Molecular Genetics

The Flow of Genetic Information

• DNA → RNA → Protein

  • DNA stores instructions.

  • RNA copies the instructions.

  • Proteins carry out the function.

• This is called the central dogma of biology.

Transcription

• What is it?

  • Transcription is the process of copying a gene from DNA into RNA.

• Where does it take place?

  • Nucleus (in eukaryotic cells)

• Purpose

  • To create an RNA copy (mRNA) of a gene so it can leave the nucleus and be used to make a protein.

RNA Types

• 1. mRNA (messenger RNA)

  • Carries the genetic message from DNA to the ribosome

• 2. tRNA (transfer RNA)

  • Brings amino acids to the ribosome

  • Has an anticodon that matches mRNA

• 3. rRNA (ribosomal RNA)

  • Makes up ribosomes

  • Helps build proteins

Codons & Anticodons

• Codon

  • A 3-nucleotide sequence on mRNA

  • Codes for one amino acid

• Anticodon

  • A 3-nucleotide sequence on tRNA

  • Complementary to the codon

• Example:

  • mRNA codon: AUG

  • tRNA anticodon: UAC

Start and Stop Codons

• Start Codon

  • AUG

  • Signals the ribosome to begin translation

  • Codes for Methionine

• Stop Codons

  • UAA, UAG, UGA

  • Tell the ribosome to stop building the protein

RNA Splicing

• After transcription:

  • Introns = noncoding sections (removed)

  • Exons = coding sections (kept)

• Splicing removes introns and connects exons to form mature mRNA.

Translation

• What is it?

  • The process of building a protein from mRNA instructions.

• Where does it occur?

  • Ribosome (in cytoplasm)

• Purpose

  • To assemble amino acids into a protein.

How Ribosomes Read mRNA

• The ribosome attaches to the mRNA

• Reads one codon at a time

• tRNA brings matching amino acids

• Amino acids are joined together

• What bonds form?

  • Peptide bonds form between amino acids.

Mutations

• A mutation = a change in the DNA sequence.

• Types:

  • Silent → no change in protein

  • Missense → different amino acid

  • Nonsense → early stop codon

• Mutations can:

  • Change protein shape

  • Make protein nonfunctional

  • Sometimes have no effect

DNA Replication

• What is it?

  • Copying DNA before cell division.

• When?

  • S phase of interphase.

Semiconservative Model

• Each new DNA molecule:

  • Has 1 original strand

  • Has 1 new strand

• Think of the original strands as blue and the new strands as gray — each daughter's DNA has one of each.

Enzymes in DNA Replication

• DNA Helicase

  • Unwinds DNA

  • Breaks hydrogen bonds between bases

• DNA Polymerase

  • Adds new complementary nucleotides

  • Builds new strand in 5' → 3' direction

• DNA Ligase

  • Seals fragments together (especially on the lagging strand)

Hershey-Chase Experiment

• Scientists used viruses to prove:

  • DNA is the genetic material, not protein.

• They labeled:

  • DNA with radioactive phosphorus

  • Protein with radioactive sulfur

• Only DNA enters bacteria → DNA carries genetic info.

Structure of DNA

• Double helix shape

• Two strands twisted

• Sugar-phosphate backbone on the outside

• Nitrogen bases in the middle

• Base pairing:

  • A pairs with T

  • C pairs with G

• Hydrogen bonds hold bases together.

Nucleotides

• Each nucleotide has:

  • Sugar

  • Phosphate group

  • Nitrogen base

• DNA sugar = deoxyribose

• RNA sugar = ribose

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The Search for the Genetic Material

• Early 1900s Mystery

  • Genes known to be on chromosomes

  • Chromosomes are made of DNA + protein

  • Unsure which molecule carried hereditary information

• Why Protein Seemed Likely

  • Proteins = 20 amino acids → high complexity

  • DNA = 4 nucleotides → seemed too simple

  • Scientists assumed complexity = information storage

🧪 Frederick Griffith (1928) – Transformation

• Studied two strains of pneumonia-causing bacteria:

  • Harmless strain

  • Disease-causing strain

• Heat-killed pathogenic bacteria mixed with live harmless bacteria

• Result:

  • Some harmless bacteria became virulent

  • Change was heritable

• Key Insight

  • A chemical from dead bacteria caused the transformation

    • → Called the “transforming factor.”

