Glossary

Glossary

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2D gel electrophoresis (also 2-DE)
“A form of gel electrophoresis commonly used to analyze proteins. Mixtures of proteins are separated by two properties in two dimensions on 2D gels.” Source: Two-dimensional gel electrophoresis. (2023, March 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Two-dimensional_gel_electrophoresis

3′ untranslated region (3′ UTR)
The region of DNA that is downstream (3′) of the transcription termination site.

5′ untranslated region (5′ UTR)
The region of DNA that is upstream (5′) of the transcription start site.

A

A/B compartments
Distinct chromosomal regions. The A compartment tends to be located closer to the center of the nucleus and contains more genes. The B compartment contains relatively more constitutive heterochromatin and is more likely to be at the nuclear periphery.

acetylation
A chemical modification that can be added to a variety of biomolecules to change their function. In this process, an acetyl group is added to the molecule at a specific location.

actin filaments
Polymers of actin subunits that are part of the cell’s cytoskeletal system.

actin-binding proteins (ABP)
Proteins that bind to actin (monomers or filaments) in vivo to modulate their function.

activator proteins
A DNA binding protein that has positive control over gene expression, often causing an increase of transcription of a particular gene.

adaptor protein
Proteins that play an important role in vesicle formation, where they help to gather scaffold proteins that are needed to form the clathrin coat of the vesicle.

adenylyl cyclase
An enzyme responsible for making cAMP (cyclic AMP) from ATP. Also called adenylate cyclase.

affinity
In the context of proteins, refers to the favorability of a binding interaction. For instance, the protein when phosphorylated has greater affinity for its substrate. This means that the protein is likely to bind more tightly when the protein is phosphorylated.

agarose gel electrophoresis
A method of gel electrophoresis used in biochemistry, molecular biology, genetics, and clinical chemistry to separate a mixed population of macromolecules such as DNA or proteins in a matrix of agarose, one of the two main components of agar. Source: Gel electrophoresis. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Gel_electrophoresis

aggregation
When referring to proteins, it means that they cluster together into clumps. Oftentimes these clumps are no longer functional.

allele
“A variation of the same sequence of nucleotides at the same place on a long DNA molecule.” Source: Allele. (2023, April 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Allele

alpha helix (α-helix)
“A common motif in the secondary structure of proteins and is a right hand helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence.” Source: Alpha helix. (2023, July 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Alpha_helix

alternative splicing
“An alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. This means the exons are joined in different combinations, leading to different (alternative) mRNA strands.” Source: Alternative splicing. (2023, June 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Alternative_splicing

amino acyl tRNA synthetases
Responsible for putting the amino acid on the tRNA.

amphipathic
A chemical compound or molecule that possesses both a hydrophilic region and a hydrophobic region. Phospholipids that make up the majority of the structure of phospholipid bilayers are an example of an amphipathic molecule.

anaphase
The stage of mitosis when the chromosomes are separated.

anaphase A
In this part of Anaphase, the kinetochore microtubules shorten to facilitate chromosomes moving closer to their respective spindle poles.

anaphase B
In this part of Anaphase, the interpolar microtubules lengthen. This pushes the spindle poles further apart.

anaphase-promoting complex (APC)
Causes the degradation of the cohesion proteins that bind sister chromatids together, which releases the daughter chromosomes so that they can be pulled toward their respective spindle pole.

anterograde traffic
Involves movement of coated vesicles in the “forward” direction. Depending on the trafficking pathway, this can be different destinations.

antiparallel
Refers to two molecules that bind in a head-to-tail orientation.

apoptosis
A regulated process of cell death.

Arp2/3
An actin-binding protein that binds to actin filaments and promotes a new branched actin filament.

arrays (cytoskeletal)
Networks of either actin or microtubules.

astral microtubules
Microtubules that start at the spindle pole but extend toward the plasma membrane to anchor the spindle pole.

asymmetric division
When cell division does not equally split a cell in half. This occurs in a variety of cell types.

ATP synthase
A large protein complex that uses the flow of protons to synthesize ATP from ADP and inorganic phosphate. It dimerizes and is found in the cristae membrane of mitochondria.

autocrine
In this type of signaling, the signal is released and received by the same cell.

autotroph
An organism that creates its own complex biomolecules (carbohydrates, proteins, lipids) from simple substrates (carbon dioxide and water).

B

beta barrel
“A beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta barrels are arranged in an antiparallel fashion. Beta barrel structures are named for resemblance to the barrels used to contain liquids.” Source: Beta barrel. (2022, May 5). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Beta_barrel

beta sheet
“A common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation.” Source: Beta sheet. (2022, September 9). In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Beta_sheet

bilayer
Generally refers to a lipid bilayer that has two lipids stacked tail to tail with the polar head groups facing the aqueous environment.

binary fission
A type of asexual reproduction where an organism divides into two of the same.

bioinformatics
“An interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex.” Source: Bioinformatics. (2023, July 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Bioinformatics

biological membrane
A selectively permeable barrier that is designed to separate the cell from the external environment, allows communication of activities between cells, and functions to form intracellular compartments. It is composed of lipids, proteins, and carbohydrates.

brightfield light microscopy
“The simplest of all the optical microscopy illumination techniques. Sample illumination is transmitted (i.e., illuminated from below and observed from above) white light, and contrast in the sample is caused by attenuation of the transmitted light in dense areas of the sample.” Source: Bright-field microscopy. (2023, May 8). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Bright-field_microscopy

C

carbon-fixation reactions
The biochemical reactions that occur in the chloroplast stroma, where carbon dioxide is used to make three carbon sugar molecules.

cargo protein
Proteins that are carried within vesicles to a particular location. These can be proteins that are secreted but also other resident proteins that need to travel to a particular destination in the endomembrane system.

cargo receptor (protein)
Responsible for binding to specific forms of cargo like proteins. Cargo receptors help the cargo get loaded into the correct vesicle for transport.

cell cortex (also known as the actin cortex, cortical cytoskeleton, or actomyosin cortex)
“A specialized layer of cytoplasmic proteins on the inner face of the cell membrane.” Source: Cell cortex. (2023, February 12). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cell_cortex

cell cycle
“The series of events that take place in a cell that causes it to divide into two daughter cells.” Source: Cell cycle. (2023, June 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cell_cycle

cell fractionation
“The process used to separate cellular components while preserving individual functions of each component.” Source: Cell fractionation. (2023, February 22). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cell_fractionation

cell plate
The site at which a new cell wall forms when a plant cell undergoes cytokinesis.

cell wall
“A structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. It provides the cell with both structural support and protection, and also acts as a filtering mechanism.” Source: Cell wall. (2023, March 30). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cell_wall

centriole
A cylindrical organelle at the center of a centrosome in animal cells.

centromere
A structural region of a chromosome where the two sister chromatids are connected. Additionally, the kinetochore and mitotic spindle fibers attach to the sister chromatids during mitosis and meiosis.

centrosome
A microtubule organizing center (MTOC) in animal cells. It contains a pair of perpendicular centrioles.

chaperone protein
“Proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes.” Source: Chaperone (protein). (2023, April 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Chaperone_(protein)

checkpoints (cell cycle)
Molecular mechanisms that ensure that proper cellular conditions are met prior to allowing a cell to enter the next phase of the cycle.

chemiosmotic coupling
Refers to the cellular mechanism that harnesses the potential energy stored in a chemical gradient to power a biochemical reaction.

ChIP-seq
“A method used to analyze protein interactions with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.” Source: ChIP sequencing. (2023, May 9). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/ChIP_sequencing

cholesterol
A molecule in the sterol family that plays a role in the fluidity of membranes.

chromatid
Represents one-half of a replicated chromosome. Two sister chromatids together form one chromosome.

chromatin
In the simplest terms, the combination of DNA and protein. When DNA is packaged using proteins, this combination structure is referred to as chromatin.

chromatin fiber (30 nm fiber)
A structure of chromatin that contains the nucleosome core as well as histone H1. This is considered the most abundant form of chromatin in the interphase nucleus.

chromatin immunoprecipitation (ChIP)
“A type of immunoprecipitation experimental technique used to investigate the interaction between proteins and DNA in the cell. It aims to determine whether specific proteins are associated with specific genomic regions, such as transcription factors on promoters or other DNA binding sites.” Source: Chromatin Immunoprecipitation. (n.d.). In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Chromatin_immunoprecipitation

chromatin remodeling
“The dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.” Source: Chromatin remodeling. (2023, May 24). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Chromatin_remodeling

chromatin remodeling complexes
Protein complexes responsible for making changes to chromatin structure. This can include nucleosome sliding, nucleosome eviction, and nucleosome swapping.

chromosome
Long strands of DNA that contain the genetic material of the given organism. Chromosomes usually contain histone and nonhistone proteins that add to the packaging of the DNA strand.

chromosome territory
A region in the nucleus preferentially occupied by a chromosome.

cilium
A specialized structure in Eukaryotic cells containing microtubules and a specialized MTOC called a basal body.

