Genetics Exam 4
Important features of siRNAs
1. 5'-monophosphate 2. 3' OH 3. Two-nucleotide 3' overhang beyond core base paired region 19 nucleotide
Translation Initiation Positioning in Bacteria
1. AUG initiation Codon in mrna preceded by a special sequence the Shine-Dalgarno sequence 2. This sequence base pairs with the 3' 16s rRNA in the small subunit 3. This correctly positions the AUG in the P site where the initiator tRNA will bind
Explain Allosteric Effectors
1. Activator and Repressor exists in two states: one that can bind its DNA target and another that cannot 2. The allosteric site on each acts as a sensor and interacts with effectors 3. The effectors bind to the regulatory proteins and 4. Causes them to change shape 5. Allow them to now bind either the Activator binding site or the operator 6. Some activator and repressor can still bind dna without allosteric effectors
What happens in eukaryotic after the charged met-tRNA mets the mRNA?
1. ElF4E consists of three IF and bind the 5' end so cap structure 2. Has helicase activity the unwinds 5' UTR so ribosome can scan for AUG and position in the p site
catabolite repression
1. Glucose is the breakdown product of lactose or catabolite 2. Glucose levels control the lac operon in positive control
Describe what occurs in the situation of: lactose present, no glucose present so high cAMP high
1. Lactose inactivates repressor 2. cAMP joins with CAP to create CAP-cAMP that will activate transcription
Describe what occurs in the situation of: glucose present, low cAMP, lactose present
1. Lactose is present so it will inactive the repressor 2. low cAMP so no binding to CAP to enhance the pathway 3. very little lac mRNA produced
Describe Nonsense Suppressor Mutations
1. Mutation created that produce nonsense mutations or stop codons resulting in truncated proteins 2. Usually the stop codon would prematurely cut off the protein chain, but a suppression mutation recognizes the stop Codon and translation continoues 3. Normally no normal tRNA recognize stop codons only RF, but mutation produced an anticodon that reads stop codon
Describe what occurs in the situation of: glucose present, cAMP low, no lactose
1. No lactose so repressor can bind so no lac mrna created
Describe capping process
1. RNA polymerase 2 produces a new mrna strand with ppp end 2. TP enzyme removes the terminal phosphate from the first nucleotide so pp 3. GT adds a guanine (G) to nucleotide but phosphate is attacked to base so ppp now 4. MT added a methyl group 5. TP, GT, MT: all three enzymes are positioned to act on the mRNA after is emerges from RNA polymerase 2 because of their association with the CTD that is phopholoyated on serine 5 6. First nucleotide in mrna is modified by the addition of m7G cap
Torpedo Termination Model
1. RNA polymerase II continues to transcribe past the site of cleavage and the pre-mRNa is cleaved from polymerase. 2. The remaining 5' monophophorlayed end stil attached to polymerase is then digested one nucleotide at a time by 5' to 3' exonuclease called Xrn2 3. Xnr2 reaches rna polymerase 2 and causing it to fall off DNA strand
RNA interference RNAi features?
1. RNAi very specific: need complementarity to the dsRNA to be affected 2. RNAi very potent only a few dsRNA molecules required per cell to inhibit expression of targeted gene= catalytic process 3. RNAi can affect cells and tissues that are far removed from introduction site 4. Affect progeny so shows that it is heritable
What did Jorgensen see on her petunia experiment?
1. She injected pale pink petunias with an enzyme nesccary for the synthesis os purple-blue pigment 2. Injected same gene into plants with deep violet color 3. None of the transgenic had darker colors rather that they were purely white or a variety of white patterns 4. The transgene suppressed the expression of its own mrna as well as the mrna produced from the original pigement gene 5. Called co-supression
Identify the true statements about RNA interference.
