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Exam 3, Share much in common with retro viruses - Coggle Diagram

- - - - EIf4
        
        also cap binding
    - - IF1, IF3
      - eIF1,eIF3,eIF6
    - - IF2
        
        comes with GTP
      - eIF2
    - - eIF5
  - - - EF-Tu
      - eEF1
    - - EF-G
      - eEF2
      - 23 3 S catalyzed movement
        
        ribozyme
    - - RF1, RF2
        
        Rf1
        
        UAA, UAG
        
        Rf2
        
        UAA, UGA
        
        class one
      - eRF1
    - - RF3
      - eRF3
  - - - aliphatic
    - - benzene ring
    - - alpha carbon
      - r group
        
        and hydrogen
        
        switch places to get specific amino acid
        
        such as polar group having a hydroxyl group
        
        charged has an acid amine group
      - Positive terminal (n) and negative terminal (c) never switch
        
        Carboxyl
        
        amino
      - Long chain of amino acids called poly peptide
        
        many peptide bonds
        
        connects carboxyl with amino via release of water
  - - - gene is defective of making this enzyme
  - - - synthesized by biochemical pathway
        
        a bunch of enzymes
        
        plate divided into five sections
        
        wild type grows fine
        
        Each progressive mutant strain had mutated enzyme coding genes
        
        Progressive strains unable to code for next progressive enzyme in the pathway
        
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  - - - Assembles amino acids based on those codes
      - Adapter
    - - brings amino acids based on codes read on the mRNA
    - - always attached to adenine
        
        ester bond
    - - isoacceptor stem
      - 76 nucleotides in tRNA
        
        there will be three stem loops
        
        middle stem loop will have anti codon
        
        hydrogen bonds with codes on messenger RNA
    - - adenine deaminated to give inosine
        
        Sometimes methylated
      - uradins can be modified to give pseudo uradin
        
        pseudo uradin labeled p
      - These modification allow for enzymes that attach amino acid to be attached to tRNA
        
        Amino acyl transfer rna synthetase
        
        20 of these
        
        requires second reading (Reading of tRNA)
        
        2 steps
        
        Activation of amino acid
        
        ATP
        
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        Amino acid
        
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        aminoacyl transfer RNA synthetase
        
        Also can help bind to anti codon
        
        150 nucleotide modification
  - - - rRNA
        
        bulk of ribosome
      - Protein
      - assembled separately in nucleolus
    - - mitochondrial
      - chloroplasts
      - cytosol
    - - 70s coefficient
        
        small subunit
        
        30s
        
        16srRNA
        
        comp to sd
        
        21 proteins
        
        large subunit
        
        50s
        
        23srRNA
        
        34 proteins
        
        5 srRNA
    - - 80s
        
        large sub unit
        
        60s
        
        5.8 srRNA
        
        28 srRNA
        
        49 proteins
        
        small subunit
        
        40s
        
        18srRNA
        
        33 proteins
    - - large sub unit
        
        A site
        
        Aminoacyl site
        
        All following tRNA enter through A site
        
        P site
        
        Peptidyl site
        
        1st TransferRNA that does process of translation enters here
        
        Methionine is always the amino acid bound to the transfer RNA so that is why it is marked
        
        E site
        
        Exit
  - - - mimic will cause end
- - - - Both parental strands of DNA remain together following DNA replication
      - Original arrangement is conserved and daughter strands remain together
    - - Double stranded DNA is half conserved following the replication process
      - Newly made DNA contains one parental strand and one daughter strand
    - - Mix of parental and daughter DNA within one strand
    - - N15 represented parental while N14 represented daughter
      - First gen showed half heavy so conservative and semiconservative were possible
        
        Second gen showed half heavy and half light which is only consistent with semi conservative
  - - - Capable of doing double stranded break and therefore can relieve
    - - Three sequences within OriC region
        
        DnaA boxes
        
        Causes the two strands of DNA to separate
        
        Also need DnaA proteins
        
        Bind to DnaA boxes in the form of 20-40 DnaA ATP complexes
        
        DnaA wraps around protein and tension causes first break in two strands
        
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        There are 5 DnaA boxes
        
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        THIS SHIT IS NOT RELATED AT ALL TO ADNA DO NOT MIX THIS UP YOU FUCKING DUMBASS PIECE OF SHIT FUCK YOU
        
