DNA Structure and Nucleotides (sugars, bases, base pairing, and antiparallel strands)

DNA Structure and Components: Key Ideas

  • DNA (deoxyribonucleic acid) determines a lot about an organism (e.g., which proteins are made, hair type, height). The order of bases in DNA encodes genes and traits.
  • The basic building blocks of DNA are sugars, phosphate groups, and bases, which together form nucleotides that link into a long backbone with attached bases.
  • The gene sequence concept: a gene can be thought of as a sequence of letters (A, T, C, G) that code for specific traits. Example snippet: A T C G A A T C … showing the order matters for encoding information.
  • DNA is a long, negatively charged molecule due to its phosphate groups, which play a key role in its structure and in applications like DNA profiling.

Pentose Sugars: Deoxyribose vs Ribose

  • DNA uses a pentose sugar called deoxyribose; RNA uses ribose. The only difference is that deoxyribose is missing an oxygen atom compared to ribose at the 2' carbon (hence the name deoxyribose).
  • Both sugars have a ring structure with an oxygen at the top and a four-carbon ring; each carbon has a place for bonding. Hydrogens and hydroxyl groups fill the remaining bonds.
  • In the sugar rings:
    • Ribose (RNA) has an -OH on the 2' carbon.
    • Deoxyribose (DNA) has an H on the 2' carbon (no oxygen there).
  • On the right side of the sugar ring, there is a hydroxyl group (OH) and at the top there is a CH₂OH group (often drawn as HO-CH₂). The exact orientation of these groups helps distinguish DNA from RNA.
  • Important note for labeling on a fact sheet:
    • Label both sugars as pentose sugars.
    • Indicate which is found in DNA (deoxyribose) and which in RNA (ribose).
    • Carbons can be labeled 1', 2', 3', 4', 5' in textbooks, but the numbers are not required for this exercise; if drawn, circle them to show they’re carbons, not extra bonds.

Phosphate Backbone

  • DNA strands are linked by phosphate groups that connect sugars from adjacent nucleotides, forming a sugar–phosphate backbone.
  • Pattern described: sugar — phosphate — sugar — phosphate — sugar … continuing in a chain. This repeats along the length of the molecule and holds the backbone together.
  • Each phosphate group is negatively charged (due to the oxygens attached to phosphorus). This contributes to the overall negative charge of DNA.
  • A ball-and-stick view of phosphate shows phosphorus atom with multiple negatively charged oxygen groups and a double-bonded oxygen; this is the moiety that links sugars between nucleotides.
  • Why it matters: the negative charge of the phosphate backbone is critical for DNA’s behavior in solution and plays a role in DNA profiling and interactions with proteins.

Nitrogenous Bases and Base Pairing

  • There are four bases in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G).
  • The bases are labeled by their starting letters: A, T, C, G.
  • Base pairing rules (complementarity):
    • Adenine (A) pairs with Thymine (T) via two hydrogen bonds.
    • Cytosine (C) pairs with Guanine (G) via three hydrogen bonds.
  • Purines vs pyrimidines (structure-based grouping):
    • Purines: adenine (A) and guanine (G) have two-ring structures.
    • Pyrimidines: cytosine (C) and thymine (T) have one-ring structures.
  • Why the pairing rules exist: to keep the width of the DNA double strand consistent (two-ring purine-purine or pyrimidine-pyrimidine pairs would widen or narrow the helix improperly). The A–T and C–G pairings maintain uniform spacing.
  • Hydrogen bonds (concept): a hydrogen bond is an attraction between a slightly positively charged region (e.g., a nitrogen atom’s H-bond donor) and a slightly negatively charged region (e.g., a nearby electronegative atom). These are weaker than covalent bonds and are represented with dotted/dashed lines in drawings.
  • In practice:
    • A–T pairing involves 2 hydrogen bonds.
    • C–G pairing involves 3 hydrogen bonds.
  • Visual notes for drawing:
    • Use dotted lines to indicate hydrogen bonds, not solid lines.
    • A and T and C and G should be drawn with their characteristic ring structures (A and G as purines with two rings; C and T as pyrimidines with one ring).

