BIOL 230: DNA Structure, Function, and Genomic Organization

Course Information, Agenda, and Announcements

• Course Administration:

  • Course Title: BIOL 230: Cell and Molecular Biology

  • Class Session: Class #6

  • Date: Friday, September 4, 2026

  • Instructors:

  • Dr. Blake Riggs, Associate Professor

  • Dr. José de la Torre, Professor

• Central Agenda Questions:

  • How does the structure of DNA, and its hydrogen bonds, relate to its function?

  • How do parts of DNA store the code for how to build traits?

  • How are these codes used to build proteins, which are the basis of traits?

• Class Agenda Outline:

  • Welcome, Agenda, & Announcements

  • Big Idea: Connecting Hydrogen Bonds and the Structure-and-Function of DNA

  • Mini-Lecture: SIX Big Ideas about DNA Structure and Function

  • Activity: Using Concept Mapping to Identify Confusions ("What do you know about how genes code for traits?!")

  • Activity: Becoming RNA Polymerase & Being the Ribosome

  • Homework Assignments

• Active Participation Protocol:

  • PollEverywhere Link: https://pollev.com/josedelatorre814

  • Participation credit is awarded for engagement rather than correctness to encourage independent, courageous scientific reasoning.

Scientist Spotlights & Endosymbiotic Theory

• Scientist Spotlight #1 Key Figures:

  • Rosalind Franklin: Biophysicist and X-ray crystallographer whose famous Photo 51 provided crucial structural evidence demonstrating the double helical structure of DNA.

  • Rick Kittles: Human geneticist whose pioneering research focuses on genetic ancestry, health disparities, and complex disease susceptibility in diverse populations.

• Endosymbiotic Theory:

  • Key Proponent: Lynn Margulis.

  • Core Concept: Eukaryotic cells and their membrane-bound organelles (specifically mitochondria and chloroplasts) originated from free-living prokaryotes that were engulfed by ancestral host cells, establishing a mutually beneficial endosymbiotic relationship.

  • Etymology:

  • Endo = inside.

  • Symbiotic = life working together.

  • Three Key Lines of Evidence Supporting Endosymbiotic Theory:

  1. Double Membranes: Mitochondria and chloroplasts are bounded by double membranes, consistent with an engulfment event via endocytosis.

  2. Independent Circular DNA: Mitochondria and chloroplasts contain their own circular DNA genomes, structurally similar to bacterial plasmids and distinct from nuclear linear chromosomes.

  3. Prokaryotic Ribosomes & Binary Fission: Both organelles divide independently within host cells through binary fission and contain $70S$ ribosomes that resemble prokaryotic ribosomes rather than eukaryotic $80S$ ribosomes.

Homework Assignments and Exam #1 Details

• Homework Due Date: Wednesday, September 9, 2026 (both assignments must be turned in on physical paper in class, clearly labeled with full name and lab section number).

• Required Paper Assignments:

  1. Concept Map: "On Genes, Mutations, Proteins, and Traits" (instructions posted on CANVAS).

  2. Puzzle Activity: "Becoming RNA Polymerase and Being the Ribosome" activity completed for all FIVE ALLELES of the Mystery Gene.

• Required Online Media:

  • Four overview modules on Utah Learn Genetics (http://learn.genetics.utah.edu/content/basics/):

  • What are traits?

  • What are genes?

  • What are proteins?

  • What is a mutation?

• Optional Textbook Readings (Campbell's Biology):

  • Pages $328-331$: From genes to proteins.

  • Pages $344-348$: Mutations, genes, and transcription and translation.

• Exam #1 Logistics:

  • Date & Time: Friday, September 18, 2026, from $10:00$ to $10:50\,\text{AM}$ sharp ($50\,min$ exam period).

  • Coverage: Lectures #1 through #10 (August 26 to September 18, 2026).

  • Required Items:

  • #2 pencil(s) and eraser.

  • Scantron Test Form No. 882-E.

  • Knowledge of exact lab section number.

  • Format: Mix of Multiple Choice and Short Answer questions.

