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