Molecular Biology: Polynucleotide Structure
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Questions and Answers

What is the orientation of the two strands in double-stranded DNA?

  • The strands are parallel.
  • The strands must be anti-parallel. (correct)
  • One strand has 5' at the top, while the other has 3' at the top.
  • Both strands have the same orientation.

    • Which of the following base pairs is correctly paired with its corresponding number of hydrogen bonds?

  • A and T - 2 H-bonds (correct)
  • G and T - 2 H-bonds
  • A and U - 3 H-bonds
  • G and C - 4 H-bonds

    • What is the complementary DNA strand for 5’ CACTGC 3’?

  • 3’ GTGACG 5’ (correct)
  • 3’ CAGCGT 5’
  • 5’ GTGACG 3’
  • 5’ CTGACG 3’

    • How many hydrogen bonds are present in a DNA molecule consisting of 4 G/C pairs and 2 A/T pairs?

    <p>16</p> Signup and view all the answers

    Which base pairing occurs when forming a complementary RNA strand from DNA?

    <p>A and U</p> Signup and view all the answers

    What stabilizes the structure of DNA apart from hydrogen bonds?

    <p>Base stacking interactions</p> Signup and view all the answers

    What is the typical number of base pairs in one helical turn of DNA?

    <p>10.5</p> Signup and view all the answers

    What is the primary reason DNA strands exhibit electrostatic repulsion?

    <p>The negative charge of the sugar-phosphate backbone</p> Signup and view all the answers

    Which grooves of DNA are important for protein recognition?

    <p>Major grooves only</p> Signup and view all the answers

    How many helical turns would be present in a 1000 bp DNA molecule?

    <p>95.2</p> Signup and view all the answers

    Which forces are considered destabilizing for DNA structure?

    <p>Electrostatic repulsion between strands</p> Signup and view all the answers

    Which representation of DNA structure emphasizes the orientation and connectivity of bases?

    <p>Stick representation</p> Signup and view all the answers

    In the context of DNA structure, what do major and minor grooves represent?

    <p>Spaces between the strands with varying accessibility of bases</p> Signup and view all the answers

    What determines if a polynucleotide is DNA or RNA?

    <p>Presence of deoxyribose at the 2’ position</p> Signup and view all the answers

    What type of bond links the 3’ and 5’ positions of adjacent nucleotides?

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

    In a DNA structure, where are the phosphate groups located relative to the double helix?

    <p>On the outside of the helix</p> Signup and view all the answers

    In which direction are DNA and RNA sequences synthesized?

    <p>5’ to 3’ direction</p> Signup and view all the answers

    Which of the following bases is present in RNA but not in DNA?

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

    What critical evidence did Rosalind Franklin provide for the structure of DNA?

    <p>X-ray diffraction images</p> Signup and view all the answers

    What structural feature of DNA allows for its replication?

    <p>Complementary base pairing</p> Signup and view all the answers

    What is the significance of the 5’ and 3’ terminus in a polynucleotide strand?

    <p>They direct the synthesis and reading of the strand</p> Signup and view all the answers

    What effect does heating DNA to 95°C have on its structure?

    <p>It destabilizes the double stranded structure.</p> Signup and view all the answers

    In what conditions is A-DNA formed?

    <p>High salt and low humidity.</p> Signup and view all the answers

    Which form of DNA is the most common under normal conditions?

    <p>B-DNA</p> Signup and view all the answers

    What characterizes Z-DNA?

    <p>It is formed by sequences of alternating purines and pyrimidines.</p> Signup and view all the answers

    Which sugar pucker conformation has the C3' position protruding?

    <p>C3'-endo</p> Signup and view all the answers

    Which glycosyl bond conformation is associated with being spatially less crowded?

    <p>Anti-conformation with purines.</p> Signup and view all the answers

    What is the result of the sugar pucker conformation on the phosphate groups in DNA?

    <p>It increases the distance between neighboring phosphate groups.</p> Signup and view all the answers

    Which type of DNA is characterized by a right-handed helix and an anti glycosyl bond conformation?

    <p>B-DNA</p> Signup and view all the answers

    What does the left-handed helix structure of Z-DNA imply about its nucleotide sequences?

    <p>It typically forms from alternating purines and pyrimidines.</p> Signup and view all the answers

    Which conformation does B-DNA exhibit regarding its sugar pucker?

    <p>C-2' endo</p> Signup and view all the answers

    What is the primary difference between A-DNA and B-DNA?

    <p>Sugar pucker and helix sense</p> Signup and view all the answers

    Which of the following forms of DNA exists as a left-handed helix?

    <p>Z-DNA</p> Signup and view all the answers

    The glycosyl bond conformation in pyrimidines (C, T, U) always adopts which orientation?

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

    Study Notes

    Polynucleotide Structure

    • Polynucleotides are formed by linking nucleotides through phosphodiester bonds, connecting the 3’ and 5’ ends.
    • The backbone consists of phosphate and sugar components, which are negatively charged at pH 7 due to deprotonation.
    • Bases in DNA include adenine (A), cytosine (C), guanine (G), and thymine (T); RNA contains uracil (U) instead of thymine.

    Directionality

    • DNA and RNA sequences are synthesized and read in the 5’ to 3’ direction.
    • The structure has defined 5’ and 3’ termini based on the sugar configuration.

    Structure of Double-Stranded DNA

    • Watson and Crick elucidated the double helix structure using X-ray diffraction data, notably Rosalind Franklin's images.
    • The two strands of DNA are complementary and anti-parallel, ensuring proper base pairing and replication.

    Base Pairing Rules

    • Adenine pairs with thymine (A-T) in DNA, forming two hydrogen bonds; guanine pairs with cytosine (G-C), forming three hydrogen bonds.
    • In RNA, adenine pairs with uracil (A-U) and guanine with cytosine (G-C).

    DNA Structure Characteristics

    • Double-stranded DNA has a uniform width, with approximately 10.5 base pairs per helical turn.
    • Major and minor grooves allow proteins to recognize specific DNA sequences, particularly in transcription factors.

    Stabilizing and Destabilizing Forces

    • DNA stability is maintained by hydrogen bonds in base pairs and base stacking, which involves hydrophobic and electrostatic interactions.
    • Electrostatic repulsion occurs between negatively charged phosphate backbones, which can destabilize the structure.

    Denaturation of DNA

    • Heating (95°C) or alkaline conditions can disrupt hydrogen bonding or base stacking, leading to denaturation.

    Structural Forms of DNA

    • B-DNA is the most common form under normal conditions.
    • A-DNA appears in high salt and low humidity environments, while Z-DNA features a left-handed helix formed by specific nucleotide sequences.

    Sugar Pucker Conformations

    • The sugar pucker conformation affects the distance between phosphate groups, impacting DNA structure.
    • C3’-endo and C2’-endo configurations determine the position of the sugar relative to the base.

    Glycosyl Bond Conformation

    • Glycosyl bonds can exist in syn (crowded) conformation, typical of Z-DNA and limited to purines, or anti (less crowded) conformation, favored in B-DNA with pyrimidines adopting only the anti form.

    Key Differences among DNA Forms

    • B-DNA: Right-handed helix, anti glycosyl bond, C2’-endo sugar pucker.
    • A-DNA: Less common, forms in specific conditions.
    • Z-DNA: Left-handed helix with different base pairing sequences and structural characteristics.

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    L3. Polynucleotide Structure PDF

    Description

    Explore the intricate details of polynucleotide structure, including the formation of DNA and RNA. This quiz covers nucleotides, base pairing rules, and the significance of the double helix as explained by Watson and Crick. Test your understanding of molecular biology fundamentals.

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