Chapter 4 - Nucleic Acids & DNA Replication Objective

Nucleic Acids

  1. Know the structure of nucleic acids; differences between nucleoside and nucleotide 

  • Nucleic Acid: A macromolecule composed of nucleotide monomers. Generally used by cells store or transmit hereditary information. Includes ribonucleic acid and deoxyribonucleic acid.

  • Polymers of nucleotides, each containing a sugar, phosphate group, and nitrogenous base 

    • Sugar: give-carbon sugar, deoxyribose in DNA and ribose in RNA

    • Phosphate group: links sugars together 

    • Nitrogenous base: nitrogen-containing base 

      • DNA bases: adenine (A), guanine (G), cytosine (C), and thymine (T)

      • RNA bases: adenine (A), guanine (G), cytosine (C), and uracil (U)

  • Primary structure is the sequence of these nucleotides linked by phosphodiester bonds

    • linear sequence of nucleotides in a single strand 

    • phosphodiester bonds form a long chain with a sugar-phosphate backbone and a sequence of bases 

    • sequence is read from the 5’ to 3’ direction 

      • 5’: free phosphate group, 3’ free hydroxyl group 

  • Secondary structure: 3D shape of nucleic acid strands 

    • DNA’s secondary structure is a double helix of two antiparallel strands, held together by hydrogen bonds between complementary base pairs (A-T and G-C) 

      • bases on opposite strands pair up 

    • RNA is often a single strand that can fold into complex shapes like hairpins or loops 

  • Nucleotide vs Nucleotide 

    • Nucleotide: composed of a five-carbon sugar (deoxyribose/ribose)

      • contains a phosphate group (one or more)

      • components: nitrogenous base and sugar and phosphate group 

      • function: building block for DNA and RNA, involved in energy metabolism and cell signaling 

      • ex: ATP, GTP, cAMP

    • Nucleoside:

      • doesn’t contain a phosphate group 

      • components: nitrogenous base and sugar 

      • function: building block for nucleotides

      • ex: adenosine

  1. Know the reaction of how they are joined and the name of the bond 

  • Condensation reaction that forms a covalent phosphodiester bond linking the phosphate group of one nucleotide to the sugar of the next 

    • creates a sugar-phosphate backbone and releases a water molecule 

    • reaction occurs between the 5’ phosphate group of one nucleotide and the 3’ hydroxyl group of another forming a long chain in the 5’ —» 3’ direction 

  1. List several functions for nucleic acids 

  • Main functions (DNA & RNA): store and transmit genetic information, direct protein synthesis

    • DNA: stores genetic blueprint for an organism 

    • RNA: Uses genetic information to build proteins which are essential for all cellular functions 

  • Store & Transmit Genetic Information 

    • DNA: stores the genetic blueprint of an organism, includes instructions for its development, growth, and reproduction 

    • Heredity material: DNA is passed from parents to offspring, ensuring the transmission of heritable traits from one generation to the next 

  • Direct Protein Synthesis: 

    • Protein synthesis: nucleic acids are central to the process of creating proteins, which perform most the chemical processes in a cell 

    • mRNA: messenger RNA; carries the genetic code from DNA to the ribosome 

    • tRNA: transfer RNA; brings the correct amino acids to the ribosomes 

    • rRNA: ribosomal RNA; a structural component of ribosomes, the site of protein synthesis 

  • Gene expression: nucleic acids regulate which genes are turned on or off 

  • Cellular processes: involved in processes like DNA replication, repair, and recombination to maintain genetic integrity —» highly organized 

  • Energy transfer: modified nucleotides like ATP are crucial for energy processing in cells 


  1. Explain experiments that helped to define the structure of DNA

  • Erwin Chargaff - analyzed composition of DNA from different species 

    • method: chromatography and UV spectrophotometry to measure the quantity of each of the 4 nitrogenous bases in DNA 

    • findings: 2 rule where the amount of A=T in DNA and G=C; and ratio of (A+T) to (G+C) varies from species to species 

    • bases are paired in a specific, non-random, way 

  • Rosalind Franklin and Maurice Wilkins - X ray diffraction analysis 

    • method: Franklin purified DNA fibers and sued a focused x-ray beam to produce diffraction patterns which revealed the position of atoms within crystal structure 

    • findings: Franklin captured “photo 51” a clear diffraction image that shows a cross-shaped pattern characteristic of a helical structure —» analysis showed key measurements and confirmed that the sugar-phosphate backbone of DNA molecule was on the outside 

  • James Watson and Francis Crick 

    • method: used existing data from Chargaff, Franklin, and Wilkins, and knowledge of chemical bonding to assemble a physical model of DNA 

