are limited to certain types of host cells

True

True/False: Viruses are obligate intracellular parasites

True

True/False: When you make mRNA the synthesis proceeds 5' to 3' just as in DNA

True

True/False: While Eukaryotes have repeated sequences; Prokaryotes do not have very many repeated sequences.

True

True/False: While prokaryotes, eukaryotes, and some viruses use DNA for their genetic material, bacteria and archaea differ in genome structure

True

True/False: While some Archaea have introns, bacteria have no introns

True

True/False: all living things are close to 50% Proteins in dry weight

True

True/False: in a modulon each operon has a specific repressor protein and an inducer but all respond to positive regulation by CRP

True

True/False: incompatible plasmids normally share the same replication or partition mechanisms.

True

True/False: plasmids can spread to unrelated organisms such as in the transfer of antibiotic resistance plasmids

True

True/False: The biochemistry of transcription is different in Eukaryotes and Prokaryotes

True: RNA polymerase binds directly to the promotor sequence by means of sigma protein subunit in prokaryotes

True/False: eggs can be used as an aseptic incubator (sterile environment) to grow viruses

True; The shell provides protection from bacterial contamination, These are used fro large batches of viruses for vaccines

True/False: Some bacteria can have linear DNA or have DNA in many pieces; not all DNA for bacteria is in the Single covalently closed circular form.

True; This is the type of DNA that humans have as well

True/False: DNA and RNA strands have 5' ends and 3' ends

True; This means that they are directional

Define Plaque Assay

Used for virus isolation, purification, and as way to measure the infectivity of viruses; Viruses and host cells are mixed The bacteria cover the pit dish as a "lawn" and eukaryotic cells cover the bottom of the dish. Multiplication of viruses leads to release and spread and to destruction of nearby cells. Vitale as holes, plagues, on bacterial lawn and eukarotic cells in culture are first stained for easier view to see plagues

Describe the relative size of the following: viruses, ribosomes, bacteria, plasmids

Viruses range from 20nm to 300nm Ribosomes 30nm smallest known bacteria are about 200nm plasmids are roughly about 100nm

define Sporulation

When cells slow down their metabolism and become resting cells; Some will change shape and develop a thick coat, Endospores form within cells and are very resistant. Spores are generally for survival NOT reprocution

Describe how the lac operon works

When lactose is NOT present, the cell does not need these enzymes, The lac repressor, a protein coded for by the lac I gene, binds to the DNA at the operator preventing transcription. When lactose is present and the enzymes for using it are needed, allocates bind to the repressor protein, causing it to change shape and come off the operator, allowing RNA polymerase to find the promoter and transcribe. Lactose is not actually the inducer; low basal levels of betagalactosidase exist in the cell. This converts some lactose to the related allocates which binds to the lac repressor protein. Think induction.

Define polysomes

When multiple ribosomes attach to the mRNA and begin translating. Some stings of ribosomes can be seen attached to the mRNA

Define Assimilation

When something is taken up and becomes a part of you; when the organism takes up a nutrient that it needs but that needs to be broken down for the organism itself ; Only takes up/ carries out the reaction that is needed to make another bacterium; The cell limits this reaction to limit energy loss; only does it when it needs to. Trying to make more cell biomass. Taking sulfate and making hydrogen sulfide

Describe the lytic life cycle (AKA lytic infection) of bacteriophages; Note that this is the life cycle of most bacteriophages

When they multiply then lyse the cell Viruses replicates its parts (nucleic acid and protein) the virus assembles into many new virions Then the bacterial cell lyses

Can regulation be fine tuned?

Yes

Does DNA code for tRNAs and rRNAs?

Yes

Does every type of organism have a virus that infects it?

Yes

Does prokaryotic DNA differ from Eukaryotic DNA?

Yes

Does supercoiling occur in both eukaryotes and prokaryotes?

Yes

Does the insertion of DNA elements alter nearby DNA?

Yes

Can plasmids be used in disease models? If so how?

Yes, developents in Adeno-associated virus recombination techniques and Zinc finger nucleases have enabled that creation of a new generation of isogenic human disease models. *explain in more detail

Can bacteria change the environment when metabolizing? If so, how?

Yes; Fermenting bacteria maintain low pH for themselves, Ecological succession ex. compost Aerobic bacteria use up the oxygen and anaerobes begin to grow Degradation in compost raises the temperature and thermophiles take over Fermentation lowers pH.

Can bacteria change their size due to being limited on nutrients?