1. Small RNAs interfere with gene expression by interacting with mRNA, bringing about mRNA degradation. 2. Duplex RNA is cleaved by the Dicer enzyme complex 3. Duplex RNA (dsRNA) can suppress the expression of a gene
Describe Jacob and Monod experiment regarding partial diploids and why they were important
1. Studied bacteria (haploid) so made diploid by injecting with bacteria that carried lac region of genome making diploid: 2. Created mutant strains that were heterozygous for lac operon mutations but haploid for rest of genome: Partial diploids 3. Allowed them to distinguish mutations in regulatory dna site (lac operon) from mutations in regulator proteins (lac repressor encoded by the I gene) remembered I gene not apart of lac operon
Process of splicseome chemical reactions
1. The 2' OH of brand point adensonine attacks the phosphorsdieaster bond at 5' splice site 2. two intermediates a 5' exon and intron-3 3. 3' OH of 5' exon attacked phosphodieaster bond at 3' splice site producing linked exons and released lariat intron
Translation Initiation Positioning In Eukaryotes
1. The 5' cap of mRNA is bound to a translation initiation factor 2. Which in return binds other IF to recruit the small ribosomal subunit 3. The ribsomsome scans the mRNA in the 5' to 3' direction until it encounters the first AUG codon 4. Sequence surrounding AUG Condon effects effeincey of initiation this is called Kozak sequence
Explain why high glucose results in no cAMP in cell while low glucose does?
1. The cell captures more energy from glucose breakdown therefore it will break down glucose before going through energy expensive process of creating genes to break down lactose 2. Therefore when high glucose then no breakdown of glucose so no cAMP catabolite 3. When low glucose then it has been broken down so high cAMP catabolite
What happens next in bacteria when the Shine-Dargarno sequence base pairs with the 16s rRNA ?
1. The charged tRNA with fMet with anticodon complementary to AUG start codon in mRNA binds with help of Initiation factors 2. This occurs in P site 3. More IF come and recruit the 50s or large subunit 4. 70s ribosome generated
Describe negative regulation in terms of lac operon when their is lactose?
1. There is lactose so genes will be transcribed to make proteins to break it down 2. Repressor produced by I gene, but lactose acts as an inducer to stop repressor from binding operator 3. Rna polymerase allowed to transcribe down molecule Allosteric effector is lactose (inducer) since it causes a share change in repressor not allowing it to bind dna
What are the two mechanism for trp regulation?
1. Trp repressor in the presence of tryptophan switches off the operon 2. Attenuation: mrna production will decrease when tryptophan is plentiful
Process of spliceosome
1. U1 binds 5' splice site 2. U2 binds branch point with snRNA base pairing with nucleotides across brand point except for key adenosine 3. u4, u5, u6 snRNP's join spliceosome 4. u1 and u4 release 5. first catalytic step 6. second catalytic step
Describe negative regulation in terms of lac operon when their is no lactose? cis and trans elements?
1. When no lactose is present it will not make the proteins by transcribing the genes since no lactose to break down 2. Repressor protein made by I gene and does not allow rna polymerase to move along strand cis: promotor and operator trans: repressor
Process of attachment of amino acid?
1. aminoacyl-tRNA synthetase charges tRNAs with correct amino acid 2. AA is transferred to the A of the CCA sequence at the 3' end of tRNA
How are amino acids attached to tRNAs?
1. an enzyme called aminoacyl-tRNA synthetase will charge tRNA with an amino acid. 2.
What does the AAUUAAA sequence do ?
1. bound to a protein called CPSF which contains the endonuclease enzyme that executes the cleavage step 2. CPSF also recruits PAP (poly a polymerase) the will add a string of A's onto 3' OH end of the mrna
4 ways transcription is more complex in eukaryotes than bacteria?
1. many genes that are spaced far apart 2. Three rna polymerases whereas bacteria only has 1 3. Location in the nucleus 4. Dna in eukaryotes are packaged with proteins in chromatin
Functions of 5' cap
1. protect rna from decay by exonuclease which often relation 5' phosphates to recognize substrates 2. binding site for proteins 3. crucial for translation
Two criteria needed to gene regulation mechanism?
