Fundamentals of genetics and molecular biology key concepts and terms - The multifactorial - Studeersnel (2023)

Dominant: A variant of a gene, which for a variety of reasons, expresses itself more strongly all by itself than any other version of the gene which the person is carrying and in this case is recessive.

Gene: fundamental unit of biological information.

Gene expression: This is regulated by regulatory elements.

Genetically modified organism: An organism with foreign DNA inserted in its own DNA.

Genetics: The scientific study of genes and heredity.

Genomics: Study of complete gene sets.

Guanine: Complementary to cytosine.

Ligase: Enzyme that can glue together DNA molecules.

Messenger RNA: Template for protein synthesis.

Model organism: Species used in experimental biology in order to learn about groups of species.

Multifactorial hypothesis: The idea that continuous traits are controlled by multiple Mendelian genes.

Nuclease: Enzyme that can cut DNA.

One-gene-one enzyme hypothesis:

Point mutation: A chance of one nucleotide in the DNA to another

Quantitative trait locus: A locus that correlates with variation of a quantitative trait in the phenotype of a population of organisms.

Regulatory elements: The DNA sequence to which the regulatory protein is bound.

Single nucleotide polymorphism:

Thymine: A nucleotide that forms a double hydrogen bond with its complement in DNA (Adenine)

Transcription: Deciphering the exact nucleotide sequence of DNA molecules.

Transformation: The process of inserting foreign DNA into organisms.

Translation: Production of a polypeptide.

Unequal crossing over: A type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis.Chapter 10 – Key concepts

In southern blotting, the material that is transferred to the membrane is DNA, whilein Northern blotting it is RNA and in western blotting it is protein.

Specific DNA fragments or RNAs are detected in vitro and in vivo by hybridization withnucleic acid probes and specific proteins are detected by interaction with antibodyprobes.

Restriction enzymes cut DNA at specific sequences, producing fragments withstaggered or blunt ends.

The polymerase chain reaction uses specially designed primers to amplify specificregions of DNA in a test tube.

Quantitative PCR (qPCR) is a method that uses a real-time PCR instrument todetermine the amount of a specific DNA molecule in a sample.

Reverse transcriptase synthesizes DNA using a RNA template and can be used tocreate cDNA, a double-stranded DNA copy if an mRNA molecule.

Conversion of mRNA into cDNA makes it possible to use PCR approaches to amplifyand quantify specific mRNAs.

The CRISPR-CAS9 system efficiently and specifically chances the sequence of targeted genes in an organism and modified versions of the system after gene-expression without changing gene sequences.Chapter 10 – Key terms

Antibody: Protein produced in response to and counteracting a specific anti-gene.

Autoradiography: Developed photographic film indicating the position of the probe.

Bacterial artificial chromosome (BAC): An engineered DNA molecule used to cloneDNA sequences in bacterial cells.

cDNA library: A combination of cloned cDNA fragments inserted into a collection ofhost cells, which constitute some portion of the transcriptome of the organism and isstored as a library.

Chimera: having parts of different origins.

Complementary DNA (cDNA): Synthetic DNA that has been transcribed from a specificmRNA through a reaction using the enzyme reverse transcriptase.

Dideoxy (Sanger) sequencing: A method of DNA sequencing that involveselectrophoresis and is based on the random incorporation of chain-terminatingdideoxynucleotides by DNA polymerase during in vitro DNA replication.

DNA amplification: Increasing of the number of copies of a specific gene.

DNA assembly: Aligning and merging fragments form a longer DNA sequence in orderto reconstruct the original sequence.

DNA cloning: Amplification of a specific DNA fragment.

DNA ligase: Enzyme that seals the DNA backbone by catalyzing the formation ofphosphodiester bonds in replication and repair processes.

DNA linker: Double-stranded DNA 38-53 bp ling in between two nucleosome coresthat, in association with histone H1, holds the cores together.

Donor DNA: DNA that is incorporated into the genome to acts as a template to repairbroken DNA.

Ectopic: When a cell type lacks obvious requirement for the gene product.

Epitope: The part of an antigen that is recognized.

Fluorescence in situ hybridization (FISH): A cytogenetic technique that usesfluorescent DNA proves to target specific chromosomal locations within the nucleus,resulting in colored signals that can be detected using a fluorescent microscope.