        AT Rich region
        
        GATC methylation sites
        
        Every adenine in GATC site must be methylated
        
        Methylation of cytosine is silencing transcription while methylation of adenine is beginning replication
    - - Polymerase
        
        Two drawbacks
        
        Cannot initiate synthesis
        
        Can only catalyze the addition of nucleotides in 5' to 3' direction
        
        incoming nucleotides can only be attaches to 3rd carbon of pre-existing sugar
        
        How many polymerases are present in bacteria
        
        Eukaryotes have 12
        
        Prokaryotes have 5 distinguished by roman numerals
        
        we only look at 1 & 3
        
        DNA polymerase 1
        
        is only made of one subunit
        
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        DNA polymerase 3
        
        Made of several protein units
        
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        2,4,5 are involved in repair
        
        Dna polymerase 3 continues synthesis in 3' direction
        
        DNA polymerase 1 will remove RNA primer and substitute with DNA nucleotides
        
        As this substitution is done, one phosphodiester bond will be missing between strand made by DNA polymerase 1 & 3
        
        This ester bond will be catalyzed by an enzyme called DNA ligase
        
        Eukaryotes
        
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        prokaryotes
        
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        If a strand is synthesized in the 5' to 3' direction the template is 3' to 5'
        
        Strand types
        
        Leading strand
        
        One RNA primer is made at the origin, DNA pol III attaches nucleotides in a 5' to 3' direction as it slides toward the opening at the replication fork
        
        By looping template parent strand strand in small segments you can reverse direction of strand
        
        Each fragment formed with each fragment formed with each loop is 1000-2000 bp loop
        
        Lagging strand
        
        Template loop in the form of Okazaki fragments
        
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        This strand will have hyperactive DNA ligase and primase
        
        There is very little time lag between leading strand and lagging strand
        
        3' and 5' refer to the carbon of the nucleotide which is being added to
        
        DNA can only be added on the 3' carbon
        
        Nucleotides come in the form of triphosphate
        
        For example: deoxyadenosin triphosphate, two phosphates will be released because of water in cell (hydrolysis)
        
        Monophosphate will form ester bond
        
        This bond break actually provides the energy
      - Because DNA polymerase cannot initiate synthesis DNA primase comes in first
        
        similar to RNA polymerase
        
        Makes tiny strand (10-12 RNA nucleotides)
        
        These are called RNA primer
    - - Takes place at a point opposite of the ORiC sequence
        
        Replication goes both clock and counterclockwise
        
        When replication forks meet it is region opposite to where it started
        
        Replication ends because everything is replicated and no template remains
        
        Intertwined circles released by topoisomerase II as topoisomerase I can only perform single strand break
        
        decatenation
      - TER sequence
        
        There are two ter sequences on double stranded DNA. One strand complementary to the other
        
        TER sequences on own do not stop replication
        
        Must be bound by protein called termination utilizing substance (TUS)
        
        Only one TUS needed for two ters sequences
        
        Any particular Tus protein will either allow for counter or clock fork to continue but never both as they would overlap
        
        ASK ABOUT AT OFFICE HOURS TMMRW
      - DNA replication often results in two intertwined molecules called catenases
    - - Primosome
        
        Helicase and primase
        
        First enzymes to come into a non-covalent association
      - Replisome
        
        DNA polymerase III holoenzyme
        
        associated with the primosome
    - - multiple systems in place
        
        instability of mismatched base pairs
        
        A&T 2H bonds
        
        C&G 3H bonds
        
        Due to instability they will not form ester bond in the opposite strand
        
        Configuration of polymerase
        
        Error rate 1 per 1000 nucleotides
        
        Alpha subunit which catalyzes the formation of phosphodiester bonds
        
        If the DNA strand is distorted it will not fit in the domain of the alpha subunit and will not allow phosphodiester bond to form
        
        This reduces the error rate to 1/100,000 to 1 million
    - - one replication takes 20-200 minutes (30-40 minutes average)
        
        How is this regulated?
        