cisterna
“A flattened membrane vesicle found in the endoplasmic reticulum and Golgi apparatus. Cisternae are an integral part of the packaging and modification processes of proteins occurring in the Golgi.” Source: Cisterna. (2023, January 3). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cisterna

cisternal maturation model
A model to describe the movement of proteins through the Golgi apparatus. In this model, each cisterna matures into the next. This means that the cis cisternae become the medial, then the trans cisternae, which eventually turn into vesicles in the trans Golgi network (TGN) for further trafficking.

citric acid cycle
A series of biochemical reactions that produces ATP and the electron donors NADH and FADH2 from pyruvate. Also known as the tricarboxylic acid (TCA) cycle.

clathrin (coated vesicle)
Transport vesicles that contain a coat with clathrin triskelions. These coated vesicles participate in a variety of pathways, notably endocytosis and the lysosomal targeting pathway.

coat protein
Help support the formation of a budding transport vesicle. Coat proteins bind to adaptor proteins and cargo receptors to ensure that the proper cargo is recruited into these structures.

coding strand
“The DNA strand whose base sequence is identical to the base sequence of the RNA transcript produced (although with thymine replaced by uracil).” Source: Coding strand. (2021, December 8). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Coding_strand

cofactor
Refers to a protein to aid in regulation of gene expression.

cohesin
A protein complex that helps keep sister chromatids attached after DNA replication and also helps organize the interphase genome.

cohesin attachment regions (or CARs)
Specific sites on DNA where cohesins bind to attach sister chromatids together.

coiled coil
A form of protein structure that is produced when two alpha helices wind around each other to produce a super coiled structure.

collagen
“The main structural protein in the extracellular matrix found in the body’s various connective tissues.” Source: Collagen. (2023, July 3). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Collagen

condensin
A family of proteins with a role in DNA condensation needed for mitosis and meiosis.

confocal laser scanning microscopy
Uses a laser to excite fluorescent molecules inside cells, similar to epifluorescence. However, the light shines through a pinhole to block out-of-focus light. This allows for “optical” sectioning (dividing the cells) along an axis and can result in a sharper image.

consensus sequence
“The calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated.” Source: Consensus sequence. (2023, May 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Consensus_sequence

constitutive heterochromatin
Regions of chromatin that are packaged and inaccessible for transcription. These cannot be unpackaged. Most often these regions are important for chromosome structure and do not contain genes.

constitutive secretion
The process of continuous secretion of molecules from the cell or organelle that is not dependent on external factors. This is also considered to be the default secretory pathway.

contractile ring
A special formation of actin filaments and myosin motors that will continually rachet smaller. This structure is needed for cytokinesis in animal cells.

COPI (vesicle coat)
Transport vesicles that contain a coat with COPI units. These coated vesicles participate in a variety of pathways, notably Golgi to ER (retrograde pathway).

COPII (vesicle coat)
Transport vesicles that contain a coat with COPII units. These coated vesicles participate in a variety of pathways, notably ER to Golgi (anterograde pathway).

core histones
H2A, H2B, H3, and H4 are the histone proteins that make up the core of the nucleosome. Two copies of each are needed to create the octamer.

crista
“A fold in the inner membrane of a mitochondrion. The name is from the Latin for crest or plume, and it gives the inner membrane its characteristic wrinkled shape, providing a large amount of surface area for chemical reactions to occur on.” Source: Crista. (2022, November 5). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Crista

critical concentration (Cc)
Can be thought of in three ways: the monomer concentration needed to initiate polymer formation, the monomer concentration at reaction equilibrium, and the concentration at which a polymer goes from shrinking to growth.

cryofixation
“A technique for fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy and cryo-electron microscopy.” Source: Cryofixation. (2023, May 27). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cryofixation

cyclic AMP (cAMP or 3′,5′-cyclic adenosine monophosphate)
“A second messenger, or cellular signal occurring within cells, that is important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the cAMP-dependent pathway.” Source: Cyclic adenosine monophosphate. (2023, April 30). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cyclic_adenosine_monophosphate

cyclin
“A family of proteins that controls the progression of a cell through the cell cycle by activating cyclin-dependent kinase (CDK) enzymes or group of enzymes required for synthesis of cell cycle.” Source: Cyclin. (2023, January 29). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cyclin

cyclin-CDK complex
A complex of a cyclin protein with a cyclin-dependent kinase (CDK). When this complex is activated, it promotes progression to the next stage of the cell cycle.

cyclin-dependent kinase (CDK)
A protein kinase that, when activated, phosphorylates target proteins needed for progression to the next stage of the cell cycle. Activation requires binding with a cyclin protein as well as phosphorylation of particular locations within the protein.

cytokinesis
The process of cytoplasmic division.

cytoplasmic streaming
“The flow of the cytoplasm inside the cell, driven by forces from the cytoskeleton.” Source: Cytoplasmic streaming. (2023, July 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cytoplasmic_streaming

D

darkfield microscopy
“Describes microscopy methods, in both light and electron microscopy, which exclude the unscattered beam from the image. As a result, the field around the specimen (i.e., where there is no specimen to scatter the beam) is generally dark.” Source: Dark-field microscopy. (2022, September 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Dark-field_microscopy

Delta G (ΔG)
The change in Gibb’s free energy. When this term is negative, it suggests that a reaction will be spontaneous and occur without the input of energy from the environment.

Delta H (ΔH)
The change in enthalpy between two states. In the case of proteins, usually a bound and unbound state. Enthalpy encompasses the amount of bound energy in the system. When applied to proteins, this can relate to the amount of energy contained within all the bonds of the molecule. A positive ΔH indicates there is more bond energy in the second state compared to the first state, usually as a result of more bonds or stronger bonds.

Delta S (ΔS)
The change in entropy of the system. Entropy is the measure of motional freedom within the system. Different molecules will have more and less freedom. A higher ΔS indicates that the resulting state will have more motional freedom than the original in a chemical reaction.

dephosphorylation
The process of removing a phosphate chemical group from a protein.

desmosome
“A cell structure specialized for cell-to-cell adhesion.” Source: Desmosome. (2023, May 27). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Desmosome

diacylglycerol (DAG)
“A glyceride consisting of two fatty acid chains covalently bonded to a glycerol molecule through ester linkages.” Source: Diglyceride. (2022, November 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Diglyceride

dichroic mirror
A special filter that allows some wavelengths of light to pass through but reflects others. These are used in microscopy to shine certain wavelengths of light on the sample but not others.

dimer
“The word dimer has roots meaning ‘two parts,’ di- + -mer. A protein dimer is a type of protein quaternary structure.” Source: Protein dimer. (2023, May 15). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Protein_dimer

dimerize
The process of two biomolecules binding.

diploid
Refers to organisms that contain two copies of each chromosome.

direct staining
When colored or fluorescent dyes are added to a biological sample to help differentiate cellular structures under the microscope.

disulfide bridge
The covalent linkage of thiol groups between two thiol residues. Commonly, these are found on the R groups of cysteine amino acids.

docking sites
Protein locations where other biomolecules are able to bind.

domain map
A schematic representation of the protein sequence with highlighted areas indicating protein domains (regions of the protein with a particular function).

downstream
Refers to the region of the DNA that is 3′ of the area referenced. For example, in a sentence, you could say, “The transcription stop site is located downstream of the transcription start site.”

dynamic instability
“Refers to the coexistence of assembly and disassembly at the ends of a microtubule. The microtubule can dynamically switch between growing and shrinking phases in this region.” Source: Microtubule. (2023, July 15). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Microtubule

dynamin
Part of a large family of enzymes known as GTPases that play a crucial role in endocytosis, cytokinesis, scission of newly formed vesicles, and division of organelles.

dynein
A molecular motor that uses microtubules. All known dynein motors move toward the minus end. Plants do not have dyneins and instead use minus-end directed kinesin to fulfill this role.

