Lec1 DNA and chromosome structure PDF

DNA and chromosome structure  DNA History Deoxyribonucleic acid, or DNA, was discovered in the late 1860s. It was ignored because it seemed too simple: A,C, G, T. In the 1940s scientists discovered that chromosomes, which carry hereditary information, consist of DNA an...

DNA and chromosome structure  DNA History Deoxyribonucleic acid, or DNA, was discovered in the late 1860s. It was ignored because it seemed too simple: A,C, G, T. In the 1940s scientists discovered that chromosomes, which carry hereditary information, consist of DNA and proteins. Experiments conducted throughout the 1940s showed that DNA actually seemed to be the genetic material.  DNA: The Genetic Material Griffith (1920s) discovered a “Transforming Principle” that carried heritable (genetic) information. In the 1940’s, Avery and colleagues identified the transforming principle as DNA. Griffith experiment Avery experiment Hershey-Chase Experiment  The Structure of the Nucleotide DNA and RNA are long polymers whose monomer units are called nucleotides A nucleotide consists of: 1. Nitrogen containing heterocyclic base Purine Pyrimidine 2. Five-carbon sugar ring Ribose Deoxyribose 3. Phosphoryl group Ring structures are found in both the base and the sugar Base rings are numbered as usual Sugar ring numbers are given the designation (' )or prime  Major Purine Bases Nitrogenous bases are heterocyclic amines – Cyclic compounds with at least 1 N atom in the ring structure – Purines are a double ring structure A 6-member ring fused to a 5-member ring NH2 O C N C N1 6 5C 7 HN C N 8 CH CH 2 HC 3 4C 9 C C N N N N H H2N H Adenine Guanine  Major Pyrimidine Bases Pyrimidines consist of a single 6-membered ring NH2 O O C C CH C N3 4 5CH HN C 3 HN CH C2 16 O N CH C CH C CH O N O N H H H Cytosine Thymine Uracil in DNA in RNA  Nucleotides The nitrogen base is attached b to – ribose (RNA) base – deoxyribose (DNA) The sugar is phosphorylated at carbon 5‘ phosphate C NH2 Covalent bond between the sugar ester N CN CH and the phosphoryl group is a 2- HC C N N phosphoester bond O3PO CH2 O H H Bond between the base and the H H sugar is a b-N-glycosidic linkage OH H joining the 1'-carbon of the sugar and a nitrogen atom of the base deoxyribose sugar  Deoxythymidine 5'-Monophosphate linkages between NH2 – The nitrogenous base C CH3 thymidine and the 5- HN C carbon sugar C C deoxyribose O N 2- – The deoxyribose and O3PO CH2 O the phosphoryl group H H H H OH H Deoxythymidine 5'-monophosphate dTMP  The Specific Ribonucleotide, Adenosine Triphosphate Schematic labels the different portions of the molecule indicating the change as sequential phosphoryl groups are added Functions of Nucleotides  20.2 The Structure of DNA and RNA Nucleotides combine to form a chain or polymerize in a series of 3' to 5' phosphodiester bonds – The 5' phosphate on one unit esterifies to the 3' OH on the adjacent unit – The terminal 5' unit retains the phosphate Backbone of the polymer (in blue) is called the sugar- phosphate backbone because it is composed of alternating units of deoxyribose and phosphoryl groups  Helical Structure of DNA DNA consists of two chains of nucleotides coiled around one another in a right-handed double helix – Sugar-phosphate backbones of the two strands spiral around the outside of the helix like the handrails on a spiral staircase – Nitrogenous bases extend into the center at right angles to the acids of the helix as if they are the steps of the spiral staircase  Chargaff’s Rules Base composition varies between species Base composition is the same within the species Base composition remains the same during the individuals development In all DNAs, A = T and G = C Thus A + G = T + C Nucleotides must be paired in a specific way  Hydrogen Bonding of the DNA Helix A-T base pairs have two H- bonds. Figure 2.6ab: Normal base pairs in DNA: adenine and thymine G-C base pairs have three H-bonds Figure 2.6cd: Normal Base Pairs in DNA: guanine and cytosine 19 Models courtesy of Antony M. Dean, University of Minnesota. 