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DNA Structure and Replication Quiz
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DNA Structure and Replication Quiz

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Questions and Answers

What is the expected banding pattern after one generation of DNA replication in a semiconservative mechanism?

  • Two heavy bands
  • Two light bands
  • One heavy band only
  • One heavy and one intermediate band (correct)

    • What characterizes the DNA molecules after four generations of semiconservative replication?

  • All molecules contain parental strands only
  • Most of the DNA has shifted to light density (correct)
  • There are no new strands present
  • All DNA molecules contain both parental and new strands

    • In the context of semiconservative replication, how many DNA molecules will contain one parental and one new strand after two generations?

  • One
  • Four
  • Two (correct)
  • Three

    • Which experimental method is used to observe the banding patterns in DNA density?

    <p>CsCl density gradient centrifugation</p> Signup and view all the answers

    What does the presence of intermediate density bands after replication suggest about the DNA strands?

    <p>They consist of both parental and new strands</p> Signup and view all the answers

    What mechanism of DNA replication suggests that each new DNA molecule contains one old strand and one new strand?

    <p>Semiconservative replication</p> Signup and view all the answers

    What isotopes were used by Meselson and Stahl to enrich the E.coli DNA in their experiment?

    <p>2H and 15N</p> Signup and view all the answers

    In which form of DNA does the double helix consist of alternating sugar and phosphate groups?

    <p>A double-stranded DNA</p> Signup and view all the answers

    What allows the E.coli DNA to be replicated while remaining compact inside the cell?

    <p>Circular structure of DNA</p> Signup and view all the answers

    Which property allows the heavy DNA to sediment faster in density gradient centrifugation?

    <p>Incorporation of isotopes</p> Signup and view all the answers

    What is the primary structural difference between purines and pyrimidines in DNA?

    <p>Size of the nitrogenous base</p> Signup and view all the answers

    What was the outcome of the first generation of E.coli after being shifted to normal media in the Meselson-Stahl experiment?

    <p>A mix of heavy and normal DNA</p> Signup and view all the answers

    What characteristic of E.coli DNA allows for rapid replication?

    <p>Circular structure</p> Signup and view all the answers

    What is the relationship defined by Lambert-Beer Law used for?

    <p>To measure absorbance related to concentration</p> Signup and view all the answers

    Which components are essential for a spectrophotometer to function?

    <p>A light source, sample chamber, and detector</p> Signup and view all the answers

    In the context of DNA structure, what is a phosphodiester bond?

    <p>A bond between the sugar of one nucleotide and the phosphate of another</p> Signup and view all the answers

    How does the molar absorptivity of protein compare to nucleic acids?

    <p>It is lower for protein</p> Signup and view all the answers

    What is one application of scanning spectrophotometers in experiments?

    <p>To monitor spectral changes in proteins</p> Signup and view all the answers

    Which part of the DNA is considered to have a free hydroxyl group relevant to its structure?

    <p>The deoxyribose ring's 5-carbon</p> Signup and view all the answers

    What does A = εbC represent in biochemical analysis?

    <p>Absorbance of the compound in solution</p> Signup and view all the answers

    What is the main limitation when measuring protein concentration with UV absorption?

    <p>Nucleic acids interfere with protein readings</p> Signup and view all the answers

    What component of nucleic acids acts as a redox coenzyme?

    <p>NADH</p> Signup and view all the answers

    Which process is not facilitated by nucleic acids?

    <p>Cell membrane formation</p> Signup and view all the answers

    What is the primary reason nucleic acids are considered anionic compounds at physiological pH?

    <p>Presence of deprotonated phosphate residues</p> Signup and view all the answers

    Which best describes the structure of purines compared to pyrimidines?

    <p>Purines have two fused ring structures.</p> Signup and view all the answers

    Which type of nucleic acid is primarily responsible for signaling within the cell?

    <p>cAMP</p> Signup and view all the answers

    What distinguishes the monomer units of nucleic acids from those of proteins and carbohydrates?

    <p>Nucleic acids consist of multiple components: nitrogenous bases, sugar, and phosphate.</p> Signup and view all the answers

    Which statement is true about the nitrogenous bases in nucleotides?

