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What is a silent, synonymous mutation?
Single nucleotide substitutions that do not change the peptide sequence. Neutral with respect to fitness. Sometimes slightly deleterious
What is a Missesne, replacement, non-synonymous substitution?
single nucleotide substituations that change a single amino acid in a peptide sequence
What is a nonsense mutation?
Single nucleotide substituation that create a stop-codon where there used to be an amino acid
What is a Frameshift mutation?
A single nucleotide deletions or insertions that change the reading frame downstream of the mutation. Result in multiple amino acid changes and often premature stop
What is a transversion of base pairing?
A change from Purine to pyrimidine or purine to pyrimidine
What is a Transition of base pairing?
A change from purine to purine or Pyrimidine to pyrimidine
What is more common, transition or transversions?
What is an Ames Test?
THe test uses an Auxotrophic strain of Salmonella Typhimurium that can be reverted to prototrophy by a mutation. The Salmonella bacterium is plated on medium that it cannot grow on unless it mutates.
Who developed the Ames test?
What did Salvador Luria and Max Delbruck notice?
That E.coli somethimes became resistant to the phage T1
What is a Mutation Hotspot?
Regions with particularly high mutation rates
What is the Luria-Delbruck experiment?
- Start with manu indiepedend tcultures of E.Coli that are sensitive to T1 phage
- Plated on Petri dishes with T1 phage
Analyzed the distrobution of resistant (mutation) E.Coli to determine if resistant to bacteria existed prior to exposure to phage or became resistant after exposure to phage
When did Delbruck and Salvador get their nobel prize?
What did Joshua Lederberg do?
He used replica printing to demonstrate that E. coli mutants resistant to phage or the anitbiotic streptomycin existed prior to exposure to the phage or the antibiotic
What is an Operon?
- A group of closely linked genes that produces a single messenger RNA molecule in transcription
- Operons consist of structural genes and regulating elements (as an iperator and promotor)
From left to right state each part of the Lac Operon.
- Lac Z
- Lac Y
- Lac A
What three enzymes are produced by the lac operon? From left to right
What is Clonal Reproduction?
- Daughter cells inherit copies of the genome carried by the mother cell
- No gametes, no fertilization, no zygotes
What is Transformation in Genetic exchange bacteria?
Uptake of naked DNA
What is Conjugation in Genetic exchange bacteria?
- Transfer of genes facilitated by conjugative plasmids
- Transfer of DNA through a pilus
- Mediated by a plasmid that contains the gene requires
- The F factor in E. coli is an example
What is transduction in Genetic exchange bacteria?
Transfer of genes by bacteriophages
What are Competent cells?
Cell capable of DNA uptake
What are Plasmids?
Self-replicating circular double stranded DNA milecules
What is an F-factor?
A plasmid that exist in 1-2 copies per cell
What is an Hfr chromosome?
- These chromosome with an integrated F are called Hfr chromosomes
- Hfr (high frequecy recombination)
How long does Conjugation take?
- 100minutes to trasfer the whole E
- . Coli chromosome between cells
What is the oriT?
Origin of transfer, the particular point where gene transfer between cells starts in the F factor
What are R plasmids?
- Conjugative plasmids can carry antibiotic resistance genes and these plasmids are often called R plasmids
The process that copoes the genetic information from DNA to RNA
The process that translates the genetic information from RNA to a protein sequence
The RNA molecules that are components of ribosomes
A complex protein and RNA molecules that splices intorns from mRNA molecules
Define an enhancer.
Binding sire for proteins (Activators) that increase the rate of transcription of the genes they regulate. Enhancers can be far upstream of the genes they control
What genetic block did Archibald Garrod discover in patients with Alkaptonuria?
The enzyme that transfers Homogentisic acid to 4-maleylacetoacetic acid
Beadle and Tatum were able to hypothesis what, from their experiment using Neurospora fungus?