E

ectotherm
“An animal in which internal physiological sources of heat are of relatively small or of quite negligible importance in controlling body temperature.” Source: Ectotherm. (2023, June 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ectotherm

electrochemical gradient
“A gradient of electrochemical potential, usually for an ion that can move across a membrane. The gradient consists of two parts: 1) The chemical gradient, or difference in solute concentration across a membrane. 2) The electrical gradient, or difference in charge across a membrane.” Source: Electrochemical gradient. (2023, July 18). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Electrochemical_gradient

electron carrier (donor)
“A chemical entity that donates electrons to another compound. It is a reducing agent that, by virtue of its donating electrons, is itself oxidized in the process.” Source: Electron donor. (2022, August 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Electron_donor

electron tomography
The chemical gradient or difference in solute concentration across a membrane.

electron transport chain (ETC)
“A series of protein complexes and other molecules that transfer electrons from electron donors to electron acceptors via redox reactions (both reduction and oxidation occurring simultaneously) and couples this electron transfer with the transfer of protons (H+ ions) across a membrane.” Source: Electron transport chain. (2023, May 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Electron_transport_chain

emitted light microscopy (a.k.a. fluorescence light microscopy)
A microscopy technique where samples are illuminated with light of a particular wavelength. The fluorescent molecules in the sample become excited and emit light of a longer wavelength. The microscope catches this light to display the location of the fluorescent molecules bound to a cellular structure of interest. There are two main types of fluorescent light microscopy: epifluorescence and confocal microscopy.

endocrine
A long-range signaling pathway where a cell secretes a signaling molecule that is picked up by target cells not in the local vicinity.

endocytic pathway
The pathway by which materials are brought into the cell. Once materials are in the cell, they transit to the endosome and then to the lysosome.

endocytosis
The process in which outside materials and cargo are brought into the cell after passing through the membrane and forming a vesicle once inside. Endocytosis includes pinocytosis, phagocytosis, and receptor-mediated endocytosis.

endoplasmic reticulum (ER)
“The transportation system of the eukaryotic cell… [that] has many other important functions such as protein folding. It is a type of organelle made up of two subunits—rough endoplasmic reticulum (RER), and smooth endoplasmic reticulum (SER). The endoplasmic reticulum is found in most eukaryotic cells and forms an interconnected network of flattened, membrane-enclosed sacs known as cisternae (in the RER), and tubular structures in the SER.” Source: Endoplasmic reticulum. (2023, June 12). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Endoplasmic_reticulum

endosome
Intracellular sorting centers that are the first location molecules are delivered to once they are endocytosed. There are two classifications of endosomes, early and late, which are marked by different cellular markers. Some vesicles from the TGN can be routed to the endosome as well. Endosomes sort materials that need to go to the lysosome from those that need to go back to the Golgi or cell membrane.

endosymbiont theory
“The leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes (more closely related to the Bacteria than to the Archaea) taken one inside the other in endosymbiosis.” Source: Symbiogenesis. (2023, May 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Symbiogenesis

endotherm
“An organism that maintains its body at a metabolically favorable temperature, largely by the use of heat released by its internal bodily functions instead of relying almost purely on ambient heat.” Source: Endotherm. (2023, April 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Endotherm

enhancer region
“A short (50–1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.” Source: Enhancer (genetics). (2023, July 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Enhancer_(genetics)

epifluorescence
The most general ubiquitous form of fluorescence light microscopy. Light at the excitation wavelength is applied to the sample. Then the detector will pick up the emission wavelength of light emitted from the sample.

epigenetics
“The study of stable changes in cell function (known as marks) that do not involve alterations in the DNA sequence.” Source: Epigenetics. (2023, July 5). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Epigenetics

ER exit site
The site on the endoplasmic reticulum (ER) where vesicles accumulate and bud off bound for the Golgi.

ER insertion sequence
A sequence of hydrophobic amino acids (approx. 8–10) that serve as a binding site for SRP. This triggers its cotranslational insertion into the ER. There are several variations of this sequence depending on the location in the protein’s sequence, including N-terminal START sequence, internal START sequence, and internal STOP sequence.

ER lumen
The interior fluid of the endoplasmic reticulum (ER).

ER resident protein
“Refers to proteins that remain in the endoplasmic reticulum, or ER, after folding has finished and are not exported to other organelles.” Source: ER resident proteins. (n.d.). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Endoplasmic_reticulum_resident_protein

ER retention signal (KDEL)
A targeting sequence defined by the amino acids KDEL (lysine, aspartate, glutamate, and leucine). If these proteins travel to the Golgi, this sequence helps them to be recognized by a receptor to be returned to the ER.

euchromatin
Loosely packed chromatin with regions rich in genes that can be transcribed in order to be later translated into proteins.

exon
A coding region within a DNA sequence that is spliced together after the introns have been removed from an mRNA sequence allowing for the formation of a mature mRNA segment.

exon skipping
“A form of RNA splicing used to cause cells to `skip’ over faulty or misaligned sections (exons) of genetic code, leading to a truncated but still functional protein despite the genetic mutation.” Source: Exon skipping. (2023, January 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Exon_skipping

exportin
The nuclear export receptor. They bind to proteins with a nuclear export receptor to aid in transport of proteins through the nuclear pore out of the nucleus into the cytosol. They are closely related to importins (which help protein enter the nucleus) and together form a larger family of proteins known as the karyopherins.

extracellular matrix (ECM)
“A network consisting of extracellular macromolecules and minerals, such as collagen, enzymes, glycoproteins and hydroxyapatite that provide structural and biochemical support to surrounding cells.” Source: Extracellular matrix. (2023, June 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Extracellular_matrix

F

facultative heterochromatin
Regions of chromatin that are densely packaged and not accessible for transcription. However, these regions contain genes and can be opened for transcription when needed by the cell.

feedback loop
A regulatory mechanism whereby the product of a process will influence (upregulate or downregulate) itself.

filamentous protein
“Made up of elongated or fibrous polypeptide chains which form filamentous and sheet-like structures.” Source: Fibrous protein. (2022, September 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Fibrous_protein

flagellum
“A hairlike appendage that protrudes from certain plant and animal sperm cells, and from a wide range of microorganisms to provide motility.” Source: Flagellum. (2023, July 13). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Flagellum

flippase
“Transmembrane lipid transporter proteins located in the membrane that belong to ABC transporter or P4-type ATPase families. They are responsible for aiding the movement of phospholipid molecules between the two leaflets that compose a cell’s membrane (transverse diffusion, also known as a ‘flip-flop’ transition).” Source: Flippase. (n.d.). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Flippase

flow cytometer
A machine that analyzes properties (such as fluorescence) as it passes through.

fluorescence recovery after photobleaching (FRAP)
A method to determine the mobility of molecules within a membrane. A region of the cell is photobleached (the fluorescent molecules are destroyed). The same area is monitored over time to determine if fluorescence returns to the bleached area.

fluorescence-activated cell sorting (FACS)
“In this process, a sample containing cells or particles is suspended in a fluid and injected into the flow cytometer instrument. The sample is focused to ideally flow one cell at a time through a laser beam, where the light scattered is characteristic to the cells and their components. Cells are often labeled with fluorescent markers so light is absorbed and then emitted in a band of wavelengths. Tens of thousands of cells can be quickly examined and the data gathered are processed by a computer.” Source: Flow cytometry. (2023, June 27). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Flow_cytometry

fluorescent light microscopy (a.k.a. emitted light microscopy)
A microscopy technique where samples are illuminated with light of a particular wavelength. The fluorescent molecules in the sample become excited and emit light of a longer wavelength. The microscope catches this light to display the location of the fluorescent molecules bound to a cellular structure of interest. There are two main types of fluorescent light microscopy: epifluorescence and confocal microscopy.

G

g-actin
The monomeric actin subunit that is not attached to any other actin units.

G-protein-coupled receptors (GPCRs)
“A large group of evolutionarily related proteins that are cell surface receptors that detect molecules outside the cell and activate cellular responses. They are coupled with G-proteins.” Source: G-protein-coupled receptor. (2023, April 16). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/G_protein-coupled_receptor

G-proteins (guanine nucleotide-binding proteins)
“A family of proteins that act as molecular switches inside cells and are involved in transmitting signals from a variety of stimuli outside a cell to its interior. Their activity is regulated by factors that control their ability to bind to and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP).” Source: G-protein. (2023, July 21). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/G_protein

G0 phase
A life stage that exists outside of the cell cycle. Cells can enter this phase due to poor environmental conditions, terminal differentiation, or other cellular cues.

G1 (Gap or Growth 1) phase
“The first of four phases of the cell cycle that takes place in eukaryotic cell division. In this part of interphase, the cell synthesizes mRNA and proteins in preparation for subsequent steps leading to mitosis. G1 phase ends when the cell moves into the S phase of interphase. Around 30 to 40 percent of cell cycle time is spent in the G1 phase.” Source: G1 phase. (2022, December 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/G1_phase

G1/S checkpoint
A cell cycle checkpoint that regulates the progression of a cell into the S (synthesis) stage of the cell cycle.

G2 (Gap or Growth 2) phase
“The third subphase of interphase in the cell cycle directly preceding mitosis. It follows the successful completion of S phase, during which the cell’s DNA is replicated. G2 phase ends with the onset of prophase, the first phase of mitosis in which the cell’s chromatin condenses into chromosomes.” Source: G2 phase. (2022, December 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/G2_phase

G2/M checkpoint
A cell cycle checkpoint that regulates the progression of a cell into the M (mitosis) stage of the cell cycle.

gain-of-function experiment
An experiment where a protein is given a new function through introducing a mutation and the result on the system is measured. Gain-of-function experiments are used to explore what the absolute minimum requirements are for a particular function (i.e., what is sufficient).

gain-of-function mutation
A form of mutation that causes a gene to produce altered products that have gained new molecular functions compared to the unaltered gene products.

gamma-tubulin
A specialized tubulin network that acts as a nucleating site for microtubule growth.

gel electrophoresis
“A method for separation and analysis of biomacromolecules (DNA, RNA, proteins, etc.) and their fragments, based on their size and charge.” Source: Gel electrophoresis. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Gel_electrophoresis

general transcription factors (GTFs)
“A class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA.” Source: General transcription factor. (2023, April 11). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/General_transcription_factor

genetic code expansion (GCE)
A biochemical technique to encode designer amino acids into genetically engineered proteins.

glycocalyx
“A glycoprotein and glycolipid covering that surrounds the cell membranes of bacteria, epithelial cells, and other cells.” Source: Glycocalyx. (2023, July 9). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Glycocalyx

glycolysis
“The metabolic pathway that converts glucose (C6H12O6) into pyruvate.” Source: Glycolysis. (2023, July 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Glycolysis

glycosylation
“The reaction in which a carbohydrate (or ‘glycan’), i.e., a glycosyl donor, is attached to a hydroxyl or other functional group of another molecule.” Source: Glycosylation. (2023, June 21). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Glycosylation

glycosyltransferase
An enzyme that adds a carbohydrate group (‘glycan’) to a biological molecule.