Hershey–Chase Experiment (1952)

• Scientists: Alfred Hershey & Martha Chase

• Goal

  • Determine whether DNA or protein is the genetic material

• Model System

  • Virus Phage T2

  • Infects Escherichia coli (E. coli)

Experimental Design

• Radioactive labeling:

  • Sulfur-35 (³⁵S) → labels protein

    • Proteins contain sulfur

    • DNA does NOT

  • Phosphorus-32 (³²P) → labels DNA

    • DNA contains phosphorus

    • Proteins mostly do NOT

Procedure

• Let labeled phages infect bacteria

• Use blender → knock off viral coats

• Use centrifuge

  • Pellet = bacteria

  • Liquid = viral parts 

Phage T2 Replication Cycle

• The virus attaches to the bacterium

• Injects DNA only

• Host produces:

  • Viral DNA

  • Viral proteins

• Cell lyses → releases new phages

• DNA contains instructions

Structure of DNA & RNA

• Nucleic Acids

  • DNA & RNA = polymers of nucleotides

Nucleotide Components

• Each nucleotide contains:

  • Nitrogenous base

    • DNA: A, T, C, G

    • RNA: A, U, C, G

  • Sugar

    • DNA → Deoxyribose

    • RNA → Ribose

  • Phosphate group

Sugar-Phosphate Backbone

• Covalent bonds connect sugar ↔ phosphate

• Forms repeating backbone

• Bases project inward 

Nitrogenous Bases

• Two Types

  • Pyrimidines (single ring)

    • Thymine (T)

    • Cytosine (C)

    • Uracil (U in RNA)

  • Purines (double ring)

    • Adenine (A)

    • Guanine (G)

Base Pairing Rules

• A ↔ T (2 hydrogen bonds)

• G ↔ C (3 hydrogen bonds → stronger)

• Complementary pairing

DNA Double Helix Discovery (1953)

• Scientists:

  • James Watson

  • Francis Crick

• Built on X-ray data from:

  • Rosalind Franklin

  • Maurice Wilkins

Franklin’s Contributions

• DNA = helix

• Uniform diameter: 2 nm

• Bases stacked 0.34 nm apart

Watson–Crick Model

• Key Features

  • Double helix

  • Sugar-phosphate backbones on the outside

  • Bases on inside

  • Purine + Pyrimidine pairing

    • Maintains uniform width

  • Strands run antiparallel

Chargaff’s Rules

• Scientist: Erwin Chargaff

  • %A ≈ %T

  • %G ≈ %C

• Explained by complementary pairing 

Why Sequence Matters

• Pairing rules don’t restrict order

• Base sequence can vary enormously

• Genes = unique nucleotide sequences

• Information stored in base order

Recognition

• 1962 Nobel Prize:

  • Watson

  • Crick

  • Wilkins

• Franklin was not included (passed away in 1958)

Big Picture Impact

• Discovery of DNA structure:

  • Confirmed molecular basis of heredity

  • Explained:

    • Information storage

    • Accurate copying

    • Inheritance

Structure ↔ Function in DNA

• Biology theme: Structure determines function

• Watson & Crick’s insight:

  • Specific base pairing explains DNA’s shape

  • Also explains how DNA copies itself

• Famous line (1953):

  • “Specific pairing immediately suggests a copying mechanism.”

Complementary Base Pairing

• Rules:

  • A ↔ T

  • G ↔ C

• Knowing one strand → you can infer the other

DNA Replication Overview

• Basic Steps

  • Parental strands separate

  • Each strand becomes a template

  • Free nucleotides align via base pairing

  • Enzymes link nucleotides

  • Two identical daughter DNA molecules

Semiconservative Model

• Eachdaughter'sr DNA contains:

  • One old (parental) strand

  • One new strand

• “Semi” = half conserved

• Confirmed experimentally (1950s)

Why Replication Is Complex

• Challenges:

  • The double helix must untwist

  • Two strands copied simultaneously

  • Extremely fast

  • Extremely accurate

Speed of Replication

• E. coli

  • ~4.6 million base pairs → copied in < 1 hour

• Humans

  • 6 billion base pairs → copied in a few hours

• Remarkable efficiency

Accuracy of Replication

• Error rate: ~1 mistake per several billion nucleotides

• Thanks to:

  • Base pairing rules

  • Proofreading enzymes

Origins of Replication

• Replication begins at origins

• Origins = specific DNA sequences

• DNA opens → forms replication bubbles

Replication Bubble Behavior

• Replication proceeds in both directions

• Strands elongate outward

Eukaryotic Advantage

• Many origins per chromosome

• Hundreds/thousands of bubbles at once

• Faster genome duplication

DNA Strand Directionality

• Each strand has:

  • 5′ end

    • Phosphate attached

  • 3′ end

    • –OH group attached

• Strands run antiparallel

DNA Polymerase Rules

• Adds nucleotides ONLY to the 3′ end

• New strand grows 5′ → 3′

• Cannot grow 3′ → 5′

Replication Fork Consequences

• At each fork:

• Leading Strand

  • Synthesized continuously

  • Polymerase moves toward the fork

Lagging Strand

• Synthesized discontinuously

• Made in short pieces

Okazaki Fragments

• Short DNA segments on the lagging strand

• Named after Reiji & Tsuneko Okazaki

• Later joined by:

• DNA ligase

DNA Ligase Function

• “Glues” DNA fragments together

• Forms a continuous strand

Proofreading & Repair

• DNA Polymerases

  • Proofread the new DNA

  • Remove mismatches

Repair Roles

• Polymerase & ligase help fix damage from:

  • UV light

  • X-rays

  • Toxic chemicals (e.g., tobacco smoke)

Why Replication Matters

• Ensures:

  • All somatic cells have the same DNA

  • Genetic info passed to next generation

Genotype → Phenotype

• Key Definitions

  • Genotype = organism’s genetic makeup (DNA)

  • Phenotype = observable traits (appearance, function)

• Molecular connection:

  • DNA → RNA → Protein → Trait

• Proteins are the bridge between genes and traits.

