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Molecular Week 4 Notes

by: Kiara Lynch

Molecular Week 4 Notes Bio 413

Marketplace > La Salle University > Biology > Bio 413 > Molecular Week 4 Notes
Kiara Lynch
La Salle

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These notes cover the information covered during week 4 (2/8-2/12; info from Chapter 6)
Dr. Stefan Samulewicz
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This 3 page Class Notes was uploaded by Kiara Lynch on Wednesday February 17, 2016. The Class Notes belongs to Bio 413 at La Salle University taught by Dr. Stefan Samulewicz in Spring 2016. Since its upload, it has received 21 views. For similar materials see Molecular in Biology at La Salle University.

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Date Created: 02/17/16
CHAPTER 6: How Cells Read the Genome: From DNA to Protein  Pathway from DNA to protein o Transcription: DNA to RNA o Translation: RNA to protein o Expression of genes  Some genes are expressed at higher levels  When they are activated and how much they are expressed leads to different phenotypes  Ex: If gene A is transcribed and translated much more efficiently than gene B, A has a higher level of expression (more protein) than B  RNA structure o Ribose instead of deoxyribose- ribose has an additional hydroxyl group o Uracil instead of thymine- absence of CH3 group in uracil that is in thymine  Uracil base pairs with adenine  Caution: making many copies can lead to silent mutations  However, RNA is temporary and multiple codons can code for one amino acid, so proofreading is not needed. o Phosphodiester chemical linkage between nucleotides in RNA is the same as in DNA o RNA can fold into specific shapes  Internal base pairing  Folds like protein and can form domains  Interact with other molecules like enzymes o Needed for transcription:  Building blocks  Nucleases  Polymerase/ligase  Prokaryotic RNA Polymerase o Eukaryotic and prokaryotic RNA polymerases look identical o Attracted to promoter region o Requires  Double stranded DNA template  4 activated precursors (GACU)  Divalent metal ion- usually Mg or Mn o Doesn’t require free 3’ hydroxyl like DNA polymerase o Rutter peels new RNA sequence off DNA o Copies exons and introns: not copying whole genome, only segments o Consensus sequence in promotor (-35)  TATA box (-10)  downstream effects  In eukaryotes, the TAT box is further upstream (-25), CAT box (- 75), enhancer sequence can be located anywhere o Evolution  Double-psi barrel antiparallel beta sheet  Dimerization and insertion of large loops  Acquisition of 2 lysines to position template and 2 aspartic acids to chelate Mg at the active site o Multiple transcripts can be made simultaneously  Electron micrograph- start site is shorter and shows fewer nucleotides  Transcription cycle of bacterial RNA polymerase o Sigma factor finds and reads promotor o Holoenzyme- (RNA polymerase core enzyme plus sigma factor) assembles and locates promoter  Scans double stranded genome in proximal cells looking for a promoter  Has 2 binding sites and a TATA consensus region  Active site must be open and polymerase must be pointed in right direction  Unwinds DNA at start site for transcription (exposing template in active site) and begins transcribing  Abortive initiation- relatively inefficient o Once about 10 nucleotides are synthesized, the promoter and sigma factor break off  Few nucleotides polymerized in active site (slow process)  Not committed to transcribing  Abortive synthesis  Loss of interaction with sigma factor o 2 conformational changes  Clamps down committed  Dissociates transcript from template so DNA can re-hybridize rutter  Synthesis accelerates greatly o Elongation phase  Polymerase leaves DNA template and releases newly transcribed RNA when it encounters a termination signal o Termination signal  GC base pairs loop and hydrogen bond with each other and form a hairpin loop  Polymerase becomes tangled in rutter  Forces rutter to open and release template  Sigma factor binds to polymerase to transcribe another gene  Gene regulation o Don’t want genes on all of the time o Consensus sequence for E coli promoters are recognized by RNA polymerase and sigma factors o Allow for mutations (base pair substitutes) in promoter elements  Harder for sigma factor to bind  Regulates how often gene is activated o RNA polymerase recognizes promoters as double stranded DNA o Ideal spacing between -35 and -10 hexamer sequences  Ideal #=17  higher expression  If spacing is too small, the polymerase needs to squeeze and if spacing is too large, it needs to stretch so the gene won’t be expressed as often  RNA polymerase orientation is important o DNA is in 3’ to 5’ direction o Direction of RNA polymerase movement determines which of 2 DNA strands will serve as a template for RNA synthesis o Polymerase direction is determined by the orientation of the promoter sequence  Promoter sequence- site at which RNA polymerase begins transcription; at the beginning of each gene  RNA polymerases in eukaryotic cells o RNA polymerase I- 5.8S, 18S, and 28S rRNA genes o RNA polymerase II- all protein-coding genes, snoRNA genes, miRNA genes, sIRNA genes, and most snRNA genes o RNA polymerase III-tRNA genes, 5S rRNA genes, some snRNA genes and genes for other small RNAs o The larger the S value the larger the RNA o Structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase  Alpha helices & beta sheets  Metals that help maintain structure  About 120 proteins that bind to start site  Initiation of transcription of eukaryotic gene by RNA polymerase II o Need transcription factors (TF)  TFIID  1 to bind  TATA binding protein- binding site for TATA box  TFIIH  Acts as a helicase- pries apart DNA  Acts as a kinase to phosphorylate CTD o CTD- carboxy terminal domain; 52 repeats of a 7 amino acid sequence (has serines that can be phosphorylated)


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