Exam 3 MicroBio
DNA function and properties
- Genetic code for RNA and proteins - heritable and transferable molecule within cell - double stranded, anti-parallel, complementary base-paring
LOGOS
- a pictorial representation of a consensus sequence - larger letter means the more represented the nucleotides is - allows for all bases to be viewed
Avery-MacLod-McCarty experiments
- used heat killed smooth cells - isolate DNA, protein and others, mix with rough live bacteria to prove DNA is transforming substance
Zinc transport regulation
- used when the cell needs zinc - not used when the cell has a lot of zinc - Zur senses zinc and can act as a repressor if zinc is high in cell
E. coli will consume all the _____BEFORE it consumes any ______!
- uses the most energetically favorable substrate first answer: 1) Glucose 2) Lactose
Making cells competent in a lab
- using calcium chloride - electroporation (makes small holes in cells) -both of these work by destabilize the cytoplasmic membrane of the cell - but in nutrient rich environment so that cell can recover
Genetic transfer
- vertical gene transfer: transfer of genes from organism to offspring - horizontal gene transfer: transfer of genes bt cells in a manner other than traditional repo
Can you come up with an example of a mutation that would be beneficial?
-Acquisition of an antibiotic (bla) gene - allows survival in the presence of that specific antibiotic
Missense mutation
-Amino acid changed; polypeptide altered - different amino acid incorporated in translation or protein
Nonsense mutation
-Codon becomes stop codon; polypeptide is incomplete - Premature stop of translation - can result in a nonfunctional protein -most drastic and severe
Plasmids and Medicine: Diabetes and types
-Diabetes mellitus (DM) are metabolic diseases resulting from high blood sugar levels over a long period of time. -Type 1 DM: Failure to produce insulin -Type 2 DM: Failure to respond to insulin, insulin resistance (Adult onset)
Meselson-Stahl Experiment
-E.coli used Used isotope of nitrogen to change the weight of DNA N15 (heavy nitrogen) & moved cells to a N14 (light nitrogen) medium, demonstrated that the semi-conservative model is the best description of replication. - any new molecule synthesized will have n-14 nitrogen
lacY: lactose transport
-Lacy protein is a simple transporter - transport lactose into the cell across the cytoplasmic membrane
Mutant
A strain of any cell or virus differing from parental strain in genotype -TMNT
A) ________ is the main genetic element that is essential for the cell's survival B)_______is a extrachromosomal DNA element that encodes non-essential genes C)_______is a specific genetic element within the chromosome that encodes the information to make a specific RNA D)________is entire complement of genes in cell
A) Chromosome B) Plasmid C) Gene D) Genome
Which of the following uses correct genetic nomenclature when referencing the gene for the lactose simple transporter? A. lacY(i) B. lacY C. LacY D. LacY(i)
A) correct B) not italicized C) not italicized, capital L D) capital L
Which of the following uses correct genetic nomenclature when referencing the lactose simple transporter protein? A. lacY(i) B. lacY C. LacY D. LacY(i)
A) italicized, lowercase L B) lowercase L C) correct D) italicized
Which of the following uses correct genetic nomenclature? A. Vibrio Cholerae B. Vibrio cholerae C. Vibrio cholerae(i) D. V. Cholerae
A) species cap B) not italicized c) correct D) species cap
incorrect reading frame
moving +1 or -1 - result in incorrect translation
Prophage
When the DNA of a bacteriophage is recombined into the bacterial host's chromosome. (Non-replicating)
Theta replication
named because as replication proceeds around the single, circular chromosome, it takes on the appearance of the Greek letter theta.
what strand of DNA does RNA polymerase actually read to make an RNA transcript
non-coding/ template strand
genome size (#bases/Genes)
on average a bacterium will encode 1 gene for every 1k nucleotides within its genome
Replication
process of copying DNA prior to cell division
transcriptional regulation
regulates the amount of RNA that is produced in transcription - considered the most efficient form of regulation
Transcriptional Regulation of the znuABC operon is an example of what type of genetic regulation?
repression
Operons
sets of genes that are transcribed off a single promoter
most common sigma factor
sigma 70 RpoD - for most genes, factor for normal growth
Types of point mutations
silent, missense, nonsense
Bacterial genome size
small compared to multicellular organisms like humans (3bill base pairs) - average size of bacterial chromosome nucleotides is bt 2-4 million base pairs
The +1 site refers to what?