Central Dogma (Francis Crick)

• Flow of genetic information:

• Transcription: DNA → RNA

• Translation: RNA → Protein

• Mnemonic:

  • “DNA makes RNA makes protein”

Genes & Enzymes

• Archibald Garrod (1909)

  • Proposed genes affect phenotype via enzymes

  • “Inborn errors of metabolism”

• Example: Alkaptonuria

  • Dark urine due to alkapton buildup

  • Cause: missing enzyme

Beadle & Tatum (1940s)

• Studied Neurospora crassa

• Found:

  • Nutritional mutants lacked specific enzymes

  • Each defect is traced to one gene

• One gene–one enzyme hypothesis

Modern Update

• Now understood as:

  • One gene–one polypeptide

• Because:

  • Not all proteins are enzymes

  • Many proteins have multiple polypeptides

DNA & RNA as “Languages”

• Both are polymers of nucleotides

• DNA bases: A, T, C, G

• RNA bases: A, U, C, G

• Genetic info = linear base sequence

Genetic Code Logic

• Why triplets?

  • 1 base → 4 possibilities 

  • 2 bases → 16 possibilities 

  • 3 bases → 64 possibilities 

• Enough for 20 amino acids

Codons

• 3-base “words”

• Nonoverlapping

• Specify amino acids

Cracking the Code

• Marshall Nirenberg (1961)

  • Used artificial RNA: poly-U

  • Only codon: UUU

  • Produced phenylalanine

• UUU = Phenylalanine (Phe)

Genetic Code Features

• 64 codons total

• 61 → amino acids

• 3 → stop codons

Special Codon: AUG

• Codes for Methionine (Met)

• Start signal

Redundancy

• Multiple codons → same amino acid

• No ambiguity

• Example:

  • UUU & UUC → Phenylalanine

Nearly Universal Code

• Shared across life

• Enables genetic engineering

Transcription (DNA → RNA)

• Where?

  • Eukaryotes → nucleus

  • Prokaryotes → cytoplasm

Process

• Enzyme: RNA polymerase

• Steps:

  • DNA strands separate

  • One strand = template

  • RNA nucleotide pairs (A–U, G–C)

  • RNA strand synthesized

Promoter

• “Start transcription” signal

• RNA polymerase binding site

Phases

• Initiation

• Elongation

• Termination (at terminator)

RNA Processing (Eukaryotes)

• Occurs before mRNA leaves the nucleus.

5′ Cap

• Modified G nucleotide

• Protection & ribosome binding

Poly-A Tail

• 50–250 A nucleotides

• Stability & export

Introns vs Exons

• Introns = noncoding

• Exons = coding

RNA Splicing

• Introns removed

• Exons joined

• Allows:

  • Multiple proteins from one gene

mRNA (Messenger RNA)

• Carries genetic instructions to the ribosome

• Translated into protein

Translation (RNA → Protein)

• Requires:

  • mRNA

  • tRNA

  • Ribosomes

  • Amino acids

  • ATP

tRNA (Transfer RNA)

• Structure

  • Single RNA strand (~80 nucleotides)

  • Folded via base pairing

Key Regions

• Anticodon

  • Matches the mRNA codon

• Amino acid attachment site

Charging tRNA

• Enzyme: aminoacyl-tRNA synthetase

  • One enzyme per amino acid

  • Uses ATP

  • Attaches the correct amino acid

Ribosomes

• Made of:

  • rRNA

  • Proteins

• Two subunits:

  • Large

  • Small

Medical Relevance

• Some antibiotics target bacterial ribosomes:

  • Tetracycline

  • Streptomycin

Translation Mechanics

• tRNA Binding Sites

  • A site = incoming tRNA

  • P site = growing polypeptide

Initiation

• mRNA binds the small subunit

• Initiator tRNA binds AUG

• Large subunit joins

Elongation

• tRNAs bring amino acids

• Peptide bonds form

• The ribosome moves along the mRNA

Termination

• Stop codon reached

• Polypeptide released

• Ribosome disassembles

Speed

• Protein made in < 1 minute

• Multiple ribosomes per mRNA (polyribosomes)

Protein Folding

• Polypeptide → 3D structure

• Determines function

Mutations

• Definition

  • Change in DNA nucleotide sequence

Types

• Nucleotide Substitution

  • Replace one base pair

Silent Mutation

• No amino acid change

Missense Mutation

• Different amino acid

Nonsense Mutation

• Stop codon created

• Truncated protein

Insertion / Deletion

• Often causes frameshift

  • Alters the reading frame

  • Usually disastrous

Example: Sickle-cell disease

• Single nucleotide change

• Glutamate → Valine

• Alters the hemoglobin shape

Causes of Mutations

• Spontaneous

  • Replication errors

Mutagens

• Physical:

