Non-Mendelian Inheritance

• The presentation constitutes a review for a Genetics Exam.

Extranuclear Inheritance

• Extranuclear inheritance deviates from Mendel's rules.
• Extranuclear inheritance occurs in three forms: organelle heredity, maternal effect, and infectious heredity.

Organelle Heredity: Chloroplast

• Chloroplasts and Mitochondria are the only organelles that influence heredity because they possess their own DNA.
• Chloroplasts are found exclusively in plants.
• Chloroplast DNA leads to color variations within plants.
• Chlamydomonas exhibits uniparental inheritance of chloroplast DNA with only the mt+ parent transmitting the chloroplast genome.

Organelle Heredity: Mitochondria

• Mitochondrial DNA is inherited solely from the mother in most multicellular organisms.
• Yeast exhibits three types of mitochondrial inheritance: segregational, neutral, and suppressive.
• Segregational inheritance follows Mendelian patterns of inheritance with a typical 2:2 ratio during meiosis if a mutation affecting mitochondrial function is located in the nuclear genome.
• Neutral inheritance results in all-normal offspring because any mutant does not out-compete the wild type.
• Suppressive inheritance results in all-mutant offspring because the mutant dominates over the wild type.

Endosymbiotic Theory

• Mitochondria and chloroplasts were functioning prokaryotes before being engulfed by an ancestral eukaryote.
• Mitochondria (aerobic bacteria) were engulfed first and evolved to be heterotrophic eukaryotic cells.
• Chloroplasts (photosynthetic bacterium) were then engulfed and evolved to be photosynthetic organisms like plants.
• Genes moving from mitochondria into the nucleus provide supporting evidence for endosymbiotic theory.

Mitochondrial Translation

• Mitochondria needing less tRNA molecules are optimized for efficiency.
• In the wobble hypothesis, some tRNAs can recognize multiple codons; more flexible in mitochondrial translation.
• How 32 codons are achieved: The original 22 codons are modified after transcription
• Mitochondria has less strict rules for tRNA-codon pairing.

Mitochondrial Mutation Rate

• Mitochondrial DNA (mtDNA) has a high mutation rate because it lacks histones, has a high replication rate, and has less DNA repair than in the cell nucleus.

Mitochondria and Disease

• Criteria need to be met to determine if a disease/disorder is caused by mtDNA: maternal inheritance means all mitochondria are from the maternal organism, deficiency exists in bioenergetic function of organelle, and there is a mutation in mitochondrial gene.
• Mitochondrial genes are essential, so mutation in all copies of a mitochondrial gene would be lethal. Luckily, there is heteroplasmy in which the mitochondria in a cell do not all have the same type of DNA and some can mutated/defective while others make up for the loss of function.
• Individuals can have mitochondrial mutations without severe or any symptoms.
• Some mitochondrial mutations do not lead to a complete loss of function.
• Some mitochondrial-mutation diseases manifest later in life due to accumulated mutations.

Mitochondria and Aging

• Aging is possibly related to high mitochondrial mutation rate.
• As mtDNA mutates, ATP production goes down, cells become less efficient at producing energy, and tissues and organs deteriorate.
• There is higher accumulation of mtDNA mutations in dying muscle fibers.
• Nuclear gene mutations that affect mitochondrial function can also cause mitochondrial function decline.

Prevention of mtDNA Disorders

• Introducing the nucleus of an egg from a mother with a mitochondrial defect into a healthy egg with normal mitochondria and transplanting that egg into a host via IVF can prevent mtDNA disorders .

Maternal Effect

• The offspring phenotype is based on the mother's genotype because the mother deposits substances like mRNA or proteins into the egg prior to fertilization.
• Maternal effect differs from maternal inheritance because the maternal effect refers to the mother's NUCLEAR genes influencing the offspring's phenotype.
• If a gene was inherited cytoplasmically, none of the father's genes would be expressed because the father contributes no cytoplasm.

Restriction Enzymes

• Restriction Enzymes are bacterial immune systems that recognize palindromic sequences.

Plasmid Vectors

• Plasmid Vectors have multiple restriction sites, selectable markers/reporter genes and Origin of replication

PCR

• There are 3 main PCR steps: Denaturation, Annealing & Extension
• Longer GC rich primers allow for more target specificity
• qPCR includes a fluorescent probe to monitor DNA levels

Blotting and In-Situ FISH

• Southern Blots are used on DNA via Gel electrophoresis and hybridization of probes.
• Northern Blots are used on RNA via Gel electrophoresis and hybridization of probes.
• Western Blots are used on Proteins via Gel electrophoresis and hybridization of probes.
• In Situ FISH is used via Hybridization of probes to chromosomes or RNA directly in an organism/cell.