Nucleotides and Nucleotide Structure

  • A nucleotide is the basic unit of DNA (and RNA) and consists of three parts: a nitrogenous base, a sugar, and a phosphate group.
    • Base: A, T, C, G (or U in RNA for uracil; U is not used in DNA).
    • Sugar: ribose in RNA, deoxyribose in DNA.
    • Phosphate group: links to the sugar and to the next nucleotide, forming the backbone.
  • Example from transcript: Adenosine Monophosphate (AMP)
    • AMP contains ribose (RNA sugar) attached to adenine (A) with one phosphate group.
    • This is an RNA nucleotide (not DNA) and illustrates how nucleotides are named (adenosine + phosphate = AMP).
  • Full nucleotide definition (as used in the activity): base + sugar + phosphate.
  • Practical labeling on worksheets:
    • Label a nucleotide as: Phosphate — Ribose — Adenine, or more generally: Phosphate Ribose Adenine.
    • This helps identify the RNA nucleotide structure and contrast with DNA nucleotides (which would use deoxyribose instead of ribose).
  • Note: In the teaching exercise, there is discussion of assembling a single nucleotide and then using those building blocks to assemble longer strands (DNA or RNA) in model activities.

Building DNA Models: Backbone and Antiparallel Strands

  • The class activity uses model tiles to build a DNA-like double strand. Some tiles may be RNA-like (ribose) to illustrate the concept.
  • Step-by-step modeling concept:
    1) Create a sugar–phosphate backbone: alternating deoxyribose (DNA sugar) and phosphate groups linked together.
    2) Attach bases to each sugar (one base per sugar).
    3) Pair bases across the two strands: A with T (two H-bonds) and C with G (three H-bonds).
    4) Extend the strands to create a long chain, forming a ladder-like structure that resembles the DNA double helix.
  • Antiparallel orientation:
    • The two strands run in opposite directions. One strand goes in one direction (e.g., 5' to 3'), while the other runs in the opposite direction (3' to 5').
    • When paired, one side of the ladder runs in the opposite direction to the other, producing the characteristic antiparallel arrangement of DNA.
  • Practical tips from the session:
    • Share materials when there aren’t enough tiles; work collaboratively.
    • If using RNA-type tiles, pretend they are DNA by adjusting the representation (one sugar missing an oxygen is the DNA difference).
    • Leave enough room on the page for the entire model; do not crowd all components in a single space.
    • You may need to rearrange or jiggle the bases to ensure correct pairings and steric fit on the two strands.

Connections, Implications, and Practical Takeaways

  • Relevance to real-world biology:
    • The sequence of bases encodes genetic information, which is read and translated into proteins, guiding phenotype and cellular function.
    • The phosphate backbone’s negative charge is a key feature exploited in techniques like gel electrophoresis and DNA profiling.
  • Conceptual connections:
    • The base-pairing rules explain why DNA keeps a constant width and how the two strands can store complementary information.
    • The antiparallel arrangement explains directional reading of genetic information and the mechanics of DNA replication.
  • Ethical and practical implications (brief):
    • DNA profiling leverages the properties of DNA (including the phosphate backbone and base order) to identify individuals, which raises privacy and ethical considerations in data use and law enforcement.

Quick Reference: Key Formulas and Concepts (LaTeX format)

  • Base pairing rules:
    • A ext{ pairs with } T ext{ via } 2\text{ hydrogen bonds}
    • C ext{ pairs with } G ext{ via } 3\text{ hydrogen bonds}
  • Nucleotide composition (generic):
    • ext{Nucleotide} = ext{Base} + ext{Sugar} + ext{Phosphate}
  • DNA backbone concept: the repeating unit is a sugar–phosphate linkage that forms the chain with negatively charged phosphates.
  • Purines vs pyrimidines:
    • Purines: A, G (two rings)
    • Pyrimidines: C, T (one ring)

Study Tips and Instructor Cues

  • When labeling: keep bases and sugars clearly distinguished; use dashed lines for hydrogen bonds.
  • Do not crowd the page; leave space for the rest of the notes and future additions.
  • Remember the key distinctions: deoxyribose (DNA) vs ribose (RNA); A/T vs C/G pairings; antiparallel strand orientation.
  • Think of DNA as a ladder-like scaffold where the rungs are base pairs and the sides are sugar–phosphate backbones; the ladder twists into the famous double helix in three-dimensional space.