start of transcription
a38 rpos a54 rpon a32 rpoh
stress response nitrogen heat shock
Why is there a lag phase in between glucose and lactose utilization?
the cells are switch from using glucose to using lactose
Recombination
the exchange of genetic material between organisms - not involved in central dogma
consensus sequence
the most commonly occurring bases within a sequence element - can be used to find genetic motifs
repression and de-repression is not affected by
the presence of absence of glucose
coding strand
the strand of DNA that is not used for transcription and is identical in sequence to mRNA, except it contains uracil instead of thymine - T in DNA replaced with U in RNA - identical to the RNA sequence - 5 to 3
Central Dogma
theory that states that, in cells, information only flows from DNA to RNA to proteins
When would a bacterium repress the expression of znuABC?
high zinc
plasmids can be transferred
in horizontal and vertical gene transfer events - they are non-essential chromosomes - horizontal gene transfer: original plasmid cell makes copy and pass it to other cell
Transformation horizontal gene transfer
in which free DNA in the environment is taken up by a cell - can be with linear DNA fragments or circular plasmids -DNA fragments: can be degraded bc its seen as a invader -competent: bacteria that can naturally uptake DNA from environment (some cells can be forced to do this)
Types of Mutations
insertion, deletion, point mutations
When would the lacZYA operon be transcribed?
lactose present - this operon codes for proteins that used the disaccharide sugar lactose and the cell will only want to use its energy to make these when lactose is available
not involved in transcription
leading and lagging strands
Translation
mRNA converted to protein
purpose of many sigma factors
helps cell coordinate gene expression - uses sigma factor to transcribe genes
Transcriptional Regulation of the luxCDABE operon is an example of what type of genetic regulation?
activation
polycistronic mRNA and operons
allows for genes to be expressed at the same time and at similar levels
What type of mutations will lead to a change in the reading frame?
deletions and insertions
simple transport
driven by the energy in the proton motive force
Knowing where to bind?
each promoter region has its own unique DNA sequence
Lacz gene
encodes beta-galactosidase which breaks down lactose into glucose and galactose - glucose is then used in glycolysis (to produce energy)
LacA gene
encodes transacetylase - role is not fully understood
CAP-cAMP complex
enhances promoters affinity for RNA polymerase *CAP Protein will only bind to the lac promoter region when bound by cAMP
Transcription of genes and protein products is always on
false Ex: genes in flagella are not always on but when the cells needs to move
-10 and -35 meaning
genetic motifs are about 10 and 35 base pairs away from the +1 site - its an average and not always accurate
non-coding strand (template strand)
- 3 to 5 - strand of DNA that RNA polymerase reads
Which One Is Wrong? 5'-TACT A CGTAGCTG-3' 3'-ATGA G GCATCGAC-5' ch3 ch3
- A does not go with G - The new strand (non-methylated) needs to be fixed (A to C) DNA is not methylated Which strand is old (served as the template in DNA replication)? Older DNA is methylated Which strand is newly synthesized? Newly synthesized DNA is not methylated
Insertions
- Addition of DNA into the genome can be - Single nucleotide (one base added) - Whole gene(s) (lacZ)
general transduction and advantages
- Antibiotic Resistance Genes - Lactose Utilization Genes (lacZYA) (can use lactose as energy source)
CAP
- Catabolic Activating Protein - is an ACTIVATOR of the lac operon - recruits RNA poly to promoter region - only activates when there is NO Glucose
frameshift mutation
- Deletions or insertions that result in a shift in the reading frame - Often result in complete loss of function of protein
Mismatch Repair: Mut System
- Do not need to know every protein - recognizes error and replacing it with the correct sequence
Insulin
- E.coli was made to produce human insulin - amino acid composed of a and b chain (linked by disulfide bonds)
Bioluminescence
- LuxI: autoinducer synthase (makes autoinducer molecule) - LuxR: transcriptional activator protein (activated at high cell density) why: vibrio fischeri grow in the light organ of the Hawaiian bobtail squid. the light helps the fish evade predators while feeding at night (squid loses shadow)
Selectable mutations
- Mutations that result in a growth advantage/disadvantage under certain conditions/environments - Allows you as a researcher to selectively grow the mutant and isolate it from non-mutant strains.