2. The diameter of the helix is 2 nm or 20 Å Distance dictated by the dimensions of the purine- pyrimidine base pairs 2 nm  complementarity Purine-purine = TOO WIDE ◼The A-T and G-C base pairs are the only ones that can fit the physical dimensions of the helical model. Purine-pyrimidine = JUST RIGHT Space between sugar-phosphate backbones  Complementary DNA Strands The two DNA strands are complementary strands – The sequence of bases on one automatically determine the sequence of bases on the other strand The chains run antiparallel – Only when the 2 strands are antiparallel can the base pairs form the H bonds that hold them together  Hydrogen Bonds link Nucleotides to form a ladder (DNA) + The two strands show opposite polarity, therefore oriented in opposite directions (5’→ 3’ AND 3’→ 5’)  Schematic Ribbon Diagram of DNA Double Helix 2 strands of DNA form a right-handed double helix Bases in opposite strands hydrogen bond with AT/GC rule 2 strands are antiparallel per their 5' to 3' directionality 1 complete 3600 turn of the helix, 10 nucleotides 1 complete turn is 3.4 nm and 1 nucleotide is 0.34 nm 0.34 nm 3.4 nm, 10 base pairs per turn  DNA Segment Sugar-phosphate backbone Chain 2 Chain 1 Hydrogen bonded base pairs in the core of the helix The Major and Minor grooves grooves are large enough to allow protein molecules to make contact with the bases.  RNA Structure Sugar-phosphate backbone for ribonucleotides is also linked by 3'-5' phosphodiester bonds – RNA molecules usually single-stranded – Ribose replaces deoxyribose – Uracil replaces thymine Base pairing between U and A and G and C can still occur – This H bonding results in portions of the single- strand that become double-stranded DNA Denaturation and Renaturation (Annealing ) What is causing DNA to denature? Heat and extreme pH Disruption of hydrogen bonds between paired bases Annealing in two steps 1. two strands have to find each other by random collisions (slow) 2 base pairing of the two strands (fast) From Lehninger Principle of Biochemistry Relationship between Tm Heat Denaturation of and the GC content of DNA DNA (melting curve) The higher the G C content , the higher the melting point Tm is the temperature at which equal % age of single strands and double strands is present (measured by spectrophotometry) From Lehninger Principle of Biochemistry  Prokaryotic Chromosomes Chromosomes are pieces of DNA that contain the genetic instructions, or genes, of an organism Prokaryotes (single chromosome) – No true nucleus – Additional DNA (plasmid) – Chromosome is a circular DNA molecule that is supercoiled, meaning the helix is coiled on itself – At approximately 40 sites, a complex of proteins is attached, forming a series of loops – This structure is the nucleoid Eukaryotic Chromosome Levels of Structure  Chromosomes The complex of DNA and proteins is called chromatin. Chromatin condenses; during mitosis or meiosis This makes division of copies of chromosomes to nucleus possible. Chromosomes and cell division  chromosomes The first level of compaction, winding around histone cores (proteins) → nucleosomes. Histone Proteins  Structural role in chromatin  Present in amounts equivalent to amounts of DNA  Major histone types: H1, H2a, H2b, H3, and H4  Basic proteins  Arginine and Lysine are Abundant  Highly conserved proteins  chromosomes A nucleosome contains a core of 8 histone molecules: 2 of (H2A, H2B, H3, and H4) with 146 bp of DNA wrapped around it. Histone H1, clamps the DNA to the core →facililates the next level of packaging nucleosomes  Nucleosomes→ chromosome Nucleosomes→30 nm polynucleosome fiber (nucleofilament)→loops anchored by a scaffold of proteins→ additional paccking→ chromosome  Anatomy of a chromosome Chromosomes are categorized by : 1. The size 2. the relative location of their centromere. The portion of the chromosome to each side of a centromere is called a chromosome arm. The telocentric is not present in humans  Centromeres are the largest constriction of the chromosome Site of attachment of spindle fibers 100,000s of 171 base pair repeat, called alpha satellite sequences  Telomeres are: At the tips of chromosomes Many repeats of the sequence TTAGGG