    <p>Purines consist of two fused ring structures.</p> Signup and view all the answers

    What differentiates the functions of DNA and RNA?

    <p>DNA stores information, while RNA transcribes information.</p> Signup and view all the answers

    What is the difference between D-ribofuranose and 2-Deoxy-β-D-ribofuranose?

    <p>D-ribofuranose carries a hydroxyl group, while 2-Deoxy-β-D-ribofuranose carries a hydrogen atom.</p> Signup and view all the answers

    What results from the combination of a heterocyclic base and a sugar?

    <p>A nucleoside.</p> Signup and view all the answers

    What type of bond connects the base and the sugar in a nucleoside?

    <p>β-N-glycosidic linkage.</p> Signup and view all the answers

    Which of the following is a ribose-containing nucleoside?

    <p>Uridine.</p> Signup and view all the answers

    What identifier is used for carbon atoms in the ribofuranose ring?

    <p>Prime numbers following the main numbers.</p> Signup and view all the answers

    What is the term used when more than one phosphate is added to a nucleoside?

    <p>Nucleotide.</p> Signup and view all the answers

    Which of the following nucleosides can be derived from deoxyribose?

    <p>Thymidine.</p> Signup and view all the answers

    What is the common nomenclature confusion regarding the term thymidine?

    <p>It can refer to both ribothymidine and deoxythymidine.</p> Signup and view all the answers

    What is the expected distribution of DNA after four generations of semiconservative replication?

    <p>Half of the DNA molecules contain one parental and one new strand.</p> Signup and view all the answers

    How does the banding pattern of DNA change after one generation of replication?

    <p>Intermediate density bands are introduced.</p> Signup and view all the answers

    What does the presence of both parental and new strands in the DNA molecules after two generations indicate?

    <p>The replication mechanism is semiconservative.</p> Signup and view all the answers

    What is indicated by the presence of a heavy band at the initiation of the CsCl density gradient centrifugation?

    <p>Only parental DNA is present.</p> Signup and view all the answers

    What can be concluded about the DNA replication process after observing the banding patterns change over generations?

    <p>The replicated DNA molecules contain varying combinations of parental and new strands.</p> Signup and view all the answers

    What direction do the two strands of DNA run relative to each other?

    <p>One strand runs 5' to 3' and the other runs 3' to 5'</p> Signup and view all the answers

    How many base pairs are there per turn of the DNA double helix?

    <p>10 base pairs</p> Signup and view all the answers

    What type of bond is most commonly present between complementary bases in DNA?

    <p>Hydrogen bond</p> Signup and view all the answers

    Which model of the DNA double helix emphasizes the non-covalent interactions between bases?

    <p>Ribbon model</p> Signup and view all the answers

    What characterizes the structure of the DNA double helix in terms of phosphate residues?

    <p>They are negatively charged and located on the outside</p> Signup and view all the answers

    How many hydrogen bonds typically form between adenine and thymine base pairs in DNA?

    <p>Two hydrogen bonds</p> Signup and view all the answers

    Which feature of the DNA double helix allows for its stability and structure?

    <p>Presence of major and minor grooves</p> Signup and view all the answers

    What is the role of the deoxyribose-phosphate backbone in the DNA structure?

    <p>It acts as a stabilizing framework for the DNA strands</p> Signup and view all the answers

    What mechanism underlies the DNA replication process proposed by Watson and Crick?

    <p>Semiconservative replication</p> Signup and view all the answers

    Why were heavy isotopes used in the Meselson-Stahl experiment?

    <p>To increase the DNA's density for separation</p> Signup and view all the answers

    After how many generations of growth in normal media were DNA samples taken in the Meselson-Stahl experiment?

    <p>1, 2, 3, and 4 generations</p> Signup and view all the answers

    What characteristic of E.coli DNA allows for efficient replication despite its compact size?

    <p>The DNA is circular and highly coiled</p> Signup and view all the answers

    What results were anticipated in the Meselson-Stahl experiment after the first generation of growth in normal media?

