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Biology LibreTexts


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  • Introduction


    An anomaly is anything that deviates from the standard/what is expected. Biological anomalies help us understand what is biologically possible, rather than just what is biologically “normal.”


    The set of all biological characteristics of an organism. This includes anatomy, physiology, and behavior.

    Developmental Biology

    Describes/studies anatomy, physiology, and genetics of an organism over time. Typically it refers to embryological development (from a single cell to an independent organism), and/or juvenile development (from a new independent organism to an adult). However, development occurs throughout an organism’s lifespan, for example stem cell differentiation. We can also think about the development of single celled organisms as they “mature” in response to environmental changes and reproduce.

    SNP/RFLP testing

    Genetic testing that looks for small “polymorphisms” (DNA sequence differences) in individuals. SNP stands for “Single Nucleotide Polymorphism,” a single nucleotide location that can vary in sequence in a population. For example some people might have a T and some might have a C at the same location. We say this location is “polymorphic.” RFLP stands for “Restriction Fragment Length Polymorphism,” a DNA locus with a “length” polymorphism after cutting with a specific endonuclease (enzyme that cuts DNA). The difference in length of a DNA fragment among individuals may be caused by a small mutation that removes or adds a cut site or a larger scale deletion or insertion of DNA.

    Teratogenic anomalies

    Anomolies caused by a teratogen, an environmental agent that affects development.


    The same patterning process can be used to create larger or smaller versions of the same body plan.


    An unfertilized egg cell (note: depending on the species, this can specifically refer to an immature egg cell, but here I use it to refer to any unfertilized egg cell regardless of maturity).


    A tissue, cell, or molecule that creates a chemical/protein gradient that affects cells close to it or far away from it differentially to form an organized group.

    Concentration gradient

    A gradient formed by a high number of molecules on one side and a low number on the other with intermediate numbers in between.

    Diffusion gradient

    A concentration gradient formed by diffusion – the random movement of molecules away from a point source.


    Messenger RNA, this acts as the intermediary step between DNA and protein.

    SSD model

    Sythnesis, Solute, Diffusion model for the Bicoid protein concentration gradient in Drosophila melanogaster. This model has Bicoid protein diffusing from a point source to create a diffusion gradient.


    Proteins that “organize” head and tail tissues in Drosophila melanogaster and other flies. They form opposing concentration gradients which have cascading effects that end up in an embryo with distinct regions along its anterior/posterior axis.


    The process of making RNA using a DNA template


    The process of making protein (or a peptide) from an mRNA template by joining together amino acids in a ribosome.

    Gene Expression

    Making a functional product from a DNA template (i.e. transcription and/or translation). While most cells in a multicellular organism have all of the organisms genes represented in their DNA, only a small subset of these genes get made into product (expressed) in an individual cell.

    RNA interference

    A small RNA can interfere with translation if it is a reverse complement to an mRNA.

    Untranslated Regions

    Portions of the genome that do not code for protein.


    Adding a phosphate group (PO4) to a protein. This changes the function of the protein.

    Allosteric inhibition/activation

    Inhibiting or activating a protein by interfering with a site outside the “active site.” The active site is where the substrate binds.

    Homo and heterodimers

    A dimer is two peptides/proteins bound together to perform a new function. A homodimer is made up of two of the same protein. A heterodimer is made up of two different proteins.


    Adding a sugar/carbohydrate group to a protein. This changes the function of the protein.

    Proteolytic cleavage

    Cleaving a protein between two amino acids. This can destroy the function of a protein or activate a function (e.g. pepsinogen -> pepsin).



    Chemicals that attract a particular type of cell or organism. For example, chemicals that attract axons during neurogenesis, or chemicals secreted by egg cells that attract sperm from the same species.

    Cortical rotation

    The rotation of the cell cortex (outer layer) in relation to the cell inner-layer. This is mediated by the cytoskeleton and only happens in certain species.

    Ventralized embryo

    An embryo that is primarily made up of ventral tissues (i.e. endoderm). Often called a “belly piece.” This embryo will not continue development past early stages.


    Any manipulation of an embryo that results in an overabundance of ventral structures. Ventralization leads to a ventralized embryo.

    Spemann-Mangold organizer

    The region of a vertebrate embryo that will differentiate into the notochord. The notochord itself has organizer activity – it induces ectoderm above it to become the neural tube. Ectoderm farther from it becomes skin. This organizer is located at the edge of the blastopore in vertebrates and, more specifically, at the dorsal-lip of the blastopore in frogs.