Important Genetic Motifs
- ORI: ensure that cells copies and passes gene to new daughter cells - Antibiotic resistance: selectively grow cells -Gene of interest: the one your tying to express Promoter: driving transcription of gene of interest
Biodegradable plastics
- PHB is metabolized by bacteria in the soil - bacterial cells are transformed by plasmids to encode the enzymes to synthesize PHB
The Regions of the lac Operon - promoter - operator -CAP -Pi
- Promoter: The -10/-35 RNA Polymerase Binding Site -Operator: The binding site for the lactose sensor LacI -CAP: The binding site for the Catabolite Activating Protein (CAP) -Pi: The promoter for the lacI gene
Ribosome
- Protein:RNA Complex where amino acid subunits are linked together to form a protein. - Reads codons within RNA transcript
Deletions
- Removal of DNA from the genome - Single nucleotide - Whole gene(s)
+Glucose / + Lactose
- Same as +Lactose - operon is not repressed - RNA poly is not fully and consistently binding to promoter region - to fully turn on Lac operon and get lots of transcription of LacZYA the help of an activator protein is needed
+Glucose / No Lactose
- Same as - Lactose: Repression - LacI will not be bind to lactose and will repress transcription
If there is lactose present, does the cell transcribe the lac operon?
- The cell will not repress transcription and transcribe the Lac operon - De-repression event: repressor protein is no longer repressing -LacI: is bind to lactose and unable to bind to the operator region
Induced mutations
- Those made environmentally or deliberately - Result from exposure to external intervention
Spontaneous mutations
- Those that occur without external intervention result of: DNA Replication Errors - ~1/100,000,000 (10-8) - Repair enzymes decrease this rate to 1/10,000,000,000 (10-10)
UV light
- UV light mutates DNA - UV light induces thymine dimers (occurs with bases bind with adjunct nucleotide rather then complimentary base resulting in kink)
Stop Condon
- Uncharged tRNA Will Enter A-Site - Ribosome will Dissociate and mRNA and polypeptide will be released - does not encode for a amino acid
replication of DNA
- begins at origin (ori) - bi-directional - stops at termination site
diauxic growth
- cellular growth in two phases - E.coli second growth phase - instead of going into death phase like in a normal graph they go into a second growth phase
Spontaneous Mutation Rates
- changes based on genome size -higher eukaryotes like human have lower mutation rates - RNA viruses have high mutation rates bc poly to copy DNA do not have proofreading activity (no mistakes fix/permeant)
Plasmid vs chromosome division
- chromosomes must be copied to pass to daughter cells - Plasmid does not need to be transfer - plasmids can intergrade with DNA and will be passed in cell division
Phage
- composed of a protein coat and a DNA genome - bind to bacteria surface and inject their genetic material
Why regulate gene expression?
- conserve energy - express certain genes in an environment -efficiency: don't want to waste energy by creating unimportant proteins
Flow of genetic information
- expression: central dogma (DNA to RNA to protein) - Recombination: Transformation, conjunction and Transduction: flow of info bt cells of the same generation (horizontal gene transfer) - replication: parent to daughter cells
S. pneumoniae
- gram + - human pathogen - Two strains 1) smooth: capsule, virulent 2) Rough: No capsule, Non-virulent
Non-Selectable mutations
- harder to isolate from non mutant cells in population -Those that do not result in a growth advantage nor a growth disadvantage.
Recombinant DNA Technologies
- herbicide - insect resistant crops - crops that produce nutrient substance (Ex: golden rice) - HGH to help patients with pituitary disorders - blood clotting factor 8 - vaccines (ex: yeast to produce vaccine against the hep B virus)
RNA polymerase holoenzyme
- includes core complex plus sigma factor
Insulin production
- insulin production was induced by a non metabolized lactose analogue called iptg - two e.coli encode for a and b chain separately
Transcription Termination: Rho-dependent
- involves RHO protein - function is to stop transcription by separating RNA polymerase from template - Rho and RNA polymerase have the same speed and Rho catches up with poly hits termination sequence and stalls -Rho pulls RNA poly off template and transcription is complete
cAMP
- is produced in the absence of glucose -Acts as an alarm signal -Informs the cell that it is out of a key energy source
Mut System steps
- know old and new DNA base on methylation so errors need to be fixed before new DNA is methylated 1. MutS recognizes mismatch 2. MutH nicks dsDNA upstream of mutation on NON-METHYLATED STRAND 3. DNA is degraded on NON-METHYLATED STRAND, by a nuclease, past the site of the mutation 4. New DNA is synthesized by DNA Polymerase 5. DNA Ligase seals the ends of the newly synthesized DNA to the chromosome. 6. New DNA eventually becomes methylated
rolling circle replication
- linked with plasmid replication
quorum sensing
- mech bacteria use to talk to each other - regulation of gene expression as a response to cell population density changes
post-transcriptional regulation
- modification of protein - regulating the activity/function of produced proteins
Replication and speed
- multiple rounds can occur at once - allows cells to divide quickly - replication occurs very quickly
Plasmids and Research
- plasmids are mobile and Allow for the ectopic expression of non-native genes/proteins
16S rRNA
- prokaryotes - component of 30s - involved in translation initiation - contains anti-ribo binding site that helps ribo bind
RNA polymerase sigma factor
- recognizes specific DNA sequences within promoter region - tells if there is a gene that needs to be transcribed - recognizes -10 and -35 region (initiates binding of RNA polymerase to this region of DNA)
How do we know a cell was transformed?