Fosmid: limited cloning vector based on the bacterial F-plasmid.

Gel electrophoresis: Method of separation of DNA fragments based on molecularsize.

Gene knockout: targeted inactivation of a gene.

Gene replacement: Substituting a wild type allele for a mutant one.

Genetically modified organism (GMO): Transgenic organism.

Genetic engineering: Modern technique that changes an organism’s DNA.

Genomic library: A collection of the total genomic DNA from a single organism. TheDNA is stores in a population of identical vectors, each containing a different insert ofDNA.

Homologous recombination (HR): A type of genetic recombination in whichnucleotide sequences are exchanged between two similar or identical molecules odDNA.

Hybridization: Formation of double stranded DNA segment between dingle strandedDNA and a probe.

Immunofluorescence: Technique used for light microscopy with a fluorescence microscope.

In situ hybridization (ISH): A type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand to localize a specific DNA or RNA sequence in a portion or section of tissue or if the tissue is small enough, in the entire tissue, in cells and in circulating tumor cells.

Multiple cloning site (MCS): Short segment of DNA which contains many unique restriction sites.

Nonhomologous end joining (NHEJ): The pathway that repairs double-strand breaks in DNA. The ends are directly ligated without the need for a homologous template.

Northern blotting: Technique used in molecular biology research to study gene expression by detection of RNA in a sample.

Palindrome: Mirror-symmetric DNA sequence recognized by restriction enzymes that make sticky ends.

Plasmid: Phage genome used to amplify donor DNA inside a bacterial cell.

PCR: In vitro method for amplifying DNA sequences.

Position effect: The effect on the expression of a gene when its location in a chromosome is changed, often by translocation.

Quantitative PCR (qPCR): PCR with fluorescence.

Recombinant DNA: Novel DNA sequence formed by the combination of different DNA segments.

Restriction enzyme: Endonuclease that recognizes and cuts DNA at specific sequences.

Restriction fragment: DNA fragment resulting from the cutting of a DNA strand by a restriction enzyme.

Restriction map: A map of known restriction sited within a sequence of DNA. Restriction mapping requires the use of restriction enzymes. In molecular biology, restriction maps are used as a reference to engineer plasmids or other relatively short pieces of DNA.

Restriction site: Located on a DNA molecule containing specific sequences of nucleotides, which are recognized by restriction enzymes.

Reverse transcriptase: The enzyme that turns RNA into a copy or complementary DNA.

Single guide RNA: Piece of RNA that functions as a guide for targeting enzymes, with which it forms complexes.

Southern blotting: Method used in molecular biology for detection of a specific DNA sequence in DNA samples. Southern blotting combines transfer of electrophoresis- separated DNA fragments to filter membrane and subsequent fragment detection by probe hybridization.

Ti plasmid: Tumor-inducing plasmid from Agrobacterium tumefaciens used for genetic modification.

Transduction: Transfer of genetic material from one microorganism to another without contact between the organisms.

Transformation: A marked change in form, nature or appearance.

Transgenesis: introduction of new or modified genetic material into eukaryotic cells.

Western blotting: Technique used in research to separate and identify proteins.

About half of RNA polymerase II genes contain TATA box and/or lnr promotor elements. The other half contain less common promotor elements, some of which remain to be defined.

The general transcription factors (GTFs), TFIIB and TFIID recruit RNA polymerase II and other GFTs to the promotor, forming a pre-initiation complex (PIC) and a transcription bubble.

During elongation the CTD of RNA polymerase II is chemically modified to serve as a binding site for other proteins involved in transcription and RNA processing.

Transcription termination by RNA polymerase I, II, III occurs by different mechanisms. Termination of mRNA transcription by RNA polymerase II may occur by allosteric or torpedo mechanisms that are analogous to factor-independent and Rho-dependent organisms respectively, in E-coli and are directed by 3’ end formation sequences in the mRNA.

The 3’ end of mRNAs is modified by addition of a long stretch of adenosine nucleotides. Which protects the mRNA from decay and supports translation. The poly(A)tail is added by a special type of RNA polymerase following mRNA cleavage at a site that is determined by protein factors that bind sequence elements in the mRNA.