        Methylated strand of GATC is parent while non methylated is daughter strand
        
        together they make hemi methylated DNA
        
        When bacteria has grown and is ready to replicate enzyme called DNA adenine methyl transferase converts hemi methylated strand to fully methylated strand
        
        This is the control
  - - - The question was why does DNA replication still occur even with mutated DNA polymerase I
        
        Experiment:
        
        Expose bacteria to mutagenic agent
        
        Put on AGAR plate
        
        Take round velveteen sheet and touch with colonies
        
        One in permissive
        
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        One in non permissive
        
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        Slow stop mutants
        
        mutations in initiation process
        
        Rapid stop mutants
        
        mutations in replication process
  - - - Each is about 150-200 bp long in bacteria
        
        ORiC
      - In Eukaryotes each is about 50 bp
        
        ARS (Autonomously replicating sequence
      - Three or four copies of the same sequence (many As and Ts)
        
        Similar to bacterial A boxes
    - - The first part of the preRC formed is the ORC (origin recognition complex)
        
        Combines with ATP and allows for helicase attachment
        
        Similar to DnaA ATP complex
        
        Promotes the binding of
      - Present from end of mitosis until G1 phase
        
        getting ready to assemble onto ARS
      - 14 proteins
        
        6 member protein
        
        Cell division control protein
        
        Homolog 6 or protein 6 homolog (also arrives with ATP)
        
        CDT 1
        
        Controls chromosome licensing and DNA replication
        
        MCM helicase (complex of 6 proteins)
        
        All of these proteins assembled by end of G1 phase
        
        Then DNA replication licensing occurs
        
        Ensures entire stretch of protein replicated once and only once
        
        ASK ABOUT THIS AT OFFICE HOURS
        
        MCM helicase is bound at origin of replication allowing formation of two replication forks
        
        This occurs during the G1 phase
        
        s phase
        
        Then Firing occurs
        
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    - - Normal replication in prokaryotes involves 2 polymerases (1 &3)
        
        (five overall)
      - Normal replication in eukaryotes involves four
        
        (over a dozen overall)
        
        Alpha
        
        Delta
        
        All 3 nuclear
        
        Epsilon
        
        Gamma
        
        Mitochondrial
        
        PCNA acts as a clamp and allows DNA polymerase to move
      - Very specific polymerases deal with errors
        
        DNA polymerase Kappa
        
        Remove any kind of mismatched bp because of benzokirene (that is not what it is)
        
        DNA polymerase Beta
        
        Involved in base excision repair
        
        If one mismatched pair will be removed and put in correct bp
        
        DNA polymerase eta
        
        Removes thymine dimers that occur from sunburns and such
        
        Translesion polymerases
        
        Work on original DNA strand rather than on the replicated strand
        
        Daughter strand of other template strand used as template
        
        Unlikely to have errors as unwinding is usually when errors occur
        
        Will stall otherwise
        
        ASK ABOUT THIS AT OFFICE HOURS
    - - Keeps strands separated
        
        Just like single strand protein in prokaryotes
    - - Prokaryotes just have DNA primase responsible for synthesizing the first strand of DNA
        
        Eukaryotes also have DNA primase
        
        However, it is present in complex with DNA alpha polymerase
        
        Always synthesizes 10 bp RNA strand followed by a 20-30 bp strand of dna (overall 30-40 bp long strand)
        
        Alpha polymerase will then detach and be replaced by either a delta or an epsilon polymerase
        
        This is known as a polymerase switch
        
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        Associated with primase and helicase (primosome)
        
        forming the replisome
      - Beta subunit of DNA polymerase III in prokaryotes was responsible for processivity
        
        Eukaryotes do not have that
        
        Processivity in eukaryotes
        
        proliferating in Euks= Proliferating cell nuclear antigen (PCNA)
      - DNA polymerase I in proks removes RNA primer
        
        DNA ligase catalyzes phosphodiester bond in prokaryotes (NAD+ source of energy)
        
        Ligase still functions in Eukaryotes
        
        Catalyzes the formation of ester bonds in strands synthesized by alpha epsilon or delta DNA polymerase
        
        Eukaryotes use ATP rather than NAD+
      - How are the ends of Eukaryotic chromosomes replicated
        
        Telomerase
        
        telomerase RNA component (TERC)
        
