Microbiology MCC Scott Quinton Exam 3
mRNA (messenger RNA)
"A riboswitch" that regulates translation. A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
transformation
"naked" DNA, in solution from the environment
Translation (RNA to protein)
*Initiation*: Initiation factors bind ribosome to 1st codon, AUG *Elongation*: EF-Ts, EF-Tu, EF-G bring GTP energy -Polymerization, movement of ribosome along mRNA *Termination*: Releasing factors undock ribosome from mRNA
Describe DNA replication
1) Unwinding of DNA molecule 2) Breaking parent strands apart hydrogen bonds broken 3) Assembly of new DNA strands DNA polymerase assembling new strands of DNA complementary deoxyribonucleotides paired e.g., AATCGATCG paired with TTAGCTAGC via hydrogen bonds 4) Restoration of DNA to coiled double helix
Transcription (DNA to RNA)
1. Initiation 2. Elongation 3. Termination Unit: stretch of DNA that codes for a polypeptide or RNA (tRNA, rRNA) RNA Polymerase II: Separates DNA strands and transcribes mRNA. Attaches to promoter (start of gene), stops at terminator (end). mRNA elongates in 5' - 3' Uracil replaces thymine when pairing to adenine
RNA processing in eukaryotes
1. initiation 2. elongation 3. termination *4. "tail step"-splice and dice*
DNA is synthesized in what direction?
5' to 3' at the replication fork, the leading strand is synthesized continuously and the lagging strand (3' to 5') discontinuously
Nucleic acids only grow in
5-->3-'OH
Gene
A segment of DNA on a chromosome that codes for a specific trait
terminator
A special sequence of nucleotides in DNA that marks the end of a gene. It signals RNA polymerase to release the newly made RNA molecule, which then departs from the gene
DNA polymerase
An enzyme that catalyzes the formation of the DNA molecule. proofreads new molecules of DNA and removes mismatched bases before continuing DNA synthesis
RNA polymerase
Binds to promoter; transcription begins at AUG; the region of DNA that is the end point of transcription is the terminator; synthesizes a strand of RNA from on strand of double-stranded DNA, which serves as a template
shuttle vectors
Can exist in several different species, plasmids and viruses can be used as vectors
chemical mutagens
Chemicals (nitrogen/nitrogenous bases)that cause genetic mutations
What is tryptophan?**
Corepressor because if there is too much trypt, made, it'll bind and help to repress the operator gene
Four tools of biotechnology that every technique uses
Cut, amplify, insert, grow
Define and describe: Transduction
DNA is passed from one bacterium to another in a bacteriophage and is then incorporated into the recipients DNA, generalized description: any bacterial gene can be transferred
How can mutations be repaired?
DNA polymerase, and photolyases(for uv radiation only)
describe the process of dna replication
DNA replication fork; DNA is copied; DNA unzips, one strand serves as the template and creates 2 new DNA molecules
central dogma
DNA-transcription-RNA-translation-protein
Southern Blotting uses
DNA; DNA probes detect specific DNA in fragments (RFLPs) searated by electrophoresis
restriction enzymes
Enzyme that cuts DNA at a specific sequence of nucleotides
Define and describe: Transformation
Genes are transferred from one bacterium to another as "naked" DNA in a solution
Describe how DNA serves as genetic information.
Genetic information is encoded by the sequence of bases along a strand of DNA.
What is the role of cAMP in catabolite repression?
Is a co-inducer, super promoter. Makes it go fast
inducible operon (lac operon)
Lac is always "off" uless lactose is present-active repressor binds to the operator -inducer (lactose) binds to and inactivates the repressor
How do you repair thymine dimers from UV radiation(nonionizing) ?
Photolyases; light repair mechanism to separate dimers
Four tools of biotech: step 2 amplify
Polymerase chain reaction (PCR)
Operon model of gene expression
Promoter: segment of DNA where RNA polymerase initiates transcription of structural genes Operator: segment of DNA that controls transcription of structural genes Operon: set of operator and promoter sites and the structural genes they control
Northern blotting uses
RNA
Define and describe: Transposons
Small segments of DNA that moves from one region to another of the same chromosome or to a different chromosome or plasmid. Complex versions can carry any type of gene; including antibiotic resistant genes
nonsense codons
Stop codons (UAA, UAG, and UGA)
What is CAP?
Super promoter for RNA polymerase
explain how mutant microorganisms can be used to detect chemical carcinogens
The Ames test is inexpensive and fast for identification of possible chemical carcinogens, test assumes the mutant cell can revert to a normal cell in presence of a mutagen and that many mutagens are carcinogens
non-coding strand (anti-sense strand)
The DNA strand that forms the template for the transcribed mRNA. This strand is the opposite strand of the coding strand. contains anticodons.
tRNA (transfer RNA)
The form of RNA that carries each amino acid to the ribsome to form the polypeptide chain (protein)
leading strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.