    <p>One band at an intermediate density</p> Signup and view all the answers

    How does the density of heavy isotopes affect the sedimentation of DNA in centrifugation?

    <p>It increases the rate of sedimentation of the DNA</p> Signup and view all the answers

    What does the term 'density gradient centrifugation' refer to in the context of the Meselson-Stahl experiment?

    <p>A procedure to separate molecules based on density differences</p> Signup and view all the answers

    What is the significance of the DNA double helix model introduced by Watson and Crick?

    <p>It reveals the structural basis of genetic replication</p> Signup and view all the answers

    What is the primary reason most of the DNA shifts to light density after four generations of semiconservative replication?

    <p>The replacement of both parental strands with new strands.</p> Signup and view all the answers

    Which observation is indicative of the semiconservative nature of DNA replication after two generations?

    <p>The formation of DNA molecules with both parental and new strands.</p> Signup and view all the answers

    Why is there a lighter band present at the intermediate density after one generation of replication?

    <p>It represents DNA containing both parental and new strands.</p> Signup and view all the answers

    How does the pattern of DNA replication change over generations in the experiment?

    <p>The relative amount of light density DNA increases significantly.</p> Signup and view all the answers

    What is the significance of detecting a single heavy band at the initiation of the experiment?

    <p>It reflects the initial state of DNA as entirely parental.</p> Signup and view all the answers

    What is the main advantage of ATP hydrolysis in biological systems?

    <p>It couples favorable reactions with energetically unfavorable reactions.</p> Signup and view all the answers

    How much energy is released from the hydrolysis of ATP to ADP and inorganic phosphate?

    <p>7.3 kcal/mol</p> Signup and view all the answers

    What type of bond in ATP releases significantly less energy upon hydrolysis compared to phosphoanhydride bonds?

    <p>Phosphoester bond</p> Signup and view all the answers

    In which metabolic pathways is ATP primarily produced from the breakdown of organic compounds?

    <p>Glycolysis and TCA cycle</p> Signup and view all the answers

    What is the standard energy conversion factor between kcal and kJ mentioned in the context?

    <p>1 kcal = 4.18 kJ</p> Signup and view all the answers

    What biological roles does ATP fulfill beyond energy provision from hydrolysis?

    <p>Promoting muscle contraction and transporting ions</p> Signup and view all the answers

    What characteristic of the base components of nucleotides allows them to absorb ultraviolet light?

    <p>Conjugated double bond systems</p> Signup and view all the answers

    In the context of ATP production, which element is crucial for coupling energy from the breakdown of organic compounds?

    <p>Synthesis of ATP</p> Signup and view all the answers

    What is the primary reason that GC base pairs provide greater stability than AT base pairs in DNA?

    <p>GC pairs have more effective hydrogen bonding configurations.</p> Signup and view all the answers

    Which statement correctly describes the interaction between purines and pyrimidines in DNA?

    <p>A purine must bond with a pyrimidine.</p> Signup and view all the answers

    What is the bond distance between the 1' C of the deoxyribose of one DNA strand and the corresponding carbon of the opposite strand for an AT base pair?

    <p>1.11 nm</p> Signup and view all the answers

    What is a significant factor for the stability of the DNA double helix structure?

    <p>Consistent hydrogen bonding between purine and pyrimidine bases.</p> Signup and view all the answers

    What accounts for the greater energy requirement to separate DNA strands with GC base pairs compared to those with AT pairs?

    <p>The number of hydrogen bonds in GC pairs.</p> Signup and view all the answers

    What is the purpose of the hydrogen bonds formed between complementary bases in DNA?

    <p>To maintain a stable double helix structure.</p> Signup and view all the answers

    How many hydrogen bonds are formed between guanine and cytosine in DNA?

    <p>Three hydrogen bonds</p> Signup and view all the answers

    Which of the following statements best describes the role of base pairing in molecular biology?

    <p>Base pairing is essential for DNA replication, transcription, and translation.</p> Signup and view all the answers

    How many hydrogen bonds are present between guanine and cytosine base pairs in DNA?

    <p>Three hydrogen bonds</p> Signup and view all the answers

    Which pair represents a mismatch in DNA base pairing?

