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Nucleic Acids and RNA World - General Biology

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  • What is a nucleic acid?

    Nucleic acid is a polymer of nucleotide monomers, each consisting of a phosphate group, a five-carbon sugar, and a nitrogenous base.

  • What are the three components of a nucleotide?

    Phosphate group, five-carbon sugar, and nitrogenous base.

  • Difference between ribonucleotides and deoxyribonucleotides?

    • Ribonucleotides are monomers of RNA, and have ribose sugar with an -OH group at 2′ carbon

    • deoxyribonucleotides are monomers of DNA, and have deoxyribose sugar with H at 2′ carbon.

      • Both sugars have -OH group bonded to 3' carbon

  • What are purines and pyrimidines?

    The two groups of nitrogenous bases:

    • Purines have two rings (adenine, guanine)

    • Pyrimidines have one ring (contain 6 atoms in their one ring - cytosine, uracil in RNA, thymine in DNA - "CUT of Py")

  • How do nucleotides polymerize to form nucleic acids?

    Via condensation reactions, forming phosphodiester linkages between the phosphate group on the 5' carbon of one nucleotide and the 3′ OH of another.

    • Produces DNA polymers or RNA polymers

  • What is the directionality of DNA and RNA strands?

    They have 2 diff ends: the 5′ end has unlinked phosphate grp, the 3′ end has unlinked hydroxyl grp (-OH), so the strand runs 5′ → 3'

    • U only read it 1 way

      • If have, 5′ — A T T A G C — 3′, its not same backwards, 5′ — C G A T T A — 3′

        • 5' , 3'--> unlinked phos., hydroxyl

        • A T T A G C - nitrog. bases

  • What powers nucleic acid polymerization?

    Activated nucleotides (nucleoside triphosphates) provide energy; energy is released when 2 phosphates are removed during polymerization.

  • Describe the secondary structure of DNA.

    DNA forms an antiparallel double helix with complementary base pairing (A-T, C-G) held by hydrogen bonds, with a sugar-phosphate backbone.

    • *Antiparallel - parallel to each other but pointing in opposite directions; ex: ↑ ↓

  • What causes the DNA strands to twist into a helix? What stabilizes the helix?

    • Hydrophobic interactions - hydrophobic bases hide from water in the cell by stacking inside DNA, with the phosphate group on the outside

    • Van der Waals interactions stabilize strands.

  • What is the tertiary structure of DNA? Two forms?

    DNA forms more compact, three-dimensional structures in cells.

    • Forms supercoils - wound too tightly or loosely

    • Wraps around DNA-binding histone proteins

  • How does DNA store biological information?

    Information is stored in the sequence of nucleotide nitrogenous bases, which function like letters in an alphabet.

  • What are the three steps of DNA replication?

    1. Strands separate by breaking hydrogen bonds.

    2. The original strands stay in place, while free nucleotides floating around the cell find and pair with their matching bases (A–T, C–G).

    3. Phosphodiester bonds form to create a complementary strand

  • How does RNA differ structurally from DNA?

    RNA contains ribose sugar instead of deoxibrose, uracil instead of thymine, and has a reactive 2′-OH group making it less stable than DNA (-H group).

  • What is RNA's secondary structure?

    RNA folds back on itself → complementary bases pair (A–U, G–C) → hydrogen bonds form between the bases → creates a hairpin structure. The paired sections are antiparallel, meaning they run in opposite directions (5′→3′ and 3′→5′).

  • What is RNA's tertiary structure?

    Complex 3D shapes formed by folding of secondary structures, allowing diverse size, shape, and reactivity.

  • What are some types of RNA? What roles do they play?

    mRNA, rRNA and tRNA are key in protein synthesis.

  • Why is RNA considered versatile?

    RNA folds into various complex shapes (different than DNA's structure - always a helix), regulates mRNA production, and can catalyze chemical reactions.

  • What are ribozymes?

    RNA molecules with catalytic activity and have active sites that can catalyze phosphodiester bond formation and potentially self-replicate.

  • What is the RNA world hypothesis?

    Proposes early life used RNA both to store genetic information and catalyze its own replication before DNA and proteins.

  • What evidence supports RNA as the first life-form molecule?

    RNA can store information, catalyze reactions, and replicate, fulfilling key life characteristics before proteins evolved.

  • What are some functions of nucleotides besides forming nucleic acids?

    Energy carriers (ATP), coenzymes (NAD+), and chemical messengers (cAMP).

  • What did Chemical Evolution lead to?

    Production of a molecule that could self replicate

  • What does DNA do? How does it replicate?

    • Stores genetic information

    • Replicated using proteins

  • What is the RNA world hypothesis?

    Proposes time in evolution where RNA both stored genetic information and catalyzed its own replication

  • What are the phosphate group and nitrogenous base bonded to in a nucelotide?

    A 5-carbon sugar molecule

  • What is a condensation reaction?

    A chemical process where two smaller molecules (monomers) join together to form a larger molecule, releasing a water molecule as a byproduct

  • What does it mean if a group is unlinked in a molecule?

    • "Unlinked" means the molecule has a free group at the end that isn't connected to another nucleotide.

      • Ex: 5' phosphate group in the sugar-phosphate backbone of a DNA or RNA strand is unlinked bc its at the end and isnt connected to another nucleotide.

  • Nucleoside vs. Nucleotide

    • Nucleoside = sugar + nitrogenous base (3 phosphates needed to polymerize - provide energy, releases 2 P in reaction)

    • Nucleotide = S + NB + ≥1 P (needs 2 P )

    • Nucleotide disphosphate = S + NB + 2 P (needs 1 P)

    • Nucleotide triphosphate = S + NB + 3 P (Activated; no P needed for energy --> can react)

  • What did Watson and Crick determine about DNA?

    DNA has 2 antiparallel strands with A–T & C–G base pairing; H-bonds hold them together, forming a double helix with the sugar-phosphate backbone outside and bases inside.

  • What are van der waals interactions? When do they usually occur?

    • Weak attractions between nearby atoms caused by temporary charges.

    • occur when atoms/molecules are very close together, especially between nonpolar molecules or hydrophobic groups

  • What is complimentary base pairing? What does it allow for?

    • Where bases pair with their specific match: A–T and C–G

    • Complementary base pairing allows each strand to be copied exactly producing two identical daughter molecules

  • What makes the DNA double helix stable?

    Phosphodiester bonds, hydrogen bonds, and hydrophobic interactions --> make it good for storing genetic information, bc their stability prevents DNA from breaking down.

  • What is the theory of chemical evolution?

    Life may have started as a free RNA molecule in water, not enclosed by a membrane. To reproduce, it needed to provide a template and build a copy using monomers. RNA can do both → so scientists propose that early life may have been made of RNA.

  • Why does RNA possibly preceed proteins?

    Most modern ribozymes aid protein production, if removed, proteins could not be made

  • Nucleotide functions?

    • Energy carriers - ATP

    • Coenzymes (NAD+)

    • Chemical messengers (cAMP)

    • Building blocks for nucleic acids