BMB 251 1st Edition Lecture 18 Outline of Last Lecture I. Homologous RecombinationII. Strand invasion III. DNA renaturation IV. HeteroduplexV. RecA/Rad51 proteinsVI. Review from in-class for Exam Two materialOutline of Current Lecture VII. ClickersVIII. Central dogmaIX. RNAX. Transcriptiona. RNA polymeraseb. mRNAc. rRNAd. tRNAe. snRNAf. RNA holoenzymeg. RNA core enzymeh. Sigma factorXI. Promoters/terminatorsCurrent Lecture- Clicker Question 1: You would then surmise RNA polymerase… o Synthesizes 5’ to 3’ and reads the template strand 3’ to 5’- Clicker Question 2: The promoter is found:o On the 5’ side of the gene, on the coding strando Nature doesn’t know about template and coding, we read the sequence on the coding strand, sequence is always the coding strand because we made it up and decided to do itthat way- DNA in genomes does not direct protein synthesis directly  uses RNA as intermediaryo When cell needs a protein, DNA is transcribed into RNA, which is then translated into the protein via direct synthesis (this is known as the central dogma)- RNA transcripts in eukaryotes are subject to series of processing steps (such as RNA splicing) before they can leave the nucleusThese 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.- Many RNA’s can be the final structure  folding into 3D conformations resembling those of proteins (serves structural, catalytic, and regulatory roles in the cell)- Many identical RNA copies can be made from the same gene that code for the same protein  proteins can be synthesized rapidly and in large quantities when needed- RNA: linear polymer made up of four different types of nucleotide subunits linked by phosphodiester bondso Differ from DNA by: Nucleotides in RNA are ribonucleotides (containing the sugar ribose) Use uracil base in place of thymine  RNA = single-stranded, therefore, RNA can fold up on itself like a protein- Transcription: begins with opening and unwinding a small portion of DNA double helix as template for RNA synthesiso RNA chain has covalently linked bases and elongates one nucleotide at a timeo RNA strand does not remain H-bound to DNA; it is replaced and DNA double helix reforms, allowing RNA to be released from the DNA templateo RNA is much shorter than DNA (a few thousands of nucleotide bases compared to the approximate 250 million on a DNA molecule)o RNA polymerase: enzyme that performs transcription (catalyze the formation of phosphodiester bond)  **RNA polymerase unwinds DNA (NOT HELICASE!!!)  Growing RNA chain is extended one base at a time in the 5’ to 3’ direction  Substrates = nucleoside triphosphates  high energy bonds provide energy needed to drive the reaction RNA polymerase can start DNA chain without use of primers RNA polymerase can still proofread: if wrong nucleotide is added, polymerase can back up and its active site can then perform an excision reaction similar to that of reverse polymerization- Other than Mg2+ in catalytic sites, DNA and RNA polymerases seem unrelated to one another- Messenger RNA (mRNA): RNA molecules directly copied from DNA-coding sequences- Small nuclear RNA (snRNA): direct splicing of pre-mRNA to form mRNA- Ribosomal RNA (rRNA): core of ribosomes- Transfer RNA (tRNA): form adaptors that select amino acids and hold them into place on ribosome for incorporation into protein- Transcription unit: each transcribed segment of DNAin bacteria: RNA polymerase core enzyme = multisubunit complex that synthesizes RNA using DNA as a guide (**detachable subunit = sigma factor, which associates with core enzyme and assists in reading signals in DNA of where to start)- RNA polymerase holoenzyme: combination of sigma factor and core enzyme slides along DNA rapidly until promoter is found and then it binds onto DNA tightly - After about first ten nucleotides, core enzyme breaks interaction with promoter, weakens its interaction with sigma factor and synthesizes conformational changes of RNA polymerase holoenzyme and DNA - Termination signal consists of a string of A-T nucleotide pairs proceeded by a “two-fold symmetric” DNA sequence  forms hairpin in RNA- Consensus nucleotide sequence: common features between promoters recognized by sigma factor; compares many sequences with the same basic functions and tallies up most commonnucleotide found at each position (aka summary or average of large number of individual nucleotide sequences)- Promoters for genes that encode for abundant proteins = much stronger than those associated with genes coding for rare proteins - Terminator sequences = even more heterogeneous than promoter because almost an unlimited number of nucleotide sequences have the potential of forming hairpins - A gene typically only has one promoter and because promoter’s nucleotide sequence is asymmetric, RNA polymerase can only bind in one orientationo Polymerase synthesizes RNA in the 5’ to 3’ direction can only transcribe one strand per geneo **The DNA strand used for RNA template varies from gene to gene, depending on the location and orientation of the