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Cell biology is a branch of biology that studies the structure, function, and behavior of cells. All living organisms are made of cells. A cell is the basic unit of life that is responsible for the living and functioning of organisms. Cell biology is the study of the structural and functional units of cells. Cell biology encompasses both prokaryotic and eukaryotic cells and has many subtopics which may include the study of cell metabolism, cell communication, cell cycle, biochemistry, and cell composition. The study of cells is performed using several microscopy techniques, cell culture, and cell fractionation. These have allowed for and are currently being used for discoveries and research pertaining to how cells function, ultimately giving insight into understanding larger organisms. Knowing the components of cells and how cells work is fundamental to all biological sciences while also being essential for research in biomedical fields such as cancer, and other diseases. Research in cell biology is interconnected to other fields such as genetics, molecular genetics, molecular biology, medical microbiology, immunology, and cytochemistry.
The endoplasmic reticulum (ER) is a part of a transportation system of the eukaryotic cell, and 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, and tubular structures in the SER. The membranes of the ER are continuous with the outer nuclear membrane. The endoplasmic reticulum is not found in red blood cells, or spermatozoa.
The endomembrane system is composed of the different membranes (endomembranes) that are suspended in the cytoplasm within a eukaryotic cell. These membranes divide the cell into functional and structural compartments, or organelles. In eukaryotes the organelles of the endomembrane system include: the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes, and plasma (cell) membrane among others. The system is defined more accurately as the set of membranes that forms a single functional and developmental unit, either being connected directly, or exchanging material through vesicle transport. Importantly, the endomembrane system does not include the membranes of plastids or mitochondria, but might have evolved partially from the actions of the latter.
Protein targeting or protein sorting is the biological mechanism by which proteins are transported to their appropriate destinations within or outside the cell. Proteins can be targeted to the inner space of an organelle, different intracellular membranes, the plasma membrane, or to the exterior of the cell via secretion. Information contained in the protein itself directs this delivery process. Correct sorting is crucial for the cell; errors or dysfunction in sorting have been linked to multiple diseases.
A signal peptide is a short peptide present at the N-terminus of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles, secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, most type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide.
The translocon is a complex of proteins associated with the translocation of polypeptides across membranes. In eukaryotes the term translocon most commonly refers to the complex that transports nascent polypeptides with a targeting signal sequence into the interior space of the endoplasmic reticulum (ER) from the cytosol. This translocation process requires the protein to cross a hydrophobic lipid bilayer. The same complex is also used to integrate nascent proteins into the membrane itself. In prokaryotes, a similar protein complex transports polypeptides across the (inner) plasma membrane or integrates membrane proteins. In either case, the protein complex are formed from Sec proteins, with the heterotrimeric Sec61 being the channel. In prokaryotes, the homologous channel complex is known as SecYEG.
COPI is a coatomer, a protein complex that coats vesicles transporting proteins from the cis end of the Golgi complex back to the rough endoplasmic reticulum (ER), where they were originally synthesized, and between Golgi compartments. This type of transport is retrograde transport, in contrast to the anterograde transport associated with the COPII protein. The name "COPI" refers to the specific coat protein complex that initiates the budding process on the cis-Golgi membrane. The coat consists of large protein subcomplexes that are made of seven different protein subunits, namely α, β, β', γ, δ, ε and ζ.
The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide, referring to the free amine group (-NH2) located at the end of a polypeptide. Within a peptide, the amine group is bonded to the carboxylic group of another amino acid, making it a chain. That leaves a free carboxylic group at one end of the peptide, called the C-terminus, and a free amine group on the other end called the N-terminus. By convention, peptide sequences are written N-terminus to C-terminus, left to right (in LTR writing systems). This correlates the translation direction to the text direction, because when a protein is translated from messenger RNA, it is created from the N-terminus to the C-terminus, as amino acids are added to the carboxyl end of the protein.