    <p>G with T</p> Signup and view all the answers

    What is the result of purine-purine pairings in DNA?

    <p>Overlap repulsion</p> Signup and view all the answers

    In terms of the structure of a double helix, what defines the major and minor grooves?

    <p>The distance between the complementary bases</p> Signup and view all the answers

    What type of structure do the larger purine bases have?

    <p>Double-ringed</p> Signup and view all the answers

    What is the effect of aromatic stacking on DNA structure?

    <p>It provides additional stabilization</p> Signup and view all the answers

    Which of the following statements is true about the geometrical structure of nitrogenous bases?

    <p>Bases tilt slightly with respect to each other</p> Signup and view all the answers

    What key feature differentiates RNA base pairing from DNA base pairing?

    <p>RNA replaces thymine with uracil</p> Signup and view all the answers

    Which suffix is correctly used to identify purine-containing nucleosides?

    <p>-osine</p> Signup and view all the answers

    What type of bond links the phosphate groups in ATP?

    <p>Phosphoanhydride bonds</p> Signup and view all the answers

    Which form of nucleotides has phosphates esterified to the 3' hydroxyl group?

    <p>3'-dGMP</p> Signup and view all the answers

    What is the favored orientation between the nitrogenous base and sugar in nucleotides?

    <p>Anti orientation</p> Signup and view all the answers

    Which of the following statements about nucleotides is true?

    <p>Nucleotides consist of a base, sugar, and at least one phosphate group.</p> Signup and view all the answers

    Which identifier is used to refer to adenosine with a single phosphate group at the 5' position?

    <p>5'-AMP</p> Signup and view all the answers

    What distinguishes the hydroxyl groups available for phosphorylation in ribonucleotides compared to deoxyribonucleotides?

    <p>Ribonucleotides have a hydroxyl group at the 2' position.</p> Signup and view all the answers

    What type of sugar is found in nucleotides that contain ribonucleotides?

    <p>Ribofuranose</p> Signup and view all the answers

    What base is found in RNA but not in DNA?

    <p>Uracil</p> Signup and view all the answers

    What type of sugar is found in RNA nucleotides?

    <p>Ribose</p> Signup and view all the answers

    Which bond type links the sugar residues in RNA?

    <p>3’-5’-phosphodiester bonds</p> Signup and view all the answers

    Which structure represents the relative orientation of RNA nucleotides?

    <p>5’ end to the left and 3’ end to the right</p> Signup and view all the answers

    What is the implication of the hydroxyl groups at the 2’ position in RNA?

    <p>Increases reactivity and instability</p> Signup and view all the answers

    What is the primary function of a spectrophotometer in biochemical experiments?

    <p>To measure changes in absorbance related to substrate-product conversion.</p> Signup and view all the answers

    Which equation represents the relationship described by Lambert-Beer Law?

    <p>A = ε × b × C</p> Signup and view all the answers

    What characteristic is observed in the structure of supercoiled mitochondrial DNA?

    <p>Tightly twisted and kinked</p> Signup and view all the answers

    During which process is it observed that DNA strands separate to form a loop?

    <p>Replication</p> Signup and view all the answers

    What describes the relationship between the length of the light path and absorbance in a sample?

    <p>Absorbance is directly proportional to the length of the light path.</p> Signup and view all the answers

    What limits accurate measurement of protein concentration when nucleic acids are present?

    <p>The lower molar absorptivity of proteins compared to nucleic acids.</p> Signup and view all the answers

    What are the two types of ends observed in RNA structures?

    <p>Hydroxyl and phosphorylated ends</p> Signup and view all the answers

    Which component is essential for a spectrophotometer to function effectively?

    <p>A silica cuvette that holds the sample solution.</p> Signup and view all the answers

    What types of bonds are involved in forming a 3’-5’-phosphodiester linkage in DNA?

    <p>Phosphoester bonds connecting deoxyribose sugars.</p> Signup and view all the answers

    How do scanning spectrophotometers enhance biochemical experiments?

    <p>By monitoring a range of wavelengths simultaneously.</p> Signup and view all the answers

    In the context of DNA structure, where does the free hydroxyl group reside?