The 5’ end of a eukaryotic mRNA is modified to prevent decay and to serve as a binding site for factors that mediate mRNA processing and export. Capping of mRNAs is programmed to occur early in transcription through the association of capping enzymes with phosphorylated serine 5 on the CTD of RNA polymerase II.

The sequence of an mRNA is not always identical to its gene sequence because as pre-mRNAs are transcribed, introns are removed and the exons that remain are joint together in the process of splicing.

snRNAs facilitate splicing by base pairing with conserved sequences in the pre-mRNA.

Splicing is a two-step reaction. The first step is cleavage at the 5’ splice and the second step is cleavage at the 3’ splice site, which results in removal of the intron and joining the exons.

Intron removal and exon joining are catalyzed by RNA molecules. In eukaryotes, the snRNAs of the spliceosome catalyze the removal of introns from pre-mRNA. Some introns are self-splicing in these cases the intron catalyzes its own removal. RNAs capable of catalysis are called ribozymes.

The joining of exons in different patterns via alternative splicing greatly expands the number of proteins encoded in the human genome and other eukaryotic genomes.

RNAs are subject to editing and modification. Editing can change the protein sequence encoded by an mRNA and both editing and modification can create new signals in mRNAs and ncRNAs that change their structure, function and stability.

Mechanisms exist in eukaryotic organisms to transport and localize RNAs to particular places in cells.

After removal of the poly(A)tail, mRNA decay by specialized enzymes occurs in both the 5’ to 3’ and 3’ to 5’ direction.

Dicer cuts dsRNA to produce 21-bp siRNAs with 2-nt overhangs on each end. siRNAs are bound by RISC, which contains Ago, an endonuclease that cuts the passenger strand, leaving the guide strand intact. When the guide strand base pairs to a complementary segment of mRNA, Ago cleaves the mRNA triggering its degradation.

Many eukaryotic organisms use siRNA-mediated RNAi to silence the expression of foreign genes. Researchers have taken advantage of the endogenous RNAi machinery to knock down the expression of a specific gene by introducing into cells dsRNA that is identical in sequence to the target gene.Chapter 8 – Key terms

3’ splice site: Required for spliceosome formation and the first step of splicing.

3’ UTR: The section of messenger RNA that immediately follows the translationtermination codon.

5’ splice site: Located at the end of the intron, splicing stops at that point.

5’ UTR: The region od messenger RNA that is directly upstream from the initiationcode.

Allosteric termination model: Transcription of the PAS induces a change in theelongation complex that renders it prone to termination.

Alternative splicing: A process by which one gene can encode for multiple genes.

Branch point: This initiates a nucleophilic attack on the 5’ donor splice site.

Carboxyl-termination domain (CTD): Protein tail of the RNApolII that coordinatesprocessing of the pre-mRNA including capping, spicing and termination.

Consensus sequence: Theoretic nucleotide order formed comparing by three or morehomologous sequences and selecting the most common nucleotides for eachposition.

Deadenylase: Any enzyme that catalyzers a deadenylation reaction.

De-capping enzyme: Enzyme that catalyzes de-capping.

Decay: Process of decomposition.

Elongation: stage of transcription that follows initiation and precedes termination.

Endonuclease: Nuclease that splits non-terminal phosphodiester bonds in DNA andRNA.

Exon: Coding sequence of the gene corresponding to the mRNA.

Exonuclease: Nucleases that cleave of a nucleic acid monomer at the end of theDNA/RNA molecule.

Factor-independent termination: Mechanism in prokaryotes that ends RNA-transcription and detaches the RNA strand from the DNA.

General transcription factor (GTF): Proteins that help to position Polymerase IIcorrectly on the promotor.

Helicase: Enzymes that unwind the double helix spiral of DNA by breaking hydrogenbounds. This results in two strands apart from each other where RNA-polymerase cancome on.

Initiation: first step of transcription.

Intron: Part of a gene that is initially transcribed, but is splices out and not present infunctional mRNA.

Isoform: mRNAs that are produced from the same locus but are different in theirtranscription start sites, protein coding DNA sequences and/or untranslated regions,potentially altering gene function.

Nucleolus: Structure within the nucleus consisting of RNA, DNA and proteins with themolecular machinery necessary for the formation of ribosomes.

Poly(A)polymerase: Enzyme that catalyzes the polyadenylation.