1. recognize enviromental conditions in which they should activate or repress the transcrption 2. must be able to toggle on or off like a switch the transcription of specific gene or group of gene
Allosteric Termination Model
1. rna polyemase transcribes through site of cleavage and pre-mRNA is cute 2. also going through cleavage causes elongation factors to dissociate 2. Leading to conformation change within active site of rna polymerase II 3. Release from DNA
Describe the trp mRNA leader sequence
1. usually long 160 baes and works as an attenuator to govern further transcription 2. Right after the operator and before 1st structural gene 3. attenuator region 4. two tryptophan codons 5. Forms four segments of stem- loop rna structures
Bacteria/Eukaryote translation elongation steps
1.EF-TU escrots charged tRNAs to A site and positions them for peptide bond formation: tRNA plus Ef-TU = ternary complex 2. Decoding center recognition of codon-anitcodon checks 3. Ef-Tu leaves 4. Ribosome changes shape and two amino acids are juxtaposed in the peptidyltransferase center of large subunit 5. Peptide bon formed of fMet and amino acid in A site 6. Ef-G binds A site and shifts tRNA in A and P site to P and E site: translocation 7. Ef-G leaves so A site open again 8. Process repeated with growing amino acid chain in the p site
How many aminocyl-tRNA synthetase?
20 for the 20 amino acids
Bacteria ribosome subunits
30s and 50s to make 70s
Eukaryotic ribosome subunits
40s and 60s to make 80s
What are Is mutations
A mutant repressor is produced from the I gene and its allosteric site is changed so it can no longer bind the inducer so will always bind the operator and stop transcription. It is also dominant over I+ so will bind both copies of operator and prevent transcription
TATA box
A promoter DNA sequence (-30) upstream of transcription start site (+1)
How was a nonoverlapping code proven?
A single nucleotide mutation would only alter one Codon and therefore one amino acid. If the code was overlapping one nucleotide mutation would effect more than one amino acid
What can 5' anticodon bind to in the 3' codon? (A, C, G, U, I)
A= U C=G G= C or U U= A or G I= A, C, U
How are Activator and Repressor different then General Transcription Factors?
Activator and Repressor are GENE SPECIFIC and regulate certain gene expression due to responses to environmental changes while GTF are general mechanisms not specific
Linear sequence of nucleotides in gene determines linear sequence of what?
Amino acids in a protein
A site
Amino-acyl tRNA binding site: binds incoming aminoacyl-tRNA whose anitcodon is complementary to the mRNA codon in the A site of the small subunit
RNA editing
Another way for rna sequences to change. This occurs by changing nucleotide sequences in RNA's after transcription. Adding a nucleotide, methyl or changing base, insertion or deletion
cis-acting elements
Are apart of the DNA strand so promotor and operator
What is the first amino acid Brough to the P site in translation initiation?
Bacteria: a charged methionine (fMet) with a formyl group Eukaryotes: methionine (Met)
Why is Oc called cis-acting?
Because it only affects the genes on the SAME chromsome. If O+/Oc then the O+ is still subject to repression
How does cAMP-CAP enhance transcription?
Bends DNA which in turn aids the binding of RNA polymerase to the promotor
Describe two pathways of mrna decay?
Both have the poly A tail removed by deadenylase 1. One mechanism will remove the m7g cap by decapping enzyme (Dcp1/Dcp2) 2. This leaves behind a 5'-monophosphate that serves as substrate for digestion by 5' to 3' exonuclease Xrn1 1. Another mechanism where digestion occurs 3' to 5' exonuclease called exosome 2. Following decay by exosome a different decapping enzyme called DcpS removes m7g cap
How does poly A tail come about?
CPSP binds to AAUUAAA sequence which recruits PAP and this will add a string of A's onto 3' OH of the mrna stand
Where is the binding site for mRNA in ribosomes ?
Completely in the small subunit
E site of ribosome
Contains deacylated (no amino attached ) tRNA and is ready to be released from the ribosome
Difference in decay between eukaryotes and bacteria?
Decay in eukaryotes is initiated by a exonuclease NOT a endonuclease like in bacteria
ternary complex
EF-Tu binds charged tRNA to bring to A site
What is the most common type of editing?
Editing of adenosine to inosine
5' splice site and 3' splice site sequence and Branch points?
GU and AG sequences and branch point is located upstream of the 3' splice site . These sites direct the splicisome to act at specific places in the pre-mrna binding to these sequences
Describe trp operon
Genes that encode enzymes that are in the same metabolic pathways are generally organized into operons. the order to operon genes and the order in which products are created are directly related
Why can you not use the genetic approach with haploid organisms?