Golgi apparatus
A compartment at the heart of the endomembrane system responsible for sorting and processing proteins in that system.

grana
“Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum).” Source: Thylakoid. (2023, May 24). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Thylakoid

green fluorescent protein (GFP)
A naturally occurring protein found in jellyfish that glows green when excited with blue wavelength light. It is commonly fused genetically to proteins of interest to visualize the interior of cells.

GTP cap
A buildup of GTP bound beta subunit accumulates at the end of a microtubule, protecting it from depolymerization (catastrophe).

GTPase
Enzyme that functions as a molecular switch. GTPases bind to GTP and GDP. Depending on their bound state, they will have different functions. This is a large class of proteins with a wide variety of functions.

GTPase-activating protein, or GAP
A family of proteins that helps a G protein accelerate its GTPase activity (converting GTP into GDP).

guanine-exchange factor, or GEF
A family of proteins that will swap a GDP for GTP on a G protein.

H

haploid
Refers to organisms that contain one copy of each chromosome.

hemidesmosomes
“Very small stud-like structures found in keratinocytes of the epidermis of skin that attach to the extracellular matrix.” Source: Hemidesmosome. (2023, April 21). In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Hemidesmosome

heterochromatin
Tightly packed chromatin that is not transcriptionally active.

heterotroph
“An organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly plant or animal matter.” Source: Heterotroph. (2023, February 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Heterotroph

histone
Proteins that bind to DNA to package into nucleosomes. They are highly basic, resulting in a positive charge. This allows them to bind to the negative backbone of DNA nonselectively.

histone exchange
A chromatin remodeling process where an enzyme removes one histone core and replaces it with a histone core with slight variations in composition.

histone-modifying enzymes
“Enzymes involved in the modification of histone substrates after protein translation and affect cellular processes including gene expression.” Source: Histone-modifying enzymes. (2023, May 9). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Histone-modifying_enzymes

hormone
“A class of signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and behavior.” Source: Hormone. (2023, July 24). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Hormone

hyaluronic acid (HA)
A carbohydrate polymer often found in the extracellular matrix and often serves a lubrication function.

hydropathy index
An index (reported on the y axis) that is a measure of the average hydrophobicity of a given amino acid residue (hydropathy score) and the average hydropathy score of a range of amino acids on either side combined into one value.

hydropathy plot
A graph used to predict the number of position of transmembrane domains in an amino acid sequence. Each amino acid’s hydropathy score is plotted with the N terminus of the protein starting at position 0 on the x axis. A peak on this plot above the threshold indicates a potential transmembrane domain.

hydropathy score
A set value indicating the hydrophobicity of a given amino acid.

hydrophilic
Latin for “water loving.” Refers to chemical groups that readily associate with polar molecules like water.

hydrophobic
Latin for “water fearing.” Refers to chemical groups that do not readily associate with polar molecules like water. Instead, these are generally nonpolar in nature and group with other nonpolar molecules.

hydrophobic effect
“The observed tendency of nonpolar substances to aggregate in an aqueous solution and exclude water molecules.” Source: Hydrophobic effect. (2023, June 13). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Hydrophobic_effect

I

immunolabeling
“A biochemical process that enables the detection and localization of an antigen to a particular site within a cell, tissue, or organ. Antigens are organic molecules, usually proteins, capable of binding to an antibody.” Source: Immunolabeling. (2023, February 9). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Immunolabeling

immunoprecipitation
A technique that uses an antibody bound to an insoluble bead to selectively isolate a protein out of a solution. This will purify and concentrate a protein of interest and anything that is bound to that protein.

importin
“A type of karyopherin that transports protein molecules from the cell’s cytoplasm to the nucleus. It does so by binding to specific recognition sequences, called nuclear localization sequences (NLS).” Source: Importin. (2022, November 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Importin

in silico
Refers to experiments conducted in a computer; computer simulations.

inositol
A ringed sugar molecule that is commonly used in signaling pathways.

integral membrane protein
A type of protein that is embedded into biological membranes. Transmembrane proteins are an example of integral membrane proteins that span the entire biological membrane and are used to transport material from one side to the other.

intermediate filaments
A family of proteins that polymerize to form ropelike structures. These provide mechanical strength as part of the cytoskeletal system.

intermolecular forces (IMF)
“The force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighboring particles, e.g., atoms or ions. Intermolecular forces are weak relative to intramolecular forces—the forces which hold a molecule together.” Source: Intermolecular force. (2023, June 22). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Intermolecular_force

internal START transfer sequence
A start signal sequence that is somewhere internal on the protein as opposed to at the N-terminus of the protein. The START sequence is always either the first ER insertion sequence or one that directly follows a START (if there are multiple ER insertion sequences). Unlike the N-terminal START sequence, this is not cleaved off after the transfer of the protein has been completed.

interphase
All phases of the cell cycle that are not mitosis or meiosis. This stage contains G1, S, and G2 phases.

interpolar microtubules
The microtubules emanating from a spindle pole that attach in the center (between the two poles).

intron
A region of noncoding DNA that is usually located between two exons and is spliced out of the mRNA segment after transcription.

ion-channel-coupled receptors
When a signal binds to this type of receptor, an ion channel is opened as a result.

IP3 (inositol triphosphate)
“An inositol phosphate signaling molecule. It is made by hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2), a phospholipid that is located in the plasma membrane, by phospholipase C (PLC). Together with diacylglycerol (DAG), IP3 is a second messenger molecule used in signal transduction in biological cells.” Source: Inositol trisphosphate. (2023, May 1). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Inositol_trisphosphate

J

juxtacrine
In this contact dependent signaling pathway, a cell attaches to another cell to initiate the signaling pathway.

K

karyopherin
“Proteins involved in transporting molecules between the cytoplasm and the nucleus of a eukaryotic cell.” Source: Karyopherin. (2023, February 22). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Karyopherin

KDEL
A targeting sequence defined by the amino acids KDEL (lysine, aspartate, glutamate, and leucine). If these proteins travel to the Golgi, this sequence helps them to be recognized by a receptor to be returned to the ER.

KDEL receptor
A protein that binds to the KDEL amino acid sequences in the Golgi to help load them into vesicles back to the ER.

kinase
An enzyme that adds a phosphate chemical group to another enzyme. These can be added on serines, threonines, or tyrosine.

kinesin
A molecular motor that uses microtubules. Most kinesin motors move toward the plus end, but not all.

kinetochore
“A disc-shaped protein structure associated with duplicated chromatids in eukaryotic cells where the spindle fibers attach during cell division to pull sister chromatids apart.” Source: Kinetochore. (2023, March 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Kinetochore

kinetochore microtubule
A microtubule emanating from the spindle pole that attaches to the kinetochore of a chromosome during mitosis.

lag phase
A beginning stage of a chemical reaction where the reaction proceeds slowly.

lamellipodium
“A cytoskeletal protein actin projection on the leading edge of the cell.” Source: Lamellipodium. (2022, November 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Lamellipodium

lamin (nuclear)
“Fibrous proteins in type V intermediate filaments, providing structural function and transcriptional regulation in the cell nucleus. Nuclear lamins interact with inner nuclear membrane proteins to form the nuclear lamina on the interior of the nuclear envelope.” Source: Lamin. (2023, January 21). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Lamin

lamin-associated domain (LAD)
Areas on the nuclear lamina that link the nuclear lamina to specific regions of chromosomes.

lariat loop
The intronic DNA between two exons that is ‘looped’ out during the splicing process by the spliceosome. It is so called because the shape mimics a lasso loop used by farm hands when wrangling animals.

leading edge
The portion of the cell that is at the “front” with respect to the direction of movement.

leaflet
A single layer of a lipid bilayer.

ligand (signaling)
A molecule that binds to a receptor to initiate a signaling cascade.

light-dependent reactions
The biochemical reactions that occur in the plant chloroplast that depend on light. These include the process of photophosphorylation.

linker DNA
The DNA between two nucleosomes.

lipid raft
A distinct membrane region that contains specialized lipids and proteins. Often these regions are a bit thicker than surrounding membrane areas and provide specialized functions like cell signaling.

liposomes
“A small artificial vesicle, spherical in shape, having at least one lipid bilayer.” Source: Intermolecular force. (2023, June 22).
In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Intermolecular_force

loss-of-function experiment
An experiment designed to test how the functional inhibition of a protein/gene impacts the system. Loss-of-function experiments help us determine what aspects of the system are required (i.e., necessary).

loss-of-function mutation
A form of mutation that causes a gene to produce proteins that are lacking molecular functions present in the nonmutated protein.

lumen
The area inside a membrane-bound organelle. For instance, the ER lumen, Golgi lumen, and lysosomal lumen.

lysosomal pathway
Refers to the vesicle trafficking pathway originating at the TGN and ending at the lysosome for lysosomal resident proteins. Proteins are recognized by a receptor at the TGN and transported to the endosome where the protein is disassociated from the receptor. The protein then travels to the lysosome. The receptor is transported back to the TGN for further rounds of trafficking.

lysosome
A roughly spherical membrane-bound organelle that contains digestive enzymes. This compartment breaks down materials delivered from the endocytic pathway.

