DNA — Interactive Lab

🏠 Where is it?

DNA is mostly found in the nucleus of each of our cells, packed into structures called chromosomes. We have 46 chromosomes (23 pairs) — 23 from our mother and 23 from our father!

📝 What does it do?

DNA holds the instructions your body needs to make proteins - the "tools" that do almost everything in your body: from the color of your eyes to the way you digest your food!

🪜 The parts of the "ladder"

The sides (backbone): Made of sugar (deoxyribose) and phosphate groups — they give it stability.

The rungs: The nitrogen bases that pair up with each other!

🎨 The 4 Bases

DNA uses only 4 "letters" to write all the instructions for life:

• Adenine (A) - Always pairs with Thymine
• Thymine (T) - Always pairs with Adenine
• Guanine (G) - Always pairs with Cytosine
• Cytosine (C) - Always pairs with Guanine

📐 Dimensions

📏 Chargaff's Rules

Erwin Chargaff discovered that in every DNA molecule:

• The amount of Adenine (A) = the amount of Thymine (T)
• The amount of Guanine (G) = the amount of Cytosine (C)
• So: A + G = T + C (purines = pyrimidines)

📋 Types of RNA

• mRNA (messenger): Carries the information from DNA to the ribosomes
• tRNA (transfer): Carries amino acids for protein synthesis
• rRNA (ribosomal): Structural component of the ribosomes

📊 Human Chromosomes

🔬 Homologous Chromosomes

Homologous chromosomes are pairs of chromosomes (one from each parent) that:

• Have the same size and shape
• Carry the same genes in the same spots (loci)
• Can have different alleles of the same gene

📦 DNA Packaging

How do 2 meters of DNA fit inside a nucleus only a few micrometers wide?

🧬 What Is a Gene?

A gene is a piece of DNA that holds the instructions for building a protein. It sits at a specific spot (locus) on the chromosome.

🎭 Types of Alleles

🔀 Problems & Solutions

Problem: DNA polymerase only works in one direction (5' → 3').

Solution: One strand (the leading strand) is built non-stop, while the other (the lagging strand) is built in pieces (Okazaki fragments) that are then joined together by ligase!

🧮 Numbers

🧬 From DNA to Protein

Here is how the information flows:

Transcription: DNA is copied into RNA

Translation: The RNA is "read" to build a protein

🔤 The Genetic Code

Every triplet of bases (codon) matches one amino acid:

• AUG → Methionine (start signal)
• UUU → Phenylalanine
• UAA, UAG, UGA → stop codons (end signal)

There are 64 codons for only 20 amino acids — the code is "degenerate"!

❓ What exactly are they?

Polymorphism = a spot in the DNA where 2 or more versions (alleles) exist in the population, with the rarest one showing up in >1% of people.

📊 Types of Polymorphisms

• SNP (Single Nucleotide Polymorphism): A change in a single letter. E.g. ...AAGCTAA... vs ...AAGCCAA... - The most common type!
• Insertions & deletions (indels): Small pieces of DNA that get added or removed
• STRs (Short Tandem Repeats): Repeats of short sequences. E.g. CAGCAGCAG... - These are used in DNA tests!
• CNVs (Copy Number Variations): Differences in the number of copies of large pieces

🎯 Why do they matter?

• Traits: Eye color, hair color, height, blood type
• Health: Risk of disease, how you react to medicines
• Identification: Forensics, paternity tests
• Ancestry: Genealogy tests, population studies

🧪 Example: Blood Types

The ABO gene has 3 alleles: I^A, I^B, i

Combinations → Blood types:
I^AI^A or I^Ai → A | I^BI^B or I^Bi → B | I^AI^B → AB | ii → O

🔄 Mutation vs Polymorphism

📝 Types of Mutations

Mutations fall into two big categories:

1️⃣ Point mutations — one base changes. Depending on what that does to the protein, they split into:

• Silent: the amino acid doesn't change (because the code is degenerate) → no effect at all
• Missense: a different amino acid goes in → the protein may work less well
• Nonsense: an early stop codon appears → a cut-short protein that usually doesn't work

2️⃣ Frameshift mutations — insertion or deletion of bases:

• Reading frame shift: if the number of bases inserted or deleted isn't a multiple of 3, the whole reading shifts from that point on → every amino acid after it changes!

