BIOL 3451 1st Edition Lecture 17 Outline of Last Lecture I. 13.2 Early Studies Established the Basic Operational Patterns of the CodeII. 13.3 Studies by Nirenberg, Matthaei, and Others Led to Deciphering of the CodeIII. 13.4 The Coding Dictionary Reveals Several Interesting Patterns among the 64 CodonsIV. 13.5 The Genetic Code Has Been Confirmed in Studies of Phage MS2V. 13.6 The Genetic Code Is Nearly UniversalVI. 13.7 Different Initiation Points Create Overlapping GenesVII. 13.8 Transcription Synthesizes RNA on a DNA TemplateVIII. 13.9 Studies with Bacteria and Phages Provided Evidence for the Existence of mRNAIX. 13.10 RNA Polymerase Directs RNA SynthesisX. 13.11 Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several WaysOutline of Current Lecture I. 13.11 Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several WaysII. 13.12 The Coding Regions of Eukaryotic Genes Are Interrupted by Intervening SequencesIII. 13.13 RNA Editing May Modify the Final TranscriptIV. 13.14 Transcription Has Been Visualized by Electron MicroscopyV. 14.1 Translation of mRNA Depends on Ribosomes and Transfer RNAsVI. 14.2 Translation of mRNA Can Be Divided into Three StepsCurrent LectureI. 13.11 Transcription in Eukaryotes Differs from Prokaryotic Transcription in Several Wayso Table 13.7o RNA polymerase II (RNP II): responsible for wide range of genes in eukaryotes- Has to recognize everything that is a protein- Has core promoter: somewhat small, determines exactly where RNP II binds (if bind, then where binds); can’t do it without core promotero Other types of sequences - proximal-promoter elements Because other sequences can be enhancers and act at a distance; has massive increase in activity; a. Changed activity of promoter when doesn’t have anything stimulating it from 1 to 100.  Silencers: cut it back; do the opposite of enhancers in a waya. more up and down, rather than on and offThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- TATA box: core promoter element that binds to TATA-binding protein (TBP) of transcription factor TFIID and determines start of site of transcription Looks like a 10- sequence Have to have TBP, just don’t have to have TATA box to bind with TATA-less promoters are more variable in starting spoto Enhancers and Silencers- Can be upstream, within (middle-), and downstream of gene Why be within….because of introns Many of these sequencers are conserved (meaning they are really important)- In order for them to work, need to bind with protein- Can increase or decrease transcription depending on cell’s requirement- Modulate transcription from a distanceo 2 broad categories- General transcription Factors: necessary, but not sufficient; framework for activators to act, but in and of itself, it can’ turn gene on and off- Transcription activators and repressors: influence efficiency (meaning turn on and off)o RNA polymerase opens up and separates (by denaturation) strand so template strand can pass through active site during RNA synthesis; then, hits termination andRNA enzyme complex separateso Transcripts that have incompletely processed results in heterogeneous nuclear RNA- Can have a dozen or more bands in between largest (just removed from DNA) and smallest (processed first)- Add 5’ cap to protect- Add poly-A tail to help transcript get out of nucleus and to cytoplasm- Introns removed by splicing- Fig 13.10: II. 13.12 The Coding Regions of Eukaryotic Genes Are Interrupted by Intervening Sequenceso Introns: intervening sequences are regions that are removed by splicing - Size of mature RNA usually much smaller than initial RNA (introns can be really large) Further you go down in simplicity of eukaryotes, the less introns used andsize of them decreases Fig. 13.12: note how much larger the introns are Table 13.8: shows size comparisons of RNA, gene size, and # of intronsa. Dystrophin: gene affected in X-linked muscular dystrophy; used to be largest gene discovered (over 2 million bases): why so fairly common because it IS so long and there are many places for mutations to hitb. Often have multiple promoters (in eukaryotes)o Pre-mRNA introns are spliced by spliceosome in a reaction involving formation of a lariat structure (Fig 13.14)- RNA could have been original catalysts (not enzymes) because makes more simple DNA replaces RNA as genes, and proteins are better at catalyzing (so now that’s what we have=this is a theory)- Fig 13.14: certain Us are important for intron-exon junctions GU on left junction (5’) AG on right junction (3’) These are always conserved A is in the middle at branch point, and if taken out, they can bind to another A close by and use it (though they may not be happy) Connected two branches in RNA (which is normally not branched)III. 13.13 RNA Editing May Modify the Final Transcripto Splicing: removing something from the middleo Editing: changed the sequence- 2 types: Substitution editing: identity (base) is altered; done by oxidization (oxidizethe C and get Uracil; thus it can change what protein it codes for) Insertion/deletion editing: nucleotides can be added or deleted in the middle (within exons); much more complex than substitutionIV. 13.14 Transcription Has Been Visualized by Electron Microscopyo RNA strands come from many transcription events happening along each gene- Ribosomes attached next to RNA polymerase and more ribosomes on it (polyribosomes) Happens in both prokaryotes and eukaryotes Fig 13.15: spacing not as open as shown in picture; thus, there are more like bubbles where parts have reattachedV. 14.1 Translation of mRNA Depends on Ribosomes and Transfer RNAso Translation: biological polymerization of amino acids into polypeptide chains- Need: Amino acids mRNA tRNA Translation factors/ribosomes- *When say Factor, means protein; and element means amino acid sequence*- tRNAs:  have anticodon that complement mRNAs carry corresponding amino acid small in size and very stablea. about 75-90 nucleotidesb. can have introns, but not usually transcribed from DNA and contain posttranscriptionally modified basesa. modify bases enhances hydrogen bonding efficiency during translation 2-dimensional structure is cloverleaf (but it is wrong; just easier