The roll of a specific gene is to produce a specific enzyme
A bacteria that is a histadine auxotrph should be grown on a medium that?
Contains a histidine
We know that the one gene one enzyme hypothesis is not entirely accurate because?
- Many genes conde for proteins that are not enzymes
- A single gene codes for a single polypepetide chain, and many enzymes are made up of more then one polypeptide chain
- Many genes code for RNA molecules that have no enzymatic activity
The coding sequence for beta-galactosidase, Lac Z, in E. coli is 3072 nucleotides long, including both the start and the stop codons. How many amino acids does Lac Z protein contain?
- But the start doesnt code for an amino acid so - 1
What are the two key regions of prokaryotic promoters?
the -10box (Pribnow box) and the -35 box
A strain of an organism that does no require nutritional supplemntation
Define the TATA box.
The name given to the -25 region of a eukaryotic promoter
Define a purine.
- A type of base with a double ring structure
Define the initiator protein.
Protein that binds to the origin or replication
Define the sigma facor.
A protein that assists RNA polymerase binding in prokaryotes
If the DNA sequence of one stand of the double helix is 5'-CACAGATAT-3'. what is the DNA sequence of its complimantary strand? (include the 5' and 3' orientation)
If the DNA sequence of one stand of the double helix is 5'-CACAGATAT-3'. iF this DNA sequence codes for the amino acid sequence isoleucine-serine-valine, is teh DNA sequence given in the quesion the template strand or the coding strand?
The template strand
Introns are removed from precursor mRNAs by?
mRNAs are synthesized by?
RNA poltmerase II
If the template strand of DNA is 3'CATTACGCTT5' what is its corresponding mRNA sequence?
Why is the promotor of a bacteria gene needed?
It is required for initiation of transcription
Death cap mushrooms produce a substance called alpha-amanitin. Alpha-amanitin blocks synthesis of mRNA but not of tRNA or rRNA in eukaryotic organisms. How is this possible?
Alpha-amantin interferes with the action of RNA poly II, but not RNA poly I or III
Where is the Polyadenylation signal found?
Down stream of the 3' end on DNA
T/F, Multiple origins of replication can be found on the E. coli chromosome??
What does the 5' polyA tail do on the mRNA?
Stablizes the mRNA in the cytoplasm
How many nucleotides can be found in one turn of the double helix?
What binds to the enhancer regions?
The TATA box (-10 or pribnow box) has what characteristics?
- It is upstream of most genes
- It is part of the binding site for RNA polymerase
- It is part of a consensus sequence of the promotor
What is the function of the A site?
It accepts new charged tRNA molecules into the ribosome-mRNA comples, and uncharged amino acid acids exit from the E site. Teh P (peptidyl) site hold the tRNA that is attached to the growing peptide chainuntil charged tRNA enters the A site. The peptide chaing is then transferred to the amino acid on the charged tRNA in the A site.
What happens when the ribosome encounters a stop codon during translation?
A release factor enters the A site and recognizes the stop codon, resulting in the release of the polypeptide chain. The ribosomal subunits dissociate from the mRNA and each other.
What are ribosomes comprised of?
rRNA and proteins
During translation, what does the ribosomes do?
- Hold mRNA and tRNA togehter
- catalyzes the addition of amino acids from tRNAs to the growing peptide chain
- Move along the mRNA and eject uncharged tRNA
AS the ribosome translocates along an mRNA molecule by one codone, what happens?
- The tRNA that was in the A site moves to the P site
- The tRNA that was in the P site moves to the E site and is released.
What happens during the termination of translation?
- A stop codon causes the A site to accept a peptide release factor
- The newly formed polypeptide is released.
- The two ribosomal subunits seperate.
- Translation stops
What is the difference between E.coli cells that are F+,Hfr and F-?
F+ cells contain an F plasmid. F- cells do not contain an F plasmid. In Hfr cells, the F plasmid is integrated into the chromosome.