    • findings: proposed double-helical structure for DNA and in their model the sugar-phosphate backbones form the outside the helix, nitrogenous bases (A,T,C,G) pair up in the middle forming rungs of the ladder, specific base pairing (A with T and C with G), and two strands run in opposite directions (antiparallel)

    • important since the structure itself suggested a mechanism for how 

  • Meselon-Stahl Experiment 

    • experimentally confirmed the “semi-conservative” model of DNA replication 

    • method: grew bacteria in a medium containing “heavy” nitrogen isotope N15, causing bacteria to incorporate it into their DNA; transferred bacteria to a ‘light” nitrogen isotope N14 medium and allowed them to replicate over several generations; density of DNA at each stage was analyzed using a centrifuge 

    • findings: after one generation, all DNA was a hybrid of heavy and light nitrogen; after two generations half the DNA was hybrid and half was entirely light; pattern perfectly patched the prediction of the semi-conservative model, where each new DNA molecule consists of one old strand and one new strand 

    • contribution: final confirmation that the double helix model was correct and accurately explained the mechanism of genetic inheritance 


  1. Compare and contrast RNA and DNA

  • Both carry genetic information but differ in structure, sugar, and bases 

  • DNA: 

    • deoxyribonucleic acid 

    • structure: double-stranded helix 

    • sugar: deoxyribose 

    • bases: adenine (A), thymine (T), guanine (G), cytosine (C)

    • function: long-term storage of genetic information 

    • stability: more stable due to its structure and sugar 

    • location: primarily in nucleus (eukaryotes) 

  • RNA: 

    • ribonucleic acid 

    • structure: single-stranded (can fold into complex shapes)

    • sugar: ribose

    • bases: adenine (A), uracil (U), guanine (G), cytosine (C)

    • function: carries out protein synthesis, acting as a messenger (mRNA), and is a component of ribosomes (rRNA) and transfer (tRNA)

    • stability: less stable due to its single strand and sugar structure 

    • location: nucleus and cytoplasm 


  1. Provide the characteristics of the W-C model of DNA

  • Double-helix structure, composed of two antiparallel strands with sugar-phosphate backbones on the outside and nitrogenous bases on the inside 

  • Strands are held together by specific base pairing rules via hydrogen bonds, creating a uniform diameter and a consistent shape for the molecule 

  • Structure: double helix, antiparallel strands, nitrogenous bases, major and minor grooves

  • Base pairing: complementary base pairing, hydrogen bonds


  1. Know the Scientists involved in determining the structure of DNA 

  • Watson and Crick proposed double helix idea 

    • work was built on the foundational research of others including Franklin, Wilkins, and Chargaff 

DNA Replication 

  1. Know the proteins involved in the process 

  • Enzymes: 

    • DNA polymerase: synthesizes new DNA strands by adding nucleotides to the 3’ end of the growing strand 

    • Helicase: unwinds the DNA double helix at the replication fork 

    • Primase: synthesizes RNA primers, which provide a starting point for DNA polymerase 

    • Topoisomerase/Gyrase: relieves DNA supercoiling during unwinding 

    • DNA ligase: joins Okazaki fragments on the lagging strand 

  • Telomerase: in eukaryotic cells, synthesizes telomere sequence at the ends of linear chromosomes 


  1. Describe the process step by step with attention to orientation of the strands 

  • 1. Unwinding the DNA 

    • origin of replication: replication begins at a specific site on the DNA helix 

    • helicase: enzyme DNA helicase unwinds the double helix by breaking the hydrogen bonds between base pairs which creates a Y-shape structure called a replication fork 

    • single-strand binding proteins: proteins bind to the separated DNA strands to prevent them from re-pairing and becoming a double-helix again 

    • topoisomerase: ahead of the replication fork, the DNA becomes overwound or supercoiled; topoisomerase enzymes alleviate this strain by cutting, unwinding, and re-ligating the DNA

  • 2. Building new Strands 

    • RNA primers: DNA polymerase cannot start a new strand from scratch. An enzyme called primase must first create a short RNA primer, which provides a starting point with a free 3’-OH group for DNA polymerase to begin synthesis 

  • 3. Synthesis of the Leading Strand 

    • the leading strand is the template strand that runs in the 3’ to 5’ direction toward the replication fork 

    • continuous synthesis: because DNA polymerase synthesizes in the 5’ to 3’ direction, it can move along the template strand continuously following the unwinding helicase 

    • single primer: only one RNA primer is needed for the entire leading strand 

  • 4. Synthesis of the Lagging Strand 

    • the lagging strand in the template strand that runs in the 5’ to 3’ direction opposite to the movement of the replication fork 