  • UV light

  • X-rays

Chemical:

• Base analogs

• Example:

  • AZT (resembles thymine)

  • Blocks viral DNA replication

Importance of Mutations

• Despite risks:

  • Source of genetic diversity

  • Drives evolution

  • Essential research tools

Viruses: “Genes in a Box”

• Basic Structure

  • A virus consists of:

    • Nucleic acid (DNA or RNA)

    • Capsid = protein coat

    • Sometimes a membrane envelope

• Viruses are obligate intracellular parasites

  • Can only replicate inside host cells

• The host provides machinery for:

  • Replication

  • Transcription

  • Translation

Viral Replication Cycles

• Lytic Cycle

  • Outcome: Host cell is destroyed

  • Steps:

    • Virus injects DNA

    • Viral genes hijack a cell

    • Viral components produced

    • New viruses assembled

    • Cell lyses → viruses released

  • Fast, deadly to host

Lysogenic Cycle

• Outcome: Host survives (initially)

• Key Idea:

  • Viral DNA integrates into the host chromosome

Prophage

• Integrated viral DNA

• Usually inactive

• When a bacterium divides:

  • Copies the prophage DNA along with its own

• Result:

  • Many infected daughter cells

  • No immediate cell death

Advantages of Virus

• Spreads without killing the host

• Can remain dormant indefinitely

Genetic Switch

• Triggered by stress:

  • Radiation

  • Toxic chemicals

  • Environmental damage

• Prophage excises → enters lytic cycle

Medical Relevance

• Prophage genes can make bacteria more dangerous

• Examples of toxin-linked diseases:

  • Diphtheria

  • Botulism

  • Scarlet fever

• Bacteria become harmful due to viral genes

Emerging Viruses

• Definition

  • Viruses that:

    • Appear suddenly

    • Are newly recognized

Examples

• Human immunodeficiency virus

  • Identified early 1980s

Ebola virus

• Identified 1976

• Causes severe hemorrhagic fever

West Nile virus

• Appeared in North America, 1999

Severe acute respiratory syndrome

• Emerged 2002

• Caused by coronavirus

Why Do New Viral Diseases Appear?

• Three Main Causes

• Mutation

  • Especially in RNA viruses

  • Reason:

    • Lack proofreading

    • High error rates

  • Rapid evolution of new strains

  • Example:

    • Influenza → yearly vaccines needed

Cross-Species Transmission

• Viruses jump between species

• ~75% of new human diseases originate in animals

• Example:

  • H5N1 avian flu

Spread from Isolated Populations

• Previously rare viruses expand due to:

  • Global travel

  • Social change

  • Medical practices

• Example:

  • AIDS pandemic

Retroviruses & HIV

• HIV Structure

  • Envelope with glycoprotein spikes

  • Two RNA strands

  • Enzyme: reverse transcriptase

Why “Retrovirus”?

• Because:

  • RNA → DNA (reverse of usual DNA → RNA)

Reverse Transcription

• Enzyme: reverse transcriptase

• Steps:

  • Viral RNA → DNA strand

  • Complementary DNA strand added

  • Viral DNA enters the nucleus

  • Integrates into host DNA

Provirus

• Integrated viral DNA in an animal cell

• Like a prophage in bacteria

Consequences

• Host machinery:

  • Transcribes viral RNA

  • Produces viral proteins

  • Assembles new viruses

Disease Mechanism

• HIV infects white blood cells

• Result:

  • Weak immune system

  • Vulnerable to secondary infections

Viroids

• Definition

  • Small circular RNA

  • Infect plants

  • No capsid

  • Do not encode proteins

• Replicate using host enzymes

• Effects:

  • Abnormal growth

  • Stunting

Prions

• Definition

  • Infectious proteins

  • No nucleic acid (!)

Mechanism

• Misfolded protein:

  • Converts normal proteins → misfolded form

• Effects:

  • Protein clumping

  • Brain damage

Diseases

• Examples:

  • Scrapie (sheep)

  • Chronic wasting disease

• No cure yet

Bacteria as Genetic Models

• Bacterial DNA

  • Single circular chromosome

  • Highly folded

Reproduction

• Binary fission (asexual)

• Offspring genetically identical

Genetic Variation in Bacteria

• Despite asexual reproduction:

  • Genes can move between cells

Three Mechanisms

• Transformation

  • Uptake of “naked” DNA from the environment

• Classic experiment:

  • Frederick Griffith

Transduction

• DNA transferred by bacteriophages

  • Error during the lytic cycle:

    • Host DNA is packaged into the virus

    • Injected into a new bacterium

Conjugation

• Direct DNA transfer via sex pilus

• Features:

  • Cytoplasmic bridge forms

  • The donor replicates DNA during transfer

DNA Integration

• Transferred DNA may:

  • Recombine with the recipient chromosome

• Mechanism:

  • Crossing over

• Result:

  • Recombinant chromosome

F Factor (Fertility Factor)

• Definition

  • Special plasmid

  • Contains genes for conjugation

  • Has the origin of replication

Two Forms

• Integrated F Factor

  • Part of a chromosome

  • Transfers chromosomal genes

Plasmid F Factor

• Separate circular DNA

• Entire plasmid transferred

  • Recipient becomes:

    • Donor

Plasmids

• Definition

  • Small circular DNA

  • Independent of the chromosome

  • Self-replicating

Medical Importance: R Plasmids

• Carry:

  • Antibiotic resistance genes

• Examples:

  • Penicillin resistance

  • Tetracycline resistance

Why is the problem increasing?