Genetic approach studies the phenotype of mutants so you must compare two alleles to determine dominance so you need TWO alleles not one like in haploid
If code is continuous what would an insertion or deletion cause? If discontinuous what would occur?
If insertion or deletion was in a continuous code then then it would cause a shift in the reading frame starting at the mutation to the end of the code. In a discontinuous code it would only effect one codon. Was found that code is continuous so no gaps and are nucleotides are arranged side by side
What is the advantage of wobble base pairing?
It allows the anticodon of some tRNAs to pair with more than one codon
Describe error rate in aminocyl-tRNA synthetase?
It has two proofreading mechanism: since amino acids only differ by their side chains which can be very similar these mechanisms work to reduce error rate 1. Activation site rejects AA that do not fit 2. Another active site with specific size requirements 3. Ensure that synthetases charge tRNA's with correct amino acid
decoding center of ribosome
Located in the A site of small subunit and makes sure tRNA anticodon matches Codon of mRNA and will accept them If matches
What binds to 5' cap?
Many proteins that perform slicing or polyadenyation and Cap Binding Protein (CBP) which is needed for translation
Does one codon stand for more than one amino acid?
No one codon only encodes one amino acid but different codonons can encode the same amino acid
trans-acting elements
Not apart of the dna molecule so activator and repressor
Translation Elongation continues until?
One of the three stop codons: UGA, UAA, or UAG comes and there is no Trna to recognize. RF do recognize so trigger release of polypeptide from the tRNA in the P site. Ribosome subunits disscoacaite from one another and from the mRNA by RRF (ribosome recycling factor )
P site of ribosome
Peptidyl site; Facilitates along with the A site for formation of a peptide bind between their amino acids. The P site amino acid will disconnect from its tRNA and transfers to A site to grow chain
What did they see when there as an TrpR repressor protein in a presence of tryptophan? absence?
Presense: halted transcrption Absense: transcprtion continuous
What decides where cleavage occurs ?
Sequence elements within the 3' UTR region
What binds the INR and DPE
TAF's
What binds to the TATA box?
TATA-binding protein (TBP) of the TF2D
What GTFs has kinase and helicase activity?
TFIIH which is position right in front of rna polymerase 2 and will initiate opening the transcription bubble and phosphorylation of the CTD
I-Z-Y+/I+Z+Y- what would the phenotype look like
The I+ creates enough repressor to bind the operator in the I- chromosome so it will have the wild type phenotype of -+-+
Example of allostery
The Is mutation which allosteric site is mutated so that is can never bind inducer so always binds operator and prevents expression
Describe the Oc mutation or the operator mutation
The Oc mutation results in a mutation in the operator so the repressor can NEVER bind therefore always expressing the genes. In a O+/Oc the O+ binds the repressor like normal but the Oc still produces genes. Would be called cis acting since effects nearby genes
Once dicer cuts into siRNAs what happens?
The RISC assembles (RNA induced silencing complex), which as Ago in I which will cut and displace the passenger strand (same sequences as target mrna) leaving guide strand behind (complementary sequence to target mRNA) which will find the complementary mrna and ago cleaves the mrna and triggers degradation = silencing
What happens first in the splicing process?
The U1 binds the 5' splice site and aU2 binds the branch point
What happens when the U1 binds the 5' splice site?
The U1 snRNA recognizes the 5' splice site and base pairs to form 8 connective base pairs with the 5' splice site
What determines splicing efficiency ?
The ability of U1 sn RNA to base pair with the 5' splice site
negative regulation
The absence of the bound repressor allows transcription to begin 1. Repressor binds to operator and no transcription occurs 2. No repressor then transcription occurs
Anticodon complementary to?
The anticodon found in the tRNA is complementary to the mRNA codon for the amino acid carried by the tRNA
What makes up the PIC or preinitiation complex?
The assemblage of the GTF's and the RNA polymerase II, which will serve to position polymerase at start site and generation transcription bubble
What is the first step in preintiaiton complex forming in eukaryotes ?