M

M (mitosis) phase
The stage of the cell cycle where mitosis and cytokinesis occur.

magnification
Refers to enlarging the apparent size of an image. This is akin to scaling or zooming in on an image and does not change its inherent resolution.

mannose-6-phosphate (M6P)
A mannose sugar phosphorylated on the sixth carbon with a phosphate.

mannose-6-phosphate receptor (M6PR)
The protein receptor that recognizes M6P on proteins.

MAP kinase cascade
A three-part signaling cascade where a MAPKKK phosphorylates a MAPKK, which then phosphorylates a MAPK. These are part of a larger signaling pathway.

matrix
The area inside the mitochondria where the TCA cycle, mitochondrial DNA, and mitochondrial ribosomes are located.

messenger RNA (mRNA)
“A single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of synthesizing a protein.” Source: Messenger RNA. (2023, June 7). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Messenger_RNA

metaphase
The stage of mitosis where chromosomes are lined up in a line on the metaphase plate.

metaphase checkpoint
Ensures that chromosomes are properly lined up prior to starting the next phase, anaphase.

metaphase plate
An invisible axis where chromosomes line up during metaphase.

methylation
“Denotes the addition of a methyl group on a substrate, or the substitution of an atom (or group) by a methyl group.” Source: Methylation. (2023, July 4). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Methylation

microtubule organizing center (MTOC)
“A structure found in eukaryotic cells from which microtubules emerge.” Source: Microtubule organizing center. (2023, March 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Microtubule_organizing_center

microtubules (MT)
“Polymers of tubulin that form part of the cytoskeleton and provide structure and shape to eukaryotic cells.” Source: Microtubule. (2023, July 15). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Microtubule

minus end
The portion of the microtubule filament that grows slower and has a higher critical concentration. This is the end with alpha tubulin exposed.

mitochondrial processing peptidase (MPP)
“An enzyme complex found in mitochondria which cleaves signal sequences from mitochondrial proteins.” Source: Mitochondrial processing peptidase. (2023, January 29). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Mitochondrial_processing_peptidase

mitochondrion
A membrane-bound organelle in a cell known to produce and secrete a chemical currency called ATP.

mitosis
A cellular process of nuclear division.

mitotic chromosome
Refers to the structure of a chromosome during the cellular process of mitosis. In this stage, the DNA is fully condensed, and the DNA appears as the characteristic X’s.

mitotic spindle
A microtubule arrangement established during mitosis.

molecular switch (protein)
“Proteins can switch between active and inactive states, thus acting as molecular switches in response to another signal. For example, phosphorylation of proteins can be used to activate or inactivate proteins.” Source: Molecular switch. (2023, June 10). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Molecular_switch

monolayer-associated protein
A protein that is embedded in a biological membrane but only interacts with one layer of the bilayer.

monomer
Composed of one unit. With a protein, this refers to having a single polypeptide chain.

monomeric
Existing as a single unit. With a protein, this refers to having a single polypeptide chain.

motor proteins
Proteins that bind to cytoskeletal filaments and use energy to move along them.

myosin
A molecular motor that uses actin filaments. Most myosin motors move toward the plus end, but not all.

N

N-linked glycosylation
“The attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine [Asn] residue of a protein), in a process called N-glycosylation.” Source: N-linked glycosylation. (2023, July 9). In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/N-linked_glycosylation

N-terminal START transfer sequence
A sequence of hydrophobic amino acids located at the N-terminus of a protein. This sequence will be cleaved after the protein has been imported into the ER.

native gel electrophoresis
“Native gels are run in non-denaturing conditions so that the analyte’s natural structure is maintained. This allows the physical size of the folded or assembled complex to affect the mobility, allowing for analysis of all four levels of the biomolecular structure.” Source: Gel electrophoresis. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Gel_electrophoresis

negative feedback loop
A regulatory mechanism whereby the product of a process will negatively influence (downregulate) itself.

negative staining
“An established method, often used in diagnostic microscopy, for contrasting a thin specimen with an optically opaque fluid. In this technique, the background is stained, leaving the actual specimen untouched, and thus visible.” Source: Negative stain. (2021, December 4). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Negative_stain

neuronal
Referring to neurons, an electrically excitable cell that is associated with the brain.

neurotransmitters
“A signaling molecule secreted by a neuron to affect another cell across a synapse.” Source: Neurotransmitter. (2023, April 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Neurotransmitter

nitric oxide (NO)
“In mammals, including humans…a signaling molecule in many physiological and pathological processes.” Source: Nitric oxide. (2023, July 11). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Nitric_oxide

nonhistone chromatin-associated protein
A protein whose function aids in maintenance of DNA packing but is not in the histone family.

nonpolar
Refers to molecules that have do not have one end of the molecule that is different from the other end. Most often, this refers to electron distribution. Nonpolar molecules share electrons evenly and never carry a dipole or charge. Nonpolar can also refer to the symmetrical shape of molecules, such as the tetrameric form of intermediate filaments.

nuclear bodies
Membraneless structures found in the nucleus. A common example is the nucleolus.

nuclear envelope
The lipid bilayer that surrounds the nucleus. It is a double bilayer with a perinuclear space in between. The outer membrane is continuous with the ER, and nuclear pores go through both layers of the envelope.

nuclear export receptor
A protein that binds to a nuclear export signal to help proteins exit the nucleus.

nuclear export signal (NES)
A short targeting sequence found in proteins that allows them to bind to the nuclear export receptor to be transported out of the nucleus into the cytoplasm.

nuclear import receptor (NIR)
A protein that binds to a nuclear localization signal (NLS) to help proteins enter the nucleus through the nuclear pore.

nuclear lamina
Fibrous mesh formed by intermediate filaments and membrane-associated proteins found just inside the nuclear envelope of cells. It functions as a structural support and helps maintain chromosome organization among other functions.

nuclear lamins
A type of intermediate filament found in animal cells. They polymerize to form the nuclear lamina.

nuclear localization sequence (NLS)
A sequence of amino acids (KKKRK) that marks the protein to be sent to the nucleus of the cell via nuclear transport. Without an NLS tag, the protein will remain in the cytosol and won’t be capable of entering the nucleus.

nuclear pore
A complex of proteins that spans the double membrane of the nuclear envelope, which surrounds a cell’s nucleus. The pore serves as a method of transport for molecules to be able to enter or exit the nucleus through either a passive or active process.

nuclear receptors (signaling)
“A class of proteins responsible for sensing steroids, thyroid hormones, vitamins, and certain other molecules. These intracellular receptors work with other proteins to regulate the expression of specific genes thereby controlling the development, homeostasis, and metabolism of the organism.” Source: Nuclear receptor. (2023, May 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Nuclear_receptor

nucleation sites
A preformed structure that allows molecules in a reaction to be more favorably arranged. In regards to the cytoskeleton, nucleation sites include small preformed pieces of cytoskeleton. These make it easier for other cytoskeletal monomers to attach and thus speeds up the rate of reaction.

nucleolus
A membraneless organelle within the nucleus where ribosome biogenesis takes place.

nucleolus organizing regions (NORs)
“Chromosomal regions crucial for the formation of the nucleolus.” Source: Nucleolus organizer region. (2022, October 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Nucleolus_organizer_region

nucleoplasm
The fluid and molecules found within the nucleus.

nucleosome
“The basic structural unit of DNA packaging in eukaryotes. The structure of a nucleosome consists of a segment of DNA wound around eight histone proteins and resembles thread wrapped around a spool.” Source: Nucleosome. (2023, June 18). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Nucleosome

nucleosome eviction
A chromatin remodeling process where an enzyme removes a core set of histone from a region of DNA. This opens up this region so that it is able to be accessed by other proteins.

nucleosome sliding
A chromatin remodeling process where a chromatin remodeling enzyme moves a nucleosome thereby exposing the DNA that was originally around the histone core. This opens up this region so that it is able to be accessed by other proteins.