Yes; You want to have a large surface area to volume area; This optimizes absorption; This is why cells are small; The smaller you are the greater SA to volume area there is; They can also get long and thin

Binding of small molecules to proteins can cause what?

a Shape change; This is characteristic of many DNA-biding proteins; can lead to increased binding to DNA or decreased binding to DNA; The binding of these proteins to DNA affects the amount of transcription- in many instances the binding of the protein decreases the amount of transcription that occurs; but still in some cases the binding increases transcription

define gene

a section of DNA with the information for making a protein or a mRNA

Define Gene:

a section of DNA with the information that is inherited that can be copied into RNA

Define Domain

a section of super coiled DNA; There are about 50 of these estimated to exist

Define plasmid

a small (usually circular) DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently; they often carry genes that benefit the survival of the organism; They are normally very small. They are "naked" DNA meaning that they do not encode the genes necessary to encase the genetic material for transfer to a new host, however, some classes encode the conjugative "sex" plus necessary for their own transfer; They typically provide a selective advantage under a given environmental state by carrying genes that provide resistance to naturally occurring antibiotics in a competitive environmental niche, or the proteins produced may act as toxins under similar circumstances, or by allowing the organism to utilize particular organic compounds that would be advantageous when nutrients are scarce; genetic elements that exist exclusively or predominantly outside of the chromosome and can replicate autonomously; almost always carry at least one gene; can provide bacteria with the ability to fix nitrogen; they are generally circular and linear plasmids require specialized mechanisms to replicate their ends ; They can also be used to make large amounts of proteins and can be used in genetic engineering in making things such as insulin (an inserted gene); often used to purify a specific sequence. 1-10% of the total genome.

What is a microenvironment

a variety of conditions in a small space such as a soil particle. Different metabolic types completing and complementing. oxygen available in some places but not in others.

Define bacteriocin plasmid

codes for bacteriocins= proteins that kill related bacteria

Define Niche

describes the location of the microbe and its function/ role in that location; The certain location can change the role of the microbe

True/False: Pure cultures exist naturally

false; They are laboratory artifacts this is because habitats support mixed groups of microbes/ no microbe is on an island; They both compete (nutrients are limited) and cooperate (waste for one = nutrients for another) These things are dynamic meaning what is happening over time.

What can plasmids be used for in Gene therapy?

gene transfer into human cells to potentially allow the lacking proteins to be expressed within the cells, some require the insertion of therapeutic genes at preselected chromosomal target sites within the human genome. Plasmid vectors are used for this purpose. Zinc finger nucleases (SFNs) offer a way to cause a site-specific double-strand break to the DNA genome and cause homologous recombination. these could help deliver therapeutic gene to a specific site so that cell damage and cancer causing mutations or an immune response is avoided

List the essential components of viruses

genetic material: could be double stranded DNA, Single stranded DNA, single stranded RNA or double stranded RNA They do not have a ton of genes because space is limited A covering: This is to protect the genetic material This covering is known as a capsid that is made of one or more proteins Capsid+nucleic acid= nucleocapsid

Define virulence plasmids

has the genes needed for the bacterium to infect the host

list the possible shapes for viruses

helical, polyhedral, and complex

Describe the benefits of cell culture

it allows for specific amplification and isolation the tissue homogenate with virions added to cell culture, viruses specifically infect and multiply in cells, The ratio of Virions to cellular material is compared to original sample greatly increase, virions lot and cells usually are attached Virions in large number can be more easily separated from cell debris This also allows for the creation of antiviral drugs and their effects can be tested under controlled conditions and answer questions such as will this drug prevent viruses attachment, replication etc.

Describe RNA polymerase

it is a multi-component enzyme- it has a quaternary structure many come together to make this machinery; polypeptides can pop on and pop off it needs a template (a DNA strand to copy - produce a complimentary DNA), but it does not need a primer In bacteria, a component (sigma- more than one of these) recognizes the promoter as the place on DNA to start synthesis- protein that is part of the polymerase that recognizes the start of a gene. - reads the DNA and tells the polymerase where to start- recognizes the beginning of the coding sequence that wants to be copied, There is many different types of sigmas in one organism; This is what gives the organism its flexibility on the types of genes that are going to be transcribed and translated.

some plasmids or microbial hosts include an addiction system or prostsegregational killing system what does it do? Do all biotechnological used plasmids contain this system?