🔥 Causes of Mutations

• Spontaneous: Mistakes during replication (~1/10⁹ bases)
• UV radiation: Creates thymine dimers
• Chemicals: Smoke, certain chemical substances
• Ionizing radiation: X-rays, gamma rays

✅ Repair Mechanisms

The cell has "repair crews" that fix the damage:

• Checking during replication (proofreading): DNA polymerase checks every base it puts in
• Repair of mismatched bases (mismatch repair): Spots wrong pairings after replication
• Repair by cutting out (excision repair): Cuts out and replaces damaged sections

🔬 Types of Cells

🧫 Organelles of the Cell

• Nucleus: Holds the DNA, controls the cell
• Mitochondria: "Power plants" — they make ATP
• Ribosomes: They build the proteins
• Endoplasmic Reticulum: Transport and processing
• Golgi Apparatus: "Post office" — it packages proteins
• Lysosomes: "Digestive system" — they break materials down

🔄 The Flow of Genetic Information

This is the "Central Dogma" of Molecular Biology!

🔬 Mendel's Experiment

Mendel crossed pea plants that had different traits:

• Seed color: Yellow vs Green
• Seed shape: Round vs Wrinkled
• Plant height: Tall vs Short
• Flower color: Purple vs White

1️⃣ Law of Dominance (Uniformity)

When you cross two pure lines with different alleles for a trait, all the offspring of the first generation (F1) are the same and show the dominant trait.

2️⃣ Law of Segregation

When gametes are made, the two alleles of a gene separate and each gamete gets only one. In the F2 generation you see a 3:1 ratio!

3️⃣ Law of Independent Assortment

The alleles of different genes (the ones sitting on different chromosomes) are inherited independently of each other.

📊 Punnett Square

A tool for predicting the offspring of a cross:

Result: 25% AA, 50% Aa, 25% aa → Phenotype 3:1

🧬 Examples in Humans

The classic school examples, in their simplified form:

• Eye color: Brown is dominant over blue
• Earlobe: Free is dominant over attached
• Tongue: Being able to "roll" it is dominant
• Freckles: Presence is dominant over absence

📌 Example 1: Pea Seed Color

Yellow color (Y) is dominant over green (y).

Cross: Homozygous yellow (YY) × Homozygous green (yy)

📌 Example 2: F1 × F1 Cross

Continuing from example 1: we cross two heterozygous yellow plants (Yy).

Cross: Yy × Yy

📌 Example 3: Plant Height

Tall (T) is dominant over short (t).

Cross: Heterozygous tall (Tt) × Homozygous short (tt)

📌 Example 4: Eye Color in Humans

Brown color (B) is dominant over blue (b).

Question: A man with brown eyes (Bb) marries a woman with blue eyes (bb). What eye color will their children have?

⚠️ Simplified model. In reality, eye color is decided by many genes, so the real ratios don't come out this neat.

📌 Example 5: Blood Types (Codominance)

Blood types are decided by 3 alleles: I^A, I^B, i

I^A and I^B are codominant with each other, but both are dominant over i.

Question: Father with type A (I^Ai) × Mother with type B (I^Bi)

📌 Example 6: Dihybrid Cross (3rd Law)

We look at 2 traits at the same time in pea plants:

• Color: Yellow (Y) is dominant over green (y)

• Shape: Round (R) is dominant over wrinkled (r)

Cross: YyRr × YyRr (dihybrids)

📌 Example 7: Incomplete Dominance — Flower Color

In Mirabilis jalapa flowers (the four o'clock flower), neither allele is fully dominant!

• RR = Red

• Rr = Pink (in between!)

• rr = White

Cross: Pink (Rr) × Pink (Rr)

📌 Example 8: Sex-Linked Inheritance — Color Blindness

Color blindness (daltonism) is a recessive trait carried on the X chromosome.

• X^N = Normal vision

• Xⁿ = Color blindness

Females: X^NX^N (normal), X^NXⁿ (carrier), XⁿXⁿ (color blind)
Males: X^NY (normal), XⁿY (color blind)

Cross: Carrier female (X^NXⁿ) × Normal male (X^NY)

✏️ Exercise 1: Coat Color in Rabbits

Black (B) is dominant over brown (b).

Question: If we cross two heterozygous black rabbits (Bb × Bb), what color will the babies be?

✏️ Exercise 2: Earlobes

The free earlobe (F) is dominant over the attached one (f).

Question: A man with free earlobes (Ff) marries a woman with attached earlobes (ff). What is the chance that their child has attached earlobes?

✏️ Exercise 3: Blood Type

Question: A mother has blood type O (ii) and the father has type AB (I^AI^B). Which blood types can their children have?

✏️ Exercise 4: Dihybrid Cross

In guinea pigs: Black (B) > white (b), Short hair (S) > long (s)

Question: Two dihybrids (BbSs × BbSs) are crossed. What is the chance of getting a white guinea pig with long hair?