The binding of TFIID at a promotor element that is the first step in the sequential assembly of other GTF's and rna polymerase
Describe the amino acid structure
The central a-carbon is bonded to two function groups: amino group (NH3) and Carboxyl group (COO-) and also an attached H and side chain (R)
How are amino acids grouped together?
The chemical structure of the side chains based on polarity and charge
What is the outcome of capping?
The first nucleotide in an mrna strand is modified by addition of an m7G cap
The level of trp operon gene expression is governed by what?
The level of tryptophan 1. trp is absent in growth medium then trp gene expression high
Describe changes in the CTD?
The pattern of amino acid modification in the CTD changes as the polymerase transcribes through the gene. The modifications (phosphorylation of serines 2 and 5, dephosphorylation by phosphates ) create a code that directs the binding of factors at specific stages of transcription
TP GT and MT are associated with 5' cap and they are located near pre-mrna strand because they are associated with what?
The phosphorlayted Serine 5 in the CTD
What is apart of the lac operon?
The promotor, operator, and Z, Y and A gene, but the lac I gen is not apart even though it produces the lac repressor that is crucial for proper regulation of the lac operon
tRNA amino acid attachment site
The sequence 5' -CCA- 3' is found at the very end of all tRNAs and the 3'OH of the A is the site of attachment of amino acids
What differentiates one amino acid from another?
The side chain or R group resulting in 20 unique amino acids
Select the definition of gene silencing
The structure or location of a gene prohibits access by transcriptional enzymes.
Co-suppression
The transgene inhibits both the expression of the transgene AND the endogenous gene
Lac is switched off when?
There is no lactose (inducer) in the cell so repressor binds operator and no transcription
Kozak sequence
This sequence in eukaryotic cells guides the small ribosomal subunit to the correct initiation codon bu surrrodung the AUG start codon
Why would TF2D stay at the promotor rather than dissociate like other GTF's do when RNA polymerase elongates transcript?
To attract the next rna polymerase 2, in this way multiple rna polymerase 2's can simultaneously synthesize transcripts from a single gene
The Stem and loop structure of the leader sequence results what?
Two conformations 1. High Tryptophan: Segment 1 of leader mrna is translated so ribosome enters 2 and the 3rd and 4th segment for a stem and loop the results in termination of transcription 2. Low Tryptophan: ribosome is stalled at codons in segment 1 thus segment 2 and interact with segment 3 and 3 and 4 won't pair so transcription continues
What is upstream of poly A site and downstream?
Upstream: highly concerned AAUUAAA sequence Downstream: GU rich sequence element
What lead scientist to discover trp used a second mechanism for regualtion?
When trp repressor mutant was combined with no tryptophan the production of trp mrna further increased several folds. Even without the repressor there was regulation
In the torpedo model of transcription termination what controls Xrn2?
Xrn2 is positioned to act in termination through its association with the CTD phosphorylated on serine 2
transgene
a gene introduced by researchers into the chromosomes of an organism
What is RNA polymerase 2 responsible for transcribing?
all the mRNAs and numerous ncRNAs like snRNAs and miRNAs
Where is cleavage site in mrna?
also known as the Poly A site
What starts and ends an intron?
begin with GU 5' splice site so cut before and end with AG 3' splice site cut after
What is the first step in initiation of transcription?
binding of the TF2D at a promotor then other GTFs' come and then rna polymerase 2
What is bound to the poly A tail
binding proteins PABP which protect the mrna from decay by exonuclease and promotes translation
What does beta-galactosidase do? What does premease do?
breaks down lactose and permease transports lactose into the cell
Efficiency of decay pathways?
can be enhanced or suppressed by RNAs and proteins that bind specific sequences within the 3' UTRs and affect the recruitment of decay factors
Tranfers RNA's
carry out the decoding work of translation; associating three-nucleotide sequences in an mRNA strand with their corresponding amino acids
Two events that happen at the 3' end of mrna strand
cleavage from the rna polymerase 2 and poladenlyation which adds 50-200 A's to end of cleaved mrna
Proteins are made of what?