it produces both a long-lived poison and a short lived antidote (remedy to counteracting poison; Daugher cells that retain a copy of the plasmid survive while the daughter cell that fails to inherit the plasmid dies or suffers a reduced growth rate because of the lingering poison from the parent cell. This prostsegregational killing system enhances the overall productivity of its host cell No, they do not contain toxin-antitoxin addiction systems and thus need to be kept under antibiotic pressure to avoid plasmid loss

Define maxiprep/bulkprep as a method to isolate plasmid DNA from bacteria

larger volumes of bacterial suspension are grown from which a maxi-prep can be performed, essentially a scaled up mini prep followed by additional purification production relatively large amounts of very pure plasmid DNA

list some wasteful activities that bacteria try to avoid doing. How do they accomplish this?

making unneeded enzymes ; by using biochemical (feedback inhibition of key enzymes) and genetic controls (DNA binding proteins controls transcription)

Define copy number and state how it is determined

normal number of copies of a specific plasmid that may be found in a single cell. This is determined by how the replication initiation is regulated and the size of the molecule

What is mRNA assembled from? And how many phosphate groups are lost each time a base is added?

nucleoside triphosphate monomer units ; two This is equivalent of losing 2 phosphates from an ATP

Define Genetic code

patterns of 3 bases (codons) indicating amino acids needed

Define cryptic plasmids

plasmids that have no observable effect on the phenotype of the host cell or its benefit to the host cell cannot be determined

Define integrative plasmids and state what they are referred to as occasionally within prokaryotes.

plasmids that insert into the host chromosome, however at some stage they exist as an independent plasmid molecule. Episomes -refers to the plasmid that is capable of integrating into the chromosome within prokaryotes

Bacteria are frequently attached to....... state why

soil particles, Polymeric debris (decaying leaf litter), and other bacteria This is because they seek associate with nutrient sources, They use fimbriae and slime to attach, they form pellicles at water surfaces and they grow clumped in lab

What migrates faster through gel and why? supercoiled DNA or linear and open-circular DNA.

supercoiled DNA because of its tight conformation

define tumor-inducing plasmid

the Tumor inducing plasmid (Ti plasmid) is found in Argobacterium tumefaciens. Codes for plant growth hormones. When the bacterium infects the plant cell, the plasmid is passed to the plant cell and the genes are expressed causing local overgrowth of plant tissue= gall. Very useful plasmid for cloning genes into plants. Plasmids can go from bacteria to plant

Define prophage

the genetic material of a bacteriophage, incorporated into the genome of a bacterium and able to produce phages if specifically activated. Mobile DNA element consisting of phage DNA This phage can transfer bacterial DNA from one bacterium to another via transduction There is evidence that this DNA got there from somewhere else and can be copied and moved else where- meaning it is part of the mobilome Some prophages remain active because of stimulations by DNA damages, and mutations which cause them to be terminate.

Define Bioinformatics software

these programs record the DNA sequence of plasmid vectors, and help to predict cut sites of restriction enzymes, and to plan manipulations. Ex. ApE, Clone manager, GeneConstructionKit etc.

Define col plasmids

they contains genes that code for bacteriocins= proteins that can kill other bacteria

define episomes when referring to eukaryotes

this is non-integrated extrachromosomal closed circulated DNA molecule that may be replicated in the nucleus. viruses are the most common example of this. Within Eukaryotes the DNA is sadly maintained and replicated with the host cell

When glucose enters the cell it is shutting down adenylate cyclase; What does this do?

this prevents the conversion of ATP to cAMP

What is the goal of biochemical regulation?

to shut down the enzymes that make the small molecules when the small molecules are not needed so that energy is not wasted on their synthesis

True/False: untranslated regions do not have codons

true; This is because a Codon is what codes for a specific amino acid on the mRNA following the start codon

What is the role of the GTP-dependent release factor (protein) in translation

when the stop codon is in the A site and no tRNA binds to it the GTP-dependent release factor (protein) removes the polypeptide from the rNA in the P site; basically releases the created protein from the ribosome.

Because cells are obligate intercellular parasites they require a host cell list some possible ways to grow viruses and explain them

whole organism such as animal models or human volunteers (humans require consent safety and pay) eggs organ/tissue/cell culture- this is minced tissue separated into cells by enzyme treatment that are grown in a sterile plastic dish with nutrient solution, cells are prepared this way grow only until the dish is covered then they stop. When growth stops you can scrape some off and move to another dish to continue growth but there are a limited amount of times that this can occur. Transformed cells such as ones with cancer properties grow faster. This cell culture is a major reason for advances in virology