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Week 14 notes

by: Cassidy Zirko

Week 14 notes BCH 110

Cassidy Zirko

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About this Document

These notes cover transcription and replication and codons/genetic code
Intro Biology for Biochemist
Scott Samuels
Class Notes
geneticcode, codons, transccription, replication, tRNA, mRNA
25 ?




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This 6 page Class Notes was uploaded by Cassidy Zirko on Monday May 2, 2016. The Class Notes belongs to BCH 110 at University of Montana taught by Scott Samuels in Spring 2016. Since its upload, it has received 12 views. For similar materials see Intro Biology for Biochemist in Biology at University of Montana.


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Date Created: 05/02/16
Transcriptional Regulation 4/25/16  Sigma factors recognize promoter  cycles off during elongation   Alternate sigma factor  o Determines which gene is translated  o Bacteria can regulate which genes are expressed by utilizing different sigma  factor  it directs the RNA polymerase to a different set of genes   Developmental regulation by cascade of alternative sigma factors  o Bacillus subtillis­ cousin of anthrax  o Has many sigma factors  o Hijacks RNA polymerase  manipulating sigma factor  o Carries genes that encode replication units  o Late genes  structural component of the virus  o Has about 2 dozen factors  o Enzootic cycle­ lyme disease bacterium is regulated by sigma factors   Only has three sigma factors   Alternative sigma factor Rpos controls genes involved in tick transmission and mammalian factor   Induction or repression of Lac operon  o Transcription factor  Repressors­ prevent RNA polymerase form binding to promoter or  initiating transcription   Activators­ facilitate RNA polymerase binding or initiation  o Bacterial Transcription Factor  interact with small molecules, post  translationally modified in response to environment  o Operon­ how bacteria organize genes  o 2 or more genes transcribed together from same promoter  o Produce polysistranic RNA (many genes on one mRNA) o Allows for coordinate regulation of functionally related genes   Lac Operon  o First operon to be discovered  o 3 structural genes involved in metabolism of lactose  o Cods a catabolic pathway  o Operon turned on when lactose is present and glucose is absent  o Glucose is always the easiest way to go   DNA encods more than just genetic information  origin of replication and promoter:  Many signals   Cast of Lac operon o Lac Z­ structural gene encoding beta­galactosidase (Breaks down lactos)  o Repressor (Lac I)­ transcription factor encoded by Lac I­ that binds to operator,  not actually part of operon   Inhibits transcription of lack operon  o Operator­ adjacent to Lac promoter  o DNA sequence where repressor (Lac I) binds  o Repression   Repressor point encoded by Lac I gene   Absence of lactose­ Lac I repressor binds to operator   Transcription of lac operon is off   Lac I­ tetramer (most are dimers)   Promoter and operator right next to each other, RNA polymerase cant bind  Without repressor­ lactose broken down into Beta galactosidase  o Induction­ turning on of Lac operon   Requires presence of lactose and absence of glucose   Inducer­ allolactose (isomer of Lactose)  o Induction Mechanism   Inducer binds to Lac I Repressor   Repressor changes conformational shape  o Repressor/inducer complex cannot bind to operator  o Lac operon transcribed  responds to presence or absence of nutrient  o Allalactose­ beta (16) galactosidase vs. lactose beta (14) galactosidase   Two binding sites on DNA  o Promoter­ RNA polymerase binding site  o Repressor Binding site   Positive Control  o Glucose is favorite sugar (easiest to break down for energy)  o No need to use lactose if glucose is present  o Lac operon (operons encoding catabolism of other sugars) kept off if glucose is  present  o Glucose  repressor on lac operon  o Lactose and no glucose  lac operon active   cAMP o cyclic AMP (nucleotide)  only has one phosphate­ 5’ carbon and 3’ carbon  o signals low in glucose  o binds to CAP­ catabolite activator protein  o fight or flight signal  inhibited by caffeine  o also hunger signal   CAP­ activator promoter  o Receptor for cAMP in bacteria  o Also called CRP­cAMP receptor Protein  o cAMP­CAP complex binds near promoter and facilitates RNA polymerase  binding  o cAMP  increases with hunger  o cAMP and CAP helps RNA polymerase finds promoter   DNA protein interactions  o Promoter and RNA polymerase, Operators and Lac I repressor and CAP binding  site and cAMP binding site   Protein­ protein interactor  o RNA polymerase and Lac I repressor  o RNA polymerase and cAMP and CAP binding   Transcriptional regulator machinery responds to presence of lactose and absence of  glucose  4/27/16  Negative control­ turning gene off­ turning expression off  o Repressor binding to DNA at promoter (induction­ small molecule removing)   Positive control: catabolite repression (CAP)   Allolactose is negative control­ relieves repression   Cyclic AMP is induction­ relieving repression, CAP bound to cAMP turning on gene  expression   Attenuation: trp operon  o Operon that