  • Exam Protocol: Exams will be pre-distributed in bins upon arrival; students must leave exams in bins until instructed to start. (Patience is required as BIOL 240 vacates the hall immediately prior).

  • Study Recommendations: Study daily in small increments; avoid last-minute cramming; form active study groups with lab section peers; study for long-term comprehension.

Chemical Structure of DNA and Base Pairing Rules

• Deoxyribonucleic Acid (DNA) Structure:

  • DNA is a nucleic acid polymer composed of nucleotide monomers.

  • Each nucleotide monomer contains three structural components:

  1. A phosphate group ($PO_4^{3-}$) covalently bound to the $5'$ carbon of deoxyribose.

  2. A pentose sugar (deoxyribose) with specified $3'$ carbon (bearing a hydroxyl $-\text{OH}$ group) and $5'$ carbon ($-\text{CH}_2-$) positions.

  3. A nitrogenous base bound to the $1'$ carbon of the sugar.

  • Structural Distinctions:

  • Nucleoside: Nitrogenous base + Pentose sugar.

  • Nucleotide: Nucleoside + Phosphate group.

• Nitrogenous Bases and Mnemonic:

  • Adenine (A)

  • Thymine (T)

  • Guanine (G)

  • Cytosine (C)

  • Mnemonic: "AT is where it's at!" ($A$ pairs with $T$; $G$ pairs with $C$).

• Erwin Chargaff's Findings (1949):

  • Chargaff's Rules:

  • Quantitative analysis shows that within any DNA molecule, the percentage of Adenine equals Thymine ($\%A = \%T$) and the percentage of Guanine equals Cytosine ($\%G = \%C$).

  • The ratio of $(A+T)$ to $(G+C)$ varies across different organismal species ($\%(A+T) eq \%(G+C)$).

  • Hypothesis: The specific linear sequence of nitrogenous bases carries genetic information.

• Quantitative Base Pair Calculations:

  • Concept Check 1: If $20\%$ of the nucleotides in a DNA molecule are Adenine, what percentage is Cytosine?

  • Since $\%A = \%T$, Thymine $= 20\%$.

  • Total $\%A + \%T = 20\% + 20\% = 40\%$.

  • Remaining percentage for $\%G + \%C = 100\% - 40\% = 60\%$.

  • Since $\%G = \%C$, Cytosine percentage $= \frac{60\%}{2} = 30\%$ (Option A).

  • Concept Check 2: If $15\%$ of the nucleotides in a DNA molecule are Guanine, what percentage is Thymine?

  • Since $\%G = \%C$, Cytosine $= 15\%$.

  • Total $\%G + \%C = 15\% + 15\% = 30\%$.

  • Remaining percentage for $\%A + \%T = 100\% - 30\% = 70\%$.

  • Since $\%A = \%T$, Thymine percentage $= \frac{70\%}{2} = 35\%$ (Option B).

The SIX Big Ideas of DNA Structure and Function

• Big Idea #1: Double Helix Geometry

  • The structural architecture of a DNA molecule is a DOUBLE HELIX.

  • Analogy: Functions identically to a spiral or helical staircase.

• Big Idea #2: Spatial Mapping of Nucleotide Sub-units创

  • Sugar-Phosphate Backbone: Forms the structural outer "handrails" of the double helix via repeating covalent phosphodiester bonds.

  • Nitrogenous Base: Forms half of a stair step extending inward from each backbone strand.

  • Information Storage: Genetic information is stored in the specific sequential order and variety of the nitrogenous base steps (the base sequence).

• Big Idea #3: Hydrogen Bonding and Molecular Dimensions

  • Hydrogen bonds hold opposing base pairs together across the two strands:

  • Adenine pairs with Thymine via $2$ hydrogen bonds ($A=T$).

  • Guanine pairs with Cytosine via $3$ hydrogen bonds ($G \equiv C$).

  • Key Structural Dimensions:

  • Helical Width: $1\,nm$ distance between base pairing points across the central axis (overall double helix diameter is $2\,nm$).

  • Helical Turn Pitch: $3.4\,nm$ length per complete $360^\circ$ turn (encompassing $10$ base pairs).

