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Lecture 8Molecular GeneticsCoding instructions of all living organisms written in same genetic language  that of nucleic acidsMust first understand structure of DNAKnew:1. Genetic material must contain complex informationa. Traits and functions of an organismb. Must have capacity to varyc. Must be stable – alterations to genetic instructions (mutations) are usually detrimental2. Genetic material must replicate faithfullya. Copied accuratelyb. Each cell division the genetic instructions must be transmitted accuratelyc. Reproduction – coding instructions must be copied with fidelity to progeny3. Genetic material must encode the phenotypea. Genetic material (genotype) codes for (determines) traits (phenotype)b. Mechanism needed to translate genetic info into amino acid sequence of proteinWatson and Crick: Discovery of the 3 dimensional structure of DNASugars and phosphates on the outside and bases on the inside of helixG-C and A-T pairingMost organisms DNA carry genetic informationA few viruses use RNADNA consists of two complementary and antiparallel nucleotide strands that form a double helixThree levels of complexity: primary, secondary, and tertiary structures of DNAPrimary  nucleotide structure and how nucleotides join togetherSecondary  DNA’s stable three-dimensional configuration, helical structureTertiary  packing arrangements of double-stranded DNA in chromosomes- Primary Structure of DNAo Consists of a string of nucleotides joined together by phosphodiester linkageso DNA is a macromolecule  large molecule Polymer  made up of many repeating units linked together Repeated units = nucleotides Nucleotides have 3 parts: 1. Sugar 2. Phosphate 3. Nitrogen-containing baseo Sugars of nucleic acids = pentose sugars RNA has –OH  so more reactive, less stable DNA  better to carry genetic info bc more stable-o Nitrogenous base  either purine or pyrimidine DNA and RNA contain A,G, C (RNA has U, DNA has T) Flat ring structures with groups sticking out Know these 5 structures In a nucleotide the nitrogenous base always forms a covalent bond with the 1’ carbon atom of the sugar A deoxyribose or a ribose sugar and a base together are referred to as a nucleosideo Phosphate group  phosphorous atom bonded to four oxygen atoms Found in every nucleotide and frequently carry a negative charge = DNA acidic Phosphate group always bonded to 5’-carbon atom of the sugar in a nucleotideo DNA nucleotides Deoxyribonucleotides or deoxyribonucleoside 5’-monophosphates 4 types of bases = 4 kinds of DNA nucleotides Equivalent RNA nucleotides = ribonucleotides or ribonucleoside 5’-monophosphate  To understand 5 prime and three prime know position on a ribose groupo Polynucleotide stands DNA made of many nucleotides connected by covalent bonds which join the 5’-phosphate group of one to 3’-carbon atom of next molecule- = Phosphodiester linkages- Strong covalent bonds Nucleotides linked like this make polynucleotide strands Backbone of stand is composed of alternating sugars and phosphates and bases project away from the axis of the strand Direction/ polarity- One end a free phosphate attach to 5’carbon of sugar in nucleotide = 5’end - Other end has free OH group of 3’-carbon of the sugar = 3’ endoo Linked by phosphodiester backbone Sugars linked by phosphodiester bondso Antiparallel 5’ phosphate  3’ hydroxyl Bases on opposite strands interact by hydrogen bonding Each base pair has different number hydrogen bonds- 2 between A-T- 3 between C-Go RNA Presence of uracil over thymine Presence of hydroxide over hydrogen on ribose moleculeo Watson-crick Base Pairing Base pairing (AT, CG)- Secondary Structureo Double helix Sugar-phosphate linkages on outside and bases stacked in interior Antiparallel strandso Strands held together by two types of molecular forces Hydrogen bonds link the bases on opposite stands  weaker than phosphodiester bonds- CG is stronger than AT because of the number of hydrogen bonds- Strands are not identical by complementary  efficient and accurate DNA replication Interaction between stacked base pairs- Help with stability of DNA molecule but don’t need a particular base to follow another- Therefore DNA molecule is free to vary, allowing DNA to carry genetic informationo Different secondary structures The 3D shape of molecule can vary depending on conditions in which the DNA is placed, or on base sequence itself Direction of helix A form, B form, Z form B-DNA is the basic physiological form- Plenty of water surround the molecule and no unusual base sequence in the DNA- Most stable configuration, and most predominate structure- Alpha helix – right handed, clockwise spiral- 10 base pairs per 360 degree rotation (turn)- .34 nm apart so each full rotation is 3.4 nm- Diameter of the helix is 2nm- Major and minor grooves A-DNA  Less water present- Alpha helix (right handed) - Shorter and wider than B-DNA (compacted helix) Z form  contains particular base sequences (stretches of C and G nucleotides)- Left-handed helix- Sugar-phosphate backbone zigzags back and forth- Rare form driven by unusual base pair compositiono- Major and Minor Grooveso  The edges of bases form a surface in each groove in each groove These surfaces will be important for protein interactionso Needs to be information in this molecule Things must be able to interact with this molecule when it is being used in a cell to make protein and is still paired in a helixoo See the base pairs sticking out into the major and minor grooves- Flow of information within cellso Central dogmao Exceptions RNA DNA via reverse transcriptaseoo Base modifications, DNA, RNA structures: more variation, more “information”- Introduction to Genomeso Variety of genome sizes and little relationship between how big genomes are and how complex they are = C value Paradoxo Number of base pairs = sizeo Paradox is that there is no relationship between size and complexity- Packing problemo 3 hierarchical levels of structure of DNA Primary (nucleotide sequences), Secondary (double-stranded helix), tertiary (high-order folding that allows DNA to be packed)o Twisting and turning can only do so mucho But like humans, 3 billion basepairs (6 feet) needs to fit in every cello Supercoiling DNA helix is subjected to strain by being overwound (positive

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UMD BSCI 222 - Molecular Genetics

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