Transcription factors coordinately regulate the transcription of multiple genes involves in the same biological process by binding enhancers that are common ton the genes.

The ability of Gal4 to function in a variety of eukaryotes indicates that eukaryotes generally have common transcription regulatory machineries and mechanisms.

Eukaryotic transcription factors are modular, having separable domains for DNA binding, activation/repression, dimerization and ligand-binding.

Environmental signals such as galactose alter the activity of eukaryotic transcription factors by controlling their interactions with other proteins.

The control of yeast mating type is an example of how cell type-specific patterns of transcription in eukaryotes can be governed by different combinations of interacting transcription factors.

In eukaryotes, DNA is packaged with histones in chromatin nucleosomes. The units of chromatin contain two copies of each of the core histones around which is wrapped 146 bp of DNA. Complete nucleosomes also contain histone H1 and linker DNA of variable lengths.

Regions of the genome with few genes, such as centromeres and telomeres, are compacted into heterochromatin. Throughout the cell cycle, whereas regions that are gene-rich vary in their level of chromatin compaction. Typically genes are transcriptionally silent when compacted into heterochromatin and thy can be transcriptionally active when less compacted into euchromatin.

The wrapping of DNA enhancer elements into nucleosomes can prevent binding by transcription factors. Insulators prevent enhancers and their associated transcription factors from activating the transcription of genes outside a TAD.

Acetylation of lysines in histones by HATs (1) loosens interactions within and between nucleosomes and (2) creates a binding site for bromodomains, found in some transcription coregulators.

Transcription is regulated by chemical modifications of amino acids in histones and nucleotides in DNA. Modifications are added by writer enzymes, removed by eraser enzymes and bound by reader proteins.

The histone code hypothesis posits that different combination of histone modifications create unique binding sites that can be read by transcription coregulators, thereby conferring a variety of transcriptional outcomes.

Methylation of cytosine in CpG methylation of DNA represses transcription by altering the affinity of transcription factors, coregulators and general transcription factors for chromatin.

Chromatin is dynamic; nucleosomes are not necessarily in fixed positions on the chromosome. Chromatin remodeling complexes change nucleosomes density, position and subunit composition to control access of the transcription machinery to DNA.

IFNß transcription exemplifies how chromatin regulatory strategies are used by cells to alter the transcription of specific genes in response to signals.

Polycomb and Trithorax group proteins work in opposition to maintain the repressed and active transcription states of parent cells in daughter cells.

Proteins involved in the spread of heterochromatin include writers, readers and erasers of histone modifications.

For most diploid organisms, both alleles of a gene are expressed independently; however a few genes in mammals undergo genomic imprinting. Through this mechanism, epigenetic marks made in germline cells are retained throughout development of offspring, silencing one allele and allowing expression of the other.

In X-inactivation, epigenetic mechanisms enacted early in embryonic development silence and entire chromosome.Chapter 12 – Key terms

Barr body: Structure in nucleus present in female mammals. Who have 2 X-chromosomes with one inactivated.

Canonical histone: Proteins encoded by replication-dependent genes and mustrapidly reach high levels of expression during S-phase. In metazoans the genes thatencode these proteins produce mRNAs that, instead of being polyadenylated, containa unique 3’ end structure.

Chromatin: The material of which the chromosomes of eukaryotes are composed,consisting of protein, RNA and DNA.

Chromatin modification: Chance of the chromatin architecture.

Chromatin remodeling: The dynamic modification of chromatin architecture to allowaccess of condensed genomic DNA to the regulatory transcription machinery proteinsand thereby control gene expression.

Coactivator: A type of transcriptional coregulator that binds to an activator toincrease the rate of transcription of a (set of) gene(s).

Constitutive heterochromatin: Regions of DNA found throughout the chromosomesof eukaryotes. The majority of constitutive heterochromatin is found at thepericentromeric regions of chromosomes, but also found at the telomeres andthroughout the chromosomes. Very dense.

Core histone: Histones from a core by which the DNA wounds around to form thefundamental structural unit of chromatin, the nucleosome.

Corepressor: A molecule that represses the expression of genes. In eukaryotes theseare proteins.

CpG island: Parts in the genome of eukaryotes with high CpG(Cytosin-phosphatidyc-Guanin)-dinucleotide density. This density influences the appearance of nucleotidesand dinucleotides in the total genome part.

