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Chapter 16

Textbook and Class Notes Collaborated - Unit 3 - Chapter 16 Bio 1A03
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Department
Biology
Course
BIOLOGY 1A03
Professor
Xudong Zhu
Semester
Fall

Description
Bio 1A03 Unit Three: Gene Structure and Expression Chapter 16: Transcription and Translation Key Concepts  After the enzyme RNA polymerase binds to a specific site in DNA with the help of other proteins, it catalyzes the production of an RNA molecule  The base sequence of the RNA produced is complementary to the base sequence of the DNA template strand  Some sections of an RNA are encoded by gene regions called exons, while others are encoded by gene regions called introns  During RNA processing, introns are removed and the ends of the RNA receive a cap and tail  Inside ribosomes, mRNAs are translated to proteins via intermediary molecules called transfer RNAs  Transfer RNA carry an amino acid and have a three base pair anticodon, which binds to a three-base long mRNA codon  The amino acid carried by the transfer RNA is then added to the growing protein via formation of a peptide bond  Mutations are random changes in the DNA that may or may not produce changes in the phenotype Introduction  A cell builds the proteins it needs from instructions encoded in its genome  Flow of information: DNA (information storage)  Transcription mRNA (information carrier)  Translation Proteins (product) 16.1 Transcription in Bacteria  First step in converting genetic information into proteins is transcription o Transcription – the synthesis of an mRNA version of the instructions stored in DNA  Transcription occurs when RNA polymerase matches the base in a ribonucleotide triphosphate with the complementary base in a gene – a section of DNA that codes for a protein or RNA o Once a matching ribonucleotide is in place, RNA polymerase catalyzes the formation of a phosphodiester bond between the 3’ end of the growing mRNA chain and the new ribonucleotide  RNA polymerase performs this synthesis by transcribing only one strand of DNA (template strand)  The sequence of the other DNA strand (non-template strand/coding strand) matches the sequence of the RNA (except RNA has uracil (U) instead of thymine (T))  Transcription consists of three phases: initiation, elongation and termination Bio 1A03 Structure and Function of RNA Polymerase  Bacterial RNA polymerase is a large, globular enzyme with several interior channels  The enzymes active site, where phosphodiester bonds are formed, is located where these channels intersect Initiation: How Transcription Begin In Bacteria  RNA polymerase cannot initiate transcription on its own  Holoenzyme – an enzyme made up of a core enzyme and other required proteins  Prokaryotic RNA polymerase is a holoenzyme made up of the core enzyme, which has the ability to synthesize RNA, and a sigma subunit  Sigma acts as a regulatory factor, telling RNA polymerase where and when to start synthesizing RNA o Sigma binds to specific sections of DNA called promoters – where transcription begins o The sigma subunit is required for the initiation phase of transcription  Transcription of bacterial genes is initiated at specific sections of DNA called promoters  Promoters have two key regions (names come from locations) o -10 box – found ten bases upstream from the transcription start site  Downstream is in the direction RNA polymerase moves during transcription; upstream is the opposite direction  Located on the non-template strand, 40-50 base pairs long, series of bases similar to TATA o -35 box  To initiate transcription, sigma identifies and binds to the -10 and -35 boxes, properly orienting the RNA polymerase holoenzyme for transcription at the start site  Next, sigma opens the DNA double helix and the template strand is threaded through the RNA polymerase active site  Incoming ribonucleoside triphosphate (NTP) pairs with a complementary base on the DNA template strand, and RNA polymerization begins  Sigma dissociates from the core enzyme once the initiation phase of transcription is completed  The reaction catalyzed by RNA polymerase is exergonic and spontaneous  Most bacteria have several different types of sigma proteins – each protein binds to a promoter box with a different DNA base sequence and thus a different gene o Controlling which sigma proteins are active is one of the ways that bacterial cells control which genes are expressed Bio 1A03 Elongation and Termination  During the elongation phase of transcription, RNA polymerase moves along the DNA template (3’5’) and synthesizes RNA in the 5’3’ direction  In the interior of the enzyme o Enzyme zipper (a group of projecting amino acids) – helps open the double helix at the upstream end o Rudder (a nearby group of amino acids) – helps steer the template and non-template strands through channels inside the enzyme o Enzymes active site – catalyzes the addition of nucleotides to the 3’ end of the