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 a general idea as to which amino acids have the most redundant number of codons and which the least You will also be asked to translate an RNA message using a codon 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 structure necessitates considerable modification of newly synthesized mRNA What additional modifications take place on the mRNA and what functional roles do these modifications play gene text definition is a discrete unit of hereditary information consisting of a specific nucleotide sequence Two fundamental kinds of genes 1 structural genes carry information for the synthesis of proteins also code for specific kinds of RNA s like ribosomal RNA s and transfer RNA s 2 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 another form namely RNA is synthesized a specific kind of RNA known as messenger RNA or 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 a sequence of amino acids thereby forming a protein fig 17 2 comparison of bacterial vs eukaryotic in eukaryotic cells the mRNA is modified 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 a sequence of nucleotides that are complementary to the nucleotides on the first strand How can four different letters produce the information needed to make proteins which consist of unique sequences of 20 different amino acids 1 fig 17 3 in the 1960 s it was discovered that amino acids are coded for by three nucleotides on the mRNA molecule these nucleotide triplets are known as codons Thus each word consists of the unique sequence of three nucleotides During translation this information is recognized and translated into amino acids fig 17 4 the code as shown in RNA reads 5 3 1 the code is redundant for many amino acids that is more than one codon codes for a particular amino acid 6 for LEU and ARG 4 for VAL SER PRO THR and ALA different groups of organisms show preference for usage of particular codons this is known as codon bias 2 AUG codes for start or MET 3 UAA UAG and UGA code for stop 4 reading frame where you begin to read the code is important starting with A starting with C 5 ACAGCCUUGGUG3 Thr Ala Leu Val 5 ACAGCCUUGGUG3 Gln Pro Trp 5 near universality the above code is common to most living organisms including prokaryotes fungi plants and animals this universality has been used as evidence for common descent of all organisms on earth However there are exceptions For instance for genes in mitochondria the RNA codon UGA is Trp not stop AUA is Met not Ile and AGA and AGG are stop not Arg Other differences are found in chloroplasts 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 the synthesized mRNA proceeds from 5 3 direction mRNA DNA 5 3 3 5 1 RNA polymerase II enzyme that catalyzes the synthesis of mRNA 2 promoter site region of the DNA where the RNA polymerase initially binds and mRNA synthesis begins consists of several regions a initiation site where mRNA synthesis begins b upstream region in eukaryotes has a sequence TATA known as the TATA box RNA polymerase II looks for this sequence associated with this 2 region are proteins called transcription factors polymerase cannot bind without these proteins being present 3 RNA polymerase II binds to region at initiation site to commence transcription fig 17 6 transcription 1 RNA polymerase II causes the DNA duplex to separate and causes the helix to untwist 2 complementary RNA nucleotides interact with corresponding nucleotides on the DNA strand 3 the polymerase catalyzes the formation of mRNA by adding nucleotides to the 3 end so the polymerase synthesizes mRNA in the 5 3 direction but reads DNA from the 3 5 4 elongation process by which the mRNA chain is lengthened text says that this occurs at a rate of 60 nucleotides sec 5 for a particular stretch of DNA more than one molecule of RNA polymerase II can be making mRNA at the same time 6 when the polymerase reaches the termination sequence AATAA in eukaryotes synthesis ceases and the newly formed mRNA is released Fate of the mRNA in prokaryotes the mRNA goes directly to translation protein synthesis not so in eukaryotes because 1 some regions of the newly formed mRNA must be excised and 2 the 3 and 5 ends must be modified to facilitate transport out of the nucleus as well as to make the message more stable 1 eukaryotic gene structure genes actually consists of bundles of regions called introns and exons fig 17 9 introns regions that must be excised from message do not contain structural information exons regions that code for specific stretches of amino acids exons often code for regions or domains of the protein which correspond to important structural and or functional components see Fig 17 11 2 fig 17 8 ends are modified in two ways a GTP is attached to 5 end to make a cap which protects the RNA from degradative enzymes as well as enhances translation b the 3 end is modified by the addition of 30 100 adenine nucleotides forming a ploy A tail this tail enhances mRNA stability and also facilitates transport out of the nucleus Fig 17 10 when mRNA is synthesized the newly formed RNA consists of a 5 leader sequence often called the 5 untranslated region b exons c introns and d 3 3 trailer sequence often called the 3 untranslated region Special protein RNA complexes known as spliceosomes cut out the introns and the remaining exons plus leader and trailer
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