    <p>On the 5-carbon of the deoxyribose ring.</p> Signup and view all the answers

    What suffix is used to refer to purine-containing nucleosides?

    <p>-osine</p> Signup and view all the answers

    In which hydroxyl group can the phosphate group of ribonucleotides NOT be esterified?

    <p>1</p> Signup and view all the answers

    Which of the following compounds includes guanine linked to a deoxyribose residue with a phosphate at the 3’ position?

    <p>3</p> Signup and view all the answers

    What orientation of the nitrogenous base relative to the sugar is favored in nucleotides?

    <p>2</p> Signup and view all the answers

    What type of bond links the phosphate groups in Adenosine 5'-triphosphate (ATP)?

    <p>2</p> Signup and view all the answers

    Which position of the ribose is the phosphate group connected to in Adenosine 5'-monophosphate (5'-AMP)?

    <p>5</p> Signup and view all the answers

    What are the main components of a nucleotide?

    <p>4</p> Signup and view all the answers

    Which type of nucleoside contains ribose and is characterized by the suffix –idine?

    <p>2</p> Signup and view all the answers

    What characteristic describes the directionality of the two strands in a DNA double helix?

    <p>One strand runs 5' to 3' while the other runs 3' to 5'.</p> Signup and view all the answers

    How many hydrogen bonds typically form between guanine and cytosine base pairs in DNA?

    <p>Three hydrogen bonds.</p> Signup and view all the answers

    What type of model emphasizes the dense packing of the DNA molecule?

    <p>Space filling model.</p> Signup and view all the answers

    What is the role of the phosphate residues in the DNA double helix?

    <p>They form the covalent backbone and are negatively charged.</p> Signup and view all the answers

    Which of the following statements is true regarding the arrangement of the DNA double helix?

    <p>The bases radiate inward and are perpendicular to the helix axis.</p> Signup and view all the answers

    What feature does DNA display regarding its base pairing?

    <p>Adenine pairs with thymine and guanine pairs with cytosine.</p> Signup and view all the answers

    What number of base pairs typically occurs per turn of the DNA double helix?

    <p>10 base pairs.</p> Signup and view all the answers

    Which model of the DNA double helix is particularly effective in showing alternating deoxyribose and phosphate residues?

    <p>Wire frame model.</p> Signup and view all the answers

    What is the primary difference between D-ribofuranose and 2-Deoxy-β-D-ribofuranose?

    <p>D-ribofuranose has a hydroxyl group at the 2' carbon, while 2-Deoxy-β-D-ribofuranose has a hydrogen atom.</p> Signup and view all the answers

    What term describes the bond formed between a heterocyclic base and a sugar in a nucleoside?

    <p>β-N-glycosidic linkage</p> Signup and view all the answers

    What is produced when one or more phosphates are added to a nucleoside?

    <p>Nucleotide</p> Signup and view all the answers

    Which of the following nucleosides is derived from ribose?

    <p>Adenosine</p> Signup and view all the answers

    Which nucleotide lacks a hydroxyl group at the 2' position?

    <p>2-Deoxyadenosine</p> Signup and view all the answers

    What is the systematic naming convention for the carbon atoms in the ribofuranose ring?

    <p>Numbers with prime designators</p> Signup and view all the answers

    What is the common naming confusion regarding the term 'thymidine'?

    <p>It can refer to thymidine derived from both ribose and deoxyribose.</p> Signup and view all the answers

    What does the 'β' in β-N-glycosidic linkage represent?

    <p>It refers to the orientation of the bond from the anomeric carbon of the sugar.</p> Signup and view all the answers

    Study Notes

    DNA Structure and Replication

    • DNA is a very long molecule, even in small cells like E. coli.
    • Its full length is packed tightly within a small region of the cell.
    • DNA replication occurs at a high speed despite its compact structure.
    • Watson and Crick proposed a model of semiconservative replication, which explains how DNA is copied.