growing RNA molecule at the rate of about 50 nucleotides per second  Termination phase o RNA polymerase encounters a transcription termination signal in the DNA template o Signal codes for RNA forming a hairpin structure  RNA sequence folds back on itself and forms a short double helix that is held together by complementary base pairing  Thought to disrupt the interaction between RNA polymerase and the RNA transcript, resulting in the physical separation of the enzyme and its product o Hairpin structure causes the RNA polymerase to separate from the RNA transcript, ending transcription 16.2 Transcription and RNA Processing in Eukaryotes  Eukaryotic transcription shares many fundamental characteristics with prokaryotic transcription o RNA polymerase does not bind directly to promoter sequences by itself  Basal Transcription Factors – proteins that initiate transcription in eukaryotes o Begin transcription by matching RNA polymerase with the appropriate promoter region in DNA  Function is analogous to that of sigma in bacteria; except that basal transcription factors interact with DNA independent of RNA polymerase  Eukaryotic cells contain three types of RNA polymerase (I, II, III) o Each enzyme transcribes different classes of RNA o RNA polymerase II – transcribes genes that code for proteins, producing mRNA o RNA polymerase I – makes the large RNA molecules that are found in ribosomes o RNA polymerase III – manufactures one of the small RNAs that are found in ribosomes and tRNA (transfer RNA) required for translation  The promoters in eukaryotic RNA are more diverse and complex than are bacterial promoters  The promoters recognized by each type of RNA polymerase differ  Many promoters recognized by RNA polymerase II include a sequence called a TATA box analogous in function to the prokaryotic -10 and -35 boxes Bio 1A03  In eukaryotes, transcription is followed by several important RNA processing steps  Eukaryotic genes do not consist of one continuous DNA sequence that codes for a product as do bacterial genes o The regions of eukaryotic genes that code for proteins come in pieces that are separated by many intervening DNA bases The Discovery of Eukaryotic Genes in Pieces  Introns – noncoding regions that interrupt the protein-coding regions of eukaryotic genes o Must be removed to make functional mRNA  Exons – the coding regions of eukaryotic genes that will be part of the final mRNA product  Eukaryotic genes are much larger than their corresponding mature mRNA Exons, Introns and RNA Splicing  The transcription of eukaryotic genes by RNA polymerase generates a primary RNA transcript that contains exons and introns  Introns are removed by splicing  snRNPs bind to 5’ exon-intron boundary; other snRNPs arrive to form spliceosomes  Spliceosomes - complex formed by small nuclear ribonucleoproteins (snRNPs “snurps”) o Catalyze splicing reaction  Once spliceosomes is formed, the intron forms a loop with an adenine ribonucleotide at its base o Adenine ribonucleoside cuts the loop out  A phosphodiester bond then links the exons on either side Bio 1A03 Adding Caps and Tails to RNA Transcripts  Primary RNA transcripts are also processed by the addition of a 5’ cap and a poly (A) tail that protect mRNA from degradation and enhance the efficiency of translation o 5’ cap  Serves as a recognition signal for the translation machinery  Consists of 7-methylguanylate and three phosphate groups o Poly (A) tail  Extends the life of an mRNA by protecting it from degradation  100-250 adenine nucleotides  With the addition of cap and tail, processing is complete; product is a mature mRNA Table 16.2 Comparing Transcription in Bacteria and Eukaryotes Aspect Bacteria Eukaryotes RNA Polymerase One Three; each produces a different class of RNA Promoter Structure Typically contains a -35 box and a -10Complex and variable often includes a box TATA box 30 from start of gene Protein(s) involved in contacting Sigma; different versions of sigma binMany basal transcription factors promoter to different proteins RNA processing steps None; translation occurs while Extensive; several processing steps transcription is still underway occur in nucleus before RNA is exported to cytoplasm for translation: 1. Enzyme-catalyzed addition of 5’ cap 2. Spicing (intron removal) by spliceosomes 3. Enzyme catalyzed addition of 3’poly (A) tail 16.3 An Introduction to Translation  The sequence of bases in the mRNA is converted to an amino acid sequence in a protein Ribosomes Are the Site of Protein Synthesis  Ribosomes – catalyze translation of the mRNA sequence into protein  In bacteria, transcription and translation can occur simultaneously o Bacterial ribosomes begin translating an mRNA before RNA polymerase has finished transcribing it  In eukaryotes, transcription and translation are separated o mRNA’s are synthesized and processed in the nucleus and transported to the cytoplasm for translation by ribosomes
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