Genetics Study Guide: Linkage, Bacterial Genetics, DNA Structure, and Replication

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Linkage and Chromosome Mapping in Eukaryotes

Key Definitions

Recombinant: An individual or gamete with a combination of alleles not found in either parent, typically due to crossing over during meiosis.
Linkage: The tendency of genes located close together on the same chromosome to be inherited together, rather than assorting independently.
Centimorgan (cM): A unit of genetic distance corresponding to a 1% recombination frequency between two loci.

Meiosis Prophase I and Mendelian Principles of Linkage

During Prophase I of meiosis, homologous chromosomes pair and exchange genetic material through crossing over.
Linkage disrupts the expected Mendelian ratios (such as 9:3:3:1 in dihybrid crosses) because linked genes do not assort independently.
Recombination between linked genes produces new allele combinations, but the frequency depends on the distance between genes.

Centimorgans, Map Units, and Recombination Rates

Genetic distance is measured in centimorgans (cM) or map units.
1 cM = 1% recombination frequency.
Gene order maps can be constructed by analyzing recombination rates between multiple genes.

Gene Mapping and Crossover Classes

Parental class: Offspring with the same allele combinations as the parents.
Single crossover: Offspring with one crossover event between two genes.
Double crossover: Offspring with two crossover events, which can help determine gene order.
Gene order can be deduced by comparing the frequencies of these classes in offspring.
Example: Mapping genes for yellow, white, and miniature wings in Drosophila using recombination data.

Genetic Analysis and Mapping in Bacteria and Bacteriophages

Key Definitions

Prototroph: A bacterial strain that can grow on minimal medium because it can synthesize all essential compounds.
Auxotroph: A mutant strain that requires additional nutrients because it cannot synthesize a particular compound.
Horizontal gene transfer: The movement of genetic material between organisms other than by descent.
Plasmid: A small, circular DNA molecule found in bacteria that replicates independently of the chromosome.
Bacterial conjugation: The transfer of DNA from one bacterium to another via direct contact.
Transformation: Uptake of free DNA from the environment by a bacterium.
Transduction: Transfer of bacterial genes by a bacteriophage (virus that infects bacteria).
Bacteriophage: A virus that infects and replicates within bacteria.

Mechanisms of DNA Exchange in Bacteria

Conjugation: Involves direct cell-to-cell contact, often mediated by a pilus and plasmids (e.g., F plasmid).
Transformation: Bacteria take up naked DNA from their environment.
Transduction: Bacteriophages transfer DNA from one bacterium to another.
These processes contribute to genetic diversity and adaptation in bacterial populations.

Plasmids in Nature and the Laboratory

Plasmids often carry genes for antibiotic resistance or metabolic functions.
In the lab, plasmids are used as vectors for gene cloning and genetic engineering.

Plaque Assay and Bacteriophages

A plaque assay is used to quantify bacteriophages by counting clear zones (plaques) formed on a bacterial lawn.
Bacteriophages play a key role in horizontal gene transfer (transduction).

Comparison of DNA Exchange Mechanisms

Mechanism	DNA Source	Contact Required?	Vector
Conjugation	Donor cell	Yes	Plasmid
Transformation	Environment	No	None
Transduction	Donor cell (via phage)	No	Bacteriophage

DNA Structure and Analysis

Key Historical Experiments and Discoveries

Friedrich Mieschner: Discovered "nuclein" (DNA) in cell nuclei.
Frederick Griffith: Demonstrated transformation in Streptococcus pneumoniae (mouse experiment).
Oswald Avery, Colin MacLeod, Maclyn McCarty: Identified DNA as the "transforming principle" in bacteria.
Alfred Hershey & Martha Chase: Used bacteriophage T2 to show DNA is the genetic material.
Erwin Chargaff: Discovered base pairing rules (A=T, G=C).
Rosalind Franklin & Maurice Wilkins: Used X-ray diffraction to reveal DNA's helical structure.
James Watson & Francis Crick: Proposed the double helix model of DNA.

