Topic 13: ORGANIZATION OF DNA INTO GENES AND THE SYNTHESIS OF PROTEINS (lecture 21-22)OBJECTIVES:1. Understand the nature of the genetic code including such issues as word size,redundancy, codon bias and reading frame. 2. You will not be required to memorize the code. However, you should have ageneral idea as to which amino acids have the most redundant number of codonsand which the least. You will also be asked to translate an RNA message using acodon dictionary.3. Know the fundamental differences between RNA and DNA.4. Review the process of transcription. Understand the roles of the promoter site,initiation site, TATA box, RNA polymerase II and transcription factors.5. Describe the structure of typical eukaryotic genes and how this structurenecessitates considerable modification of newly synthesized mRNA. What additionalmodifications take place on the mRNA and what functional roles do thesemodifications play?gene- text definition is “a discrete unit of hereditary information consisting of a specificnucleotide sequence. Two fundamental kinds of genes:1. structural genes- carry information for the synthesis of proteins; also code forspecific kinds of RNA’s like ribosomal RNA’s and transfer RNA’s2. regulatory genes- genes that control the expression (activity) of other genes.Overview of protein synthesis: two fundamental processes taking place.1. transcription- the information in the DNA is transcribed (literally written) into anotherform; namely RNA is synthesized (a specific kind of RNA known as messenger RNAor mRNA). RNA differs from DNA (fig. 5.29) in that it (a) is generally single stranded,(b) it has the pyrimidine base uracil instead of thymidine and (c) the sugar is ribose.2. translation- the information carried in the RNA molecule is translated into asequence of amino acids thereby forming a protein.fig. 17.2- comparison of bacterial vs. eukaryotic; in eukaryotic cells the mRNA ismodified prior to leaving the nucleus; translation takes place in the cytoplasm.The Genetic Code- recall that DNA molecules are polymers of four different nucleotides(A,T, G and C) strung together in s single strand; the second strand consists of asequence of nucleotides that are complementary to the nucleotides on the first strand.How can four different letters produce the information needed to make proteins whichconsist of unique sequences of 20 different amino acids?1fig. 17.3- in the 1960’s it was discovered that amino acids are coded for by threenucleotides; on the mRNA molecule these nucleotide triplets are known as codons.Thus, each “word” consists of the unique sequence of three nucleotides. Duringtranslation, this information is recognized and translated into amino acids.fig. 17.4- the code; as shown in RNAreads 5’ 3’1. the code is redundant for many amino acids; that is, more than one codon codes fora particular amino acid- 6 for LEU and ARG; 4 for VAL, SER, PRO, THR and ALAdifferent groups of organisms show “preference” for usage of particular codons; this is known as codon bias2. AUG codes for “start” or MET3. UAA, UAG and UGA code for “stop”4. reading frame- where you begin to read the code is importantstarting with A : 5’ ACAGCCUUGGUG3’ Thr Ala Leu Val starting with C : 5’ ACAGCCUUGGUG3’ Gln Pro Trp5. near universality- the above code is common to most living organisms includingprokaryotes, fungi, plants and animals; this universality has been used as evidencefor common descent of all organisms on earth. However, there are exceptions. Forinstance, for genes in mitochondria the RNA codon UGA is Trp not stop, AUA is Metnot Ile and AGA and AGG are “stop” not Arg! Other differences are found inchloroplasts and in ciliated protozoans like Paramecium.Transcriptional formation of mRNA and mRNA processing.fig. 17.7- initiation of transcription; synthesis goes from the 3’5’ end of DNA so thesynthesized mRNA proceeds from 5’3’ directionmRNA 5’ 3’DNA 3’ 5’1. RNA polymerase II- enzyme that catalyzes the synthesis of mRNA2. promoter site - region of the DNA where the RNA polymerase initially binds andmRNA synthesis begins; consists of several regions(a) initiation site- where mRNA synthesis begins(b) “upstream” region in eukaryotes has a sequence TATA known as theTATA box; RNA polymerase II looks for this sequence; associated with this2region are proteins called transcription factors; polymerase cannot bindwithout these proteins being present.3. RNA polymerase II binds to region at initiation site to commence transcriptionfig. 17.6- transcription; 1. RNA polymerase II causes the DNA duplex to separate and causes the helix tountwist2. complementary RNA nucleotides interact with corresponding nucleotides on the DNAstrand3. the polymerase catalyzes the formation of mRNA by adding nucleotides to the 3’ endso the polymerase synthesizes mRNA in the 5’3’ direction but reads DNA from the3’5’4. elongation- process by which the mRNA chain is lengthened; text says that thisoccurs at a rate of 60 nucleotides/sec5. for a particular stretch of DNA, more than one molecule of RNA polymerase II can bemaking mRNA at the same time.6. when the polymerase reaches the termination sequence (AATAA in eukaryotes)synthesis ceases and the newly formed mRNA is releasedFate of the mRNA- in prokaryotes the mRNA goes directly to translation (proteinsynthesis); not so in eukaryotes because (1) some regions of the newly formed mRNAmust be excised and (2) the 3’ and 5’ ends must be modified to facilitate transport out ofthe nucleus as well as to make the message more stable.(1) eukaryotic gene structure- genes actually consists of bundles of regions calledintrons and exons (fig. 17.9)introns- regions that must be excised from message; do not contain structural informationexons- regions that code for specific stretches of amino acidsexons often code for regions (or domains) of the protein which correspond to importantstructural
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