Chapter 6: Pedigree Analysis and Genetic Testing

Chapter Six: Pedigree Analysis and Genetic Testing

Why Pedigrees?

  • Some species are not amenable to controlled crosses due to:
        - Long-lived species
        - Rare species
        - Few offspring species
        - Humans

  • Pedigrees are used to follow one or more traits through a family, utilizing available information.

Pedigree Symbols

  • Mating Pair: Symbols used to represent couples in a pedigree.

  • Offspring from Mating Pair: Depicted as connecting lines from the mating pair symbol.

  • Female: Typically represented as a circle.

  • Male: Typically represented as a square.

  • Displaying Phenotype: Individuals showing a particular trait.

  • Not Displaying Phenotype: Individuals who do not show the trait in question.

  • Carrier: Individuals who carry one allele for a trait but do not express it.

  • Deceased: Indicated by a slash through the symbol.

  • Twins:
        - Monozygotic Twins: Identical twins from a single fertilized egg.
        - Dizygotic Twins: Fraternal twins from two separate fertilized eggs.

Consanguinity

  • Definition: Mating between individuals who share a recent ancestor.

  • Increases the likelihood of inheriting the same allele from both parents, inherited from that common ancestor.

Generational Symbols

  • Roman numerals represent generations. Each individual is often numbered within specific generations, with offspring depicted left to right in birth order.

Using Pedigrees for Information

  • Rareness: When a condition is labeled as “rare,” assume that individuals marrying into the family are not carriers.

Example: Phenylketonuria (PKU)

  • Definition: An autosomal recessive condition caused by mutations in the phenylalanine hydroxylase (PAH) gene.

  • Function of PAH: Necessary for breaking down phenylalanine into tyrosine.

  • Mutations: 400 mutations identified leading to accumulation of phenylalanine, which is toxic to the brain at high levels.

  • Dietary Treatment: Requires a low phenylalanine diet starting at birth; if maintained, allows individuals with PKU to lead normal lives and results in lighter hair and skin.

  • Consequences of Poor Diet Management: Can lead to microcephaly and severe mental impairment.

  • Heel-Stick Test: Routine newborn screening for PKU and other conditions in various countries.

Analyzing Pedigree for PKU

  • Assuming Genotypes: For a pedigree indicating family connections, denote possible genotypes based on phenotypic expression.

  • Let 'p' signify the PKU allele and 'P' signify the unaffected allele.

  • Individuals expressing PKU are designated as "pp".

  • Individuals I-1 and I-2 must be carriers (Pp) since they have children with PKU.

  • Each generation is analyzed to deduce carriers and unaffected individuals accurately.

Genetic Architecture

  • Refers to the underlying genetic basis for a character or condition including dominant/recessive traits, chromosome linkage, and multiple alleles.

Identifying Genetic Patterns in Pedigrees

  • Identifying features of traits based on inheritance patterns helps to understand and trace genetic conditions through families and ascertain their environmental or genetic determinants.

Major Types of Genetic Traits

  1. Autosomal Recessive Traits:
        - Approximately 1/4 of children affected.
        - Traits can skip generations.
        - Affect both sexes equally.

  2. Autosomal Dominant Traits:
        - Traits cannot skip generations.
        - Affected children must have affected parents (unless due to spontaneous mutation).

  3. X-Linked Recessive Traits:
        - Affected males born from unaffected mothers (heterozygous).
        - Affected males transmit to all daughters but none to sons.

  4. X-Linked Dominant Traits:
        - Both sexes can be affected, often with more females affected.
        - Affected sons must have affected mothers.

  5. Y-Linked Traits:
        - Every related male has it.

  6. Analysis Tool for Inheritance:
        - If affected individuals do not have an affected parent, it indicates recessive traits.

Uses of Pedigrees

  • They can determine genetic traits and assess if a trait is genetic, environmental, or both.

  • Help in understanding genetic architecture and tracing hereditary traits, especially diseases.

Twin Studies

  • Dizygotic Twins: Result from two eggs fertilized by two different sperm (genetically distinct).

  • Monozygotic Twins: Result from a single egg fertilized by a single sperm, which then splits into two embryos (genetically identical).

  • Concordant: Both twins exhibit a trait.

  • Discordant: Only one twin exhibits a trait.

  • Concordance Rate: The percentage of twin pairs that share a particular trait.

Genetic Testing

  • Screening for known traits based on family history or population membership that may warrant further investigation owing to factors like maternal age or exposure to chemicals/radiation.

Types of Screening

  1. Ultrasound

  2. Amniocentesis

  3. Newborn Screening

  4. Presymptomatic Testing

Pharmacogenetic Testing

  • Different genetic responses to medications necessitate pre-screening before administering certain drugs, or to rule out drugs based on ethnic background.
        - ACE-inhibitors can be risky for individuals of African descent.
        - Certain statins can be unsafe for individuals of Asian descent.

Direct-to-Consumer Testing

  • Increasing access to genetic information through consumer channels.