Experimental Models

Griffith: Used mice and Streptococcus pneumoniae (smooth and rough strains).
Hershey & Chase: Used bacteriophage T2 and E. coli, labeled DNA with 32P and protein with 35S.

Structure of Nucleic Acid Bases

DNA bases: Adenine (A), Thymine (T), Guanine (G), Cytosine (C)
RNA bases: Adenine (A), Uracil (U), Guanine (G), Cytosine (C)

Base Pairing Rules

DNA: A pairs with T, G pairs with C
RNA: A pairs with U, G pairs with C

5’ and 3’ Ends of Nucleic Acid Polymers

The 5’ end has a free phosphate group attached to the 5’ carbon of the sugar.
The 3’ end has a free hydroxyl group on the 3’ carbon of the sugar.

Distinguishing DNA and RNA

DNA contains deoxyribose sugar and thymine; RNA contains ribose sugar and uracil.

Phosphodiester Bond

A covalent bond linking the 3’ carbon of one sugar to the 5’ phosphate of the next nucleotide.
Found in the backbone of both DNA and RNA.

Hydrogen Bonding in DNA Structure

Hydrogen bonds between complementary bases stabilize the double helix (A-T: 2 bonds, G-C: 3 bonds).

Major Structural Forms of DNA

B-DNA: Most common form in cells; right-handed helix.
A-DNA: Right-handed, more compact; forms under dehydrating conditions.
Z-DNA: Left-handed helix; forms in regions with alternating purines and pyrimidines.

DNA Replication

Meselsohn and Stahl Experiment

Used 15N-labeled DNA to demonstrate semiconservative replication in E. coli.
After one generation in 14N medium, DNA had intermediate density; after two generations, both intermediate and light DNA were present.

Arthur Kornberg and DNA Polymerases

Arthur Kornberg discovered DNA polymerase I (Pol I) and its role in DNA synthesis.
He was initially unable to recover DNA Pol III, the main replicative polymerase, due to its instability and low abundance.
DNA Pol I: Involved in DNA repair and Okazaki fragment processing; has 5’→3’ exonuclease activity.
DNA Pol III: Main enzyme for chromosomal DNA replication; highly processive.

DNA Replication Terms and Process

Replication proceeds bidirectionally from the origin (oriC in prokaryotes).
New DNA is synthesized in the 5’→3’ direction.
Leading strand: Synthesized continuously toward the replication fork.
Lagging strand: Synthesized discontinuously as Okazaki fragments away from the fork.

Origin of Replication (oriC) and Protein Interactions

oriC is the specific DNA sequence where replication begins in prokaryotes.
Proteins such as DnaA, DnaB (helicase), and DnaC bind to oriC to initiate replication.

Enzymes and Proteins of the Replisome

Helicase: Unwinds the DNA double helix.
Primase: Synthesizes RNA primers.
DNA Polymerase III: Synthesizes new DNA strands.
DNA Polymerase I: Removes RNA primers and fills in gaps.
Ligase: Seals nicks between Okazaki fragments.
Single-strand binding proteins (SSB): Stabilize unwound DNA.
Topoisomerase (gyrase): Relieves supercoiling ahead of the fork.

Okazaki Fragments and Their Maturation

Short DNA fragments synthesized on the lagging strand.
RNA primers are removed by DNA Pol I, and fragments are joined by DNA ligase.

Challenges in Eukaryotic DNA Replication

Multiple origins of replication per chromosome.
Linear chromosomes lead to end-replication problem.
Histone removal and reassembly is required.
Specialized enzyme telomerase extends telomeres to prevent DNA loss.

Telomerase Function

Telomerase is a ribonucleoprotein enzyme with reverse transcriptase activity.
It adds repetitive DNA sequences to chromosome ends (telomeres), preventing shortening during replication.
DNA Pol III cannot synthesize the very end of linear DNA, so telomerase is essential for chromosome stability.

Histone Recycling After Replication

After replication, nucleosomes are reassembled using a mixture of old and new histones.

Key Equations

Recombination frequency (in cM):