        Acts as template to help synthesize the overhang
        
        Three nucleotide segment of RNA comes and binds to complementary DNA
        
        Synthesizes a 6 nucleotide long DNA repeat strand
        
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        enzyme
        
        Telomerase reverse transcriptase
        
        Comes and binds first
        
        Focused on as cure
        
        3' overhang
        
        at telomeres
        
        12-16 nucleotides in length
        
        too short to form RNA/DNA primer
        
        DNA polymerase
        
        Only synthesizes in 5'->3' direction
        
        Cannot link together first two individual nucleotides
        
        loops are 100-200 bp long
        
        If this problem was left unsolved telomeres would get progressively shorter (full length of DNA would not be replicated)
        
        blood cell and skin cell telomeres would get small
        
        rapid proliferation
        
        uncontrolled cell division diseases
        
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        Length does decrease in normal cells
        
        5'->3' template
        
        5' 3' template
        
        loops are meant to be 100-200 bp
    - - Form into octamers
      - Mixture of old and new upon replication
  - - - Endosperm
        
        Triploid
        
        two haploid nuclei from the mother one from the father
    - - Corn
        
        Colorless Kernel
        
        Colored Kernel
        
        Dominant
        
        Plant with one copy of the dominant allele
        
        Found kernels that were white/ colorless and some colored here and there
        
        hypothetically should be all colored
        
        sequence split aside by presence of dissociation sequence
        
        dissociation sequence not has gone past that sequence when colored
        
        Colored gene on chromosome 9
        
        Found interesting sequence in between
        
        dissociation sequence
        
        highly transposable element
        
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    - - Simply as a DNA sequence
        
        transposon
        
        chances much lower than retro transposon
      - RNA intermediate
        
        DNA copied into an RNA
        
        RNA reverse transcribed to DNA
        
        Then inserted
        
        Retro transposon
        
        Many more copies can be made
        
        RNA sequences are shorter
    - - two sequences on either side (inverted sequences)
        
        identical sequences opposite and below on either side
        
        Next to these (outside) direct sequences
        
        these are identical
        
        these are also on retro transposons
        
        allow to be identified
      - simple transposons
        
        have other genes not neccesary
      - highly repetitive if small moderately repetitive if larger
      - simple transposition
    - - long terminal repeats (LTR)
        
        most important enzyme
        
        Integrase
        
        Reverse transposase
      - non LTR retrotransposons
        
        inverted and direct repeats are not usually present
        
        Can start from any eukaryotic gene
        
        something like a reverse transcriptase but usually functions more like an endonuclease
        
        genes capable of identifying sequences within DNA and making cuts
        
        Alu family of genes has no viral origin for example
        
        May encode gene that functions both as reverse transcriptase and endonuclease
        
        Whenever mRNA transcript is made
        
        two modifications
        
        5' methylguanosine cap
        
        stabilizes mRNA
        
        3' end (200 nucleotides with adenine as nitrogenous base)
        
        PolyA tail
        
        Allows RNA to find out specific locations in DNA that have similar sequence
        
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        binds to Ts in DNA sequence
        
        creates tilt
    - - non-autonomous
        
        Look at dissociation sequence
        
        Cannot move anywhere
        
        without activator sequence (AS)
        
        transposase will bind to the inverted sequence
        
        proteins bind to identical sites on DNA and loop the DNA
        
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- - - - Double Helix model
        
        Sugar/ Phosphate on outside in contact with water
      - Face inward
      - Purines
        
        Two carbon
        
        Adenine and Guanine
      - Pyrimidines
        
        One carbon
        
        Thymine and cytosine
    - - Scientists
        
        Linus Pauling
        
        Found two common structures seen
        
        Alpha helical
        
        Both involve hydrogen bonds
        
        Used ball and stick to find structure
        
        Beta Region
        
        Maurice Wilkins/ Rosalind Franklin
        
        Would purify and wet DNA
        
        Expose to X-Rays
        
        Refraction pattern verified the double stranded and helically coiled rather than single stranded
        
        10 bp per turn
        
        Erwin Chargaff
        
        More interested in the role played by the nitrogenous bases (a,t,c,g)
        
        Took cells from species of different organisms
        
        Exposed to detergent to promote all unwanted components and isolate chromosome
        
        Remove histones= treat with protease
        
        Just DNA
        
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        Watson and Crick
        
        Incorrect hypothesis
    - - Mg++ crosslinks
    - - BDNA
        
        Most stable
        
        Right handed coiled double helix
        
        10 bp per turn but actually 10.5 technically
        
        Nitrogenous bases arranged perpendicular across a central axis
        
        Grooves
        
        Space filling model
        
        Every atom considered to be a sphere
        
        So each time a right handed turn takes place there is a physical groove that forms
        