O

O-linked glycosylation
“The attachment of a sugar molecule to the oxygen atom of serine (Ser) or threonine (Thr) residues in a protein.” Source: O-linked glycosylation. (2021, October 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/O-linked_glycosylation

octamer
Refers to the eight histone proteins that form the core of the nucleosome. It contains two copies of each of the four core histone proteins (H2A, H2B, H3, and H4). DNA is wrapped around this structure to create a nucleosome.

odorants
The chemicals that make up smell molecules. These are detected by odorant receptors in the nose. Subsequent signaling and activation of neurons to the brain help us sense these molecules.

oxidative phosphorylation
“The metabolic pathway in which cells use enzymes to oxidize nutrients, thereby releasing chemical energy in order to produce adenosine triphosphate (ATP).” Source: Oxidative phosphorylation. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Oxidative_phosphorylation

P

paracrine
A short-range signaling pathway where a cell secretes a signaling molecule that is picked up by target cells in the local vicinity.

PCR (polymerase chain reaction)
“A method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) to a large enough amount to study in detail.” Source: Polymerase chain reaction. (2023, June 27). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Polymerase_chain_reaction

perinuclear space
The region between the two membranes of the nuclear envelope.

peripheral membrane protein
Membrane proteins that do not embed in the biological membrane. Instead, they bind to other integral proteins or more rarely interact with the lipids themselves.

phagocytosis
The process of bringing in a large particle (like a bacterium or a cancerous cell) for digestion.

phagosome
“A vesicle formed around a particle engulfed by a phagocyte via phagocytosis.” Source: Phagosome. (2023, February 11). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phagosome

phase-contrast microscopy (PCM)
“An optical microscopy technique that converts phase shifts in light passing through a transparent specimen to brightness changes in the image.” Source: Phase-contrast microscopy. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phase-contrast_microscopy

phosphatases
Proteins that remove a phosphate from a target protein.

phosphodiesterase
An enzyme that cleaves a phosphodiester bond. These occur in between nucleic acids or within a ringed nucleotide such as cyclic AMP.

phospholipase C (PLC)
“Phospholipase C’s role in signal transduction is its cleavage of phosphatidylinositol 4,5-bisphosphate (PIP2) into diacyl glycerol (DAG) and inositol 1,4,5-trisphosphate (IP3), which serve as second messengers.” Source: Phospholipase C. (2023, June 24). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phospholipase_C

phospholipid
“A class of lipids whose molecule has a hydrophilic ‘head’ containing a phosphate group and two hydrophobic ‘tails’ derived from fatty acids, joined by an alcohol residue (usually a glycerol molecule).” Source: Phospholipid. (2023, May 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phospholipid

phospholipid bilayer
Composed of two sheets of phospholipids. The lipids are orientated so that the polar heads are facing outward and the nonpolar fatty acid tails are facing inward.

phosphomimetics
An amino acid substitution in a engineered protein to mimic the rough charge and shape of a phosphorylated protein at that location.

phosphorylation
The attachment of a phosphate group to a biological molecule. When applied to a protein, this can often change the conformation of the protein, resulting in a functional change.

photobleach
Refers to fading. Often this is in reference to a fluorescence molecule that is no longer able to be seen.

photophosphorylation
The biochemical process of turning light energy into ATP.

phragmoplast
“A plant cell specific structure that forms during late cytokinesis. It serves as a scaffold for cell plate assembly and subsequent formation of a new cell wall separating the two daughter cells.” Source: Phragmoplast. (2023, May 12). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phragmoplast

PI-3-kinase
“A family of related intracellular signal transducer enzymes capable of phosphorylating the 3 position hydroxyl group of the inositol ring of phosphatidylinositol (PtdIns).” Source: Phosphoinositide 3-kinase. (2022, October 27). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phosphoinositide_3-kinase

pinocytosis
An endocytic process that occurs continually and nonselectively. The membrane invaginates, bringing in small molecules from the external environment.

PIP (phosphatidylinositol)
A family of lipids containing a phosphate head, two fatty acid tails, and an inositol head group. These compose a small but functionally relevant component of the cytosolic side of a cell’s membranes.

PIP2
“Phosphatidylinositol 4,5-bisphosphate or PtdIns(4,5)P2, also known simply as PIP2 or PI(4,5)P2, is a minor phospholipid component of cell membranes. PtdIns(4,5)P2 is enriched at the plasma membrane where it is a substrate for a number of important signaling proteins.” Source: Phosphatidylinositol 4,5-bisphosphate. (2023, January 26). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Phosphatidylinositol_4,5-bisphosphate

pKa
A measure of a molecule’s readiness to donate a proton in solution. When an amino acid has a higher pKa, it is more likely to be a basic amino acid, preferring to keep its proton. Conversely, an amino acid with a low pKa will be willing to donate its proton and is called acidic.

plasma membrane
A biological membrane that separates the cell from the surrounding environment. It is composed of a phospholipid bilayer, proteins, and carbohydrate components.

plastid
A membrane-bound organelle found in plants. Commonly plastids will differentiate into chloroplasts, but other examples include leucoplasts and chromoplasts.

plastoglobules
“Spherical bubbles of lipids and proteins about 45–60 nanometers across. They are surrounded by a lipid monolayer. Plastoglobuli are found in all chloroplasts.” Source: Chloroplast. (2023, July 14). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Chloroplast

plus end
The portion of the microtubule filament that grows faster and has a lower critical concentration. This is the end with beta tubulin exposed.

polar
Refers to molecules that have one end of the molecule that is different from the other end. Most often, this refers to an uneven electron distribution, where extreme uneven distribution of electrons results in ionized molecules with a charge. Polar can also refer to shape differences on different ends of a molecule, as is the case with polar cytoskeletal elements.

polarity
Refers to molecules that have a distinct endedness. If referring to electron distribution, molecules with unequal electron sharing are said to be polar. Extreme versions are ions. With regards to the cytoskeleton, the protein face that is exposed is distinct and refers to the polarity in these elements.

polarized light microscopy
A subset of transmitted light microscopy where polarized light is used to enhance the contrast of the image. DIC (differential interface contrast) microscopy is one common example of this technique.

polyadenylation
“The addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation.” Source: Polyadenylation. (2023, March 21). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Polyadenylation

polymer
A strand of repeating units called monomers.

porin
A protein in the outer membrane of chloroplasts and mitochondria that allows small molecules to pass through via diffusion.

positive feedback loop
A regulatory mechanism whereby the products of a process will positively influence (upregulate) themselves.

presequence
The mitochondria and chloroplast targeting signal. It is an N-terminal sequence that forms a helical structure needed for correct receptor recognition and transport to the proper organelle.

primary endosymbiosis
“Involves the engulfment of a cell by another free living organism.” Source: Symbiogenesis. (2023, May 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Symbiogenesis

primary producers
Autotrophic organisms that provide the base of the food chain.

primary sequence (structure)
Refers to the sequence of the protein. Amino acids are joined into a polymer. The unique sequence of each polypeptide chain dictates how it will fold.

prometaphase
The intermediary mitotic phase between prophase and metaphase. Distinct in this phase is nuclear lamina breakdown and further attachment of kinetochore microtubules.

promoter
The sequence of DNA just prior to the transcription start site. General transcription factors bind here to recruit RNA polymerase to initiate the start of transcription.

prophase
The first phase of mitosis. The DNA begins to condense and the mitotic spindle begins to form.

protein aggregates
Proteins that form clusters with other proteins. The aggregation tends to be composed of misfolded proteins that join to other misfolded proteins.

protein backbone
The repeating atomic structure formed when amino acids are joined through a peptide bond. These form N-C-C repeats referring to the central atoms in the amide, R-group, carboxylic acid groups that form each amino acid.

protein cap
Proteins that bind to microtubule polymers. This prevents them from growing or shrinking.

protein coding region
The region of a gene that directly translates into protein.

protein domain
“A region of a protein’s polypeptide chain that is self-stabilizing and that folds independently from the rest.” Source: Protein domain. (2023, June 4). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Protein_domain

protein kinase A (PKA)
“A family of serine-threonine kinase whose activity is dependent on cellular levels of cyclic AMP (cAMP).” Source: Protein kinase A. (2023, July 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Protein_kinase_A

protein processing
The process of modifying proteins after they are translated.

proteoglycans
“Proteins that are heavily glycosylated. The basic proteoglycan unit consists of a ‘core protein’ with one or more covalently attached glycosaminoglycan (GAG) chain(s).” Source: Proteoglycan. (2023, February 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Proteoglycan

proteolysis
“The breakdown of proteins into smaller polypeptides or amino acids.” Source: Proteolysis. (2023, May 10). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Proteolysis

proteosome
“A protein coplex that is responsible for degrading unneeded or damaged proteins through proteolytic chemical reactions that break peptide bonds.” Source: Proteasome. (2023, January 29). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Proteasome

protofilament
A single polymerized strand of microtubules. Thirteen such strands associate into a hollow tube-like structure.

proton pump
A protein that moved protons from one side of the membrane to the other, creating a gradient.

proton-motive force
A description of the potential energy captures in a proton gradient. When the protons are allowed to flow down their gradient through ATP synthase, this allows for ATP to be made much like a hydroelectric dam makes electricity from the flow of water through turbines.

