BIOL 4003 Week 8 Lecture Notes
BIOL 4003 Week 8 Lecture Notes 4003
U of M
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This 5 page Class Notes was uploaded by Rachel Heuer on Sunday March 20, 2016. The Class Notes belongs to 4003 at University of Minnesota taught by Robert Brooker in Spring 2016. Since its upload, it has received 7 views. For similar materials see Principles of Genetics in Biology at University of Minnesota.
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Date Created: 03/20/16
Chapter 12: - Gene is segment of DNA used to make a functional product o Product can be either RNA or polypeptide - Transcription is the first step in gene expression - Structural genes (protein-encoding genes) encode amino acid sequence o Transcribed into mRNA o Determines amino acid sequence during translation o Synthesis of proteins determines traits - Path from gene to protein is the central dogma of genetics - DNA: o Promotor signals the start of RNA synthesis o Terminator signals end of RNA synthesis o Regulatory sequences influence the rate of transcription § Can be in various locations - RNA o Start codon o Stop codon o Ribosome binding site: Translation occurs near here - Stages of transcription o Initiation: Promotor functions as recognition site for transcription factors, which allows RNA polymerase to bind to promoter. Creates open complex o Elongation: RNA pol slides to synthesize RNA o Termination: RNA and RNA pol dissociate from DNA - All steps involve protein DNA interactions o Such as RNA polymerase - Promotors determine location of transcription initiation o Typically upstream of site where transcription begins o Typically have a ttgaca at -35, and a tataat at -10 o No zero base o Transcription starts at -10 o Coding strand is match to the RNA o Transcription occurs off of noncoding strand o Holoenzyme binds loosely to DNA § Scans the DNA until it encounters a promoter region § Sigma factor recognizes both the -35 and the -10 § Helix-turn-helix structure binds tighter to the DNA § Figure 12.6 § At the point initiation is complete § Sigma factor is released, allowing elongation phase to start o Elongation: § RNA binds to the 3’ end of DNA sequence, RNA built 5’ to 3’ o Termination § Occurs when RNA-DNA hydrid of open complex is forced to separate § Releases both new RNA and RNA polymerase § Two methods for termination • Rho dependent termination (figure 12.10) o Needs rho (p) protein o Rho utilization site is read and allows rho factor to bind § Tries to catch up to RNA polymerase • Rho independent manner (intrinsic termination) o U-rich region of 3’ RNA in hybrid o NusA protein stabilizes RNA to pause o When paused the weak A-U bonds are unable to hold RNA-DNA hybrid together - Transcription in eukaryotes o Many of the features are the same o More complex o Multicellularity adds another level of regulation § Must express at correct time o Three kinds of RNA polymerases § Pol I: rRNA (except for 5s) § Pol II: transcribes all protein encoding genes • mRNA • some snRNA for splicing § Pol III: tRNA • 5s o Most genes have two features § Core promotor • TATAAA o TATA box • Transcriptional start site § Regulatory elements • Affect binding of RNA polymerase to the promoter o If only core promoter but no regulatory elements, transcription rates are rather low o Transcription start site is typically an adenine base o Core promoter is relatively short o Transcription factors are needed for pol II to work o 3 proteins needed § RNA Pol II § 5 GTFs § Mediator o Initiation: Figure 12.14 § When complex becomes open, elongation can occur o Termination: occurs when polyA sequence is read § 2 types hypothesized: Allosteric and torpedo (12.15) o Processing and capping and tailing o Look at table 12.3 o Processing makes long single molecule into smaller forms that become functional rRNA and tRNA o Splicing: § Group 1,2 and spliceosome § In all three cases, introns are removed • Exon is linked by a phosphodiester linkage § Pre-mRNA splicing • Uses spliceosome o Which is composed of snRNPS o Each snRNPS has nucleic acid and proteins • U1 snRNP recognizes 5’ splice site • U2 recognizes branch site • Recruit other snRNPs • Intron loops outward to bring exons together • 5’ splice site is cut, 3’ splice site is cut • Exons are linked together o Capping § Most mature mRNAs have a 7 methylguanosine cap at the 5’ end § Needed to move RNAs into the cytoplasm § Help the early stages of translation and intron splicing o Polyadenylation § String of adenines