- selection: If you grow your transformation on media with the antibiotic, only the cells that were transformed with the plasmid will grow. - Screen: If you grow your transformation on media without the antibiotic but look for cells that express GFP, all cells will grow, but the cells transformed with the plasmid can fluoresce green
DNA replication models
- semiconservative: parental strand separated into two strands (final product is new and old DNA) - Conservative: does not happen in cell (parental remains in tack)
point mutation (substitution)
- single nucleotide modification (one base)
wild-type strain
- strain isolated from nature - the strain is not mutated and serves as a reference - Ex: normal turtle
RNA polymerase reads
- the non-coding strand at a 3-5 direction - new complementary RNA is made in the 5-3 direction
Constitutive regulation
- transcriptional reg -always on - no regulation - functions that the cell needs to survive in any environment -Ex: rpod (rna polymerase)
Translation and the genetic code
-The synthesis of proteins from mRNA - catalyzed by the ribosome complex
Coupled Transcription & Translation
-Translation can begin before transcription terminates - means: once transcription is initiated ribo can bind and start translating even before RNA poly is done - multiple proteins can result from one transcript - possible bc bacteria does not have membrane bound organelles - transcription and translation occur in the same compartment within the cell (cytoplasm)
Fredrick Griffith Experiment
-Used S.pneumoniae - mechanism not identified Experiment - Rough= live mouse -smooth= dead mouse - smooth heat killed= live mouse (showed that they need to be alive to cause illness) - rough and heat-killed smooth cells= dead mouse (only smooth virulent isolated from dead mouse) (rough transformed to smooth cells)
RNA polymerase core complex
-composed of: alpha, beta and beta prime proteins - drives synthesis of new RNA
RNA polymerase
-is a multimeric enzyme=composed of different individual proteins - two complexes: core and holoenzyme
Sites of Protein Synthesis
-ribosomes - Combination of rRNA and protein - thousands per cell - in prokaryotes: composed of two subunits (30s+50s=70s complex)
Mutations can be
-single nucleotide changes, or insertions or deletions of whole genes. - change in dna (even a change in one base is a mutation)
Transcription Termination: Rho-independent
-stem loops followed by polyu tails in RNA and A tail in DNA - unstable structure that causes RNA poly to dissociate from the template
In the Hershey Chase experiments, researchers labeled phage______with radioactive sulfur, and phage_________with radioactive phosphorous. After incubating the different phage samples with the bacteria, then separating the phage from the bacterial cells, they only ever observed radioactive________with the bacterial sample.
1) Proteins 2) DNA 3) Phosphorous
Bacterial Nomenclature
1. Binomial: genus + species 2. Genus capitalized, species lowercase 3. Both genus and species italicized
Gene/Protein Nomenclature
1. DNA/RNA: first 3 letters lowercase, final (4th) letter uppercase 2. Protein: not italicized, first and last letters are capitalized
UVR system
1. UvrA recognizes the dimer -Usually thymine dimers -Causes a bubble in DNA 2. UvrBCD removes DNA surrounding the mutation 3. New DNA is synthesized by DNA Polymerase 4. DNA Ligase seals the ends of the newly synthesized DNA to the chromosome. - does not rely on methylation of DNA and recognizes dimers
Human chromosome
23 pairs of linear double-stranded DNA
Under which of the following conditions is the LacI protein binding the operator of the lacZYA operon repressing transcription? a. No Lactose / + Glucose b. + Lactose / + Glucose c. + Lactose / No Glucose d. All of the above
A
Which of the following statements describes an operon?