What would occur if the repressor of an inducible operon were mutated so that it could not bind to the operon?
Continuous transcription of the operon’s genes
The lactose operon is likely to be transcribed when?
There is lactose but no glucose in the cell
The tryptophan operon is a repressible operon that is?
Turned off whenever tryptophan is present in the growth medium
A mutation that results in premature termination of translation is?
A nonsense mutation
An E. Coli cell without a functional lacI gene is expected to?
Always produce beta-galactosidase
If Leu+ strR recombinant are desired from the cross Hfr Leu STRs X F- Leu - strR, on what kind of medium should the recombinants to grown for identification?
Minimal medium with streptomycin
What are transversions and transitions, and which are more likely to resile in missense mutations?
Transversion mutate a pyrimidine to a purine or a purine to a pyrimidine and transition mutate a pyrimidine to another pyrimidine or a purine to another purine. Transversions are more likely to result in missense mutation because transversions cause missense mutations at two-fold degenerate sites in third base position of codons, where as transitions don’t.
A mutation in at center of a gene abolished function of the gene. A second mutation tow codons upstream of the original mutations restored function of the gene. These two mutations probably _____ mutations?
What many RNA polymerases do Eukaryotes have?
- Where is RNA poly I located?
- In the nucleolus
What does RNA I make?
Ribosomal RNA (rRNA)
What does RNA Poly III make?
What does RNA poly II synthesize?
What is a TATA box?
- It is nucleotide sequence that is 25-30 nucleotides upstream.
- It is the start sites in eukaryotes
What is the CAAT box?
its is the sequence CAAT 75 upstream
What is the GC box?
- it is -1- -200 upstream
- Sequence GGGCGG
What do snRNP’s edit?
- 1. snRNP’s and proteins assemble to form a spiceosome. The 2’ hydroxyl group on an adenine nucleoatide (A) attacks the 5’ end of the intron, breakingRNA
- 2. The 5’ end of the intron becomes attached to the A nucleotide forming a loop of RNA. The free 3’ end of one exon attacks the 5’ end of the other
- 3. The 3’ and 5’ ends of adjacent exon bond covalently, releasing the intron (which will then degrade)
How does the ribosome bind to the mRNA?
by the 5’ capping
In bacteria, where does the Promotor attach?
Contains a -35 box and a -10 box
What are sigma factors?
Proteins involved in contracting the promotor
What is the Open Reading Frame?
The length of DNA (or RNA) between a start codon (Usually AUG) and a stop codon (UAG, UAA, UGA) that can potentially be translated into a polypeptide sequence
What is an Operon?
a Single transcriptional unit that transcribes rRAN genes in prokaryotes
What is a Shine-Dalgarno sequence?
The Shine-Dalgarno (SD) sequence is a ribosomal binding site in prokaryotic mRNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon
What is actual sequence of the Shine-Dalgarno sequence?
What is the first step in the initiation of translation?
A small ribosomal subunit binds to the molecule of mRNA.
What is the 2nd step in the initiation of translation?
The arrival of a large ribosomal subunit completes the initiation complex.
What is the 3rd step in the elongation cycle of translation?
- The ribosome translocates the tRNA in the A site to the P site. The empty tRNA in the P site is moved to the E site where it is released.
What is the first step in the elongation cycle of translation?
- Codon recognition
- The anitcodon of an incoming aminoacyl tRNA base-pair with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the Accuracy and efficiency of this step
What is the second step in the elongation cycle of translation?
- Peptide bond formation
- An rRNA molecule of the large subunit catalyzes the formation of a peptide bond between the new amino acid in the A site and the carboxyl ends of the growing polypeptide in the P site. This step attached the polypeptide to the tRNA in the A site
What is the first step in the Termination of translation?
When a ribosome reaches a stop codon on mRNA, the A of ribosomes accepts a protein called a released factor instead or tRNA
What is the second step in the termination of translation?