composed of building blocks called amino acids, so a protein is a chain of amino acids and this chain is called a polypeptide
peptidyl transferase center
creates peptide bond between amino acids in A site and P site. Located in large subunit
Where does decay occur?
cytoplasm
What would happen in PABP did not bind to poly A tail
decay by Xnr 2
DSE
downstream sequence element that is U or GU rich located downstream of cleavage or poly A site
What is held within the ribosome subunits?
each subunit whether small or big contains a large rRNA and proteins. And the large subunit also has: Bacteria large ribosome subunit contain one small rRNA Eukaryotic large subunit ribosomes contain two small rRNAs
small interfering RNA (siRNA) are produced from what?
either hairpin or long double stranded RNAs that dicer will cut into the 2 nucleotide overhang structure
alternative splicing
exons in the pre-mrna can be joined together in different combinations to produce different mature manas that will encode for different protein isoforms. This is a mechanism to encode different proteins from a single gene
Where does mRNA go after processing during transcription ?
exported from the. nucleus for translation by ribosomes that reside in the cytoplasm
high glucose vs low glucose
high glucose inhibits the conversion of ATP to cAMP and as glucose decreases the conversion of ATP to cAMP is no longer blocked
How does CAP-cAMP activate transcription of the lac operon?
in the presence of low glucose cAMP molecules produced and combine with CAP to create CAP-cAMP that binds promotor and activates transcription
What do inducers do?
inactivate the repressor so relief of repression and induction or transcription can occur
Why can alternative splicing of messenger RNAs (mRNAs) be advantageous for eukaryotic organisms?
increases the variety of proteins that can be produced
Primary structure
linear sequence focusing on amino end and carboxyl end
Shine-darlgarno sequence
mRNA sequence that will bind to the 16s rRNA of the small subunit to position the ribosome correctly downstream of the AUG start codon so located in the 5' UTR
Describe how to read anitcodon and codon?
mRNA's are read 5' to 3' so anitcdons are oriented and written in the 3' to 5' direction
What does it mean that a code is degenerate?
more than one codon can specify the same amino acid
Ribosome moves in what direction alone mRNA?
moves towards 3' end
Why is there a need to regulate amino acid production like tyrphotphan ?
must be regulated so that the enzymes needed for their synthesis are produced by the bacteria only when amino acids are not available from the environment.
Explain mutations in the 5' splice site?
mutations reduce the number of hydrogen bonds and lead to a decrease in effienceity of splicing
Where is the CTD located?
near the site where new rna emerges from the polymerase so ideal place to orchestrate the binding and release of proteins needed to process the new transcript while rna synthesis continues
Mutation in the I gene results in what?
no repressor being made so consititve or always being expressed
is mRNA always the same as pre-mrna?
no since splicing occurs where introns are removed and the exons are joined
Passenger vs Guide strand
passenger: same sequence as target mrna guide: complementary sequence to target mRNA
How are amino acids linked?
peptide bonds which is a linkage of amino group (NH3) with the carboxyl group (COO-) of another amino acid with one water molecule being removed during reaction.
What forms the CTD?
phosphorylation of rna polymerase II by a protein kinase in TFIIH helps coordinate processing of mRNAs
another name of cleavage site
poly A site
secondary structure of protein
protein structure is formed by folding and twisting of amino acid chain. Most common are alpha helix and beta sheets. Forming one, neither or both
tertiary structure of protein
protein structure is formed when the twists and folds of the secondary structure fold again to from a larger 3D structure
What positions RNA polymerase in correct position ?
proteins are bound to sequences that associated with rna polymerase and position it at the correct site to start transcription
What does U1 snRNA do?
recognize the 5' splice sites by base pairing with the pre-mrna
What is the first step in both termination models of RNA polymerase 2?
recruitment of the cleavage and polyadenlyation so the pre-mrna is cut from the polymerase and a poly A site is added to rna transcript
Mutation in the 5' splice site can do what?
reduce the number of hydrogen bonds and lead to decrease in splicing. Splicing can be restored by compensatory mutations in U1 snRNA
quanterary structure of protein
refers to two the polypeptides interact with one another form a multi-polypeptide protein complex
What is splicing?
removal of introns and links together remaining segments called exons
When is the 5' cap added?
s added during transcription when the RNA is about 25 nucleotides long and has just emerged from the exit channel of RNA polymerase II.