    Cellular differentiation

    The developmental process of a cell becoming mature. This involves narrowing down its fate as well as specializing its functions.

    Radial symmetry

    An organism that has three or more fold symmetry perpendicular to a central axis. For example, anemones, jellies, and many flowers are classically considered to be radially symmetric. However, note that recent work has found that cnidarians, like anemones and jellies, may also exhibit bilateral symmetry.

    Vegetal/animal poles

    Before an embryo has clear axes that correlate to its juvenile or adult form, it may still exhibit asymmetry. One asymmetry common in animal embryos is vegetal vs. animal. The vegetal pole is rich in yolk while the animal pole is rich in cytoplasm.

    Cytoskeletal microtubules

    The cytoskeleton is the scaffolding within a cell that gives it structure and also forms the “highways” in a cell that other proteins and vesicles can travel on, instead of relying on diffusion. One major element of this are microtubules, which are long filaments made up of tubulin. Microtubules also form the mitotic/meiotic spindle and propelling structures like cilia and flagella.

    Cortical determinants

    Proteins, nucleic acids, and small molecules in a cell that help to regulate gene expression. These are often asymmetrically distributed in egg cells and early embryos. They will help to determine future axes and cell types of an organism.


    Moving part of one organism to another organism. The two organisms can be the same species or different species

    Genetic manipulation

    Experimentally modifying the genetics of an organism. This is a broad term. Usually it refers to genetic modification (aka gene editing) via genetic engineering. Genetic modification makes a permanent and heritable change to the DNA of an organism or cell within an organism.



    Diffusible molecules (often proteins) that affect cellular, tissue, or organismal morphology. They have different effects at different concentrations.

    Morphogenic gradient

    The concentration gradient of a morphogen.

    Actin Filaments

    Polymers of actin subunits, also called microfilaments. These are important components of the cytoskeleton and are especially important in cell-shape changes and cell movement.


    Early stage of embryogenesis characterized by rapid cell division and low rates of transcription and translation.


    A cleavage-stage embryo. They often appear fairly undifferentiated (a ball of cells).

    Germ layers

    A “layer” of cells formed in the early embryos through the process of gastrulation (see below). They are some of the first tissues specified in a developing animal embryo. Nearly all animals share the same three germ layers – ectoderm, mesoderm, and endoderm.


    The process of cells and tissues moving relative to each other to produce the three germ layers of an embryo and a primitive body-plan.

    Autonomous specification

    Cells or tissues whose fate is specified based on inherited factors (proteins and RNAs)

    Conditional specification

    Cells or tissues whose fate is specified based on interactions with the environment (other cells and morphogens)


    Cell movements characterized by the thinning out of a sheet of cells to cover other cells.


    A type of cell movement. Involuting cells in a sheet undergo shape changes to bend underneath the sheet of cells to form a second sheet. This has an effect similar to folding a piece of paper in half.


    Cells moving between each other to form a thinner sheet.


    Cell movements characterized by the formation of a lined pit in a sheet of cells.


    Cells in a sheet losing their affinity for the surrounding cells and leaving the sheet.


    Delaminating cells moving into a cavity in the organism.


    A map of an embryo showing the future tissues/organs cells will eventually differentiate into.


    In vertebrates, this is an embryonic structure that orients the anterior/posterior axis of the developing tissues. It is a flexible rod of mesoderm just under the future spinal-cord and brain. It signals to overlying ectoderm


    Genes or morphological characters from different species that are inherited from a common ancestor.


    A gene or morphological character that defines a taxonomic group. For example, a vertebral column in vertebrates. A synapomorphy is a homologous character that is not found in species outside the group.

    Genetic Toolkit


    A protein unique to one group of flies that specifies anterior structures. It is a “maternal effect” protein in that the egg makes Bicoid mRNA before fertilization.

    Osteogenic cell

    A bone stem-cell. They divide to produce osteoblasts.


    A non-dividing bone cell which secretes the mineral matrix that will become the hard part of bone.


    A monophyletic group of organisms that share a body-plan. We belong to Phylum Chordata along with all the other vertebrates and organisms with a notochord. Other famous phyla include Mollusca and Athropoda.