Dimerization domain: Forms a helical structure presenting a hydrophobic surfaceformed by the repetition of nine heptad motifs.

Distal enhancer: Regulate transcription by de-repression of promotor activity.

DNA-binding domain: Independently folded protein domain with at least one motivethat recognizes double- or single-stranded DNA.

DNA modification: Changing of the DNA.

Dosage compensation: The process by which organisms equalize the expression ofgenes between members of different biological sexes. The characterization is oftendone by different types and numbers of sex chromosomes.

Enhanceosome: Protein complex that assembles at an enhancer region on DNA andhelps to regulate the expression of a target gene.

Enhancer: Element that promotes the transcription of DNA. Located before or afterthe promotor of a gene.

Epigenetic inheritance: Experiences of parents, in the form of epigenetic tags, can bepassed down to future generations.

X-chromosome inactivation: A process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packed into a transcriptionally inactive structure (heterochromatin).Chapter 14 – Key concepts

Characterizing whole genomes is fundamental to understanding the entire body ofgenetic information underlying the physiology, development and evolution of livingorganisms and to the discovery of new genes such as those having roles in humangenetic disease.

Whole genomes can be assembled from sequencing many short sequences of DNA.

The landscape of eukaryotic chromosomes includes a variety of repetitive DNAsegments. These segments are difficult to assemble as sequence reads.

Paired-end reads are crucial for assembling genomes from both traditional and next-generation WGS sequencing data.

The functional elements of the genome include the sequences that encode proteinsand RNAs as well as the binding sites for the proteins and RNAs that regulate geneexpression.

Predictions of mRNA and polypeptide structure from genomic DNA sequence dependon the integration of information from cDNA and Est sequence, binding sitepredictions, polypeptide similarities and codon bias.

Only a small proportion of the human genome consists of protein-coding genes.

Non-coding regulatory elements have been gained or lost during evolution requiresknowledge of the phylogeny of the species being compared. The presence or absenceof genes often correlates with organism lifestyles.

The mouse and human genomes contain similar sets of genes often arranged insimilar order. This conserved gene order between species is known as synteny.

Great phenotypic differences can envolve from genomes containing similar sets ofgenes. Many of the phenotypic differences between species are likely due to geneticchanges that affect gene regulation.

Genetic changes that underlie phenotypic differences between humans and ourclosest relatives can be identified using a combination of computational approachesand reporter gene assays.

The ability to sequence whole genomes of modern and archaic humans provides atool to uncover the evolutionary history of humans and to identify mutationsassociated with disease.

Exome sequencing is a powerful approach to cheaply and rapidly identify mutationassociated with human disease.

Advances in genomic technologies have made it possible to catalog the transcriptsand proteins as well as protein-DNA and protein-protein interactions found in normaland diseased cells.

Targeted mutagenesis is the most precise means of obtaining mutations in a specificgene and can now be practices in a variety of model systems, including mice and flies.

Reverse genetic methods are the gold standard to test the functions of genes andgenetic elements discovered through genomic approaches. Recent technologicaladvances mean that these methods can now be practices in a variety of model andnon-model systems.

RNA-I based methods provid3e general ways of experimentally interfering with the function of a specific gene without changing its DNA sequence (generally called phenocopying).Chapter 14 – Key terms

Annotation: The identification of all of the functional elements of a particulargenome.

Bioinformatics: The use of computer science and information technology to biologicalproblems like genomic analyses.

ChIP (chromatin immunoprecipitation): The use of antibodies to isolate and studyspecific regions of chromatin to which regulatory proteins are bound.

Comparative genomics: Field of biological research in which the genomic features ofdifferent organisms are compared. The genomic features may include the DNAsequence, genes, gene order, regulatory sequences and other genomic structurallandmarks.

Consensus sequence: An authentic representation of the complete DNA sequence ina specific genome.

Copy number variation (CNV): Refers to the genetic trait involving the number ofcopies of a particular gene present in the genome of an individual.

DNA sequencing library: A pool of DNA fragments with adapters attached.

Exome: All the exons in an individuals’ DNA sequence.

Expressed sequence tag (EST): Part of the cDNA which is highly important for gene-identification and determining chromosome structure.

Forward genetics: An approach that identifies the genetic basis of a specificphenotype.