How does the spliceosome know where to cut?
sequences have boundaries between exons and introns 1. GU and AG define introns 2. branch point A
Since code is degenerate what does that say about synthetases?
some synthetases act on multiple tRNAs
wobble position
some tRNA's can recognize multiple codons through different kind of base pairings at the third position of a codon called wobble position. EX: The 5' end of anticodon G can either base pair with C or U in codon of mrna
promotor
specific region of a gene where RNA polymerase can bind. Every gene must have a promotor or is can not be transcribed. Often called promotor-driven transcription
Where does splicing by the snRNAs occur?
still in the nucleus
What changes in rna by post-transcriptional chemical modifications?
structure so in return function
Describe CTD sequence?
subunit of RNA polymerase 2 that contains the sequence YSPTSPS that was found to be consensus sequence in eukaryotes. The difference is the number of repeats of the motif. Humans have 52 repeats and yeast as 26.
What was found in bacterias small unit?
the 16S rRNA found in the small subunit of bacteria ribosomes showed a detailed secondary strcuture at the 3' end and this binds the mrna Shine-Dalgarno sequence
The 5' end of the anticodon base pairs with what?
the 3' end of the codon
What is most common rna modification?
the addition of a methyl CH3
What two ends are connected in a peptide bond?
the amino end (N-terminal end) of one amino acid and carboxyl end (C-terminal end) of another amino acid form a peptide bond
What does U2 bind to?
the branch point and base pairs to nucleotides across branch points BUT NOT the key adenosine
Mechanisms that control mrna half life regulate what?
the decay mechanism counterbalance trscrption to regulate the aobundacen of mrna in eukaryotes and this ensure proteins are only present in the cells when they are needed
What makes up an operon ?
the operator, the promoter, and the genes they control Need a Control Gene (I), Control Sites (O and P) and Structural genes
postitive regulation
the presence of the bound protein is required for transcription 1. Activator binds Activator-Binding Site and transcription occurs 2. If no Activator then no transcription
mRNA decay occurs via two general pathways that are both initiated by what?
the removal of the poly A tail at 3' end by deadenylase that cleaves phosphodieaster binds between adenosine nucleotides one at a time in the 3' to 5' direction
Where are the binding sites for tRNA in ribosomes?
there are three binding sites for tRNA molecules. With each tRNA bridging the small and large subunits. Anticodon in the small and aminoacyl end (amino acid carrying end) in the large subunit
small nuclear ribonucleoproteins (snRNPs)
these enzymes cut out introns and splice together exons in the pre-RNA
Branch point
third conserved sequence Called brand point located upstream fo 3' splice site. It is an A
Xrn2 is positioned to act in termination?
through its association with the CTD phosphorylated on serine 2
I+ gene product is what?
trans-acting meaning I+/I- will still be repressible since the I+ can produce a repressor that can act on the structural genes on I- chromosome
Why can't attenuation happen in eukaryotes?
transcpription and translation occur at different times whereas in bacertia they are couple so ribosome engagement can effects transcription
What does CTD regulate?
transcription elongation and termination and rna processing events like capping, splicing, cleavage, and polyadenylation
Describe the trp repressor
tryptophan binds trp repressor then trp binds operator and switches it off. High levels of trp results in off of the operon because there is already high levels so no need to create more
How are eukaryotic promotors recognized?
unlike in bacteria where the sigma factor recognized promotor sequences, eukaryotic promotors are recognized by GTFs that first bind sequence and RNA polymerase
What does Dicer do?
uses its PAZ domain to bind the 3' overhang and generate an siRNA from a hairpin or long dsRNA. Uses two endonuclease domains to do that
Once Dicer binds 3' overhang what occurs?
uses its two endonuclease domains to make cuts in the strands that are 21 nucleotides away and staggered by two nucleotides. Dicer can do this multiple times producing multiple siRNAs from a single dsRNA
Compensatory mutation
when 5' splice site is mutated but so is the U1 snRNA so selection of spice sites was recovered