Genetic Recombination
The regrouping of genes in an offspring that results in a genetic makeup that is different from that of the parents.
lagging strand
The strand in replication that is copied 3' to 5' as Okazaki fragments and then joined up by DNA ligase
antiparallel strands
The structure of DNA, which means there are to strands parallel to each other going in opposite directions. (5 prime to 3 prime)
Differentiate of transcription and translation
Transcription: DNA-> RNA, double strand to single strand DNA, DNA polymerase, end up with mRNA Translation: mRNA--> polypeptide --> protein
horizontal(lateral) gene transfer of foreign DNA
Transformation, transduction, conjugation
How may viruses have evolved by?
Transposons
repressible operon (trp operon)
Trp is always "on" unless tryptophan is present
Hfr cell
a cell with the F plasmid integrated into the *chromosome*
Describe a DNA molecule
a double helix with nitrogenous bases as the "rungs" and phosphate groups as the "sides"
Lac operon
a gene system whose operator gene and three structural genes control lactose metabolism in E. coli; contains genes coding for proteins in charge of transporting lactose into the cytosol and digesting it into glucose
Exon
a segment of a DNA or RNA molecule containing information coding for a protein or peptide sequence. (messenger)
Intron
a segment of a DNA or RNA molecule that does not code for proteins and interrupts the sequence of genes.
coding strand (sense strand)
a strand of DNA that is not used as a template during transcription, protects from degradation, corresponds to the base sequence of the RNA transcript produced (although with thymine replaced by uracil)
DNA chips
all DNA/RNA turned on at one time
Why is redundancy important?
allows for mistakes to be not so serious
Mutation: Nucleotide
altering chemicals, alter bases to pair with something else, example: nitrogenous bases
rRNA (ribosomal RNA)
an organelle that contains most of the RNA in the cell and that is responsible for ribosome function
Western blotting uses
antibodies; "confirmation tests" (ex. pregnancy tests)
Conjugation
bacterial sex, requires F-plasmids "sex pilus"
Transduction
bacteriophage mediated transfer of bacterial DNA
Types of mutations in DNA
base/point substitution, missense/frameshift/nonsense
Reverse transcriptionase
cDNA <---mRNA; reverse transcription
Radiation mutation: Ionizing
causes lose of electrons and breaks in chromosome
mutation
change in a DNA sequence that affects genetic information
Compare and contrast Prokaryotic and Eukaryotic chromosomes: PROKARYOTIC
circular DNA Naked (no associated proteins) Plasmids often present one chromosome only
tRNA carries
complementary anticode. every single codon has tRNA for each amino acid
How does spreading happens?
conjugative plasmids, dissimilation plasmids, R-factors
Transposons (jumping genes)
contain insertion sequences for cutting and resealing DNA (transposase)
Four tools of biotech: step 4 Grow
creating a gene library
Selection
culture a naturallly occuring microbe that produces desired product
blunt ends
cuts are straight through both DNA strands at the line of symmetry
Chemical mutations cause
deletion frameshift mutations
Vector
delivery vehicle
Describe how a mutant organism can be identified
detected & selected by testing for an altered phenotype - replica plating used for negative selection - auxotrophs (require a specific nutrient for growth) can be selected by growing cells in media without the nutrient
R factors are
encode antibiotic resistance
Operons in eukaryotes
every gene is turned off/on by multiple switches
polymerase chain reaction (PCR)
every techinque uses, requires specialized DNA polymerase and a primer
Phenotype
expression of the genes/genotype
evolution occurs by
genetic change, diversity(mutations and recombination)
Genotype
genetic makeup, its compliment of DNA
The random shotgun method is used in
genome sequencing
Anticodon
group of three bases on a tRNA molecule that are complementary to an mRNA codon to form amino acid
how can mutations be beneficial?