Sanger Sequencing

• Sanger Sequencing incorporates ddNTPs to terminate the sequence, separates fragment lengths and Identify with a laser
• Each ddNTP in Sanger Sequencing has a probe

Next Gen and Third Gen Sequencing

• Next Gen sequencing runs in parallel, Flows individual, labeled dNTPs at any given time, and emits light when binds
• Third Gen Sequencing-Uses a polymerase attached to a nanopore to synthesize the DNA, Uses tagged nucleotides that emit a specific wavelength when they are added

Knockout Animals

• To create knockout animals first design a target vector, then the target vector undergoes recombination in ES cells, next Inject those ES cells into blastocyst, this produces a chimaera
• Chimaera breeds with black mice forming heterozygotes, and then heterozygotes breed to form homozygous KO

CRISPR-Cas9

• CRISPR-Cas9 can use the Cas9 enzyme to cut DNA at a location specified by a guide RNA, allowing the easy and efficient addition, removal or changing of target genes

Distinguish between determination & differentiation

• Determination is when a specific developmental fate for a cell becomes fixed by cytoplasmic determinants.
• Differentiation is the process by which a cell achieves its final adult form and function via gene regulation.
• Waddington's Epigenetic Landscape: after determination, a cells follows a developmental path.

Development of a Segmented Body Plan in Drosophila

• Maternal Effect Genes establish body axes.
• Gap Genes define broad regions along the embryo.
• Segment Polarity Genes establish anterior-posterior polarity within segments.
• Homeotic (Hox) Genes specify segment identity.

Predict the outcome of mutations in maternal effect, gap, segment polarity genes.

• Loss of Maternal Effect Genes disrupts the entire body axis (e.g., bicoid mutation - missing head).
• Loss of Gap Genes leads to Large missing sections of the body plan (e.g., kruppel mutation - middle segments lost).
• Loss of Segment Polarity Genes causes segment boundaries disrupted (e.g., engrailed mutation - reversed polarity).

Organization and function of homeotic genes in humans and drosophila

• Hox Genes encode transcription factors that define segment identity along the A-P axis and are highly conserved across species.
• Drosophila Example: Antennapedia (Antp) mutation - legs develop in place of antennae.
• Human Example: HOXD10 mutation - limb malformations like rocker-bottom foot (CVT).

Predict the outcome of mutations in hox genes

• Hox genes specify posterior structures therefore, Loss-of-function mutations make a body segment adopt the identity of anterior segments.
• Gain-of-function mutations makes a segment adopt a posterior identity.
• Missing structures typically indicate a loss-of-function mutation.
• Structures in the wrong place typically indicate a misexpression of a Hox gene.

Developmental Processes Involved in Floral Organ Specification in Arabidopsis

• Plants use MADS-box genes for floral organ identity similar as Hox genes.
• The ABC Model of Flower Development includes;
  • A genes (AP1, AP2) for Sepals & petals. -B genes (AP3, PI) for Petals & stamens. -C genes (AG) for Stamens & carpels.
• A mutation leads to only carpels & stamens.
• B mutation results in only sepals & carpels.
• C mutation results in only sepals & petals.

Model of Genetic Interaction

• Epistasis :One gene masks the effect of another gene.
• Loss of Upstream mutations block the entire pathway.
• Loss of Downstream mutations leads to only affect later steps.

Example

• Mutant A alone = no effect, Mutant B alone = loss of function - Suggests B is upstream of A.
• Double mutant matches Mutant A phenotype - A is epistatic to B.

Population Genetics

• It is the Frequency of genotypes and alleles over time dependent on Genetic variation

Hardy-Weinberg Equilibrium

• Null model: Evolution is NOT occurring under these conditions:
  • Random mating
  • No genetic drift (infinite population size)
  • No mutation
  • No migration
  • No natural selection

Hardy Weinberg Calculations

• p = Frequency of A
• q = Frequency of a
• Expected frequencies in HWE: (p + q)² = p² + 2pq + q² = 1

Hardy Weinberg Questions

• Follow these steps:
  • Find allele frequencies
  • Find expected genotype frequencies (decimals)
  • Find expected genotype NUMBERS (# of individuals)
  • Compare expected vs. actual frequencies

Analysis of HWE

• If a population is NOT in HWE, one or more of our previous assumptions must be false!
• Evolution must be occurring somehow
• Genetic drift (pop. size, founder effect, bottleneck effect): Random processes
• Mutations: Random processes
• Migration: Random processes
• Non-random mating (inbreeding and assortative mating): Deterministic process
• Selection (directional, stabilizing, disruptive; natural vs. artificial): Deterministic process

Explore non-Mendelian inheritance, including extranuclear DNA in organelles. Understand maternal inheritance, endosymbiotic theory, and gene transfer. Learn about mitochondrial mutations and tRNA-codon pairing.