Q

quaternary structure
Refers to the interactions between two independent polypeptide chains. Not all proteins have quaternary structure. Some will only have quaternary structure transiently.

R

R group (or side chain)
A variable chemical structure off the central carbon of an amino acid. The different chemical features of the R group define each amino acid and give it its overall characteristics (size, shape, charge etc.).

Rab (protein)
A small protein that is a member of the GTPase family and is important in the processes of vesicle trafficking.

Ran cycle
A process by which the Ran protein is shuttled in and out of the nucleus to facilitate the import and export of molecules through the nuclear import channel.

Ras
“A family of related proteins that are expressed in all animal cell lineages and organs. All Ras protein family members belong to a class of protein called small GTPase, and are involved in transmitting signals within cells.” Source: RasGTPase. (2023, March 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ras_GTPase

receptor (signaling)
A protein that binds a signal molecule to transmit a cascade intracellularly.

receptor downregulation
A regulatory process where a receptor is brought into the cell via endocytosis, and then degraded in the lysosome.

receptor inactivation
A regulatory process where a biological molecule directly inhibits the cell receptor’s function.

receptor sequestration
A regulatory process where a receptor is endocytosed such that it isn’t available to bind to signal molecules on the cell’s surface.

receptor-mediated endocytosis
A process in which cargo from outside the cell enters, creating inward budding vesicles from the plasma membrane. This process is controlled by receptors located on the cell surface, and cargo is only allowed to enter after a ligand has bonded to a corresponding receptor.

receptor-tyrosine kinases (RTKs)
“The high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones.” Source: Receptor tyrosine kinase. (2022, February 19). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Receptor_tyrosine_kinase

recovery curve
The graph formed by a FRAP experiment. It measures the fluorescence intensity of a region over time to assess how much fluorescence “recovers” after the initial photobleaching step.

regulated secretion
A form of secretion that is regulated by external factors like signals that allow certain secretory vesicles to fuse with the plasma membrane.

regulatory DNA sequences
Refers to particular segments of the regulatory region that binds proteins. These proteins modify the level of gene expression. For example, there can be an enhancer protein that, when bound to the regulatory sequence, would upregulate the amount a particular gene that is expressed.

regulatory region
The region outside of the gene region of DNA that binds proteins to modify the level of gene expression for a particular gene.

repressor protein
A protein that inhibits the transcription of a particular gene when it binds to a regulatory DNA sequence.

resolution
“Quantifies how close lines can be to each other and still be visibly resolved. Resolution units can be tied to physical sizes (e.g., lines per mm, lines per inch), to the overall size of a picture (lines per picture height, also known simply as lines, TV lines, or TVL), or to angular subtense.” Source: Image resolution. (2023, June 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Image_resolution

retrograde traffic
Vesicle tracking that moves opposite of the default movement of traffic. In the secretory pathway, an example would be going from the Golgi back to the ER.

ribonucleoprotein (RNP)
“A complex of ribonucleic acid and RNA-binding protein. These complexes play an integral part in a number of important biological functions that include transcription, translation and regulating gene expression and regulating the metabolism of RNA.” Source: Nucleoprotein. (2022, July 26). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Nucleoprotein

ribosomal RNA (rRNA)
“A ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA (rDNA) and then bound to ribosomal proteins to form small and large ribosome subunits.” Source: Ribosomal RNA. (2023, July 3). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ribosomal_RNA

ribosomes
“Macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits.” Source: Ribosome. (2023, June 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ribosome

ribozyme
“RNA molecules that have the ability to catalyze specific biochemical reactions, including RNA splicing in gene expression, similar to the action of protein enzymes.” Source: Ribozyme. (2023, February 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ribozyme

RNA capping (5′ cap)
“A specially altered nucleotide on the 5′ end of some primary transcripts such as precursor messenger RNA. This process, known as mRNA capping, is highly regulated and vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis.” Source: Five-prime cap. (2023, January 31). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Five-prime_cap

rosette
A special protein structure where cellulose is made in plant cells destined for use in the cell wall.

rough ER (rER)
A section of the ER where the membrane is studded with ribosomes and is responsible for the process of protein production and protein folding.

S

S (synthesis) phase
A discrete stage in the cell cycle where the whole genome is duplicated.

saturated lipids
A lipid that has no double bonds within the hydrocarbon chain.

scaffold protein
Proteins that “interact and/or bind with multiple members of a signaling pathway, tethering them into complexes. In such pathways, they regulate signal transduction and help localize pathway components (organized in complexes) to specific areas of the cell.” Source: Scaffold protein. (2021, September 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Scaffold_protein

scanning electron microscopy (SEM)
“A type of electron microscope that produces images of a sample by scanning the surface with a focused beam of electrons.” Source: Scanning electron microscope. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Scanning_electron_microscope

scission
A term used to describe the process of vesicles detaching from the donor compartment.

scramblase
A protein that will move lipids from one monolayer (leaflet) to the other in a lipid bilayer. They are not selective in direction and do not require an energy input.

SDS-PAGE (SDS–polyacrylamid gel electroporesis)
A method to separate molecules (primarily proteins but sometimes DNA) by size. For protein separation, SDS (a detergent molecule) helps denature (unfold) the protein and gives it a consistent size-to-charge ratio. Then the proteins are loaded into a gel matrix and induced with an electric charge. The negatively charged proteins move toward the positive terminal. Larger molecules take longer to move through the gel and stay at the top, while smaller molecules can move more easily through the gel and reside at the bottom.

second messengers
Biological molecules released as part of a signaling cascade as a way to amplify the signal.

secondary endosymbiosis
“Occurs when the product of primary endosymbiosis is itself engulfed and retained by another free living eukaryote.” Source: Symbiogenesis. (2023, May 28). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Symbiogenesis

secondary structure
Refers to local repeated backbone-backbone interactions of the polypeptide chain. There are two common forms of secondary structure: alpha helices and beta sheets.

secretion
Refers to proteins leaving the cell through the secretory pathway.

secretory pathway
Refers to the protein trafficking pathway originating at the ER and ending at the plasma membrane, where soluble proteins are released into the extracellular space and integral membrane proteins are embedded in the plasma membrane. Proteins are first imported into the ER and moved to the Golgi for further processing before being sent to the plasma membrane / cell exterior. This is the default pathway for proteins targeted to the ER and does not require additional targeting sequences beyond ER insertion sequences.

selectively permeable
A feature of biological membranes that allows only certain molecules and ions to pass through to the inside of the cell. Selective permeability is useful in controlling the composition of the internal cellular environment.

self-assembly
A cellular structure that assembles without input of energy.

serine/threonine kinases
Kinases (enzymes that add a phosphate group) on serine or threonine amino acids of the target protein.

signal peptidase
An enzyme that is responsible for cleaving the N-terminal start sequences from the rest of the protein once trafficked and inserted into the ER.

signal recognition particle (SRP)
“An abundant, cytosolic, universally conserved ribonucleoprotein (protein-RNA complex) that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes.” Source: Signal recognition particle. (2022, October 18). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Signal_recognition_particle

signal transduction
“The process by which a chemical or physical signal is transmitted through a cell as a series of molecular events.” Source: Signal transduction. (2023, June 20). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Signal_transduction

signaling cascade
“A series of chemical reactions that occur within a biological cell when initiated by a stimulus.” Source: Biochemical cascade. (2023, June 16). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Biochemical_cascade

signaling protein inactivation
When a biological molecule that is part of a signaling cascade is prevented from participating in its role.

sister chromatid
Identical copies of a chromatid that are attached at the centromere after genome duplication in S phase. They will remain attached until anaphase, when they are pulled apart toward opposite spindle poles. Each sister chromatid represents one half of a replicated chromosome.

small nuclear ribonucleoproteins (snRNPs; pronounced “snurps”)
“RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.” Source: SnRNP. (2021, September 20). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/SnRNP

smooth ER (sER)
A region of the ER that does not contain any ribosomes. It is involved in many metabolic processes, including phospholipid synthesis, needed for membrane formation.

