Week 2 – 8/30-9/3DNA is not the direct template of Protein Synthesis- In the eukaryote, it was noted that DNA stayed in the nucleus while protein synthesis occurred in the cytoplasm. So DNA could not be a direct template. What was the intermediate?DNA Nucleotide In-Depth Review:-Atoms on the rings are numbered from 1-6 or 1-9(if double rings) The carbon on the ribose that connects to the base is marked as number 1: it will be labeled as 1’. The next one going clockwise is 2’, 3’, 4’ etc. The phosphate is connected to the 5’ C. the 3’ Chas a hydroxyl group on it, but the 2’C does not. It disappeared, so that is why its called deoxyribose. So has an H atom instead. RNA is a different form of nucleic acid, that actually has the 2’ OH group. RNA vs. DNA differences:1st difference: RNA is also a nucleic acid but it contains a minor modification of the sugarcomponent - it doesn’t have the deoxy-part. On the ribose, instead of having a 2’ deoxyribose, RNA has a hydroxyl group. It has a direct ribose. 2nd difference: They use different bases. Instead of thymine, RNA contains Uracil. These two bases have almost the same structure, except on the 5-C, T has a methyl but U only has an H. (this difference does not affect RNA’s ability to form double-helical structures held together by base pairing)3rd difference: RNA found mostly in cytoplasm(sometimes in nucleus) while DNAonly in nucleus, making RNA the obvious candidate for direct template. RNA usually found as single-stranded – if you find double-stranded, they are most likely composed of two parts of the same single stranded RNA molecule. Nomenclature: We have a deoxy nucleotide connected by phospoohdiester bond between 3’ C and the 5’C phosphate. The 5’ of DNA molecule has a free phosphate connected to the 5’ C of the deoxyribose of the last nucleotide – this is the 5’ end. The other end of the DNA chain is called the 3’ end – it hasa free hydroxyl group linked to the 3’carbon of the last deoxyribose of the chain.Crick’s adaptor hypothesis – People first believed that the RNA templates for protein synthesis were folded up to create cavities on their outer surfaces specific for the 20 different amino acids. Crick didn’t believe this would work because 1.) the specific chemical groups on the four bases of RNA (AUGC) should interact with water-soluble groups, yet the specific side groups of many amino acids strongly prefer interaction with water-insoluble groups and 2.) even if RNA could be folded so as to display hydrophobicsurfaces, seemed unlikely that an RNA template would be used to discriminate accuratelybetween chemically very similar amino acids(some A.A’s differ only by the presence of a single methyl group) So crick proposed that prior to incorporation into proteins, amino acids are first attached to specific adaptor molecules which possess unique surfaces that can bind specifically to bases on the RNA templates. Years later, someone discovered transfer RNA molecules which were the “adaptors” that Crick spoke of. RNA is synthesized upon DNA template by RNA PolymerasesRNA are synthesized using DNA molecules as a template, in the nucleus, by enzymes called RNA polymerases. These hold onto DNA, opening up the two strands to form a bubble. They are separated, and the polymerase will synthesize the RNA molecule from 5’->3’, using one of the DNA strands called the template strand. The other strand (non-template) strand, is often called the coding strand – it has almost identical sequence of the RNA (except T switched to U). precursors of RNA = ATP, GTP, CTP and UTP-DNA and RNA synthesis both occur 5’->3’. Major Types of RNA:• messenger RNA (mRNA): gene-specific, contains future protein sequence information.• transfer RNA (tRNA): transfer specific amino acid to the site of protein synthesis.• ribosomal RNA (rRNA): structural component of ribosomes that function as a factory of protein synthesis. • small non-coding RNA: regulatory function, don’t make protein – exist to regulate gene function and expressionmRNA-The template for protein synthesis-For the protein to be made, we need factories called ribosomes(made up of two subunits, large and small, of protein/rRNA).-Conveyor belt brings tRNAs that have attached AA’s. Get into the ribosomes, bring the AA required to synthesize protein chain. -Several ribosomes may be attached to one mRNA at one time – entire assembly = polynribosomeDetermining the Genetic Code:-One nucleotide specifies one amino acid, then can specify 4 amino acids. Going up to 3 n/aa, then you can end up with 64 amino acids. Each triplet = codon, and each codon specifies an amino acid. Lotta repetition. There are 64 codons but only 20 amino acids, which means that one amino acid has more than one codon (codon degeneracy). Codons that specify the same A.A. are called synonyms. Generally, when the first two nucleotidesare identical, the third can be C or U (or G and A, or even any of the four) and the codon will still be the same. -AUG = start codon in almost 100% of cases. UAA, UGA, and UAG are the stop codons – they tell ribosomes to stop working – this is end of protein chain. At first, it was assumed that translation of mRNA ends when the entire chain has been read. However, been discovered that translation starts and stops at internal positions. UAA, UAG, and UGA are nonsense codons that do not direct addition of a particular amino acid-they serve as translational stop signals or stop codons. AUG codes for methionines which initiates all polypeptide chains. -Seems like the code evolved in such a way to minimized the deleterious effects of mutations. For example, a mutation in the first position of a codon will often give a similar or even the same amino acid. Codons with pyrimidines in the 2nd position specify mostly hydrophobic A.A’s, whereas those with purines correspond mostly to polar amino acids. Lastly, if a codon suffers a transition mutation in the third position, will very rarely get a different amino acid. tRNA’s- Amino acids are first attached to these tRNA molecules before they are incorporated into protein. tRNA folds in on itself, has an anticodon, and the amino acid attaches to the 3’ end. First, it was proposed that a specific tRNA anticodon existed for every codon. Therefore, you would need at least 61 different tRNA’s. -It was discovered that there was a fifth base, called inosine, which arrivedthrough