at the 3’ end § Not encoded in the gene sequence (added enzymatically) § Polyadenylation sequence AAUAAA creates endonucleause cleavage 20 nucleotide downstream • PolyA polymerase adds A to 3’ end § Important for mRNA export § Length varies o Table 12.6 compares eukaryotic and prokaryotic transcription Chapter 13: Polypeptides are made by translation of codons within an mRNA into amino acid - Polypetides are units within functional proteins - Translation involves interpretation from one language into another o Relies on the genetic code o AUG is almost always the starting codon o “sense codons”: triplet corresponds to amino acid o “nonsense”: stop codons o The code is degenerate: more than one code can specify one amino acid § Third base is often “wobble” o Code is nearly universal o 5’ untranslated is upstream of the start codon o 3’ untranslated is downstream of stop codon o Most polypeptides are a couple hundred amino acids long o tRNA is complementary to mRNA (anticodon) and carries specific amino acids o Polypeptide has directionality § Parallels direction to the 5’ to 3’ mRNA (N term à C term) § Building polypeptide is a condensation reaction o Amino acids have unique side hains § 20 common § 2 uncommon § Side chains determine chemical properties § Nonpolar amino acids are hydrophobic § Polar amino acids are hydrophilic o Four levels of protein structure § Primary: Amino acid sequence • Can be folding during translation § Secondary: Local regions fold into beta sheets and alpha helix • Hydrogen bonds on backbone stabilize structures § Tertiary: Regions of secondary structures and irregular shapes worked together to become 3 dimensional § Quaternary is multiple polypetides linked together - Characteristics of cell depends of the types of proteins it makes o Key category of proteins are enzymes - tRNA o play direct role in the recognition of codons in mRNA o Adaptor hypothesis proposed mRNA had two functions: § Recognize codons § Carry amino for that codon § tRNA has cloverleaf structure • Second loop is where anticodon is located • 3’ acceptor stems carries the amino acid • Can have modified bases • tRNA is charged when it carries an amino acid • Each tRNA has an aminoacyl tRNA sythetase enzyme that attaches amino acids to it o One for each amino acid o Needs ATP input o Look at Figure 13.11 o Specific amino goes into enzyme and then ATP binds to the enzyme § Correct tRNA then binds to enzyme where amino covalently attaches to tRNA - Translation occurs on the surface of ribosomes o Bacteria have one type of ribosome o Eukaryotes have cytoplasm ribosome and organelle ribosomes o Ribosomes are composed of small and large subunits § Come together to form assembled ribosome with A,E,P sites § Named by size - Translation occurs in three stages o Initiation § Need mRNA, initiator tRNA, and ribosomal subunits § Process requires three initiation factors § Initiator tRNA recognizes start codon mRNA • tRNA^fmet • Modified with a formyl group • Bacteria can have AUG, GUG, or UUG start codon o Still brings in an N-formylmethionine § IF1 and IF3 bind to small ribosomal subunit § mRNA (shine dalgarno sequence) then binds to complementary segment of rRNA found in ribomsome § Start codon is normally only a found nucleotides downstream of SD sequence, in the P site § IF2 then binds and hydrolyzes GTP § Initiator tRNA then binds to the P site (all other tRNA binds at A site) § IF1,2,3 are released § The larger subunit associates, marking the end of the initiation phase o Elongation (Figure 13.17) § Amino acids to polypeptide one at a time § 15-20 amino acids per second in bac (2-6 in euk) § tRNA floats in and binds to the A-site (anticodon is complementary to the codon) § Polypeptide transfers from being bound to tRNA in P, to tRNA in A, § Ribozyme in ribosome catalyzes elongation § Ribosome moves left to right, while mRNA stays § tRNA that lost peptide moves to the exit site(E), tRNA will leave and get recharged § tRNA with peptide bound will move into the P site § A site is now open for new charged tRNA to bind § Cycle continues until stop codon is reached o Termination ( Figure 13.18) § Occurs when a stop (nonsense) codon is reached § These codons are not recognized by tRNAs but are recognized by release factors • Mimics structure of tRNA § No tRNA can recognize stop codon § Polypeptide is hydrolyzed off of tRNA in P site § All components are then disassembled and can be reused o Look at Table 13.7!!!
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