A set of genes transcribed of the same promoter.
Expression of the ModE transcriptional repressor results in a decreased expression of modA(i) transcription leading to a decrease in the amount of ModA produced. In the above statement, "modA"(i) is referencing which of the following?
Answer: gene gene: only last letter is capitalized, all in italics protein: first and last letter is capitalized, not in italics.
Using your knowledge on Griffith's Transformation Experiments, which of the following describes a scenario where mice would succumb to an infection and die? a. Challenge with a sample of dead smooth strain bacteria b. Challenge with a sample where live rough strains of the bacterium were incubated with heat-killed smooth strains c. Challenge with a sample of live rough strain bacteria d. Challenge with a sample where dead rough strains of the bacterium were incubated with heat-killed smooth strains
B
You are a researcher that is studying the facultative anaerobe Bacterium xyz. This bacterium does not encode the lacZYA operon and is naturally transformable (can uptake DNA). Which of the following genes would Bacterium xyz need to uptake to create a selectable mutation if you were growing the cells aerobically on a complex nutrient rich agar media with penicillin? A. lacZYA (b-galactosidase) B. bla (b-lactamase) C. ldhA (Lactate Dehydrogenase) D. znuA (Zinc Transport)
B) Because it encodes for an enzyme that can degrade antibiotics - only cells with this gene will be able to survive (meaning they are mutated) A) will not create a selectable motion based on the growth conditions presented - Nutrient rich media means the cell can use other sources of energy to grow and will not allow to select out mutants - could have been an answer if "grow cells in a minimal defined medium with lactose as the sole carbon source"
Transduction: DNA is transferred from a donor bacterial cell to a recipient bacterial cell via a
Bacteriophage: A virus that specifically infects bacteria
Regulates based on the presence/absence of GLUCOSE
CAP/cAMP
How does CAP recognize if glucose is present
CAP: Recognizes if Glucose is present in the Cell thru cAMP
Genotype
DNA
The molecule that codes genetic info in cell
DNA
Molecule that contains most of genetic info for prokaryotic microorganism (contains essential genes) - a MUST MUST for survival, cannot be lost
Chromosome
Mutation of Sigma Factor σ28 (aka: FliA) would result in which of the following? A. The cell would be unable to transcribe any DNA into RNA B. The cell would die because general "housekeeping" genes would not be transcribed C. The cell would not be able to assimilate nitrogen. D. The cell would be unable to perform chemotaxis in liquid media.
D
Which one of the following group of organisms has the LOWEST mutation rate? a. RNA Viruses b. DNA Viruses c. Bacteria d. Eukaryotic Organisms (e.g. Humans)
D
When will lacI be expressed (Transcribed & Translated)? A. Only in the presence of lactose B. Only in the absence of lactose C. Only in the absence of glucose D. It is always expressed
D LacI is the senso of lactose in the cell, it is constitutively expressed - you always want your sensor made/present to respond to its signal
Terminator (transcription)
DNA sequence that signals the end of transcription
coding sequence (transcription)
DNA template for producing RNA transcript
Transcription
DNA to RNA
Transduction horizontal gene transfer
DNA transfer mediated by a virus/phage - two types: general and specialized
Conjugation horizontal gene transfer
DNA transfer that involves cell-to-cell contact and a conjugative plasmid in the donor cell. -occurs with Pillus or mating bridge and require cell to cell contact -sex pillus made by F plasmid (f+ + f- = f+ and f+) transferred through rolling circle
Silent mutation
Does not affect amino acid sequence - no outward change in phenotype - can code for same codon Ex: UAU and UAC= tyrosine
The Model System: The lac Operon
E. coli grown on two carbon sources exhibits diauxic growth discovered by Jacob and Monod in 1942 -Genes in the lac operon code for proteins that will metabolize lactose
Which of the following best describes why E. coli exhibits diauxic growth when grown in a medium that contains glucose and lactose as the sole carbon and energy sources?