The release factor hydrolyzes the bond between the tRNA in the P site and the last amino acid of the polypeptide thus freed from the ribosome
What is the third step in the termination of translation?
The two ribosomal subunits and the other components of the assembly dissociate
What is a missense mutation?
It is a point mutation in which a single nucleotide change result in a codon that codes for a different amino acid.
What is a frame shift mutation?
- Is a genetic mutation caused by the insertion or deletion of a number of nucleotides that is not divisible by three changing the total number of nucleotides and pairing, changing the resulting protein
- Frequently result in premature stop codons
- Almost always detrimental
What is a nonsense mutation?
- A mutation in which a sense codon that corresponds to one of the twenty amino acids specified by the genetic code is changed to a chain-terminating codon
- Results in a sopt codon
- Protein will be short
- Usually detrimental
What is Nucleases?
- An enzyme that cut or degrease DNA strands
- Makes cuts in the damaged DNA strand and degrades the DNA
What are the steps in Nucleotide excision repair of DNA damage?
- 1. A thymine dimer distorts the DNA molecule
- 2. A nuclease enzyme cuts the damaged DNA strand at two points and the damaged section id removed.
- 3. Repair synthesis by a DNA polymerase fills in the missing nucleotide
- 4. DNA ligase seals the Free end of the new DNA to the old DNA, making the strand complete
What was Archibald Garrod?
Sir Archibald Edward Garrod, KCMG, FRS (25 November 1857 – 28 March 1936) was an English physician who pioneered the field of inborn errors of metabolism
What example did Garrod use?
What is Alkaptonurea?
Alkaptonuria is an inherited condition that causes urine to turn black when exposed to air.
What did Archibald Garrod call genetic defects?
Inborn errors of metabolism
What are prototrophs?
Strains that can grow on minimal media
Who was Francis Crick?
Him and his coworkers performed experiments that showed that the code has three letter word
How did Francis crick and his coworkers perform their experiment?
They used the mutagen acridine to ass and delete single nucleotide to the DNA T4. a phage that infects E/ Coli
What are the four kinds of RNA
What is mRNA?
- messenger RNA
- Transfer genetic information from the DNA molecule to the ribosomes where protein synthesis takes place
What is tRNA?
- Transfer RNA
- Bring amino acid to the ribosomes so they can be used in protein synthesis
What is rRNA?
- Ribosomal RNA
- Parts of the ribosomes along with ribosomal proteins
What is snRNA?
- Small nuclear RNA
- Forms complexes with proteins that are used in eukaryotic RNA processing
What errors to the 100 genes coding for repair enzymes repair?
- Random replication error
- DNA damage due to reactive chemical in the cells
- Radiation, X-ray and IV induced damage
What did George beadle and Edward Tatum do?
- They used a new model organism: the orange bread mold Neurospora Crassa
- They used this as a minimal medium
- From these compounds it makes everything else it need to grow to reproduce.
- They bombarded their mold with x-ray and proceeded to look for mutants that lacked the ability to make amino acids
What and when did george Beadle and Edward Tatume receive the Nobel prize in medicine for?
- In 1958
- For their discovery that genes act by regulating definite chemical events
What did Francois Jacob and Jacques Monod do?
Suggested that an RNA molecule that was complementary to one strand of the DNA molecule was the messenger between genes and proteins synthesis. They called this molecule messenger RNA, mRNA
What did Marshal Nirenberg and Heinrich Matthaei do?
- Discovered a method to make RNA of a known sequence
- They creased an RNA sequence that contained only the base urisil
- They added this RNA to an in Vitro system for synthesizing protein. The result was a gain of amino acids that contained only Phenylalanine
- The first word that was understood in the genetic code was the word UUU which translates into Phenylalanine
A knock-out allele is?
A mutated form of a gene that does not make a functioning product
Srb and Horowitz showed that _____?
Mutations of a single gene resulted in defects o one and only one enzyme