    Meselson-Stahl Experiment

    • The experiment involved using heavy isotopes 2H and 15N to label DNA in E. coli.
    • E. coli was grown in media containing heavy isotopes for many generations, resulting in heavy DNA.
    • The cells were then transferred to normal growth media and DNA samples were collected over subsequent generations.
    • Using CsCl density gradient centrifugation, the researchers observed the distribution of heavy and light DNA.

    Meselson-Stahl Experiment Results

    • At the start (time zero), only a heavy DNA band was observed.
    • After one generation, an intermediate density band appeared.
    • After two generations, the bands were about 50% intermediate and 50% light density.
    • After four generations, most of the DNA shifted to light density.
    • The observed banding patterns supported the semiconservative model of DNA replication.

    UV Absorbance Measurement

    • Many biochemical assays involve measuring light absorption by biological molecules.
    • The absorbance (A) is directly proportional to the concentration (C) and the molar extinction coefficient (ε).
    • This relationship is known as the Lambert-Beer Law.
    • Spectrophotometers are used to measure absorbance at specific wavelengths.
    • Spectrophotometers are crucial for determining the concentration of known compounds and monitoring changes in absorbance during chemical reactions.

    Phosphodiester Linkage in DNA

    • DNA consists of nucleotides linked together by phosphodiester bonds.
    • Each phosphodiester bond involves two phosphate linkages, one between the 3' carbon of one deoxyribose ring and the 5' carbon of the next deoxyribose ring.
    • The 3'-5'-phosphodiester bond forms the backbone of the DNA molecule.
    • This structure is crucial for DNA's stability and function.

    Nucleic Acid Structure and Function

    • Nucleic acids are biopolymers that contain:

      • Nitrogenous bases
      • Sugar residues
      • Phosphates

    • The phosphate groups are negatively charged at physiological pH, making nucleic acids anionic

    Nitrogenous Bases

    • Nitrogenous bases are heterocyclic nitrogen compounds
    • There are two classes:
      • Pyrimidines: single six-membered ring
      • Purines: six-membered ring fused to a five-membered ring

    Nucleosides

    • Nucleosides are formed when a heterocyclic base combines with a sugar, releasing water
    • The bond between the base and sugar is a β-N-glycosidic linkage
    • Examples of commonly occurring nucleosides:
      • Adenosine, guanosine, cytidine, uridine, thymidine (ribose)
      • Deoxyadenosine, deoxyguanosine, deoxycytidine, deoxyuridine, deoxythymidine (deoxyribose)

    Nucleotides

    • Nucleotides are nucleosides with one or more phosphate groups added
    • The phosphate groups are attached to the sugar's 5' hydroxyl group

    DNA Structure

    • DNA is a double helix
    • The two strands are antiparallel (one runs 5' to 3', the other 3' to 5')
    • The bases are complementary (Adenine (A) pairs with Thymine (T), Guanine (G) pairs with Cytosine (C))
    • Each turn of the helix contains 10 base pairs
    • The helix has major and minor grooves

    DNA Replication

    • DNA replication is semiconservative, meaning each progeny molecule contains one parental strand and one new strand
    • The Meselson-Stahl experiment confirmed the semiconservative model using heavy isotopes of nitrogen
    • The process involves:
      • Separation of parental strands
      • Replication of each parental strand to create two new strands
      • Creation of two progeny DNA molecules, each with one parental strand and one new strand

    Nucleotide Structure

    • A nucleotide is a compound containing a base, a sugar, and at least one phosphate group.
    • The phosphate can be esterified to any hydroxyl group of the sugar residue.

    Adenosine 5'-Monophosphate (5'-AMP)

    • 5'-AMP is a nucleotide with one phosphate group attached to the 5' hydroxyl group of ribose.
    • Deoxyadenosine 5'-monophosphate (5'-dAMP) is similar to 5'-AMP but has deoxyribose instead of ribose.

    3'-dGMP

    • 3'-dGMP has guanine linked to a deoxyribose residue with one phosphate group attached to the 3' hydroxyl.
    • This type of phosphoester linkage is common in DNA.

    Rotation around N-Glycosidic Bond

    • There is restricted rotation around the N-Glycosidic Bond.
    • Two orientations are possible:
      • Anti orientation: base and sugar rotated away from each other (favored).
      • Syn orientation: base and sugar lined up on the same side (less common).