In cell biology, microsomes are heterogeneous vesicle-like artifacts re-formed from pieces of the endoplasmic reticulum (ER) when eukaryotic cells are broken-up in the laboratory; microsomes are not present in healthy, living cells.
ER retention refers to proteins that are retained in the endoplasmic reticulum, or ER, after folding; these are known as ER resident proteins.
Endoplasm generally refers to the inner, dense part of a cell's cytoplasm. This is opposed to the ectoplasm which is the outer (non-granulated) layer of the cytoplasm, which is typically watery and immediately adjacent to the plasma membrane. The nucleus is separated from the endoplasm by the nuclear envelope. The different makeups/viscosities of the endoplasm and ectoplasm contribute to the amoeba's locomotion through the formation of a pseudopod. However, other types of cells have cytoplasm divided into endo- and ectoplasm. The endoplasm, along with its granules, contains water, nucleic acids, amino acids, carbohydrates, inorganic ions, lipids, enzymes, and other molecular compounds. It is the site of most cellular processes as it houses the organelles that make up the endomembrane system, as well as those that stand alone. The endoplasm is necessary for most metabolic activities, including cell division.
A secretory protein is any protein, whether it be endocrine or exocrine, which is secreted by a cell. Secretory proteins include many hormones, enzymes, toxins, and antimicrobial peptides. Secretory proteins are synthesized in the endoplasmic reticulum.
P24 protein family is a group of transmembrane proteins that are major components of COPI and COPII-coated vesicles. The family is also known as EMP24/GP25L/p24 family and TMP21-like proteins. The latter naming was after transmembrane emp24 domain-containing protein 10 that was found in the human brain. It was claimed to block the beta-amyloid peptide, which is implicated in the pathogenesis of Alzheimer's disease.
KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1, also known as KDELR1, is a protein which in humans is encoded by the KDELR1 gene.
KDEL is a target peptide sequence in mammals and plants located on the C-terminal end of the amino acid structure of a protein. The KDEL sequence prevents a protein from being secreted from the endoplasmic reticulum (ER) and facilitates its return if it is accidentally exported.
In cell biology, membrane bound polyribosomes are attached to a cell's endoplasmic reticulum. When certain proteins are synthesized by a ribosome they can become "membrane-bound". The newly produced polypeptide chains are inserted directly into the endoplasmic reticulum by the ribosome and are then transported to their destinations. Bound ribosomes usually produce proteins that are used within the cell membrane or are expelled from the cell via exocytosis.
Membrane contact sites (MCS) are close appositions between two organelles. Ultrastructural studies typically reveal an intermembrane distance in the order of the size of a single protein, as small as 10 nm or wider, with no clear upper limit. These zones of apposition are highly conserved in evolution. These sites are thought to be important to facilitate signalling, and they promote the passage of small molecules, including ions, lipids and reactive oxygen species. MCS are important in the function of the endoplasmic reticulum (ER), since this is the major site of lipid synthesis within cells. The ER makes close contact with many organelles, including mitochondria, Golgi, endosomes, lysosomes, peroxisomes, chloroplasts and the plasma membrane. Both mitochondria and sorting endosomes undergo major rearrangements leading to fission where they contact the ER. Sites of close apposition can also form between most of these organelles most pairwise combinations. First mentions of these contact sites can be found in papers published in the late 1950s mainly visualized using electron microscopy (EM) techniques. Copeland and Dalton described them as “highly specialized tubular form of endoplasmic reticulum in association with the mitochondria and apparently in turn, with the vascular border of the cell”.
Chloroplast DNA (cpDNA) is the DNA located in chloroplasts, which are photosynthetic organelles located within the cells of some eukaryotic organisms. Chloroplasts, like other types of plastid, contain a genome separate from that in the cell nucleus. The existence of chloroplast DNA was identified biochemically in 1959, and confirmed by electron microscopy in 1962. The discoveries that the chloroplast contains ribosomes and performs protein synthesis revealed that the chloroplast is genetically semi-autonomous. The first complete chloroplast genome sequences were published in 1986, Nicotiana tabacum (tobacco) by Sugiura and colleagues and Marchantia polymorpha (liverwort) by Ozeki et al. Since then, a great number of chloroplast DNAs from various species have been sequenced.