    • discontinuous synthesis: since DNA polymerase must move in the 5’ to 3’ direction, it is forced to synthesizes the lagging strand in short disconnected segments 

    • Okazaki fragments: short segments of DNA 

  • 5. Completing the DNA Copies 

    • primer removal: the RNA primers are eventually removed and replaced with DNA nucleotides by DNA polymerase I 

    • ligation: after the primers are replaced, the enzyme DNA ligase seals the gaps between the Okazaki fragments by forming phosphodiester bonds 

    • proofreading: throughout the process, DNA polymerase also proofread their work, identifying and correcting errors to ensure high yields 

  • End Result: semiconservative replication because each new double helix consists of one original or parental strand and one newly synthesized daughter strand 

  1. Compare and contrast the process in Eukaryotes and Prokaryotes 

  • Similarities

    • basic processes: semi-conservative replication model where each new DNA molecule consists of one original and one new strand 

    • key enzymes: rely on enzymes like helicase to unwind DNA and DNA polymerase to synthesize new strands 

    • direction: replication proceeds in a 5’ —» 3’ direction, requiring leading and lagging strands 

    • Okazaki fragments: both create Okazaki fragments on the lagging strand 

  • Differences

    • Prokaryotes: 

      • Origin of replication: one origin 

      • DNA structure: single, circular chromosome 

      • replication rate: faster 

      • DNA polymerases: DNA polymerase I and II are key; less types 

      • primer removal: DNA polymerase I removes RNA primers 

    • Eukaryotes: 

      • origin of replication: multiple origins 

      • DNA structure: multiple linear chromosomes

      • replication rate: slower 

      • DNA polymerases: many types 

      • primer removal:


  1. Explain how telomeres are handled during the process 

  • Linear ends of chromosomes, called telomeres, face a challenge called the “end-replication problem” 

  • Mechanism used by DNA polymerase the lagging strand cannot be fully copied to the very end 

    • most somatic cells don’t express the enzyme telomerase, so telomeres shorten with each division 

    • specialized cells use telomerase to extend their telomeres and prevent shortening 

  • End-Replication Problem 

    • DNA polymerase can only synthesizes new DNA in the 5’ to 3’ direction, to begin replication DNA polymerase needs a short RNA primer 

    • Leading strand: replication proceeds continuously towards the replication fork with a single primer and it copies the template strand completely 

    • Lagging strand: replication proceeds discontinuously in short segments, called Okazaki fragments, moving away from the replication fork, and each fragment requires a new RNA primer 

    • End-replication problem occurs specifically on the lagging strand at the chromosome’s end 

      • 1. when the final RNA primer is removed from the chromosomes end DNA polymerase cannot fill the gap 

      • 2. DNA polymerase requires a free 3’ hydroxyl group to extend the new strand, with no upstream Okazaki fragment this group is unavailable at the very tip of the chromosome 

      • 3. this leaves a non-replicated portion at the 5’ end of the new strand, leading to a net shortening of the chromosome with each cell division 

    • How cells handle telomeres 

      • 1. Telomere shortening in most somatic cells 

        • when telomeres become critically short, the cell enters a state of permanent growth arrest or triggers programmed cell death (apoptosis)

        • mechanism is a natural tumor-suppression process that prevents uncontrolled cell division 

      • 2. Telomere maintenance by telomerase in special cells 

        • some cell types that must divide continuously throughout life express the enzyme telomerase to prevent telomere shortening 

        • telomerase is made up of protein and RNA


  1. Understand how the Meselon and Stahl experiment is set up and produces the results 

  • Growing E. coli bacteria in a medium with heavy nitrogen N15 which incorporated into DNA

  • Bacteria were transferred to a light nitrogen N14 medium, and samples were taken after each round of replication 

  • Found that after the first generation, all DNA was a hybrid of one heavy N15 and one light N14 strand, proving that DNA replication is semi-conservative 

  • Results

    • generation 0 (before transfer): DNA was all heavy/N15 and formed a single band at the bottom of the centrifuge tube 

    • generation 1 (after 1st replication): DNA from bacteria grown in the light medium was a single band of hybrid DNA, so each double helix contained one heavy/N15 strand and one newly synthesized light/N14 strand which results in conservative model and produces one heavy and one light DNA molecule 

    • generation 2 (after 2nd replication): hybrid DNA replicated which results in two bands - one band of hybrid DNA N15/N14 and one band of completely light DNA N14/N14. this outcome is consistent with the semi-conservative model where the heavy parental strand separates and each template is paired with a new light strand while the previously synthesized light strands also acts as a template strand for the new light strands 

    • subsequent generations: the ratio of light to hybrid DNA continued to increase with each generation, with the light DNA band becoming more prominent as the hybrid band becomes less so