encodes catabolic pathway  o Encodes biosynthetic pathway   Trp operon  o Codes leader sequence and and five polypeptides involved in tryptophan  biosynthesis  o Only time to make trp is when there is no tryptophan  o Presence of tryptophan operon shuts down, doesn’t need to make it   Codon o Genetic code converts nucleic acid sequence to protein sequence  o Decoder ring that converts between genetic sequence to protein/amino acid  sequence  o Sequence of nucleotide in DNA and RNA specify sequence of amino acids   Trp L­ has attenuation­ all catabolic pathways has attenuator   Alternative TNA sequence  o Formed in leader sequence (trp L)   Pause structure­ binding between region 1 and 2 and 3 and 4  o Forms stem structure, G­C stem loop, followed by stretch of U­ causing end of  transcriptions  o Causes formation of just stretch of trp L  o 2 trp codons in a row­ tells to make tryptophan   Antiterminator structure  o Alternative binding between regions 2 and 3   Bacteria­ no compartmentalization between transcription and translation o Plenty of trp binds to charged tRNA   Low levels of trp­ wants operon on  o Causes low levels tRNA  o Ribosomes cant bind to sequence and needs tRNA  o Causes trp operon to turn on and increases tRNA to bind to ribosome  o Attenuation­ RNA directed processes depending on how fast the ribosome  translates   Attenuation  o Pause structure forms when ribosome passes over trp codon when tryptophan  levels are high  o Ribosome stalls at trp codon when trp levels are low and antiterminator loop  forms  o Antiterminator does just what it says  forms to not stop tryptophan production  because of low levesl of tryptophan   DNA binding proteins  o Most proteins that activate or inhbit transcription having 2 functional domains   DNA protein domain   Transcription activation   DNA binding domains  o Major them is alpha helix in major groove  o Helix turn helix (H and H)­ alpha helix and major group  o Alpha helix followed by turn followed by alpha helix  o Zinc finger­ pretty common  o 2 cytosine’s and two histidine coordinate zinc  o Alpha helix (protein) in major group of DNA  o Coordinates in Zinc­ Zinc holds structure together  o  Basic region leucine  zipper   Leucine’s  align on one side of the alpha helix formation, creates a  hydrophobic surface for dimer interaction   Every 7  amino acid is a leucine  puts hydrophobic patch on the leucine  The 2 zippers dimerize with hydrophobic interaction sin major group  creating the leucine zipper    DNA and proteins held together by weak interactions   Sequence recognition: hydrogen bonding between protein and DNA provides sequence  specificity  o Using complementary base pairs  o Maximizing bonding  can mutate sequence and binding proteins  o More information in major groove­ alpha helix fits in major groove and more  opportunities for hydrogen bonding  o Binding does not depend on G­C or A­T nucleotide bonding  o Amino acid binds to double helix based strictly on hydrogen bonds  o More bonding potential in particular pairs of nucleotide bases Genetic Code and Translation 4/29/16  Genetic flow of information: Central Dogma, DNA  RNA  Protein   Peptdies form covalent bonds between amino acids   Proteins have directionally­ orientation from the N­terminus to the C­terminus of the  amino acid   3 roles of RNA in proteins  o mRNA carries information copied from DNA in the form of a series of three base  “words”­ codons  o tRNA are adaptor molecules that bring a specific amino acid to each m RNA  codon  o rRNA forms ribosomes   Codons  o Genetic codes  Conversion of nucleic acids to protein sequence   Sequence of nucleotides in DNA transcribed by RNA then translates to  proteins  o Features of genetic code   Triplet: three base (codons) sequence are amino acids   Nonoverlapping: no bases shared between codons   Continuous­ no bases between the codons that are not used   Degenerate­ more than one  triplet can code for the same amino acid   Universal­ same in viruses, bacteria, archea and eukaryotes­ only few  exceptions  Some organelles use slightly modified genetic code  64 different codons, 20 amino acids  o Non overlapping and continuous   Ribosome moves along the mRNA three base pairs at a time   Reads one codon at a time, no commas (spaces between codon)   Mutations can shift the codon sequence  o Degenerate   64 different codons   61 codes for the 20 amino acids   3 codons for termination   More than one codon can specify the same amino acid   3  base is often ignored   Mutation on 3  codon  no or minimal change  o Start stop signals   Start codon: initiation of translation   AUG­ encodes the amino acid methionine and is usually cut off   Stop codons­ UAA, UGA, UAG­ terminates translation  o tRNA bonds to mRNA  adaptor between nucleic acid triplet code (codon) and amino acid   anticodon base pairs with mRNA codon   mRNA­ codon and tRNA­ anticodon­ work antiparallel just like DNA  o Wobble Base pairing   61 codons for amino acids but many cells have less than 61 RNAs   Some tRNA’s can recognize several codons (For same amino acid)  rd 3  position in codon (mRNA) and the first position on the anticodon (tRNA) can be less  stringent base paring 


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