BMB 462 Lecture 19 Outline of Last Lecture I. Sources of atoms for de novo synthesisII. Function and Defects of PhosphoribosyltransferasesIII. Defects in Nucleotide BreakdownIV. Nucleoside mono-, di-, and tri- phosphate conversionV. Ribonucleotide ReductaseVI. dNTP SynthesisVII. Thymidylate SynthesisVIII. Inhibition of dNTP SynthesisOutline of Current Lecture I. Function of DNA and RNAII. DNA Carries the Cell’s Genetic InformationIII. Primary DNA StructureIV. The History of DNA – Determining Secondary StructureCurrent LectureConcepts to remembers from previous courses/lectures:-I. Function of DNA and RNAa. DNA – DNA is information storagei. It provides info to cell (stored as DNA and then can be transmitted as RNAthrough the cell to make proteins)ii. It passes the info on to progeny when the cell divides (via replication - DNA replicates itself so that there is a copy for each daughter cell)b. RNAi. More diverse functionsii. Functions as information carrier in the form of mRNA (made when you transcribed; then translated into protein)iii. Acts as an adapter (tRNA; adapter between mRNA and amino acids during translation)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.iv. Stores information (i.e. in some viral genomes)v. Structural (integral part of ribosome structure)vi. Catalysis (in ribosomes there are some rRNAs that catalyze reactions; form ribozymes; some functions used to be carried out by RNA and only later did the functions transfer to proteins)vii. Regulation (miRNA (micro RNAs) - regulate gene expression by regulating either transcription or translation. Believe they're involved in a lot of cancers. siRNA (small inhibitory RNAs) - work with inhibiting certain gene expression)viii. Splicing (snRNA - small nuclear RNA)II. DNA Carries the Cell’s Genetic Informationa. DNA stores information in its linear sequence of nucleotides, and codes for proteins via RNA (rRNA)b. Passing information on to progeny - 2 processes in cell replication: mitosis (creates new cells, done by all somatic/body cells) and meiosis (only done by gametes/sex cells for reproduction)i. Information can be transferred because the DNA is double stranded. The information is then retained due to many mechanisms working to minimize change in the sequencec. DNA Information maintained by Repair Mechanismsi. Many mechanisms minimizing change use base pairing for repair.1. Mismatch repair2. Nucleotide excision repair3. Base excision repairii. These mechanisms all recognize mutations in DNA and carry out various processes of fixing them.iii. The cell spends a lot of energy to keep its DNA (information) intact.d. Process of Using DNA as informationi. Have the info in the double stranded DNA; the cell uses that to get the mRNA. Then you get a polypeptide, and then the polypeptide is folded into its 3D structure1. The making and folding of the polypeptide often happens simultaneouslyii. Information is used to make proteins and RNA - if you were to change the information sequence, you could change the function of the protein or completely destroy it1. Change in protein function is used by evolution to create new phenotypes. a. i.e. change in DNA sequence can alter an enzyme's specificity or efficiencye. Example of Evolution of DNAi. In yeast, there was a gene for a hexokinase that used glucose as a substrate.ii. A mutation occurred in the duplication of the original glucose hexokinase gene - still had one copy of the original strand that could operate under the original function, so evolutionary mutations could work on the other strand to create a mutant gene that changed the substrate specificity of the protein to galactose instead of glucose.1. Now yeast has two kinases, one specific for glucose and one specific for galactose (change of the gene caused a change in substrate specificity)iii. Change needs to be minimal to preserve function; some change is required to produce variation for evolutionIII. Primary DNA Structurea. Primary Structure relates to the sequence of nucleotides linked by phosphodiester bonds. i. DNA is written 5' to 3', and built 3' to 5' (5' end has the phosphate, the 3' end has the OH)ii. The base order then stores the information. iii. Phosphodiester bonds occur because the 3' end can attack the phosphateon a new nucleotide group and link the molecules togetherb. Stability of DNAi. DNA is more stable than RNA, because RNA has an OH group on the 2' carbon, which makes it unstable. Under slightly alkaline conditions, that extra OH can be attacked and forms a cyclic intermediate (2',3'-cyclic monophosphate derivative) and the RNA starts to be degraded1. This difference in stability may be the reason why DNA and not RNA is the main information carrierIV. The History of DNA – Determining Secondary Structurea. 1868 - Friedrich Miescher isolated DNA for the first timeb. The structure of DNA was discovered 1940 by Avery, MacLeod, and McCarthyi. Avery determined DNA was the genetic information by making a strain of Streptococcus pneumoniae virulent again; but people did not believe that DNA was the information carrier due to the fact that DNA only has 4 bases whereas proteins have 20 amino acids and have multiple functions and that better explained the variability of genes.c. Chargaff’s Rules for Base Pairingi. Different species have different ratios of the bases - % of A, T, G, C varies between species but within one species the ratios are the same. 1. They are fixed in one species, in one individual, and in all the different tissues.ii. He also noticed that A = T and G = C, and that A+G = T+C (the purines = the pyrimidines)d. Structure from Rosalind Franklin’s X-ray Diffractioni. Watson and Crick knew about the ratios of bases, but it was Franklin's image of DNA that really led them to figure out the structure1. She was a crystallographer2. Figured out that DNA has a helical structure due to noticing repeats of 34 Å [angstroms] (~3.4nm) and of 3.4 Åii. Realized the structure would only function if the phosphates had to point outside with the bases inside (others, i.e. Watson, thought it was reversed)iii. Scandal: She had a collaborator Wilkins who shared her data with Watsonwithout her knowledge. Watson and Crick took the information and madethe double helix discovery. 1. Watson, Crick and Wilkins got credit, Franklin didn't. 2. They got the noble prize, but she was already
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