    Signal transduction pathway

    A cascade of chemical interactions involving proteins that carries a signal from one part of a cell to another.


    A molecule that binds to another molecule. In signal transduction pathways, ligands are usually the signal coming from outside of the cell that bind to receptors on the cell membrane.


    Can receive and transmit a signal from a ligand. In signal transduction pathways, receptors are usually cell-membrane proteins that change conformation in response to ligand binding.

    Gene regulatory network

    The set of genes and genetic interactions leading to a particular cellular, tissue, or organismal outcome.

    Downstream effects

    In a pathway, these are events that happen after a reference event. For example, triggering a pathway has a downstream effect of turning on its effector genes.

    Wiring diagram

    A graphical representation of the genetic interactions of a gene regulatory network.

    Fate restriction

    As a cell matures, its cell-type becomes more and more restricted. For example, an ectodermal cell can be restricted to a neural fate. This neural cell can now be restricted to a (say) glial cell fate. A neural cell cannot become a skin cell, though a generic ectodermal cell can. A glial cell cannot become a neuron, though a generic neural cell can.

    Progenitor cells

    A cell that gives rise to specific cell-types.


    A type of white blood cell that is part of our innate immune system.


    Any molecule (or structure) with at least two conformations that have different effects on a system. In developmental genetics, switches are usually proteins that form different protein/protein partnerships depending on their conformation. Their conformation depends on other elements in the environment, for example a ligand. Switches in developmental genetics often determine a fate-decision by a cell.

    Paracrine signaling

    Chemically based (often protein) cell-cell communication where the two cells are nearby.

    Juxtacrine signaling

    Chemically based (often protein) cell-cell communication where the two cells must be touching.

    Autocrine signaling

    Chemically based (often protein) cell communication where a cell secretes a signal that it receives itself.


    Higher-level gene regulatory modules that make initial broad cell-fate decisions.


    Lower-level gene regulatory modules and outputs that differentiate cells


    Small gene regulatory modules that can be used in a variety of gene regulatory networks.


    Any type of development that results in differentiation across a tissue, organ, or organism.


    Cells or tissues making cell-fate decisions.


    Small blastomeres that arise from unequal cleavages in early development.

    Cis-regulatory element

    A piece of DNA that acts as a switch to help turn a gene on or off.



    The process of splitting a developing organism into different parts, often along an already defined axis. For example, differentiating frontal brain from midbrain, hindbrain, and spinal cord.

    Segmentation cascade

    In Drosophila and some other insects, the anteroposterior axis develops simultaneously. This occurs through stepwise regionalization of the embryo. First, broad regions (head vs. tail) are determined, these determinations cause differential gene expression of downstream components of the segmentation cascade leading to further divisions of the axis into smaller regions.

    Maternal effect genes

    mRNAs and/or proteins can be made by the mother and deposited in the egg before fertilization. These are maternal effect genes since the sequences of the mother’s alleles define the gene function, at least at an early stage of development. One maternal effect gene is Bicoid.

    Gap genes

    Early-acting genes in the segmentation cascade that divide the Drosophila embryo into broad regions. Loss of function mutations in gap genes often cause missing segments in the larva.

    Pair-rule genes

    Later-acting genes in the segmentation cascade that divide the Drosophila embryo into regions of two-segment periodicity. These will be divided in half by the segment polarity genes, which are expressed in every segment.

    Serial Homology

    Organs or appendages that are built in several locations along a developing body. These can differ from each other somewhat (for example arms and legs) but share common structures and a common developmental program.


    Movement, or the ability to move around.

    Apical ectodermal ridge

    A ridge of cells at the distal end of a growing tetrapod limb (arm or leg). These cells send signals to the cells under them to keep growing. They can also change their signal over time to help specify the proximal/distal axis of the limb.

    Genetic Complexity

    Positive selection

    In genetics, this refers to new genetic variants (mutants) being selected for at a locus. Over time, this increases the genetic variation across species, at least at that locus.

    Purifying selection

    In genetics, this refers to new genetic variants (mutants) being selected against at a locus. This maintains the original sequence over evolutionary periods of time.

    Organismal fitness

    The fitness of an organism, typically measured by the number of offspring it produces. Because this is highly dependent on environmental variables, this is actually measured across a population. To see if a particular allele affects fitness in a species, we can group individuals with the same genotype at a locus and compare average fitness between genotypes.