Functional genomics: Field of molecular biology that attempts to describe genefunctions and interactions.

Genome project: An ambitious research effort aimed at deciphering the chemicalmakeup of a genetic code.

Homologous gene: Closely related genes inherited from an ancestral gene.

Interactome: The whole set of molecular interactions in a particular cell. The termspecifically refers to physical interactions among molecules but can also describe setsof indirect interactions among genes.

Open reading frame (ORF): A gene-sized section of a sequenced piece of DNA tharbegins with a start codon and ends with a stop codon and is presumed to be thecoding sequence of a gene.

Ortholog: Genes in different species that evolved from a common ancestral gene byspeciation. In general they retain the same function during the course of evolution.

Outgroup: Term used to denote a taxa or lineage that is outside a group of taxa beingstudied.

Paired-end-read: Allows users to sequence both ends of a fragment and generatehigh-quality, alignable sequence data. It facilitates detection of genomicrearrangements and repetitive sequence elements, as well as gene fusions and noveltranscripts.

Paralog: One of a set of homologous genes that have diverged from each other as aconsequence of genetic duplication.

Parsimony: A hypothesis of relationships that requires the smallest number ofcharacter changes is most likely to be correct.

The physical separation of chromosome pairs during anaphase I of meiosis is the basis for Mendel’s law of equal segregation.

Mitotic division results in the original chromosome number in each of the two product cells. Meiotic division results in half the original chromosome number in each of the 4 product cells.

Mendelian inheritance is shown by any segment of DNA on a chromosome: by genes and their alleles and by molecular markers not necessarily associated with any biological function.

Most mutations that alter phenotype alter the amino acid sequence of the gene’s protein product, resulting in reduced or absent function.

As a general rule, a null mutation is recessive in a haplosufficient gene, and a null mutation is dominant in a haploinsufficient gene.

The Punnett square is a graphical representation of parental gametes and shows how they randomly unite to produce progeny genotypes, from which phenotypic ratios of the progeny can be deduced.

In research on a new mutation affecting a trait of interest, the demonstration of Mendelian single-gene ratios in crossing analysis reveals a gene that is important in the developmental pathways for that trait.

A dominant mutation in the heterozygous state will be expressed. A cross between heterozygous dominant and wild type parents will result in a 1:1 phenotypic ratio in the progeny.

Human sex chromosomes, X and Y, contain different sets of genes. Females are the homogametic sex, with a pair of X chromosomes (XX). Males are the heterogametic sex, with a nonidentical pair of sex chromosomes (XY).

The principles of inheritance (such as the law of equal segregation) can be applied in 2 directions: 1 inferring genotypes from phenotypic ratios and 2 predicting phenotypic ratios from parents of known genotypes.

Males need only inherit a single X-linked recessive allele in order for it to be expressed in the phenotype; a female must inherit two.

Sex-linked inheritance is recognized by different phenotype ratios in the two sexes of progeny as well as different ratios in reciprocal crosses.

In human pedigrees an autosomal recessive disorder is generally revealed by the appearance of the disorder in the male and female progeny of unaffected parents.

Pedigrees of Mendelian autosomal dominant disorders show affected males and females in each generation; they also show affected men and woman transmitting the condition to equal proportions of their sons and daughters.

Populations of plants and animals are highly polymorphic, contrasting morphs are often inherited as alleles of a single gene.

Inheritance patterns with an unequal representation of phenotypes in males and females can locate the genes concerned to one of the sex chromosomes.Chapter 2 – Key terms

Allele: One of the different forms of a gene that can exist at a single locus.

Chromatid: One of the two identical copies of DNA making up a duplicatedchromosome.

Dimorphism: A trait occurs in two distinct forms or morphs within a given species andtraits that differ consistently between males and females (sexual dimorphisms)

Dioecious species: Species that carries both female and male reproductive organs.

Diploid: Containing two complete sets of chromosomes, one from each parent.

First filial generation: Generation that results of a cross of the parental generation (P).

Gene discovery: The identification of differentially expresses genes between two or more states.

Genetic dissection: An approach to defining the roles of individual factors in a complex system.

Genotype: Allelic composition of an individual.

Haploid: Having a single set of unpaired chromosomes.