    Adenosine 5'-Triphosphate (ATP)

    • ATP contains three phosphate residues linked together by two phosphoanhydride bonds.
    • One phosphate is linked to a ribofuranose residue by a phosphoester bond.
    • Hydrolysis of the phosphoanhydride bonds releases energy (7.3 kcal/mol or 30.5 kJ/mol).
    • ATP is used as a reservoir of chemical energy in biological systems.

    ATP to ADP Cycle

    • The breakdown of ATP to ADP and Pi releases energy (Energy Output).
    • ATP production (Energy Input) occurs through catabolic pathways like glycolysis and the TCA cycle.
    • ATP is used in various biological processes:
      • Synthesis of biopolymers.
      • Muscle contraction.
      • Ion and metabolite transport across membranes.

    UV Absorption Spectra of Nucleotides

    • Bases in nucleotides absorb UV light in the range of 240-300 nm.
    • Each base has a unique absorption spectrum, some sensitive to changes in pH.

    DNA Structure

    • DNA is a double helix composed of two complementary strands.
    • Bases in the interior of the strands are complementary: A with T (or vice versa) and G with C (or vice versa).
    • AT pairs have two hydrogen bonds, GC pairs have three hydrogen bonds.
    • Aromatic stacking of successive bases stabilizes the helix.
    • One complete turn of the double helix takes ten base pairs.

    Base Pairing

    • Complementary bases interact on opposite strands of DNA or RNA forming a base pair (bp).
    • In DNA: A pairs with T, G pairs with C.
    • In RNA: A pairs with U (uracil replaces thymine), G pairs with C.
    • Hydrogen bonding underlies base pairing.

    Purines and Pyrimidines

    • Purines (adenine and guanine) have two rings.
    • Pyrimidines (cytosine and thymine, or uracil) have one ring.
    • Purines pair only with pyrimidines.
    • Pyrimidine-pyrimidine and purine-purine pairings are energetically unfavorable.
    • Other pairings like GT and AC are mismatches because of incorrect hydrogen bond donor/acceptor patterns.

    AT and GC Base Pairs

    • AT pairs have two hydrogen bonds and a distance of 1.11 nm between the 1' C of the deoxyribose on each strand.
    • GC pairs have three hydrogen bonds and a distance of 1.08 nm between the 1' C of the deoxyribose on each strand.
    • GC interactions have higher energy than AT interactions, making them harder to separate.

    Semiconservative Replication

    • Semiconservative replication refers to the process where each new DNA molecule contains one parental strand and one new strand.
    • CsCl density gradient centrifugation was used to demonstrate this.
    • The banding patterns evolve over generations, supporting the semiconservative model.

    ### D-Ribofuranose and 2-Deoxy- β -D-ribofuranose

    • The carbon atom in D-ribofuranose carries a hydroxyl group
    • The carbon atom in 2-Deoxy- β -D-ribofuranose carries a hydrogen atom

    ### Nucleoside Structure

    • A nucleoside is formed when a heterocyclic base combines with a sugar, releasing water
    • Nucleosides contain only a base and a sugar
    • The covalent bond between the base and sugar is a β -N-glycosidic linkage
    • The "β" in this term refers to the β orientation of the bond from the anomeric carbon of the sugar
    • The "N" refers to the bond from an anomeric carbon to a nitrogen atom of the base

    ### Numbering in Nucleosides

    • The atoms of the base and sugar in a nucleoside are numbered using conventions established by biochemists
    • The five carbon atoms in the ribofuranose ring are numbered 1-5, starting with the anomeric carbon and proceeding clockwise
    • These numbers are followed by a prime (‘) designator

    ### Naming Nucleosides

    • There are ten possible combinations of one base and one sugar
    • The ribose containing nucleosides are adenosine, guanosine, cytidine, uridine, and thymidine
    • The deoxyribose containing nucleosides are deoxyadenosine, deoxyguanosine, deoxycytidine, deoxyuridine, and deoxythymidine
    • Thymidine is sometimes called ribothymidine, but this is not generally found in RNA
    • Purine containing nucleosides end in "-osine"
    • Pyrimidine containing nucleosides end in "-idine"