SNARE
Part of a class of proteins needed for vesicle fusion. When a vesicle nears a target membrane, if there are appropriately matched SNARE proteins, they will bind. This binding causes the proteins to wind up, physically bringing the membranes in close proximity such that the lipid bilayers can fuse.

soluble protein
A protein that is not embedded in a membrane and can diffuse freely in an aqueous environment.

spliceosome
“A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins.” Source: Spliceosome. (2023, July 20). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Spliceosome

splicing (introns)
Process in which introns are removed from a pre-mRNA and exons are joined back together. This is required as part of the process to form a mature mRNA.

starch granules
“Storage areas where starch molecules are stored at night.” Source: Starch. (2023, July 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Starch

stem cells
“Undifferentiated or partially differentiated cells that can differentiate into various types of cells and proliferate indefinitely to produce more of the same stem cell.” Source: Stem cell. (2023, July 17). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Stem_cell

STOP transfer sequence
An ER insertion sequence that is located after a START sequence. It signifies to the translocation channel to stop threading the translated protein into the ER lumen. This sequence eventually is released into the membrane and exists as a transmembrane domain for the protein.

stroma
The area inside the chloroplast inner membrane that surrounds the thylakoids.

stromal processing peptidase (SPP)
A chloroplast enzyme that cleaves off the transit peptide of proteins in the stroma of chloroplasts.

structural maintenance of chromosome (SMC) complex
“Represent a large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics.” Source: SMC protein. (2023, May 23). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/SMC_protein

substrate-level phosphorylation
“A metabolism reaction that results in the production of ATP or GTP supported by the energy released from another high-energy bond that leads to phosphorylation of ADP or GDP to ATP or GTP.” Source: Substrate-level phosphorylation. (2023, March 13). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Substrate-level_phosphorylation

superresolution microscopy
“A series of techniques in optical microscopy that allow such images to have resolutions higher than those imposed by the diffraction limit, which is due to the diffraction of light.” Source: Super-resolution microscopy. (2023, May 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Super-resolution_microscopy

T

target-SNARE (t-SNARE)
A type of SNARE that is located in the membranes of target membranes and will pair with specific v-SNAREs found on vesicle membranes.

targeting sequence
A short peptide sequence located in a protein that dictates to which organelle it is transported. Proteins without any such sequences remain in the cytosol.

telomeres
A region at the end of linear chromosomes with repetitive sequences. Specialized proteins will bind to this area. In addition, these repetitive sequences contain no genes and protect the genetic loss when the chromosomes are repeatedly replicated.

telophase
The last stage of mitosis, characterized by the DNA decondensing and the nuclear envelope reforming.

temperature-sensitive mutation
Mutants of a gene where the result is a lack of activity when exposed to its restrictive temperatures. Often proper function is restored when brought back to the optimal (permissive) temperature.

template strand
The strand of DNA that is read by RNA polymerase to make mRNA during transcription. It is read 3′ to 5′.

terminal differentiation
“During terminal differentiation, a precursor cell formerly capable of cell division permanently leaves the cell cycle, dismantles the cell cycle machinery and often expresses a range of genes characteristic of the cell’s final function (e.g. myosin and actin for a muscle cell).” Source: Cellular differentiation. (2023, April 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Cellular_differentiation

tertiary structure
All the structure of the protein that is not primary or secondary or quaternary. This defines the 3D shape and encompasses interactions between side chains, side chains–backbone, and backbone-backbone (that are not local or repeated).

tether (protein)
Tether proteins in the target membrane help with vesicle docking. Tether proteins bind to the Rab proteins to bring the vesicle closer to the target membrane such that SNARE proteins are then able to bind and promote vesicle fusion.

tetramer
A group of four proteins.

thylakoid lumen
“The thylakoid lumen is a continuous aqueous phase enclosed by the thylakoid membrane. It plays an important role for photophosphorylation during photosynthesis.” Source: Thylakoid. (2023, May 24). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Thylakoid

thylakoid membrane
“The thylakoid membrane is the site of the light-dependent reactions of photosynthesis with the photosynthetic pigments embedded directly in the membrane.” Source: Thylakoid. (2023, May 24).
In Wikipedia, The Free Encyclopedia. https://en.wikipedia.org/wiki/Thylakoid

topologically associated domains (TADs)
“A topologically associating domain (TAD) is a self-interacting genomic region, meaning that DNA sequences within a TAD physically interact with each other more frequently than with sequences outside the TAD.” Source: Topologically associating domain. (2023, June 10). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Topologically_associating_domain

trans Golgi network (TGN)
The end location of the Golgi where proteins are sorted into vesicles bound for their next destination. Primary post-Golgi locations include the plasma membrane and the endosome.

transcribed region
A region of DNA that is transcribed into RNA. There are three types of transcripts: mRNA, rRNA, and tRNA.

transcription factors
Proteins involved in regulating the transcription of genes.

transcription start site (+1 site)
The location of a gene where the DNA begins to be transcribed into RNA.

transcription stop site
A specific sequence that RNA polymerase recognizes and that causes transcription of DNA to stop. Normally the transcription stop site is located and the end of a gene.

transcytosis
“A type of transcellular transport in which various macromolecules are transported across the interior of a cell. Macromolecules are captured in vesicles on one side of the cell, drawn across the cell, and ejected on the other side.” Source: Transcytosis. (2022, September 25). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Transcytosis

transduced
Refers to the process of signal transduction. When a signal is transduced, it is changed from its original form along the pathways. For example, when a signal binds to a receptor, this induces a conformational change in the receptor to activate it. The signal can be said to be transduced from a physical molecule to an activated receptor.

transfer RNA (tRNA)
A special type of RNA that carries an amino acid. During the process of translation, the tRNA binds to a correct codon and the amino acid is transferred to the growing peptide.

transit peptide
An N-terminal region of amino acids that serves as the chloroplast targeting sequence.

transitional ER (tER)
A region of ER where the rER and sER meet. Often it is the exit site for vesicles leaving the ER.

translation start site
The three-letter start codon signals the ribosome to begin translation of the messenger RNA transcript.

translation stop site (stop codon)
Termination marks the end of translation. This happens when a three-letter stop codon in the messenger RNA is reached and placed in the A site of the ribosome.

translocation channel (ER)
Channel necessary for inserted proteins into the ER. When an ER insertion sequence emerges from a protein, SRP binds and brings it to the SRP receptor, which interacts with the translocation channel. Anything after this sequence is threaded through the channel in the ER lumen unless it runs into a STOP translocation sequence.

transmembrane protein
A protein that has a region that extends through the full membrane. As a result, the protein will have exposure to both sides of the membrane.

transmission electron microscopy (TEM)
“Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a grid. An image is formed from the interaction of the electrons with the sample as the beam is transmitted through the specimen.” Source: Transmission electron microscopy. (2023, June 2). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Transmission_electron_microscopy

transport proteins
Refers to proteins in a membrane that facilitate the movement of molecules across a biological membrane.

transporter inner chloroplast membrane (TIC)
Part of the TIC/TOC complex, TIC (transporter inner chloroplast membrane) lives in the inner chloroplast membrane to help facilitate chloroplast proteins’ transfer from the cytoplasm into the chloroplast stroma.

transporter inner mitochondrial membrane (TIM)
Part of the TIM/TOM complex, TIM (transporter inner mitochondrial membrane) lives in the inner mitochondrial membrane to help facilitate mitochondrial proteins’ transfer from the cytoplasm into the mitochondrial matrix.

transporter outer chloroplast membrane (TOC)
Part of the TIC/TOC complex, TOC (transporter outer chloroplast membrane) lives in the outer chloroplast membrane to help facilitate chloroplast proteins’ transfer from the cytoplasm into the chloroplast stroma.

transporter outer mitochondrial membrane (TOM)
Part of the TIM/TOM complex, TOM (transporter outer mitochondrial membrane) lives in the outer mitochondrial membrane to help facilitate mitochondrial proteins’ transfer from the cytoplasm into the mitochondrial matrix.

triskelion
The name for clathrin monomers that form a cage-like structure around a forming transport vesicle.

tubulin
A family of proteins. Notably, alpha and beta tubulin dimers will polymerize into microtubules.

U

ubiquitin
“A small (8.6 kDa) regulatory protein found in most tissues of eukaryotic organisms.” Source: Ubiquitin. (2023, July 18). In Wikipedia, The Free Encyclopediahttps://en.wikipedia.org/wiki/Ubiquitin

unfolded protein response
A cellular response to unfolded proteins whereby they are targeted for destruction.

unsaturated lipid
A lipid that has at least one double bonded carbon in its chain.

upstream
The region 5′ of the indicated location in a piece of DNA.

V

vacuole
An organelle present in plants and fungi that is responsible for the degradation of materials originating in the endocytic pathway. Vacuoles also play a storage role that is not present in the animal lysosome, which is the functional equivalent in animal cells.

vesicle
A small membrane-bound structure containing cargo proteins destined for a particular cellular location in the endomembrane system.

vesicle budding
The process of a vesicle forming from the donor membrane in a cell or organelle.

vesicle docking
Involves the use of tether proteins to get closer to the target compartment prior to fusion.

vesicle fusion
The process of merging a vesicle membrane with the membrane of the target compartment, thereby releasing the contents into the lumen of the target (or the extracellular space in the case of the cell membrane). The process is mediated by SNARE proteins.

vesicle transport
The movement of proteins and other biological molecules through the cells in membrane compartments called vesicles.

vesicle-SNARE (v-SNARE)
A type of SNARE located in the membrane of transport vesicles.

vesicular transport model
A model describing the function of the Golgi. In this model, the cisternae stay stable in a Golgi. Proteins traveling through this system will bud from each cisterna and fuse with the next subcompartment using vesicles.

Δ

ΔG = ΔH – TΔS
The Gibbs free energy equation. When the ΔG is negative, this indicates a spontaneous reaction and does not need extra energy input to occur.

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Fundamentals of Cell Biology Copyright © 2024 by Lauren Dalton and Robin Young is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License, except where otherwise noted.

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