Endoplasmic reticulum in the context of Protein folding

Red algae, or Rhodophyta (/roʊˈdɒfɪtə/, /ˌroʊdəˈfaɪtə/; from Ancient Greek ῥόδον (rhódon) 'rose' and φυτόν (phutón) 'plant'), make up one of the oldest groups of eukaryotic algae. The Rhodophyta comprises one of the largest phyla of algae, containing over 7,000 recognized species within over 900 genera amidst ongoing taxonomic revisions. The majority of species (6,793) are Florideophyceae, and mostly consist of multicellular, marine algae, including many notable seaweeds. Red algae are abundant in marine habitats. Approximately 5% of red algae species occur in freshwater environments, with greater concentrations in warmer areas. Except for two coastal cave dwelling species in the asexual class Cyanidiophyceae, no terrestrial species exist, which may be due to an evolutionary bottleneck in which the last common ancestor lost about 25% of its core genes and much of its evolutionary plasticity.

Red algae form a distinct group characterized by eukaryotic cells without flagella and centrioles, chloroplasts without external endoplasmic reticulum or unstacked (stroma) thylakoids, and use phycobiliproteins as accessory pigments, which give them their red color. Despite their name, red algae can vary in color from bright green, soft pink, resembling brown algae, to shades of red and purple, and may be almost black at greater depths. Unlike green algae, red algae store sugars as food reserves outside the chloroplasts as floridean starch, a type of starch that consists of highly branched amylopectin without amylose. Most red algae are multicellular, macroscopic, and reproduce sexually. The life history of red algae is typically an alternation of generations that may have three generations rather than two. Coralline algae, which secrete calcium carbonate and play a major role in building coral reefs, belong there.

An organelle is a specialized subunit, within a biological cell, that has a specific function. The name organelle comes from the idea that these structures are parts of cells, as organs are to the body, hence organelle, the suffix -elle being a diminutive. Organelles are either separately enclosed within their own lipid bilayers (also called membrane-bound organelles) or are spatially distinct functional units without a surrounding lipid bilayer (non-membrane bounded organelles). Although most organelles are functional units within cells, some functional units that extend outside of cells are often termed organelles, such as cilia, the flagellum and archaellum, and the trichocyst (these could be referred to as membrane bound in the sense that they are attached to (or bound to) the membrane).

Organelles are identified by microscopy, and can also be purified by cell fractionation. There are many types of organelles, particularly in eukaryotic cells. They include structures that make up the endomembrane system (such as the nuclear envelope, endoplasmic reticulum, and Golgi apparatus), and other structures such as mitochondria and plastids. While prokaryotes do not possess eukaryotic organelles, some do contain protein-shelled bacterial microcompartments, which are thought to act as primitive prokaryotic organelles; and there is also evidence of other membrane-bounded structures. Also, the prokaryotic flagellum which protrudes outside the cell, and its motor, as well as the largely extracellular pilus, are often spoken of as organelles.

The chlorarachniophytes are a small group of exclusively marine algae widely distributed in tropical and temperate waters. They are typically mixotrophic, ingesting bacteria and smaller protists as well as conducting photosynthesis. Normally they have the form of small amoebae, with branching cytoplasmic extensions that capture prey and connect the cells together, forming a net. These extensions are dependent on the presence of light and polymerization of the actin cytoskeleton. They may also form flagellate zoospores, which characteristically have a single subapical flagellum that spirals backwards around the cell body, and walled coccoid cells.

The chloroplasts were presumably acquired by ingesting some green alga. They are surrounded by four membranes, the outermost of which is continuous with the endoplasmic reticulum, and contain a small nucleomorph between the middle two, which is a remnant of the alga's nucleus. This contains a small amount of DNA and divides without forming a mitotic spindle. The origin of the chloroplasts from green algae is supported by their pigmentation, which includes chlorophylls a and b, and by genetic similarities. The only other groups of algae that contain nucleomorphs are a few species of dinoflagellates, which also have plastids originating from green algae, and the cryptomonads, which acquired their chloroplasts from a red alga.

A hypha (from Ancient Greek ὑφή (huphḗ) 'web'; pl. hyphae) is a long, branching, filamentous structure of a fungus, oomycete, or actinobacterium. In most fungi, hyphae are the main mode of vegetative growth, and are collectively called a mycelium.

In molecular biology, post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes, which translate mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.

Post-translational modifications can occur on the amino acid side chains or at the protein's C- or N- termini. They can expand the chemical set of the 22 amino acids by changing an existing functional group or adding a new one such as phosphate. Phosphorylation is highly effective for controlling the enzyme activity and is the most common change after translation. Many eukaryotic and prokaryotic proteins also have carbohydrate molecules attached to them in a process called glycosylation, which can promote protein folding and improve stability as well as serving regulatory functions. Attachment of lipid molecules, known as lipidation, often targets a protein or part of a protein attached to the cell membrane.

Glycoproteins are proteins which contain oligosaccharide (sugar) chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as glycosylation. Secreted extracellular proteins are often glycosylated.