• Antibiotic use:

  • Kills non-resistant bacteria

  • Resistant bacteria survive & spread

Big Picture Takeaway

• Viruses reveal gene expression mechanisms

• Bacteria exchange genes despite asexuality

• Plasmids drive antibiotic resistance

• Mutation fuels emerging diseases

Viruses

• What Is a Virus?

• Non-living infectious particle

• Made of genetic material (DNA or RNA) inside a protein coat (capsid)

• Some have a lipid envelope

• Cannot reproduce on their own — must infect a host cell

Lytic Cycle 

• Goal: Make copies fast and burst the cell.

• Steps:

  • Attachment – Virus binds to specific receptors on the host cell.

  • Entry – Viral DNA/RNA enters the cell.

  • Replication – Host cell machinery makes viral nucleic acids and proteins.

  • Assembly – New virus particles form.

  • Lysis – Cell bursts (lyses), releasing new viruses.

• Key idea:

  • The host cell dies.

  • Happens quickly.

  • Causes immediate symptoms.

Lysogenic Cycle

• Goal: Hide inside the host cell.

• Steps:

  • Virus injects DNA.

  • Viral DNA integrates into host DNA → becomes a prophage (if infecting bacteria).

  • The host cell replicates normally, copying viral DNA with it.

  • Later, it can switch to the lytic cycle.

• Key idea:

  • The cell does NOT immediately die.

  • A virus can remain dormant.

  • Makes infections harder to eliminate.

Viral Replication Cycle 

• General viral life cycle (applies broadly):

  • Attachment

  • Entry

  • Replication of the viral genome

  • Protein synthesis

  • Assembly

  • Release (lysis or budding)

• Important difference:

  • Lytic = immediate destruction

  • Lysogenic = dormancy first

Emerging Viruses

• Definition: Newly appearing viruses or viruses spreading rapidly.

• Why they emerge:

  • Mutation (especially RNA viruses)

  • Jumping from animals to humans (zoonosis)

  • Climate change

  • Global travel

  • Urbanization

• Examples: Ebola, SARS, COVID-19

• They are dangerous because:

  • Humans have little immunity

  • No immediate vaccines/treatments

HIV (Human Immunodeficiency Virus)

• A retrovirus

• Attacks T-helper cells (CD4 cells) in the immune system

• Causes AIDS

• Why It’s Dangerous:

  • Weakens the immune system

  • Makes body vulnerable to other infections

Reverse Transcriptase

• Enzyme used by retroviruses like HIV

• Converts viral RNA → DNA

• Viral DNA inserts into the host genome

• This allows:

  • Long-term infection

  • Hidden viral presence

  • Difficult treatment

Bacteria

• Bacterial Reproduction

  • Reproduce asexually by binary fission

  • Clone themselves

  • Fast reproduction rate

• Problem: Asexual reproduction = low genetic variation

• BUT bacteria have ways to increase variation without sex

Increasing Genetic Variation in Bacteria 

• Transformation 

  • Bacteria pick up free DNA from the environment

  • DNA may come from dead bacteria

  • Can incorporate it into their own genome

  • Result:

    • New traits (like antibiotic resistance)

Conjugation

• Direct transfer of DNA between bacteria

• Uses a pilus (bridge-like structure)

• Usually transfers plasmids

• Think: bacterial “DNA handshake.”

Plasmids

• Small circular DNA molecules

• Separate from the main chromosome

• Replicate independently

• Often contain helpful genes

• Example traits:

  • Antibiotic resistance

  • Toxin production

R Plasmids (Resistance Plasmids)

• Contain genes for:

  • Antibiotic resistance

• Why They’re a Threat:

  • Spread quickly through conjugation

  • Can transfer between different bacterial species

  • Create “superbugs”

  • Make infections difficult or impossible to treat

• This is a major public health concern.

Big Picture Summary

• Viruses:

  • Must infect cells to reproduce

  • Can destroy cells quickly (lytic) or hide (lysogenic)

  • Retroviruses use reverse transcriptase

• Bacteria:

  • Reproduce asexually

  • Increase variation through:

    • Transformation

    • Conjugation

    • Plasmids

  • R plasmids → antibiotic resistance crisis

Prokaryotic Gene Regulation (E. coli)

• Why Gene Regulation Matters

  • The environment changes constantly (ex, different nutrients in the intestine).