help to adapt
DNA is held together by
hydrogen bonds between the base pairs AT and CG
Describe protein synthesis
include transcription, rna processeing and translation... mRNA copies the code for the gene from the DNA in the nucleus. mRNA then carries this code to the ribosomes in the cytoplasm. A sequence of three bases is the code for a particular amino acid. Carrier molecules (tRNA) bring the bases to the ribosomes in the correct order. When the protein chain is complete, it folds up to form a unique shape which helps the protein to carry out its function
rDNA rechnology
insertion or modification of genes to produce desired proteins
Possible causes of mutations
ionizing radiation, non-ionizing(UV) radiation, spontaneous
Four tools of biotech: step 1 Cut
isolate gene of interest using restriction enzymes
DNA ligase function
joins Okazaki (lagging strand) fragments
Transposons are
jumping genes
Compare and contrast Prokaryotic and Eukaryotic chromosomes: EUKARYOTIC
linear DNA Associated with histone proteins no plasmids 2 or more different chromosomes
Genetic transformation: crossover
living took up deads ability from environment, (mouse example)
auxotrophs
lost ability to synthesize one or more organic compound
operons for prokaryotes
lots of genes translated at once (one switch)
Importance of plasmids
many different purposes in biotechnology, can be used as a tool to insert genes into bacteria to encourage their production of therapeutic proteins such as human insulin
Mutations: nucleoside analogs cause
mismatching and base substitutions
vertical transmission
mother to daughter
What is the principle behind the AMES test?
mutating it back to lost ability -ability to cause cancer
**How do bacteria evolve?
mutations, transposons, transduction, antibiotic resistance
**Nanotechnology
nanospheres used in drug targeting +delivery
Where does transcription occur?
nucleus for eukaryotes, cytoplasm for prokaryotes
clone
population of cells arising from one cell; each carries the new gene
CRISPR
powerful gene editing technique
Radiation mutation: Nonionizing
produces thymine dimers- UV light prevents replication
How do operons work?
promoter genes bind to the operator to turn on/off gene by blocking RNA polymerase from bind b/c it "coils/twists" the DNA
Proteomics is the study of
proteins
restriction enzymes
recipient DNA is usually a plasmid, evolved as bacterial DNA
gene therapy
replace defective or issing genes
tryptophan operon
repressible operon---when trp is absent, the repressor is inactive-----when trp is present and there is enough of it, the trp binds to the repressor and activates it to stop producing
Define and describe: Conjugation (Mouse example in book)
requires contact between living cells one type of genetic donor is an F+, recipient is F-. F cells contain plasmids called F factors; these are transferred to the F- cells
riplets
restriction length polymorphism(shapes); what you see with electrophoresis
horizontal gene transfer vs vertical gene transfer
same generation vs reproduction between generations of cells
Vectors
self replicating DNA, delivery device to carry gene to new cell
Define and describe: Plasmids
self replicating, circular DNA, carries genes not usually essential for cells survival. Gives a "superpower" gene; ex. antibiotic resistance, toxin carrier, bacteriocins
typical genetic modification procedure
separate 2 DNA --> transformation --> rDNA
gel electrophoresis
separates our DNA according to size "DNA fingerprint"
RNA primer
short segment of RNA used to initiate synthesis of a new strand of DNA during replication
What kind of mutation is sickle cell anemia?
single base change mutation
Mutations: frameshift
some dyes for staining DNA causes a bulge in DNA which allows for insertion/deletions
Promoter
specific region of a gene where RNA polymerase can bind and begin transcription
sticky ends
staggered ends of DNA formed after a cut
Agrobacterium
take away nasty gene and ass gene we want (ex. herbicide resistance)
transgentic
term used to refer to an organism that contains genes from other organisms
sense codons
the 61 codons that specify amino acids
Crossing-over
the exchange of genes between homologous chromosomes, resulting in a mixture of parental characteristics in offspring.
Genetics
the study of genes, how they carry information, how information is expressed, and how genes are replicated and passed to generations
metagenomics
the study of genetic material recovered directly from environmental samples
biotechnology
the use of microorganisms, cells or cell components to make a product -- foods, antibiotics, vitamins and enzymes
Why are operons important?
they change their metabolism based on the environment
Why are stem cells important?
they have the potential to develop into other cells
codon
three-nucleotide sequence on messenger RNA that codes for a single amino acid
How did E. coli acquire genes from shigella?
transduction of virus
horizontal gene transfer
transfer of genes between cells of the same generation
What processes get into cells?
transofrmation, transduction, transcription/translation, conjugation
zenotransplantation
transplant of an organ from animals
The genetic code is:
universal and redundant
bioinformatics
use of computer databases to organize and analyze biological data
Inserting foreign DNA into cells: Transformation
uses electricity or something else to allow for pores
Inserting foreign DNA into cells: Electroporation
uses electricity to make "pores"; FORCED transformation
Four tools of biotech: step 3 insert
using plasmids to transfer DNA from one organism to another, GLUE with ligase
repressible enzymes
usually function in anabolic pathways; their synthesis is repressed by high levels of the end product
inducible enzymes
usually function in catabolic pathways; their synthesis is induced by a chemical signal
genetic code
ways codons translated to amino acids