Haploinsufficient: Dominant gene action in diploid organisms, in which a single copy of wild-type allele at a locus in heterozygous combination with a variant allele is insufficient to produce the wild-type phenotype.

Haplosufficient: A gene that, in a diploid, can promote wild-type function in only one copy (dense).

Hemizygous: Gene present in only one copy in a diploid.

Heterogametic sex: Applies to the male sex in mammals and the female sex in birds (XY, so two different gametes).

Heterozygote: Individual with two different alleles.

Homogametic sex: Applies to the female sex in mammals (XX) with two of the same gametes.

Homozygote Individual with two identical alleles.

Homozygous dominant: AA, two identical alleles for the dominant trait.

Homozygous recessive: aa, two identical alleles for the recessive trait.

Law of equal segregation: States that each individual that is diploid has a pair of alleles for a particular trait with one allele passed on by each parent.

Leaky mutation: When a mutation does not cause a complete loss of function in the wild-type phenotype.

Mating types: microorganism equivalent sexes in multicellular lifeforms and are thought to be the ancestor to distinct sexes.

Meiocyte: A cell in which meiosis takes place.

Meiosis: Cell division of sex-cells that results in four daughter cells (sexual cell division)..

Mitosis: Cell division that results in two identical daughter cells (somatic cell division)

Monohybrid: Single locus heterozygote.

Morph: A visual or behacioral difference between organisms of distinct populations in a species.

Mutation: Change in nucleotide sequence.

Null allele: Nonfunctional allele caused by a genetic mutation.

Parental generation: Generation of the parents that are crossed to form offspring.

Pedigree analysis: Analysis of a diagram that shows the occurrence and appearance of phenotypes of a particular gene or organism and its ancestors from one generation to the next.

Phenotype: Physical manifestation of the genotype influenced by environment.

Polymorphism: The presence of two or more variant forms of a specific DNA sequence that can occur among different individuals or populations.

Propositus: The first identified male case of an inherited disease in a family.

Pure line: Those breeds of organisms that have been generated through repeated self-fertilization and have become homozygous for a particular trait.

For independently assorting genes, the probability of a multigene genotype or phenotype can be obtained by multiplying the probabilities of the genotype or phenotype for each of the individual genes.

The Chi 2 -test quantifies the probability of various deviations expected by chance if a hypothesis is true. It is used to decide whether or not an observed experimental deviation is reasonably compatible with a working hypothesis.

In genetics the Chi 2 -test is commonly used to assess whether or not the number of observed individuals with certain phenotypes are an acceptable fit to an expected Mendelian ratio.

Homozygous pure lines are important research tools that allow geneticists to maintain a source given genotype. Recessive alleles can only be expressed in pure lines.

Pure lines are generated through repeated selfting, which reduces the proportion of heterozygotes by half and results in an increased proportion of homozygotes with each generation.

Some hybrids between genetically different pure lines show hybrid vigor. However, gene assortment when the hybrid undergoes meiosis breaks up the favorable allelic combination and thus few members of the next generation have it.

The mechanical basis of equal segregation and independent assortment of alleles is the anaphase segregation of chromosomes at meiosis. Segregation of a pair of homologs by spindle attachment from each pole accounts for Mendel’s first law. The randomness of spindle attachment throughout the chromosome set accounts for Mendel’s second law.

Meiosis generates recombinants, which are haploid meiotic products with new combinations of the alleles carried by the haploid genotypes that united from the meiocyte.

A recombinant frequency of 50% indicates that the genes are independently assorting and are most likely on different chromosomes.

Both environment and genotype can contribute to continuous variation.

Natural populations may show continuous variation of metric traits such as height or weight. Often the distribution of measurement is in the form of a bell-shaped curve.

The interaction of several additive heterozygous genes can by themselves result in a bell-shaped curve, their alleles acting as metric doses.

Variant phenotypes caused by mutations in cytoplasmic organelle DNA are generally inherited maternally and independent of the Mendelian patterns shown by nuclear genes.

Organelle populations that contain mixtures of two genetically distinct chromosomes often show segregation of the two types into the daughter cells after one or more cell divisions. This process is called cytoplasmatic segregation.

Alleles on organelle chromosomes (1) in sexual crosses are inherited from one parent only (maternal parent) and hence show no segregation ratios of the type nuclear genes do and (2) in asexual cells can show cytoplasmic segregation.