topic 18

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Department
Biochemistry
Course
Biochemistry 2280A
Professor
Chris Brandl
Semester
Fall

Description
Topic 18 1 Topic 18: Introduction to DNA and RNA DNA - crucial molecule because carries genetic material, information passed from parent to offspring is required to produce organism RNA has many functions We are going to focus on 3 1. template for producing proteins (mRNA) 2. forms ribosomes (rRNA) and catalyzing protein synthesis (along with proteins) 3. Carries amino acids to growing polypeptide chain during protein synthesis (tRNA) Monosaccharides:  ribonucleotides contain pentose ribose  deoxyribonucleotides contain deoxyribose, which is like ribose except C2’ bears 2 H atoms instead of one H and one hydroxyl Nitrogenous bases: - Purines:  Adenine – adenosine A (don’t worry about memorizing structure)  bigger ones with 2 ring system  Guanine – G  In both DNA and RNA  Ring systems are generally flat and hydrophobic  Join to C1’ of ribose or deoxyribose via N9 position - Pryimidines:  T – DNA only  Methly CH3 group  U – RNA only  H. identical to T except U lacks CH3 group  Cytosine (C) – in both DNA and RNA  Also planar (flat) and hydrophobic  Join to C1’ of ribose or deoxyribose via N1 position Building blocks of RNA  Ribonucleotides composed of 3 parts: a sugar, nitrogenous base, and phosphate o sugar ribose – basis of ribonucleic acid o ribose always beta  Anomeric C of ribose or deoxyribose ordinarily in Beta configuration when joined to nitrogenous bases Topic 18 2  Sugars joined via N-glycosidic bond - joins sugar to nitrogen forming a nucleoside (A, G, C, D, or U) o cytosine attached  makes cytidine which is a nucleoside  N-glycosidic bond can not open or close ring  can’t go from beta to alpha, stuck in beta o this is a good thing  number starting at N – 1, O=C 2 and on sugar number as 1’, 2’ (‘ – prime) Is ribose sugar alpha or beta configuration? Beta – anomeric carbon ( 2 O bound) – OH on same side of ring as highest carbon Phosphates  Attached to C5’ position of ribose or deoxyribose by phosphodiester linkage  After phosphate is attached in this position of nucleoside, nucleotide is formed o Has all three groups: ribose, base, and phosphate  Phosphate groups are negatively charged at cellular pH  Names of nucleotides normally abbreviated using letter of nitrogenous base followed by indication of number of phosphates present o Eg ADP – adenosine diphosphate o Sometimes abbreviation of deoxyribonucleotides will being with small d (dTTP)  cytidine monophosphate – nucleotide  triphosphate attached at OCH2  ATP structural molecule that used to make RNA  Deoxycytidine triphosphate – deoxynucleotide – loss of O get 2’deoxyribosse Polynucleotides  Monomers (small units) join together to make polymers  Sugars joined via 3’, 5’ phosphodiester linkages between C3’ and C5’ o Phosphate group typically on 5’ Carbon of one pentose, which joins to hydroxyl at 3’ C of another pentose o The end of polynucleotide where 5’C is ‘free’, not attached to another monosaccharide, is still 5’ end o Likee wise, at 3’ end when the 3’ C not attached to another monosaccharide ‘free’  Not branched (unlike proteins)  always linear  Like proteins, ends are different  5’ end and 3’ end o 5’ end has phosphate (of 5’ C) (even without phosphate, still 5’) o 3’ end has OH Topic 18 3 o because ends of different, call polarity of molecules o directionality – process go from 5’ to 3’ for example Direction Convention  two polynucleotide strands are tightly but non covalently associated with each other  antiparallel strands – have opposite orientation or polarity  one strand runs 5’ 3’ and other runs 3’5’  sequences are written 5’ to 3’ by convention o eg sequence GATC – G has hydroxyl of phosphate on 5’ C and C has free 3’ hydroxyl or phosphate  not specified, assume 5’ at left end and 3’ at right end Because 4 different nomoer building blocks that can be used to assemble RNA polymers, number of possible sequence combination that can be made for RNA molecule of 100 nucleotides is: 4100 DNA double Helix: 1. Chargaffs rules  Base composition of DNA varies among species  Within species, base composition is same regardless of tissue  Composition in different species is different but always %A = %T and %G = %C 2. Diffraction Pattern  Pattern suggests periodicity of 3.4nm containing 10 repeating units – repeating structure 3. Correct Tautomeric forms of bases  Different tautomers have different H bond capabilities  In order to get correct pairing, need to get correct tautomer Double Helix: “B-DNA”  Sugar orange  Two strands come together and bases pair and meet in middle
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