  • Cells conserve energy by only making proteins when needed.

  • Gene expression = DNA → RNA → Protein.

  • A gene is “on” when it’s transcribed and translated.

  • Regulation mostly happens at transcription initiation.

Jacob & Monod (1961)

• Studied gene control in E. coli.

• Proposed the operon model.

The lac Operon (Inducible Operon)

• Purpose:

  • Controls genes for lactose metabolism.

• Structure:

  • An operon includes:

    • Promoter → where RNA polymerase binds

    • Operator → on/off switch

    • Structural genes → code for enzymes

    • Regulatory gene (separate) → makes repressor

• How It Works:

  • No lactose (OFF):

    • The repressor protein binds the operator.

    • RNA polymerase is blocked.

    • No transcription.

  • Lactose present (ON):

    • Lactose binds the repressor.

    • Repressor changes shape.

    • Cannot bind operator.

    • RNA polymerase transcribes genes.

    • Enzymes for lactose metabolism are produced.

• Key Features:

  • Inducible system (turned on by substrate).

  • Fast response: 1000× enzyme increase in 15 min.

  • mRNA degraded quickly for flexibility.

trp Operon (Repressible Operon)

• Purpose:

  • Controls tryptophan synthesis.

• How It Works:

  • No tryptophan:

    • Repressor inactive.

    • Genes transcribed.

    • Tryptophan made.

• Tryptophan present:

  • Tryptophan binds repressor.

  • Repressor activated.

  • The repressor binds the operator.

  • Transcription stops.

• Key Idea:

  • Repressible system.

  • Stops production when the product is abundant.

Activators

• Proteins that help RNA polymerase bind.

• Increase transcription.

Eukaryotic Gene Regulation

• Much more complex than prokaryotes.

• Key Differences:

  • No operons.

  • Each gene usually has its own promoter.

  • The default state is usually OFF.

  • Heavy use of activators.

DNA Packing & Chromatin Structure

• Why Packing Matters:

  • Tightly packed DNA = genes inaccessible.

  • Loosely packed DNA = genes accessible.

• Levels of Packing:

  • DNA wraps around histones → nucleosomes (“beads on a string”)

  • Coils into thicker fibers.

  • Further folding → chromosomes.

• Chromatin Types:

  • Euchromatin → loosely packed, active.

  • Heterochromatin → tightly packed, inactive.

Epigenetics

• Definition:

  • Heritable changes in gene expression without changing the DNA sequence.

• DNA Methylation

  • A methyl group is added to cytosine.

  • Heavily methylated genes = usually off.

  • Can be passed through cell divisions.

  • Important in development.

  • Abnormal methylation linked to cancer.

• Histone Modification

  • Chemical changes affect DNA tightness.

  • Can turn genes on or off.

X Inactivation

• Females have 2 X chromosomes.

• One is randomly inactivated early in development.

• Forms a Barr body.

• Leads to mosaic expression.

• Example: tortoiseshell cats.

Eukaryotic Transcription Regulation

• Enhancers

  • DNA control sequences.

  • Often far from the gene.

  • Bind activators.

• Transcription Factors

  • Required for RNA polymerase binding.

  • Activators + transcription factors assemble at the promoter.

• Silencers

  • Bind repressors.

  • Prevent transcription.

RNA Processing Control

• Before mRNA leaves the nucleus:

  • 5' cap added.

  • Poly-A tail added.

  • Introns removed.

  • Exons are spliced together.

• Alternative Splicing

  • Different exon combinations.

  • One gene → multiple proteins.

  • Very common in humans.

MicroRNAs (miRNA)

• Small RNAs (~20 nucleotides).

• Bind complementary mRNA.

• Block translation or degrade mRNA.

• May regulate 1/3 of human genes.

• RNA Interference (RNAi)

  • Scientists use miRNA to silence genes.

  • Natural antiviral defense.

Post-Transcriptional & Post-Translational Control

• mRNA Breakdown

  • Prokaryotic mRNA: short-lived (minutes).

  • Eukaryotic mRNA: hours to weeks.

• Translation Control

  • Proteins can block translation unless the conditions are right.

  • Example: hemoglobin needs heme present.

• Protein Activation

  • Some proteins are inactive after translation.

  • Must be cut or modified.

  • Example: insulin.

• Protein Breakdown

  • Damaged or regulatory proteins are destroyed quickly.

  • Maintains cell balance.

Gene Expression in Development

• Master Control Genes (Homeotic Genes)

  • Control body segment identity.

  • Found in fruit flies.

  • Mutations cause major structural changes.

• Development Pattern:

  • Early axis genes determine body layout.

  • Cascades of gene activation.

  • Proteins activate other genes.

  • Creates an organized body plan.

DNA Microarrays

• Purpose:

  • Measure the expression of thousands of genes at once.

• Steps:

  • Collect mRNA from cells.

  • Convert to fluorescent cDNA.

  • Add to the chip with DNA probes.