    ### Nucleotide Structure

    • A nucleotide contains a base, sugar, and at least one phosphate group
    • The phosphate can be esterified to any hydroxyl group of the sugar residue
    • Ribonucleotides have phosphates at the 2’, 3’and 5’ hydroxyl groups of the ribose
    • Deoxyribonucleotides have phosphates at the 3’ and 5’ hydroxyl groups of the deoxyribose
    • 5’-AMP is adenosine 5’-monophosphate
    • 5’-dAMP is deoxyadenosine 5’-monophosphate

    ### Structure of 3’-dGMP

    • 3’-dGMP is 2’-deoxyguanosine-3’-monophosphate
    • It contains guanine linked to a deoxyribose residue with a single phosphate esterified to the 3’ hydroxyl group
    • This type of phosphoester linkage is found in the backbone of DNA

    ### Restricted Rotation about N-Glycosidic Bond

    • There is restricted rotation about the N-Glycosidic bond
    • Nitrogenous bases and sugar residues can have two orientations: anti and syn
    • The anti orientation, where the base and sugar are rotated away from each other, is favored
    • The syn orientation, where the components are lined up on the same side, is less common

    ### The Structure of Adenosine 5’-triphosphate (ATP)

    • ATP has three phosphate residues linked to a ribofuranose residue by phosphoester bonds
    • The two phosphoanhydride bonds are formed by joining two phosphate groups in a reaction that eliminates water

    ### Measuring UV Absorption

    • The absorbance of light by a compound in solution (A) is calculated using Lambert-Beer Law: A = εbC
    • The molar extinction coefficient (ε) is unique to each compound
    • The length of the light path (b) and concentration (C) are also factors
    • Spectrophotometers are used to measure the absorbance of light by a compound in solution
    • Spectrophotometers contain a light source, a light filter, a sample chamber, and a detector
    • Spectrophotometers can be used to determine the concentration of a known compound, assay chemical reactions, and monitor spectral changes in electron-carrying proteins

    ### Phosphodiester Linkage in DNA and RNA

    • Deoxyadenylyl-(3’-5’)-deoxyguanosine is a short segment of DNA
    • The two nucleotide segments are joined by two phosphoester bonds: one at the 3-carbon of the upper deoxyribose ring and the other at the 5-carbon of the lower deoxyribose ring
    • These two phosphate linkages are collectively called a 3’-5’-phosphodiester bond

    ### Tetranucleotide Structure abbreviated (RNA)

    • The vertical lines in abbreviated RNA structures represent ribose residues
    • The numbers indicate the positions of the five carbon atoms
    • The diagonal lines with a central P represent the phosphodiester bonds connecting the 3’ and 5’ positions of the ribose residues
    • The orientation is 5’end to the left and 3’end to the right
    • The upper structure has free hydroxyl groups at the 5’ and 3’ ends
    • The lower structure has phosphorylated hydroxyl groups at the 5’ and 3’ ends

    ### Electron Micrograph of DNA

    • The electron micrograph shows a segment of DNA containing thousands of base pairs
    • DNA was spread on a grid and shadowed with an electron-dense material
    • The arrow points to a region where the two DNA strands have separated
    • This may be a region where DNA replication was occurring

    ### Electron Micrograph of Circular DNA

    • The graphic shows two electron micrographs of circular mitochondrial DNA
    • The left image shows a relaxed sample of mitochondrial DNA with a double helical form
    • The right image shows a supercoiled sample in which the DNA is tightly twisted
    • Supercoiling occurs during DNA replication and RNA transcription

    ### Double Helix Characteristics of DNA

    • Most DNA exists as a double helix
    • The two polynucleotide strands run antiparallel, one in the 5'->3' direction and the other in the 3'->5' direction
    • The bases in opposing strands are complementary: A-T and G-C
    • There are 10 base pairs per turn of helix
    • The typology exhibits major and minor grooves

    ### Features of the DNA Double Helix

    • The two strands run antiparallel
    • The negatively charged phosphate residues are on the outside of the helix

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