DNA REPLICATION AND TRANSCRIPTION I NUCLEIC ACID STRUCTURE A The structure of DNA 1 Chemical components of DNA a Each polynucleotide chain of DNA contains nucleotides which consist of a nitrogenous base A G C or T deoxyribose and phosphate b The bases are the purines adenine A and guanine G and the pyrimidines cytosine C and thymine T c Phosphodiester bonds join the 3 carbon of one sugar to the 5 carbon of the next sugar 2 DNA double helix a Each DNA molecule is composed of two polynucleotide chains joined by hydrogen bonds between the bases 1 Adenine on one chain forms a base pair with thymine on the other chain 2 Guanine base pairs with cytosine 3 The base sequences of the two strands are complementary Adenine on one strand is matched by thymine on the other and guanine is matched by cytosine b The chains are antiparallel One chain runs in a 5 to 3 direction the other chain runs 3 to 5 c The double stranded molecule is twisted to form a helix with major and minor grooves 1 The base pairs that join the two strands are stacked like a spiral staircase in the interior of the molecule 2 The phosphate groups are on the outside of the double helix Two hydroxyl groups of each phosphate are involved in phosphodiester bonds The third is free and dissociates its proton at physiologic pH giving the molecule a negative charge 3 The B form of DNA first described by Watson and Crick is right handed and contains 10 base pairs per turn 4 Other forms of DNA include the A form which is similar to the B form but more com pact and the Z form which is left handed and has its bases positioned more toward the periphery of the helix 1 3 Denaturation renaturation and hybridization a Denaturation Alkali or heat causes the strands of DNA to separate but does not break phosphodiester bonds b Renaturation If strands of DNA are separated by heat and then the temperature is slowly decreased under the appropriate conditions base pairs reform and complementary strands of DNA come back together c Hybridization A single strand of DNA or RNA pairs with complementary base sequen ces on another strand of DNA or RNA Biochemistry Molecular Biology and Genetics A segment of a polynucleotide strand This strand contains thymine and deoxyribose so it is a segment of DNA 2 The base pairs of DNA DNA Replication and Transcription Antiparallel strands of DNA Note that the strands run in opposite directions A adenine C cytosine G guanine T thymine Deoxyribose Phosphate 4 DNA molecules are extremely large a The entire chromosome of the bacterium Escherichia coli is circular and contains more than 4 10 base pairs b The DNA molecule in the longest human chromosome is linear and is over 7 2 cm long 5 Packing of DNA in the nucleus a The chromatin of eukaryotic cells consists of DNA complexed with histones in nucleo somes Figure 17 5 1 Histones are relatively small basic proteins with a high content of arginine and lysine Prokaryotes do not have histones 3 2 Eight histone molecules form an octamer around which about 140 base pairs of DNA are wound to form a nucleosome core 3 The DNA that joins one nucleosome core to the next is complexed with histone HI b The beads on a string nucleosomal structure of chromatin is further compacted to form solenoid structures helical tubular coils 6 Mitochondrial DNA a The mitochondrial genome is a double stranded circular DNA molecule found within the mitochondrial matrix 1 The genetic code for the mitochondria is slightly different than that of genomic DNA 2 The genome codes for 13 protein subunits of the electron transport chain a large and small ribosomal RNA rRNA and 22 transfer RNAs tRNAs The DNA double helix Biochemistry Molecular Biology and Genetics A polynucleosome Adapted from Olins DE Olins AL Nucleosomes The structural quan tum in chromosomes 4 b Mitochondrial DNA is maternally inherited 1 Mitochondria from the egg contribute exclusively to the zygote 2 The mitochondria autonomously reproduce and therefore all the mitochondria are of maternal origin c Mitochondrial DNA has a high mutation rate about 5 to 10 times greater than the nuclear genome B The structure of RNA 1 RNA differs from DNA a The polynucleotide structure of RNA is similar to DNA except that RNA contains the sugar ribose rather than deoxyribose and uracil U rather than thymine A small amount of thymine is present in tRNA b RNA is generally single stranded in contrast to DNA which is double stranded 1 When strands loop back on themselves the bases on opposite sides can pair adenine with uracil A to U and guanine with cytosine G to C 2 RNA molecules have extensive base pairing which produces secondary and tertiary structures that are important for RNA function 3 RNA molecules recognize DNA and other RNA molecules by base pairing c Some RNA molecules act as catalysts of reactions thus RNA as well as protein can have enzymatic activity 1 Ribozymes usually precursors of rRNA remove internal segments of themselves splic ing the ends together 2 RNAs also act as ribonucleases cleaving other RNA molecules e g RNase P cleaves tRNA precursors 3 Peptidyl transferase an enzyme in protein synthesis consists of RNA Messenger RNA mRNA contains a cap structure and a poly A tail 2 a The cap consists of methylated guanine triphosphate GTP attached to the hydroxyl group on the ribose at the 5 end of the mRNA 1 The N7 in the guanine is methylated 2 The 2 hydroxyl groups of the first and second ribose moieties of the mRNA also may be methylated 5 CLINICAL CORRELATES Many viruses such as the influenza virus transfer the 7 methyl G cap from host cell mRNAs to viral mRNA which functions to increase mRNA stability and increase translation of the Mrna The cap structure of messenger RNA b The poly A tail contains up to 200 adenine A nucleotides attached to the hydroxyl group at the 3 end of the mRNA 3 rRNA contains many loops and extensive base pairing a rRNA molecules differ in their sedimentation coefficients S They associate with pro teins to form ribosomes Figure 17 7 b Prokaryotes have three types of rRNA 16S 23S and 5S rRNA c Eukaryotes have four types of cytosolic rRNA 18S 28S 5S and 5 8S rRNA Mitochon drial ribosomes are similar to prokaryotic ribosomes 4 tRNA has a cloverleaf structure and contains modified nucleotides tRNA molecules are rela tively small containing about 80 nucleotides 6 The composition of ribosomes rRNA ribosomal RNA S sedimentation coefficients Biochemistry Molecular Biology and Genetics Three modified nucleosides