KKXX and for some proteins XKXX is a target peptide motif located in the C terminus in the amino acid structure of a protein responsible for retrieval of endoplasmic reticulum (ER) membrane proteins to and from the Golgi apparatus. These ER membrane proteins are transmembrane proteins that are then embedded into the ER membrane after transport from the Golgi. This motif is exclusively cytoplasmic and interacts with the COPI protein complex to target the ER from the cis end of the Golgi apparatus by retrograde transport.
HDEL is a target peptide sequence in plants and yeasts located on the C-terminal end of the amino acid structure of a protein. The HDEL sequence prevents a protein from being secreted from the endoplasmic reticulum (ER) and facilitates its return if it is accidentally exported.
References
- ↑ Rapoport T. (Nov 2007). "Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membranes". Nature. 450 (7170): 663–9. Bibcode:2007Natur.450..663R. doi:10.1038/nature06384. PMID 18046402. S2CID 2497138.
- ↑ Mariano Stornaiuolo; Lavinia V. Lotti; Nica Borgese; Maria-Rosaria Torrisi; Giovanna Mottola; Gianluca Martire & Stefano Bonatti (March 2003). "KDEL and KKXX Retrieval Signals Appended to the Same Reporter Protein Determine Different Trafficking between Endoplasmic Reticulum, Intermediate Compartment, and Golgi Complex". Molecular Biology of the Cell. 14 (3): 889–902. doi:10.1091/mbc.E02-08-0468. PMC 151567 . PMID 12631711.
- ↑ Carrie, Christopher; Small, Ian (February 2013). "A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1833 (2): 253–259. doi: 10.1016/j.bbamcr.2012.05.029 . PMID 22683762.
- ↑ Sharma, Mayank; Bennewitz, Bationa; Klösgen, Ralf Bernd (December 2018). "Rather rule than exception? How to evaluate the relevance of dual protein targeting to mitochondria and chloroplasts". Photosynthesis Research. 138 (3): 335–343. Bibcode:2018PhoRe.138..335S. doi:10.1007/s11120-018-0543-7. ISSN 0166-8595. PMID 29946965. S2CID 49427254.
- ↑ Sharma, Mayank; Kretschmer, Carola; Lampe, Christina; Stuttmann, Johannes; Klösgen, Ralf Bernd (2019-06-01). "Targeting specificity of nuclear-encoded organelle proteins with a self-assembling split-fluorescent protein toolkit". Journal of Cell Science. 132 (11): jcs230839. doi: 10.1242/jcs.230839 . ISSN 0021-9533. PMID 31085714.
- ↑ Baudisch, Bianca; Langner, Uwe; Garz, Ingo; Klösgen, Ralf Bernd (January 2014). "The exception proves the rule? Dual targeting of nuclear-encoded proteins into endosymbiotic organelles". New Phytologist. 201 (1): 80–90. doi: 10.1111/nph.12482 . PMID 24024706. S2CID 32965612.
- ↑ Ge, Changrong; Spånning, Erika; Glaser, Elzbieta; Wieslander, Åke (January 2014). "Import Determinants of Organelle-Specific and Dual Targeting Peptides of Mitochondria and Chloroplasts in Arabidopsis thaliana". Molecular Plant. 7 (1): 121–136. doi: 10.1093/mp/sst148 . PMID 24214895.
- ↑ "Pepscan Motifs". shenlab.sols.unlv.edu. Retrieved 7 April 2019.
- ↑ "Subcellular localization signal". metadb.riken.jp. Retrieved 7 April 2019.
- ↑ Lee, PA; Tullman-Ercek, D; Georgiou, G (2006). "The bacterial twin-arginine translocation pathway". Annual Review of Microbiology. 60: 373–95. doi:10.1146/annurev.micro.60.080805.142212. PMC 2654714 . PMID 16756481.