E. coli will first grow as it consumes all of the available glucose, it will then switch over to consuming the available lactose starting to grow again
Glucose and the presence of lactose
E.coli will first eat all the glucose before it will consume lactose. Even if lactose is present the cell is not fully expressing the Lac operon (the genes that code for the proteins to use lactose)
DNA polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule - uses parental strand as template - adds nucleotides in 5 to 3 direction
Under which condition(s) would cAMP be produced? A. +Glucose, +Lactose B. +Glucose, -Lactose C. -Glucose, +Lactose D. -Glucose, -Lactose E. Both A and B F. Both C and D
F cAMP production is solely tied to the presence of Glucose and is not effected by lactose levels + Glucose= No camp -Glucose= +cAMP
All mutations are bad and will result in deleterious effects on the cell, leading to death.
F
When will the lacZYA operon be repressed? A. +Glucose, +Lactose B. +Glucose, -Lactose C. -Glucose, +Lactose D. -Glucose, -Lactose E. Both A and C F. Both B and D
F - Repression occurs when LacI binds the operator region of the lac operon - LacI only binds when there is NO lactose - LacI only responds to lactose, it doesn't matter if glucose is present/absent
DNA strucutre (people)
Franklin, Crick and Watson
first to publish work on the process of transformation
Fredrick Griffith
Specific genetic element within the chromosome that encodes the information to make a specific RNA or protein
Gene
Ectopic
Gene is expressed in a cell that normally does not encode or express that gene -ex: green fluorescent protein lac promoter driving expression of GFP +Lactose/-glucose (or a lactose analogue) = +GFP = Green
entire complement of genes in cell (includes chromosomes and plasmids)
Genome
Mutation
Heritable change in DNA sequence (genotype) that may lead to a change in observable properties of an organism (phenotype
When would a population of Vibrio fischeri express luxCDABE and become bioluminescent?
High cell density
Transformation, Conjugation, and Transduction are examples of what type of genetic exchange?
Horizontal gene transfer (transfer of genes via non-reproductive methods)
mutation rates
Induced mutations and spontaneous mutations
When is LacI Repressing In this Experiment?
LACI binds to operator region when there is no more lactose available and occurs at the end of the experiment
Regulates based on the presence/absence of LACTOSE
LacI
LacI: The Sensor
LacI is a DNA binding protein that is a sensor of lactose in the cell -for this class, it sense the concentration of lactose inside the cell -repressor (similar to zur protein) -Transcription of lacI is constitutive (always on)
LacI is a [______] that directly senses the levels of [______] in the cell. CAP is a [________] that directly senses the levels of [_______] in the cell.
LacI is a [repressor] that directly senses the levels of [lactose] in the cell. CAP is a [activator] that directly senses the levels of [cAMP ] in the cell.
Repression/De-repression by LacI is only in response to
Lactose
Why does E. coli prefer to use glucose prior to using lactose?
Lactose is a disaccharide that must be cleaved (requiring energy) before is can be used, Glucose can be directly used by the cell in glycolysis (with no additional energy input).
Why Transcribe The lac Operon?
Lactose present: ON Lactose Absent: OFF
Promoter (transcription)
Located at the start of the gene. Not transcribed or translated. Only there to orient polymerase. - RNA polymerase binding sites
Are all mutations bad?
No some are beneficial -Mutation: Heritable change in DNA sequence (genotype) -The DNA the organism acquired could allow for better survival in a specific environment.
If there is no lactose, does the cell need to transcribe the lac operon?
No, bc the cell will want to repress transcription and not waste energy transcribing and translating - No lactose means no lactose bind to LacI so its able to bind to the operator region and inhibits RNA poly from transcribing the lacZYA genes
Which of the following is a type of point mutation where the mutation in the DNA results in a stop codon replacing a codon that would have encoded an amino acid?
Non-Sense Mutation
RNA polymerase directly reads the_____ strand of DNA in the 3' to 5' direction, synthesizing the RNA transcript in a 5' to 3' direction. The transcript is identical to the ______strand of DNA, except T is replaced with U.
