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Announcements

• In-person student help hours Friday cancelled (Football).
• Course Orientation Assignments are due on Wed Sept 3 – Achieve access – connect through D2L (14 day free trial) – iClicker – connect through Achieve.
• Unit 1 Assignments are due on Sunday Sept 7.
• NO CLASS next Monday – Labor Day holiday.
• We will have our first recitation partner quiz next Tuesday, and we will discuss problems from Problem Set 1.
• Exam 1 is Monday September 15.

Learning objectives

• Last time (recap):
  • Course policies and introduction.
  • Drawing models in genetics.
  • Problem solving.
• Today:
  • Review nucleic acid biology and how they function.
  • Emphasize the importance of ‘sequence’ and polarity in nucleic acids.
  • Practice problems.

The Cell Cycle

• Question reviewed: When does replication occur? Options:
  • A. G1, B. G0, C. S, D. G2, E. M.
• Answer and concept:
  • Replication occurs during the S phase of the cell cycle, i.e., in the S phase. ext{DNA replication}
    ightarrow ext{S phase}.
• Related cycle outline (as shown): G1 → S → G2 → M, with possible exit to G0; a schematic display includes G1, S, G2, M, and G0 transitions.

Key concept: Polarity

• Why is the polarity of DNA/RNA always 5' to 3'?
  • Reflects the molecular structure of nucleotides and how polymerization occurs (phosphodiester linkages form between the 5' phosphate and the 3' hydroxyl).
• Prompted exercise: draw a DNA molecule and a nucleotide; how does an RNA molecule/nucleotide differ?
• Takeaway: Nucleic acids have directionality from 5' to 3' due to the chemical linkages formed during synthesis.

Nucleic Acid Sugars

• Nucleotide structure (high-level): 5' phosphate, sugar (pentose), base.
• Sugar types:
  • RNA sugar: ribose (has an OH group on the 2' carbon).
  • DNA sugar: deoxyribose (lacks the 2' OH).
• Schematic cues seen in the figures labeling 5' and 3' ends and backbone components.

What are nucleic acids?

• Nucleic acids include DNA and RNA.
• They are polymers built from monomers called nucleotides.

What are the monomers of nucleic acids?

• Correct answer from slides: Nucleotides.
• Not monomers: Fatty acids; Amino acids; Monosaccharides.

What are the components of a nucleotide?

• Correct components (select all that apply):
  • Nitrogenous base.
  • Phosphate group.
  • Sugar.
• Not components (per slide prompts):
  • Disulfide bond.
  • Water molecule.

Nucleic acid sugars (repeat visuals)

• Key distinction reiterated:
  • RNA uses ribose; DNA uses deoxyribose.
  • 3' end of the sugar has an -OH group in both sugars shown.
• Structural note: the sugar-pentose ring and the attached base/phosphate determine backbone polarity.

Nucleic acid sugar-phosphate backbone

• Backbone components: Phosphate groups alternating with sugars.
• Ends of the strand: 5' end carries the phosphate; 3' end carries the sugar with a free 3' hydroxyl.
• Visual cues label 5' and 3' carbons (5'C and 3'C).

Nucleoside vs nucleotide

• Nucleoside: nitrogenous base + sugar (no phosphate).
• Nucleotide: nitrogenous base + sugar + phosphate group.
• Pharmacology/biochemistry note: backbone polymerization involves the phosphate group of one nucleotide and the 3' -OH of the previous nucleotide.

Nucleic acid nitrogenous bases

• Bases fall into two classes:
  • Pyrimidines: Cytosine (C), Thymine (T, in DNA), Uracil (U, in RNA).
  • Purines: Adenine (A), Guanine (G).

DNA polynucleotide strand and base-pairing directions

• DNA strands are polynucleotides with a 5' to 3' directionality.
• In a DNA double helix, strands run antiparallel to each other.
• Base-pairing rules contribute to the constant width of the double helix:
  • Cytosine (C) pairs with Guanine (G) via 3 hydrogen bonds.
  • Thymine (T) pairs with Adenine (A) via 2 hydrogen bonds.
• The sugar in DNA is deoxyribose; the sugar-phosphate backbone is on the exterior; the bases form the interior rungs.
• In RNA, Uracil (U) replaces Thymine (T).

Chargaff and foundational context

• Chargaff discovered that in DNA:
  • A = T and C = G (base-pairing principles).
• Rosalind Franklin, Watson, and Crick contributed to the structural understanding (
  image credits noted on slide).
• This historical context helps explain why base composition constrains possible sequences.

Problem: base-proportion budgeting (Chargaff-based reasoning)

• Question: You’re studying canid DNA and want to know the composition of all nucleotide bases. Cost to quantify a base proportion is $1000 per base.
• Idea: By Chargaff’s rules, you only need to measure two of the four base proportions to deduce the other two.
• Reasoning:
  • If you measure A, you know T should be equal to A: A = T.
  • Then C and G must sum to 100% minus (A + T) = 100% - 2A, and C = G, so C = G = rac{100 - 2A}{2} = 50 - A.
• Therefore, the minimum cost is $2000 (two measurements): measure A and C (or A and G, etc.).
• Example result: If A = 21%, then
  • T = A = 21 ext{
    }\%
    (unchanged by Chargaff)
  • C = G = 50 - A = 29 ext{
    }\%
    

Applying Chargaff’s rules

• Given A = 21%, predict C (and G):
  • C = G = 50^ ext{-}A = 50 - 21 = 29 ext{
    }\%
    

Your canid sequence analysis: probability of a specific 5-base sequence

• Problem: What is the probability that 5 bases in this sample are “ATTGC”? (Round to 5 decimals.)
• Using base frequencies from Chargaff: A = T = 0.21; C = G = 0.29.
• Calculation:
  • P( ext{ATTGC}) = pA imes pT imes pT imes pG imes p_C = 0.21 imes 0.21 imes 0.21 imes 0.29 imes 0.29 \