        Proteins targeting binding sites typically target major groove
      - ADNA
        
        Also Right handed
        
        Not seen often but in low humidity
        
        Occurs when there are many Cs in a sequence especially
        
        When bacteria are exposed to hazardous conditions they make endospore capable of withstanding harm created by UV radiation
        
        Accomplished by taking on A form
        
        Occurs with many terminal repeats (transposable elements) (moderately repetitive and highly repetitive
        
        seen in RNA DNA hybrid primer
      - ZDNA
        
        Much thinner, no distinctive grooves
        
        Left handed
        
        12 bases per turn
        
        Phosphates have zig zag orientation
        
        brought closer together
        
        causes them to repel each other
        
        Often seen at transcription sites
      - DNA can also form a triple helix
        
        Enzymes in yeast have capacity to bind to triplex DNA
        
        We can artificially induce third strand of DNA to bind to major strand
        
        This stops replication, transcription, and recombination
  - - - Different than dioxynucleotide because of sugar
        
        in ribose 2nd carbon has the hydroxyl group and a nitrogenous base added to the first carbon
        
        as opposed to deoxyribose
    - - RNA have complimentary regions interspersed w/ non complimental regions you will have several types of loops formed
        
        Loops form where there is absolutely non complimentary
- - - - Transcription is the first process
        
        Two major aspects
        
        Proteins recognize these sequences and carry out the process
        
        DNA sequences provide underlying information
        
        Sequences along the DNA
        
        Promoter sequence
        
        Promotes transcription
        
        Site where transcription factors come and assmeble
        
        2 more items...
        
        RNA polymerase binds after (in the case of prokaryotes)
        
        2 more items...
        
        Points out the start site of transcription
        
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        Only present along the DNA
        
        Major group sequences
        
        At -35 there is TTGACA
        
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        AT -10 there is TATAAT
        
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        Transcription also involves unwinding of DNA just like replication
        
        But does not copy DNA into DNA
        
        Copies DNA into an RNA
        
        (No change to the DNA during this process)
        
        RNA are complimentary to the template strand (no uracil in DNA)
        
        Will be similar to the coding strand
        
        Unwinding still where errors are most likely (replication still has higher likelihood of error)
        
        Structural genes
        
        Only a small percentage of uniquely repetitive sequences are structural
        
        Transcribes but also translates
        
        Large number of genes make RNA that do other functions
        
        What are the most common RNA other than mRNA
        
        Ribosomal
        
        Transfer
        
        Signal recognition
        
        Secretory proteins start synthesis in cytosol then continue and complete on rough ER
        
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        What are less common RNA other than mRNA
        
        Small cytoplasmic RNA (SCRNA)
        
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        Rnasep ribosome
        
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        SnRNA
        
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        SnoRNA
        
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        Viral RNA
        
        Actual transcription process
        
        Elongation
        
        Adding on RNA nucleotides based on nucleotides present in DNA
        
        Sliding of RNA polymerase begins at +1 nucleotide
        
        Template is 3' to 5'
        
        Synthesis is 5' to 3'
        
        Copying of DNA into RNA
        
        As copying of DNA takes place it forms a transcription bubble
        
        length of about 17 bp (open complex)
        
        2 more items...
        
        Rate of synthesis about 43 bp per sec into prokaryotes
        
        Initiation
        
        Transcription factor allows RNA polymerase (holoenzyme made of many polypeptides) to bind to and identify promoter sequence
        
        Binds at one end causing denaturation at other end
        
        Similar to DnaA boxes
        
        One segment of promoter sequence unwinds DNA when RNA polymerase and promoter sequence bind
        
        Often times in prokaryotic genes the promoter sequence may control several gene sequences
        
        Polycistronic DNA
        
        Core Enzyme= 5 subunits
        
        Two alpha subunits of the RNA polymerase catalyze the attachment of transcription factor onto the RNA polymerase
        
        Two Beta subunits ( beta and beta') catalyze phosphodiester bond s between nucleotides
        
        Omega keeps the two betas and the two alphas together
        
        Has quaternary structure
        
        2 more items...
        