Non-coding Coding
extra chromosome structure - mobile, non-essential , expendable - can be lost and cell will survive
Plasmid
general transduction
Random bacterial DNA is packaged inside a phage and transferred to a recipient cell - phage binds and injects material----->enzyme on phage DNA degrades bacteria's DNA in fragments --> new phage made (and some can accidently get bacterial DNA) --) bacterial cell lysis opens and they bind to new cells
translational regulation
Regulating the amount of protein produced in translation or mRNA to protein
Supercoiling
Repeatedly coiling DNA molecule to make chromosome shorter and wider. - allows for compaction of DNA so it fits in cell - hides DNA binding site
RBS (Shine-Dalgarno sequence)
Ribosomal Binding Site: - This is where the Ribosome binds to initiate translation - Aligns Ribosome with AUG start codon -16S rRNA contain anti-Shine-Dalgarno Site
polycistronic mRNA
Single RNA molecule that encodes all of the coding info to make each individual protein - is translated into proteins that are encoded
Autoinducers (Quorum sensing)
Small molecules produced by bacteria and secreted into the extracellular environment - constantly produced -low amounts= tells cells to express individualist behaviors
Specialized transduction
Specific bacterial genes are packaged inside a phage and transferred to a recipient cell - phage binds and injects-> Phage DNA is recombined in host chromosome (prophage) ---> phage DNA is removed and Phage results (some can contain a portion of the host cells DNA)--> bacterial cell is lysis open
AUG
Start Codon. The codon that tells the ribosome to start translating. The first amino acid in the polypeptide
UGA (UAA, UGA)
Stop Codon. The codon that tells the Ribosome to stop translating
The gens of the lacZYA operon code for proteins that will utilize the disaccharide sugar lactose
T
allosteric regulation
The binding of a molecule to a protein that affects the function of the protein at a different site.
In the Meselson-Stahl experiment demonstrating DNA is replicated in a semi-conservative manner, after one round of DNA replication, how much of the double-stranded DNA products would be N15/N15 (Parental strand all N15 and newly replicated strand all N15, both strands all N15)
The correct answer is: 0% In semi-conservative replication, each parental strand serves as the template for DNA polymerase to read and synthesize a new strand of DNA. Thus, after one round of replication the DNA products are half parental DNA and half new DNA. In the Meselson-Stahl experiment, all the DNA starts off as N15/N15. Each strand is composed of all N15 as this was the only available Nitrogen available to the cells in the media. The cells are then taken out of N15 media and moved into N14 media and allowed to grow. Any new DNA made would be N14, as this is the only Nitrogen available. Parental DNA (N15/N15) is split into its two separate strands, and a new copy is made with N14 DNA. Thus, all new double stranded DNA will be half N15 (parental strand) and half N14 (newly synthesized strand) (N15/N14). Therefore, NONE of the DNA would be all N15 (Both strands N15/N15).
antiparallel
The opposite arrangement of the sugar-phosphate backbones in a DNA double helix.
Phenotype
The observable trait
fluorescence microscopy
Traditional fluorescents: 2D view confocal scanning: 3D single molecule: allows to track single molecules
Hershey-Chase Experiment
Used radioactive material to label DNA and protein; Phage passed on DNA; helped prove that DNA is genetic material not proteins - DNA is the transforming molecule - sulfur for protein - phosphorous for DNA
Lacl with lactose
When bound by lactose, LacI is not able to bind DNA and does NOT bind the operator region -transcription - De-Repression
Lacl without lactose
When not bound with lactose (allolactose) it can bind to the promoter region of the lacZYA operon at a motif called the operator ("O") - no transcription - repression of the lac operon
Bacterial Nomenclature in paper
Write out full Genus and species once in document and then abbreviate Genus
-Insulin is produced_____ -Without insulin_____
by b-cells of the islet of Langerhans cells in the pancreas. glucose is not absorbed into the body, and results high blood glucose.
znuA, ZnuB, znuC
codes for the zinc transport system
Triplet set of nucleotide bases
codons - each codes for a specific single amino acid
Most (but not all) prokaryotic genomes
comprised of a single, circular dsDNA chromosome
How does CAP Recognizes if Glucose is present in the Cell
thru cAMP
Positive regulation
transcription is activated or lots of RNA produced - recruits RNA poly -ex: luxCDABE (bioluminescent) - activator binds near promoter region
Negative regulation/ repression
transcription is repressed and is turned off - inhibit RNA polymerase ex: znuABC - repressor blocks the -10 and -35 sites and the RNA poly would not recognize and not bind
+1 site
transcription start site
Reading frame
triplet code that determines what amino acid will be added to polypeptide chain
Transformation
uptake of foreign DNA from the surrounding environment - this DNA will allow cell to produce new molecules or structures (possible advantage for environment)
The genes in the lac operon code for proteins that will
use lactose
The genes in the lac operon encode for proteins that will
use lactose
Plasmid characteristics
usually small circles; self-replicating (contain an origin of replication); often many copies per cell; contain "dispensable" genes; provide a survival advantage under certain conditions