BIOL 3303 1st EditionExam # 2 Study Guide The Genetic Code.The genetic code is a non-overlapping code, with each amino acid + polypeptide initiation and termination specified by RNA codons composed of three nucleotides.Properties of the Genetic Code: The genetic code is composed of nucleotide triplets.o Three nucleotides in mRNA specify one amino acid in the polypeptide product.o Each codon contains 3 nucleotides The genetic code is non-overlapping. o Each nucleotide in mRNA belongs to just one codon, except in rare cases where genes overlap and a nucleotide sequence is read in two different reading frames. The genetic code is comma-free. o During translation, codons are read consecutively, one at a time. The genetic code is degenerate (partial and complete).o All but two of the amino acids are specified by more than one codon. The genetic code is ordered. o Multiple codons for a given amino acid and codons for amino acids with similar chemical properties are closely related, usually differing by a single nucleotide.These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute. The genetic code contains start and stop codons.o Specific codons are used to initiate (AUG) and terminate (UAA, UAG, UGA) polypeptide chains. The genetic code is nearly universal.o The codons have the same meaning in all living organisms, from virus to human.o Exception: mitochondrion and some protozoaTypes of Mutations in nucleotide sequence: Insertion Deletion SubstitutionTypes of mutations in amino acid sequence: Missense mutationo changes a triplet so that it specifies a different amino acid in the polypeptide product Nonsense mutationo Produces chain-terminating triplets within genes, resulting in a shorter polypeptide.o Resulting protein is often completely nonfunctional. Silent mutationo No effect on polyptide sequence or function.Beadle and Tatum’s experiment: One Gene – One Enzyme hypothesishttp://www.dnalc.org/resources/nobel/beadle_tatum.htmlProkaryotic gene expression.Because prokaryotes do not have a nuclear membrane, there is no need for an intermediary between transcription from DNA and translation on the ribosomes. This means that transcription and translation are COUPLED in prokaryotes.I. TRANSCRIPTION is the transfer of genetic information from DNA to RNA.A. RNA synthesis is similar to DNA synthesis EXCEPT thati. Precursors are ribonucleoside triphosphates instead of deoxyribonucleoside triphosphates.ii. Only ONE strand of DNA is used as a template.iii. RNA chains can be initiated de novo since primers aren’t needed.B. Synthesized RNA molecules will be complimentary and antiparallel to the template strand and identical (except Ts are Us) to the nontemplate strand.i. mRNAs are coding strands of RNA called sense strands because they specify AA sequences for proteins…they “make sense” of the code.ii. RNA synthesis occurs in the 5’  3’ direction (ribonucleotides added to 3’-OH)…..just like DNA replication.a. This is catalyzed by RNA polymeraseb. RNAps bind to specific nucleotide sequences called promoters and, with the help of proteins (transcriptionfactors), initiate RNA synthesis at transcription start sitesnear promoters.C. Prokaryotic RNA Polymerasei. Tetrameric corea. α (2) – assembly of tetrameric coreb. β – ribonucleoside triphosphate binding sitec. β’ – DNA template binding regionii. Holoenzymea. α2, β, β’b. σ – initiation of transcriptionII. Initiation of RNA chains (Figure 1)A. RNA polymerase holoenzyme binds to a promoter region in DNAi. A prokaryotic promoter is present upstream (-1, -2, -3,… vs downstream: +1, +2, +3,…) of a transcription initiation site (+1) with consensus sequences at -10 and -35.ii. σ factor binds to -35 regionB. The two strands of DNA are locally unwound by RNA polymerase to provide a single-stranded templatei. This occurs at an AT-rich region (-10 region) – why?C. Phosphodiester bonds are formed between the first few ribonucleotides in the nascent RNA chain (+1 region)Figure 1III. Elongation of RNA chainsA. Ribonucleotides are added one by one to the free 3’–OH of the growing RNA strand.B. 5’-3’ polymerase activityIV. Termination of RNA chainsA. RNA polymerase encounters a termination signali. transcription complex dissociates and RNA chain is releasedii. two types of terminating sequences in E. coli:a. rho-independent – results in termination without the involvement of rhoo contain GC-rich region followed by 6+AT bps, with As present in template strand (Us in RNA strand)i. GC-rich region has inverted repeats which produce single-stranded RNA sequences that can base-pair and form hairpin structures. These hairpins form immediatelyafter being transcribed and retard the movement of RNA polymerase, thus pausing chain extension.ii. the run of Us after the hairpin region facilitates the release of the newly synthesized RNA chains from the template at these pause sitesb. rho-dependent – results in termination only in the presence of a rho proteino also forms a hairpin structure which pauses elongationo contains 2 additional sequences, one specifying a rho factor whose helicase activity unwinds DNA-RNA base-pairing at terminus to release RNA transcriptTranscription: http://www.dnalc.org/resources/3d/13-transcription-advanced.htmlGene regulation (Lac operon): https://www.youtube.com/watch?v=oBwtxdI1zvk I. Translation is the transfer of genetic information from RNA to proteins.II. Translation occurs on ribosomes (Figure 2), which are complex macromolecular structures located in the cytoplasm (“workbenches” of the cell).WATCH THESE NOW!Figure 2A. Ribosomes are approximately half protein and half RNA.B. They are composed of 2 subunits: one large and one small (50S and 30S in prokaryotes, 60S and 40S in eukaryotes).i. These subunits dissociate after translation is completed and re-associate during initiation of translation.III. Translation involves three types of RNA:A. mRNAs – transmit genetic info to cytoplasm for translation on ribosomesB. rRNAs – present as part of the structure of each ribosomeEnzyme for proteinsynthesis(ribozyme)Recruits ribosometo mRNAi. rRNA synthesis occurs in the nucleolus and is catalyzed by RNApI (see Table 2)C. tRNAs – adaptors, mediating the incorporation of proper AAs into polypeptidesi. AAs are attached to the correct tRNA