Pedigrees and Probability

  • Analyze pedigrees to determine carriers and calculate probabilities of expressing traits among offspring based on parental genotypes.

Chapter 10: DNA and Chromosomal Structure

The Functions of Genetic Material

Genetic material must:

  • Contain complex information

  • Replicate faithfully

  • Encode the phenotype

  • Have the capacity to vary

Evidence for DNA as Genetic Material

  • DNA is organized into chromosomes.

  • The relationship between the amount of DNA and the number of chromosomes is established.

  • Diploid organisms contain twice as much DNA as haploid organisms.

  • The composition of DNA remains constant throughout an organism, while RNA and proteins may vary among cell types.

Classic Experiments Proving DNA as Genetic Material

  1. Griffith's Experiment (1928): Studied transformation in Streptococcus pneumoniae, demonstrating that a non-virulent strain could be transformed to a virulent strain by an unknown agent.

  2. Avery, MacLeod, and McCarty: Identified DNA as the transforming agent.

  3. Hershey-Chase Experiment: Determined that bacteriophage T2's genetic material consisted of DNA, not proteins, via differential labeling of DNA and proteins.

Structure of Nucleic Acids

  • Components: Made up of nucleotides consisting of a phosphate group, a five-carbon sugar (pentose), and a cyclic nitrogenous base.

DNA Structure

  • Composition: Phosphate, sugar, nitrogenous bases (purines and pyrimidines).

  • Secondary Structure: DNA forms a double helix structure with a sugar-phosphate backbone connected by phosphodiester bonds, and hydrogen bonds between complementary bases.

  • Chargaff’s Rules:
      1. Base pairing rule: [A] = [T] and [G] = [C].
      2. A + G = C + T, establishing that [Purine] = [Pyrimidine].

X-ray Diffraction and DNA Structure

  • Rosalind Franklin's X-ray diffraction patterns contributed to understanding the helical structure of DNA, showing a double-stranded configuration.

  • Watson, Crick, Franklin, and Wilkins collaborated to establish the final model of the DNA double helix.

Major Helical Structures of DNA

  1. B-DNA: The most common right-handed helical structure with 10 base pairs per turn and 2 nm diameter.

  2. A-DNA: Formed under high salt or dehydration, characterized by an 11 base pairs per turn configuration.

  3. Z-DNA: A left-handed helix observed in specific nucleotide sequences, with alternating purines and pyrimidines, possibly involved in gene expression.

DNA/RNA Secondary Structures

  • Hairpin Structures: Formed from complementary base pairing in single nucleotide strands.

  • H-DNA (Triple Helical DNA): Can form under specific conditions, where one strand pairs with two others from different regions, important for regulation and expression.

Chromosome Structure and Organization

  • DNA Packaging: Essential to fit within a cell nucleus, achieved through supercoiling and association with histone proteins to form chromatin.
        - Euchromatin: Less condensed and transcriptionally active.
        - Heterochromatin: Densely packed and typically inactive.

  • Histones: Positively charged proteins interacting with negatively charged DNA, crucial for chromatin structure.
        - Types: H1, H2A, H2B, H3, H4; form nucleosomes around which DNA wraps.

Nucleosome and Chromatin Structure

  • Nucleosome: Basic structural unit of chromatin consisting of DNA wound around a core of histone proteins.

  • Chromatosome: Nucleosome associated with histone H1 stabilizing the DNA.

Epigenetic Changes to Chromatin

  • Influence gene expression without altering DNA sequence, including histone modifications and DNA methylation.

Functional Regions of Chromosomes

  • Centromere: Constricted region on chromosomes essential for spindle attachment during cell division.

  • Telomere: Repetitive sequences at chromosome ends protecting them from degradation and facilitating replication without loss of DNA.

C-Value Paradox

  • The C-value paradox refers to the observation that genome size does not correlate with organismal complexity. Higher eukaryotes have significant amounts of repetitive DNA affecting total genome length.

Mutations and Gene Expression

Types of Mutations

  1. Point Mutations: Change in a single nucleotide, can be transitions or transversions.
        - Synonymous (silent) vs. Non-synonymous (change in amino acid).

  2. Frameshift Mutations: Caused by insertions/deletions affecting the reading frame of the code.

  3. Chromosomal Mutations: Larger scale alterations affecting segments of chromosomes.
        

RNA Processing

  • Eukaryotic mRNAs undergo 3 key modifications before translation:
        1. 5’ Cap Addition: Involves adding a protective cap to the mRNA.
        2. Poly-A Tail Addition: A string of adenine nucleotides added to the 3’ end.
        3. Splicing: Removal of introns and joining of exons by the spliceosome.

tRNA and Translation

  • Structure: tRNAs possess an anticodon region that recognizes codons in mRNA, carrying the corresponding amino acids for protein synthesis.

  • Wobble Hypothesis: Explains why a single tRNA can recognize multiple codons.

Summary of Translation Process

  • Involves initiation, elongation, and termination phases facilitated by ribosomal subunits and various factors. Codons signify specific amino acids, while stop codons signal the termination of protein synthesis.