  • Inter-base Distance: $0.34\,nm$ axial distance between adjacent stacked base pairs.

  • Antiparallel Alignment: One strand runs in the $5' \rightarrow 3'$ direction while the complementary strand runs $3' \rightarrow 5'$, terminating in a free $3'$ hydroxyl ($-\text{OH}$) group and a free $5'$ phosphate group.

• Big Idea #4: Structure Dictates Function

  • Watson & Crick (1953) Historic Insight: "It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

  • Zipper Analogy: Non-covalent hydrogen bonds holding opposing bases act like zipper teeth. This allows the two strands to easily unwind and separate ("unzip") during replication and transcription without disrupting the covalent sugar-phosphate backbones.

  • Semi-Conservative Replication: Each unwound single strand acts as an intact template for synthesizing a new complementary strand.

• Big Idea #5: The Genome as a Cellular Library

  • Genome Definition: The entirety of DNA contained within the nucleus of a cell.

  • Library Hierarchy Analogy:

  • Library Room: Cell nucleus.

  • Entire Library: Genome.

  • Individual Books: Chromosomes ($46$ total chromosomes, organized as $23$ pairs, with 1 copy inherited from each parent).

  • Sentences in Books: Genes (~$20,000$ genes in the human genome).

  • Letters in Sentences: Nucleotide base pairs (~$3 \times 10^9$ base pairs, or $6 \times 10^9$ individual bases).

  • Physical Length Scale: Unwound genomic DNA from a single human cell nucleus extends approximately $6\,ft$ ($1.8\,m$) end-to-end.

  • Hierarchy of Relative Sizes (Smallest to Largest):     $\text{Nucleotide} < \text{Gene} < \text{Chromosome} < \text{Genome}$

• Big Idea #6: Non-Coding DNA and Genomic Organization

  • Protein-Coding Fraction: Only ~$1.5\%$ of human genomic DNA (out of ~$3 \times 10^9$ base pairs) codes for functional proteins.

  • Non-Coding Fraction: ~$98.5\%$ of human genomic DNA is non-protein-coding.

  • Modern Biological Understanding (2012 ENCODE Findings):

  • Studies co-published in 2012 demonstrated that non-protein-coding DNA is not "junk," but is enriched with regulatory switches (promoters, enhancers, silencers, non-coding RNAs) controlling when and where genes are turned on or off.

Chromatin Packaging and Macromolecules

• Macromolecular Classes in Cells:

  • All cellular structures are constructed from four primary macromolecules:

  1. Proteins (amino acid monomers)

  2. Nucleic Acids (DNA & RNA; nucleotide monomers)

  3. Carbohydrates (monosaccharide monomers)

  4. Lipids (fatty acid / glycerol sub-units)

• Hierarchical Levels of Chromatin Packaging:

  1. DNA Double Helix: Naked DNA strand measuring $2\,nm$ in diameter.

  2. Nucleosomes ("Beads on a String"): DNA winds around core histone octamers ($2 \times \text{H2A/H2B}$ and $2 \times \text{H3/H4}$ dimers) forming nucleosome beads measuring $11\,nm$ in diameter.

  3. Chromatin Fiber: Nucleosomes pack tightly into a $30\,nm$ fiber.

  4. Looped Domains: The $30\,nm$ fiber forms loops averaging $300\,nm$ in width.

  5. Condensed Chromatin: Loops fold further into $700\,nm$ chromatid sections.

  6. Metaphase Chromosome: Fully condensed duplicated chromosome measuring $1,400\,nm$ across sister chromatids linked at the centromere.

• Gene Coding & Protein Translation Principles:

  • The human genome contains ~$20,000$ genes coding for ~$50,000$ distinct protein variants.

  • Gene: A molecular blueprint/recipe made of nucleic acid (DNA) that stores genetic instructions.

  • Sentence Analogy: 1 Gene = 1 literary sentence (e.g., Edward George Bulwer-Lytton's 1830 quote: "It was a dark and stormy night; the rain fell in torrents…").

  • Proteins: Long polypeptide chains of amino acids (monomers) that function as cellular machinery performing biological work.