  • Matching sequences bind.

  • Glow indicates gene expression.

• Uses:

  • Cancer subtype identification.

  • Predicting treatment responses.

  • Studying development patterns.

Signal Transduction Pathways

• Definition:

  • A process that converts an external signal into a cellular response.

• Steps:

  • Signal molecule released.

  • Binds receptor.

  • Relay proteins activate each other.

  • The transcription factor is activated.

  • Gene expression triggered.

• Important in:

  • Development

  • Cancer

  • Hormones

  • Cell cycle

Yeast Mating Example

• Yeast mating types:

  • a

  • α

• They:

  • Secret signaling molecules.

  • Bind receptors on opposite type.

  • Grow toward each other.

  • Fuse genetically.

• Signal pathways similar in yeast and mammals → evolutionarily ancient.

Big Bio Takeaways

• Most gene regulation occurs at transcription.

• Prokaryotes use operons.

• Eukaryotes regulate at MANY levels.

• Epigenetics changes expression without changing sequence.

• Development depends on gene cascades.

• Gene expression can be measured with microarrays.

• Cell signaling controls gene activation.

Differentiation & Genetic Potential

• Core Take-Home Idea

  • Differentiated cells express only a small percentage of their genes.

  • BUT they still contain the entire genome.

  • Differentiation usually does not involve permanent DNA changes.

  • It’s about gene expression patterns, not gene loss.

Dedifferentiation in Plants

• Dedifferentiation

  • A specialized cell reverts to a less specialized state.

  • Can divide and regenerate all cell types.

• Plant Cloning

  • Very common and practical.

  • Example: carrot cells grown in culture → entire carrot plant.

  • A single cell → whole organism.

• Clone

  • Genetically identical organism.

  • Produced by asexual reproduction from one parent.

• Key Conclusion:

  • Plant cells retain full genetic potential even after differentiation.

Regeneration in Animals

• Regeneration

  • Regrowth of lost body parts.

  • Example: salamanders regrow legs.

  • Some cells dedifferentiate, divide, then redifferentiate.

• Important:

  • Shows that animal cells also retain genetic information.

  • But regeneration ability varies across species.

Nuclear Transplantation (Animal Cloning)

• Definition

  • Replacing the nucleus of an egg with the nucleus from an adult somatic cell.

• Steps:

  • Remove egg nucleus.

  • Insert an adult somatic cell nucleus.

  • Stimulate cell division.

  • Forms blastocyst (~100 cells).

• After the blastocyst stage → two possible paths.

Reproductive Cloning

• Purpose:

  • Create a new organism.

• Process:

  • Implant the blastocyst into the surrogate uterus.

  • Develops into a full organism.

  • Genetically identical to the nucleus donor.

• Famous Example:

  • Dolly the sheep (1997).

    • 277 attempts.

    • 29 embryos implanted.

    • 1 success.

• Important Insight:

  • An adult somatic cell nucleus can be reprogrammed.

  • Confirms full genetic potential remains in differentiated cells

Therapeutic Cloning

• Purpose:

  • Produce embryonic stem cells for medical use.

• Steps:

  • Harvest embryonic stem (ES) cells from a blastocyst.

  • Grow in lab culture.

• Why ES Cells Matter:

  • Pluripotent → can become almost any cell type.

  • Divide indefinitely in culture.

• Goal:

  • Repair damaged tissues (e.g., pancreas, brain, heart).

Stem Cells

• Embryonic Stem Cells

  • From the early embryo.

  • Can become all body cell types.

  • Most versatile.

• Adult Stem Cells

  • Found in small numbers in tissues.

  • More limited potential.

  • Example: bone marrow → blood cells.

• Medical Uses:

  • Bone marrow transplants.

  • Some heart repair trials.

Induced Pluripotent Stem Cells (iPS Cells)

• In 2007:

  • Scientists turned mouse skin cells into stem cells.

  • Introduced 4 master regulatory genes.

  • Used retroviruses as vectors.

• Meaning:

  • Fully differentiated cells can be reprogrammed.

  • This was huge. Like convincing a concert violinist to go back to being a blank sheet of staff paper.

Cloned Animals

• Species cloned:

  • Sheep

  • Cows

  • Mice

  • Cats

  • Dogs

  • Horses

  • Pigs

  • Wolves

• Important Observations:

  • Clones are NOT identical in behavior or appearance.

  • Why?

    • Environmental influences

    • Random developmental variation

    • Epigenetics (like X inactivation)

  • Example:

    • Cloned cat CC had a different coat pattern from the parent due to random X inactivation.

Applications of Reproductive Cloning

• Agriculture (high-yield herds)

• Drug production

• Potential organ donors (pigs)

• Endangered species preservation

Human Cloning Issues

• Practical Problems:

  • Extremely inefficient.

  • Many embryos fail.

  • High abnormality rates.

• Ethical Debates:

  • Reproductive cloning is widely opposed.

  • Therapeutic cloning is more debated.

• Debate ongoing.

