BCHM 3050 1st Edition Lecture 14 Outline of Last Lecture I Nucleic Acids II Components of Nucleotides III Nitrogenous Bases IV Nucleosides V Nucleotides VI Role of ATP in Energy Metabolism VII Significance of G VIII Cyclic Nucleotides Outline of Current Lecture I Levels of Structure in DNA II Formation of Phosphodiester Bonds III B DNA Spatial Dimensions IV Stabilizing Forces in DNA V Functions of Major Grooves VI Functions of Minor Grooves VII DNA Structural Variations Current Lecture I Levels of Structure in DNA a Nucleic acids is the polymer form made up of nucleotide monomers A G C T 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 b Primary sequences of bases c Secondary double helix coil d Tertiary super coiled DNA II Formation of Phosphodiester Bonds a This is deoxyribonucleotide b Cannot have ribonucleotides in DNA c Sugar should not have OH in the second position if part of DNA d Sugar in the second position indicates an RNA component e Bonds connecting the different phosphate groups phosphoanhydride f Bond connecting different nucleotides in DNA phosphodiester g Bond connecting phosphate group to OH phosphoester h Nucleotide attaches by breaking off two phosphate group and adding to the single phosphate lef i 3rd carbon atom will always have a free OH group at the end of the chain j The first nucleotide of the chain will have free phosphate group at the 5 carbon k Nucleotides in the middle are all involved in phosphodiester bonds l Free phosphate group at 5 end m Last nucleotide has a free 3 OH group n Start with a triphosphate because they are more abundant but you loose two of these phosphate groups as the DNA chain grows o Uracil RNA p Thymine DNA q If one strand runs 5 3 in one direction the opposite strand runs 3 5 r A and T bond using a double bond but G and C bond using a triple bond stronger s In DNA start with 5 and end with 3 anti parallel to each other t Purine always bond with pyrimadine III B DNA Spatial Dimensions a B form of DNA is the form characterized by Watson Crick It was originally isolated from aqueous solutions as the partly hydrated sodium salt It is thought that this form represents most native DNA in the cell b Another form the A form is observed when DNA is extracted purified from ethanol which tends to dehydrate the molecule and make it more compact than the B form Also the angle of the base plane with the ribose plane in no longer perpendicular as in B form but tilted 20 degrees away from perpendicular c Major groove is about 2 nm across 1 nm deep This can easily accommodate a 0 5 nm alpha helix of protein d B form of DNA is the most common form e Anything with a diameter of more than 2nm can fit a protein through it DNA can fit a protein through its nucleotides f Big gap major grove g Small gap minor grove h Major and minor alternate IV i The distance between 2 turns in 3 4 nm within a turn you have one major grove and one minor grove and can fit about 10 bases j One base pair occupies about 0 34nm Stabilizing Forces in DNA a Hydrogen bonds b Hydrophobic interactions c Van der Waals Forces d Electrostatic interactions e Phosphate groups on the backbone of DNA are negatively charged so the entire backbone phosphate and sugar is highly negative f V DNA dissolves in water because of the opposite charges interact Functions of Major Grooves a The major grove attracts a protein and gives it a home it can spread out over many groves b Transcription factors proteins that commonly interact with major groves c Motif combine a bunch of secondary structures together d Helix turn helix protein motif e Leucine zipper motif VI Functions of Minor Grooves a Minor grove accommodates smaller things than proteins like vitamins co factors drugs VII DNA Structural Variations a Other forms of DNA are the A form and the Z form but they are transient and not involved in transition of genetic information b A DNA in dehydrated cells c Z form is lef handed DNA can adopt the Z form during transcription but can then revert back to the B form d A and T have very similar percentages because they bond together same with G and C e More A and T than G and C in humans
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