In proteins that have segments extending extracellularly, the extracellular segments are also often glycosylated. Glycoproteins are also often important integral membrane proteins, where they play a role in cell–cell interactions. It is important to distinguish endoplasmic reticulum-based glycosylation of the secretory system from reversible cytosolic-nuclear glycosylation. Glycoproteins of the cytosol and nucleus can be modified through the reversible addition of a single GlcNAc residue that is considered reciprocal to phosphorylation and the functions of these are likely to be an additional regulatory mechanism that controls phosphorylation-based signalling. In contrast, classical secretory glycosylation can be structurally essential. For example, inhibition of asparagine-linked, i.e. N-linked, glycosylation can prevent proper glycoprotein folding and full inhibition can be toxic to an individual cell. In contrast, perturbation of glycan processing (enzymatic removal/addition of carbohydrate residues to the glycan), which occurs in both the endoplasmic reticulum and Golgi apparatus, is dispensable for isolated cells (as evidenced by survival with glycosides inhibitors) but can lead to human disease (congenital disorders of glycosylation) and can be lethal in animal models. It is therefore likely that the fine processing of glycans is important for endogenous functionality, such as cell trafficking, but that this is likely to have been secondary to its role in host-pathogen interactions. A famous example of this latter effect is the ABO blood group system.

The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material.

The nuclear envelope consists of two lipid bilayer membranes: an inner nuclear membrane and an outer nuclear membrane. The space between the membranes is called the perinuclear space. It is usually about 10–50 nm wide. The outer nuclear membrane is continuous with the endoplasmic reticulum membrane. The nuclear envelope has many nuclear pores that allow materials to move between the cytosol and the nucleus. Intermediate filament proteins called lamins form a structure called the nuclear lamina on the inner aspect of the inner nuclear membrane and give structural support to the nucleus.

Intracellular transport is the movement of vesicles and substances within a cell. Intracellular transport is required for maintaining homeostasis within the cell by responding to physiological signals. Proteins synthesized in the cytosol are distributed to their respective organelles, according to their specific amino acid's sorting sequence. Eukaryotic cells transport packets of components to particular intracellular locations by attaching them to molecular motors that haul them along microtubules and actin filaments. Since intracellular transport heavily relies on microtubules for movement, the components of the cytoskeleton play a vital role in trafficking vesicles between organelles and the plasma membrane by providing mechanical support. Through this pathway, it is possible to facilitate the movement of essential molecules such as membrane‐bounded vesicles and organelles, mRNA, and chromosomes.

Intracellular transport is unique to eukaryotic cells because they possess organelles enclosed in membranes that need to be mediated for exchange of cargo to take place. Conversely, in prokaryotic cells, there is no need for this specialized transport mechanism because there are no membranous organelles and compartments to traffic between. Prokaryotes are able to subsist by allowing materials to enter the cell via simple diffusion. Intracellular transport is more specialized than diffusion; it is a multifaceted process which utilizes transport vesicles. Transport vesicles are small structures within the cell consisting of a fluid enclosed by a lipid bilayer that hold cargo. These vesicles will typically execute cargo loading and vesicle budding, vesicle transport, the binding of the vesicle to a target membrane and the fusion of the vesicle membranes to target membrane. To ensure that these vesicles embark in the right direction and to further organize the cell, special motor proteins attach to cargo-filled vesicles and carry them along the cytoskeleton. For example, they have to ensure that lysosomal enzymes are transferred specifically to the golgi apparatus and not to another part of the cell which could lead to deleterious effects.

Cellular compartments in cell biology comprise all of the closed parts within the cytosol of a eukaryotic cell, usually surrounded by a single or double lipid layer membrane. These compartments are often, but not always, defined as membrane-enclosed organelles. The formation of cellular compartments is called compartmentalization.

Both organelles, the mitochondria and chloroplasts (in photosynthetic organisms), are compartments that are believed to be of endosymbiotic origin. Other compartments such as peroxisomes, lysosomes, the endoplasmic reticulum, the cell nucleus or the Golgi apparatus are not of endosymbiotic origin. Smaller elements like vesicles, and sometimes even microtubules can also be counted as compartments.

In biochemistry, fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes. Two de novo fatty acid syntheses can be distinguished: cytosolic fatty acid synthesis (FAS/FASI) and mitochondrial fatty acid synthesis (mtFAS/mtFASII). Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine (by means of ester bonds) to form triglycerides (also known as "triacylglycerols" – to distinguish them from fatty "acids" – or simply as "fat"), the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surrounds the organelles within the cells (such as the cell nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, etc.).

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 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 (see below).

The nuclear membrane contains a lipid bilayer that encompasses the contents of the nucleus. The endoplasmic reticulum (ER) is a synthesis and transport organelle that branches into the cytoplasm in plant and animal cells. The Golgi apparatus is a series of multiple compartments where molecules are packaged for delivery to other cell components or for secretion from the cell. Vacuoles, which are found in both plant and animal cells (though much bigger in plant cells), are responsible for maintaining the shape and structure of the cell as well as storing waste products. A vesicle is a relatively small, membrane-enclosed sac that stores or transports substances. The cell membrane is a protective barrier that regulates what enters and leaves the cell. There is also an organelle known as the Spitzenkörper that is only found in fungi, and is connected with hyphal tip growth.