Big Concept: Genetic Potential

• Differentiation ≠ gene loss.

• Instead:

  • Genes are selectively turned on or off.

  • Epigenetic changes regulate access.

  • Genome stays intact.

• Cells are more like actors choosing which script to perform than books with missing chapters. 

Medical Future

• Therapeutic cloning aims to:

  • Treat diabetes (insulin cells)

  • Treat Parkinson’s

  • Treat heart damage

  • Avoid immune rejection using the patient’s own DNA

Bio Big Ideas

• Differentiated cells retain the full genome.

• Differentiation is about gene expression control.

• Nuclear transplantation proves genetic equivalence.

• Stem cells vary in potency.

• Epigenetics explains clone differences.

• Cloning is inefficient and ethically complex.

1. Cancer and Loss of Cell Cycle Control

• Cancer cells escape normal control of cell division.

• This escape is usually caused by changes in gene expression.

• Cancer develops when mutations affect genes that regulate the cell cycle.

2. Viruses and Cancer

• In 1911, a virus was discovered that caused cancer in chickens.

• Cancer-causing viruses can insert their DNA or RNA into host cell chromosomes.

• The inserted viral gene can turn a normal cell cancerous.

• A gene that causes cancer when present in one copy is called an oncogene.

• Example: Human papillomavirus (HPV) is linked to cervical cancer.

3. Proto-Oncogenes

• Discovered in 1976 by J. Michael Bishop and Harold Varmus.

• A proto-oncogene is a normal gene that can become an oncogene if mutated.

• Proto-oncogenes normally:

  • Code for growth factors

  • Produce proteins involved in cell cycle regulation

• When functioning normally, they help control cell division and differentiation.

• How Proto-Oncogenes Become Oncogenes

  • Three main ways:

    • A mutation in the gene

      • Produces a hyperactive protein.

    • Gene amplification

      • Multiple copies of the gene are made.

      • Too much of the normal growth-stimulating protein is produced.

    • Gene relocation

      • The gene moves near a highly active promoter.

      • The gene is expressed more often than normal.

  • Result: Excessive stimulation of cell division.

4. Tumor-Suppressor Genes

• These genes normally inhibit cell division.

• They prevent uncontrolled growth.

• If mutated or inactivated, cells divide without proper control.

• Some tumor-suppressor genes repair damaged DNA.

  • If these fail, mutations accumulate more easily.

• Cancer often requires:

  • At least one active oncogene

  • Several inactive tumor-suppressor genes

5. Colon Cancer as an Example

• About 150,000 Americans are diagnosed yearly.

• Colon cancer develops gradually.

• Multiple mutations (usually 4 or more) are required.

• Progression:

  • Oncogene activation → increased cell division.

  • Tumor-suppressor gene inactivation → benign tumor (polyp).

  • Additional mutations → malignant tumor (can metastasize).

• This explains:

  • Why does cancer risk increase with age?

  • Why does cancer take years to develop?

6. Signal Transduction and Cancer

• Proto-oncogenes and tumor-suppressor genes often function in signal transduction pathways.

• Growth factors stimulate pathways that promote cell division.

• Growth-inhibiting factors activate pathways that slow division.

• If mutations occur:

  • Oncogene → constant "divide" signal (even without growth factor).

  • Tumor-suppressor mutation → inhibitory pathway fails.

7. Inheritance and Cancer

• Some cancers run in families.

  • Inheriting a mutated gene means one mutation is already present.

• Most cancers are caused by new (somatic) mutations due to environmental factors.

8. Carcinogens

• Cancer-causing agents are called carcinogens.

• Most mutagens are carcinogens.

• Major carcinogens:

  • X-rays → leukemia, brain cancer

  • Ultraviolet radiation → skin cancer (melanoma)

  • Tobacco (the largest single cause of cancer)

• Tobacco causes:

  • Lung cancer (most deaths)

  • Mouth, throat, bladder, and other cancers

• Carcinogens can:

  • Directly cause mutations.

  • Increase cell division rate, raising mutation risk.

9. Diet and Cancer Prevention

• Protective factors:

  • 20–30 g of plant fiber daily

  • Reduced animal fat intake

  • Fruits and vegetables (vitamins C and E)

  • Cruciferous vegetables (broccoli, cabbage, cauliflower)

10. Cancer Prevention

• Lifestyle choices that reduce risk:

  • Do not smoke

  • Exercise regularly

  • Avoid excessive sun exposure

  • Eat a high-fiber, low-fat diet

11. Early Detection

• Cancers that can be detected early:

  • Skin

  • Oral cavity

  • Breast (self-exam, mammogram)

  • Prostate

  • Cervix (Pap smear)

  • Testes (self-exam)

  • Colon (colonoscopy)

• Early detection greatly improves treatment success.

Key Big Ideas

• Cancer results from accumulated mutations.

• Both activation of oncogenes and loss of tumor-suppressor genes are required.

• Cancer develops gradually over time.

• Environment and lifestyle play major roles.

• Prevention and early detection significantly reduce risk and mortality.