        Termination
        
        There is a termination sequence but that is not what causes the termination
        
        Rather it is the instability between the RNA and the DNA strand that signals termination
        
        Two different kinds
        
        Rho dependent
        
        In mRNA there is a small sequence called Rho utilization substance
        
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        A stem loop is formed where termination sequence is present along the DNA
        
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        Rho independent
        
        (no rut is present)
        
        1 more item...
        
        Stem loop will still stall
        
        Many Uracil present at the 3' end
        
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    - - Unit of heredity usually
      - For gene expression
        
        a transcriptional unit
    - - Sense strand (coding strand)
      - Template strand (anti-sense strand)
        
        Template is 3'-> 5' :
    - - Transcription
        
        Problems with eukaryotic transcription
        
        Larger organisms
        
        cellular complexity
        
        multicellularity
        
        One very long protein seen in all transcription processes
        
        Mediator
        
        does not bind to the DNA
        
        Mediates the effect of regulatory factors on the rate of transcription (especially influences TFIIH and its capacity to phosphorylate carboxyl terminal domain)
        
        Silences gene expression
        
        (TFIIH cannot fall off)
        
        Termination
        
        It is still the instability between DNA and RNA that causes termination
        
        Sequence 500-2000 bp downstream from AAUAAA will stop termination
        
        LOOK FOR THIS SEQUENCE TO DETERMINE THAT IT IS A EUKARYOTE
        
        PolyA signal sequence
        
        Exonuclease and endonuclease look for this if non existent will be digested
        
        1 more item...
        
        Two models to explain Eukaryotic termination
        
        Allosteric Model
        
        500-2000 bp past poly A either elongation factors drop off or termination factors hop on
        
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        Torpedo model
        
        Similar to the Rho dependent model in prokaryotes
        
        When RNA poly passes 500-2000 past poly A an exonuclease hops on the RNA and starts digesting nucleotides in RNA
        
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      - Nuclear DNA is transcribed by three different RNA polymerases
        
        RNA polymerase II
        
        All of the structural genes and RNA that are parts of spliceosomes
        
        Transcription factors
        
        TF IID
        
        First transcription factor to identify TATA box
        
        Has certain proteins that can identify (TATA box binding proteins)
        
        1 more item...
        
        TF IIA
        
        Will regulate the binding of transcription factor IID with TATA box
        
        Can be put in either order
        
        TF2B
        
        will recruit RNA polymerase II w/ TF2
        
        TFIIH and TFIIE
        
        TF2H has a polypeptide that does the function of helicase and ATP and Kinase activity
        
        helps switch from initiation to elongation by hydrolyzing ATP & phosphorylation a specific sequence in the carboxyl terminal domain within the RNA polymerase (a 7 amino acid sequence tail repeated 52 times in Eukaryotes (similar to tandem repeats).
        
        2 more items...
        
        Once these are assembled initiation is over
        
        When all bind it creates stress forming an open complex
        
        TFIIF
        
        Remains attached to RNA polymerase during first part of elongation
        
        Basal transcription apparatus
        
        RNA polymerase III
        
        All of transfer RNAs and 5sRNAs
        
        RNA polymerase I
        
        Synthesizes all of the rRNA aside from 5sRNA
      - Core promoter
        
        TATA box (TATAAAA)
        
        Much less than the 50 bp of prokaryotes
        
        There is still a transcriptional start site up stream
        
        Upstream from that there is usually a regulatory sequence (50-100 bp)
        
        Two types
        
        Enhancer
        
        Reulatory
        
        One mutated gene for an activator can be overcome by a regulator and vice versa
        
        Trans effect
        
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        Promoter site mutation cannot be overcome as it is necessary for transcription to occur
        
        cis effect
      - RNA modification
        
        Not as simple as in Prokaryotes
        
        For normal reasons but additionally several steps of regulation
        
        Absence of colinearity between DNA and RNA sequence (there is colinearity in prokaryotes
        
        Sequences (introns are lost in transcription from pre RNA to mRNA
        
        Splicing exons
        
        RNA modification that takes place in the nucleolus
        
        Nucleolus has two functions
        
        ribosomal subunits are assembled
        
        2Genes that deal with rRNA
        
        Trimming
        
        Transcript has sequence for three different rRNAs
        
        3 more items...
        
