Lecture 8 Molecular Genetics Coding instructions of all living organisms written in same genetic language that of nucleic acids Must first understand structure of DNA Knew 1 Genetic material must contain complex information a Traits and functions of an organism b Must have capacity to vary c Must be stable alterations to genetic instructions mutations are usually detrimental 2 Genetic material must replicate faithfully a Copied accurately b Each cell division the genetic instructions must be transmitted c Reproduction coding instructions must be copied with fidelity to 3 Genetic material must encode the phenotype a Genetic material genotype codes for determines traits phenotype b Mechanism needed to translate genetic info into amino acid sequence accurately progeny of protein Watson and Crick Discovery of the 3 dimensional structure of DNA Sugars and phosphates on the outside and bases on the inside of helix G C and A T pairing Most organisms DNA carry genetic information A few viruses use RNA DNA consists of two complementary and antiparallel nucleotide strands that form a double helix Three levels of complexity primary secondary and tertiary structures of DNA Primary nucleotide structure and how nucleotides join together Secondary DNA s stable three dimensional configuration helical structure Tertiary packing arrangements of double stranded DNA in chromosomes Primary Structure of DNA o Consists of a string of nucleotides joined together by phosphodiester linkages o 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 base o 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 o Phosphate group phosphorous atom bonded to four oxygen atoms Found in every nucleotide and frequently carry a negative charge DNA Phosphate group always bonded to 5 carbon atom of the sugar in a nucleoside acidic nucleotide o DNA nucleotides Deoxyribonucleotides or deoxyribonucleoside 5 monophosphates 4 types of bases 4 kinds of DNA nucleotides Equivalent RNA nucleotides ribonucleotides or ribonucleoside 5 To understand 5 prime and three prime know position on a ribose group monophosphate o 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 end o o Linked by phosphodiester backbone Sugars linked by phosphodiester bonds o Antiparallel Bases on opposite strands interact by hydrogen bonding Each base pair has different number hydrogen bonds 5 phosphate 3 hydroxyl 2 between A T 3 between C G o RNA Presence of uracil over thymine Presence of hydroxide over hydrogen on ribose molecule o Watson crick Base Pairing Base pairing AT CG Secondary Structure o Double helix Sugar phosphate linkages on outside and bases stacked in interior Antiparallel strands o 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 o Different secondary structures genetic information 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 composition o Major and Minor Grooves o The edges of bases form a surface in each groove in each groove These surfaces will be important for protein interactions o 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 helix o o See the base pairs sticking out into the major and minor grooves Flow of information within cells o Central dogma o Exceptions RNA DNA via reverse transcriptase o o Base modifications DNA RNA structures more variation more information Introduction to Genomes o Variety of genome sizes and little relationship between how big genomes are and how complex they are C value Paradox o Number of base pairs size o Paradox is that there is no relationship between size and complexity Packing problem o 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 much o But like humans 3 billion basepairs 6 feet needs to fit in every cell o Supercoiling DNA helix is subjected to strain by being overwound positive supercoiling or underwound negative supercoiling Supercoiled DNA occupies less space than relaxed DNA lower energy Only can happen in circular DNA or when proteins cause loops in DNA Caused by topoisomerases that add or remove rotations Makes separation of DNA easier during replication and transcription if negatively