    A gene or mutation that affects multiple aspects of an organisms phenotype. A pleiotropic constraint occurs when two different functions of the gene would be optimized with different alleles.

    Gene variants

    Different sequences of the same gene in a species, usually called “alleles.” Usually these are very very similar in sequence with only small changes between the variants.

    Synonymous changes

    Genetic changes in a protein coding region that do not cause a change in protein sequence.

    Pairwise comparisons

    Comparing two things at a time. In the context of this chapter we can compare two genetic sequences to each other at a time. So, for example, we might say humans and mice have 3 nucleotide differences in an exon, humans and maize have 10 differences, and mice and maize have 11 differences.

    Ectopic expression

    A new location or time of expression of a gene. That is, a gene is turned on in an “unusual” place or developmental time.

    Point mutations

    A single nucleotide change in a strand of DNA (note that this will result in the complementary change in the second strand of DNA).


    An insertion or deletion of bases from a genome.


    In a genome, this is a class of mutation that results in an existing sequence of DNA being duplicated elsewhere in the genome. Duplicated regions will often be found quite near their originals but they can also be found farther away, even on another chromosome.

    Genomic complexity

    The number of “parts” in a genome. For this class we are concerned with coding portions of genes and their regulatory regions. Complexity would increase if more exons (coding regions) or more regulatory regions were added to the genome.

    Organismal complexity

    The number of “parts” in an organisms phenotype. This can refer to anatomical parts, physiological processes, behavior, and/or the “extended phenotype” (the way an organism changes its environment to promote its own fitness).


    Signaling Pathway Response Element, a regulatory region of a gene that allows the gene to switch on or off in response to the activation of a Signaling Pathway. This switch may also require the presence of local activators (tissue dependent transcription factors).

    Exonic mutations

    Mutations in exons, the coding regions of genes.

    Functional domain

    A protein domain with a specific function. This may include a catalytic site, a portion that binds to DNA or other proteins, etc.

    Repressor domain

    A protein domain involved in repressing a biological function, often by binding to another protein and preventing it from acting.

    Nonsense mutation

    A mutation that converts a nucleotide codon that codes for an amino acid (protein monomer) into one that codes for a stop codon. This causes a premature end to translation and a protein missing its C-terminal end.

    Horizontal transfer

    The uptake of foreign DNA into the genome of a host. Animals typically get exogenous DNA only from retroviruses, but plants, fungi, and bacteria are more able to incorporate DNA from the environment into their genome.

    Transposon insertion

    A transposon, the remnants of a retroviral infection, is a piece of DNA that can “jump” into different portions of the genome, sometimes taking surrounding DNA with it.


    A genetic sequence resembling a protein-coding gene that does not actually code for a functional product. These may be the remnants of a genetic duplication/transposition or may be once-functional genes that accumulated mutations over time.

    Enhancer element

    A piece of regulatory DNA that may contain many individual protein-binding sites. An enhancer element typically drives gene expression under specific circumstances (for example, in the limb mesoderm during limb development).


    Functional innovation

    Mutations in an evolutionary lineage that change existing phenotypic characters so that they perform a new function. A functional innovation either increases fitness for the organisms in their ancestral ecological niche or allows them to exploit a new ecological niche.


    A new feature in an evolutionary lineage. Sometimes we restrict these to new features that are not build from existing features (functional novelty).

    Realizer genes

    Genes downstream of patterning genes that change cell and tissue characteristics to build a morphological character.


    A genetic manipulation technique that directly edits the genome of an organism. It allows researchers to target a specific genetic locus.


    A beetle’s hard wing covers. Singular: elytron

    Gin trap

    Segmentally iterated spiky defense structures on beetle pupae that disappear during metamorphosis. These are found only in abdominal segments and are thought to be serial homologs of parts of the wing.


    Population-level evolution

    Evolution within a population or a species. This level of evolution introduces new genetic variation (alleles) into a population and acts on these alleles to change their frequency.


    Evolution above the population level. That is, the origination of new species and evolutionary patterns seen at higher taxonomic levels.

    Molecular genetics

    All aspects of genetics that occur at the molecular level – for example mutations and gene expression.


    Modularity refers to discrete units being used to build up a larger structure and/or process.


    A process or structure that is resistant to change.


    A process or structure that is able to change in response to external factors.

    Weak regulatory linkage

    Processes or structures that are linked by a common regulatory event that triggers their formation.

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