        Transfer RNA takes place in the nucleus
        
        Also made from a large transcript
        
        Many enzymes present
        
        First enzyme comes at 5' end
        
        endonuclease called Rnase P
        
        2 more items...
        
        second endonuclease
        
        Rnase 2
        
        1 more item...
        
        third endonuclease
        
        Rnase D
        
        1 more item...
        
        Transfer RNA is known as an adaptor molecule
        
        (reading nucleotides) Assembles sequence of amino acids that is then attached to adenine
        
        Some tRNA do not have this sequence
        
        Additional enzyme (transfer RNA nucleotidal transferase) brings particular sequence and then assembles (primarily attaches to amino acid)
        
        Adapts to nucleotide sequence
      - Splicing (kind of)
        
        mRNA will hybridize with split DNA faster than the other strand of DNA
        
        First will form hydrogen bonds with first exon but will then be unable to form hydrogen bond with the introns
        
        Will push the intron. The intron will then form loop.
        
        of these loops= # of introns
        
        Second strand of DNA will be able to form hydrogen bonds with these loops of DNA but not with the exons which are bound to mRNA
        
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        Experiment
        
        Uses formamide to separate DNA and allow mRNA to hybridize
        
        Intron Splicing (for real)
        
        Group I
        
        Can be seen in Bacteria, Archaea, Eukaryotes, Organelles
        
        Mostly Eukaryotic organelles
        
        Intrinsic Splicing
        
        Do not need proteins
        
        Self splicing (act as own ribozyme)
        
        Sometimes maturase catalyzes
        
        Guanosine comes from outside and binds to intron sequence
        
        Guanine plus sugar
        
        Third carbon will bind at first nucleotide of the 5' end of the intron (3' end of exon)
        
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        Group II
        
        Nothing comes in as in the case with Guanosine in Group I (no external nucleophilic molecule)
        
        Within the intron there is an adenine
        
        The orientation will be such that second carbon of sugar will react at 5' end of intron and form laureate
        
        Once laureate forms and turns (twists around itself) the 3' end of the intron will break off
        
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        Spliceosomes
        
        may have evolved from intrinsic splicing
        
        RNA polymerase II will be involved in spliceosome complex
        
        Two components form the spliceosome complex
        
        rRNA
        
        small nuclear proteins
        
        snRNPS (small nuclear RNA and set of proteins)
        
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        Factors that regulate spliceosomes
        
        Splicing factors
        
        One example is the SR proteins
        
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        Alternative splicing
        
        Introns may increase stability and may allow for alternative splicing
        
        Lower eularyotes see very little alternative splicing
        
        Higher eukaryotes such as ourselves see 70% of genes have alternative splicing
        
        More cellular complexity
        
        Some exons must be present no matter what but some are organ dependent
        
        DNA sequence then makes pre mrna
        
        Those present in all mRNA
        
        Constitutive mRNA
        
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        Remove intron RNA and link Exon RNA by a phosphodiester bond
    - - DNA enters through the open mouth
        
        Triphosphates come in through the open pore
        
        Pyruphosphates are released and monophosphates form an ester bond
        
        same as in the case of DNA replication
        
        Catalytic subunit
        
        A lot of magnesium and nucleotide pore
      - Clamp
        
        Right handed wall allows DNA to move through the clamp and control rate of synthesis
      - Rudder
        
        Dissociates DNA from RNA nine nucleotides after RNA is formed
    - - occurs when translation is only 20-25 bases long
        
        If there is no capping then the mRNA will not be released from the nucleus
      - Capping first takes place on the first nucleotide of triphosphate (RNA 5' triphosphotase is first enzyme made (going to remove one of the phosphates).
      - Then GTP will arrive and bind to phosphates (brought by guanylyl transferase (then two phosphates are released as pyrophosphate and are left with a Guanine monophosphate attached)
      - Then attach methyl group to the seventh position of the guanine (nitrogenous base (via a methyl transferase)
        
        7 methyl guanosine cap
        
        seen by gatekeepers to allow passing
    - - Involves deletion or replacement of a specific type of nuceotide
      - Apoliprotein B
        
        In liver
        
        B 100
        
        Change from CAA to UAA results in shorter protein
        
        In small intestine
        
        B 48
  - - - Proteins are then tools of gene expression
  - - - Ribosomal binding site