Molecular & Cell Biology

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197 terms · Flash cards derived from the Open University S204 course text, The Core Of Life.

Eukaryote

An organism whose cells contain complex structures enclosed within membranes. The defining membrane bound structure thats sets them apart from prokaryotic cells is the nucleas or nuclear envelope within which the genetic material is carried. All species of large complex species are eukaryotes, including animals, plants and funghi.

Euchromatin

This shows as pale areas in the nucleas under electro magnification. It is a less densly packed form of chromatin; 10% is even less condensed and in this form it can be actively transcribed to produce RNA.

Heterochromatin

This shows as dark areas on the eukaryotic nucleas; it is densly packed chormatin (DNA and protein complex) which cannot be transcribed.

Histones

Special proteins around which DNA is wrapped.

Lamins

Intermediate filament proteins which protect the structure of the nucleas, they polymerize to from a network of filaments that lie just within the nuclear membrane. The network of these filament proteins is called the nuclear lamina.

Nuclear Lamina

The network of intermediate nuclear filament proteins (Lamins) which is located just below the nuclear membrane and is linked to the membrane and chromatin.

Nuclear Pores

9nm (approx) gaps in the nuclear envelope that allow the passage of RNA and ribosomes out of the nucleas and the entry of selected small proteins and small water soluble molecules.

Prokarayotes

An organism of the kingdom of Monera, comprising the bacteria and cyanobacteria. Characterised by the abscence of a distinct, membrane bound nucleas or membrane bound organelles and by DNA that is not organised in to chromosomes. Also called moneran.

Protoctist

Any of various unicellular eukaryotic organisms and their multicellular, coenocytic or colocial descendants that belong to the kingdom of Protocista according to some taxonomic systems. The protoctists include protozoans, slime moulds, various algae and other groups. In many new classification systems, all proctists are considered protists.

Signal Sequence

Affectionately known as the 'address label' of a polypeptide. A short (3-60 amino acids long) peptide chain that directs the transport of a protein. These may also be called targeting signals, signal peptides, transit peptides, or localization signals.

The amino acid sequences of these direct proteins (which are synthesized in the cytosol) to certain organelles such as the nucleus, mitochondrial matrix, endoplasmic reticulum, chloroplast, apoplast and peroxisome. Some signal peptides are cleaved from the protein by signal peptidase after the proteins are transported.

Endoplasmic Reticulum

The endoplasmic reticulum (ER) is a eukaryotic organelle that forms an interconnected network of tubules, vesicles, and cisternae within cells. Rough endoplasmic reticula synthesize proteins, while smooth endoplasmic reticula synthesize lipids and steroids, metabolize carbohydrates and steroids (but not lipids), and regulate calcium concentration, drug metabolism, and attachment of receptors on cell membrane proteins. Sarcoplasmic reticula solely regulate calcium levels.

Smooth endoplasmic reticulum

Cell organelle responsible for attachment of receptors on cell membrane proteins, synthesizing lipids and steroids, metabolizing carbohydrates and steroids (but not lipids) and regulating calcium concentration and drug metabolism.

Rough endoplasmic reticulum

Cell organelle responsible for synthesizing proteins.

Catalytic site

In molecular biology this site is part of an enzyme where substrates bind and undergo a chemical reaction.The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues (or nucleotides in ribozymes) that participate in recognition of the substrate. Residues that directly participate in the catalytic reaction mechanism are called active site residues.

Vesicles

Small lipid-bounded spheres which transport proteins, glyco proteins and newly synthesized lipids (which are imbedded in the sphere itself) from the endoplasmic reticulum to the Golgi Apparatus or from the Golgi apparatus to another destination. They move short distances by the process of difussion, moving long distances requires the assistance of proteins associated with microtubules.

Golgi apparatus

This is an organelle found in all eukaryotic cells.It was identified in 1897 by the Italian physician Camillo Golgi, after whom it is named. It processes and packages proteins after their synthesis and before they make their way to their destination; it is particularly important in the processing of proteins for secretion. Its size varies in different types of cells depending on cell function; a hormone secreting cell will contain a far larger version of this organelle than a muscle cell for example. It also forms a part of the cellular endomembrane system.

Constitutive release

The constant release of small amounts of a substances from the cell membrane.

Regulated release

The release of substances from a cell membrane only when specific conditions exist. A good example is the release of gastrointestinal hormones and digestive enzymes in response to food.

Exocytosis

The process by which substances are exported from a cell.

Phagocytosis/Endocytosis

The process by which substances or pathogens are taken in to a cell by engulfment by a vesicular structure surrounded by cell membrane.

Lysosomes

Small organelles which contain digestive enzymes with an internal pH of around 5. They are responsible for breaking down large molecules taken in to the cell by phagocytosis and also for the breaking down of old organelles.

Peroxisomes

Organelles that are plentiful in liver cells and adipocytes, responsible for breaking down fatty acids and amino acids in to hydrogen peroxide (among other things) via the action of an enzyme known as catalayse.

MItochondrian

Sausage shaped organelles with a double membrane. The inner membrane folds in to cristae. This organelle plays a fundamental role in the production of ATP in eukarayote cells and they are abundant in cells which require high amounts of energy such as muscle cells.

Cristae

Internal compartments formed by the inner membrane of a mitochondrion. They are studded with proteins, including ATP synthase and a variety of cytochromes. The maximum surface for chemical reactions to occur is within the mitochondria. This allows cellular respiration (aerobic respiration since the mitochondrion requires oxygen) to occur.

Mitochondrial DNA

The DNA located in mitochondria
It can be regarded as the smallest chromosome, and was the first significant part of the human genome to be sequenced. In most species, including humans, mtDNA is inherited solely from the mother. The DNA sequence of mtDNA has been determined from a large number of organisms and individuals (including some organisms that are extinct), and the comparison of those DNA sequences represents a mainstay of phylogenetics, in that it allows biologists to elucidate the evolutionary relationships among species. It also permits an examination of the relatedness of populations, and so has become important in anthropology and field biology.

Mitochondrial Matrix

This matrix contains soluble enzymes that catalyze the oxidation of pyruvate and other small organic molecules.
It also contains the mitochondria's DNA and ribosomes. The word "matrix" stems from the fact that this space is viscous, compared to the relatively aqueous cytoplasm.

Cell Wall

An extracellular structure in plants which is rigid and surrounds the cell membrane giving it shape and support, like playtex for plants lol! It is primarily composed of cellulose which is a polysaccharide.

Plastids

These are major organelles found in the cells of plants and algae. They are the site of manufacture and storage of important chemical compounds used by the cell, often containing pigments used in photosynthesis. The types of pigments present can change or determine the cell's color.These organelles are responsible for photosynthesis, storage of products like starch and for synthesis. All types are derived from proplastids (formerly "eoplasts", eo-: dawn, early), which are present in the meristematic regions of the plant. Proplastids and young chloroplasts commonly divide, but more mature chloroplasts also have this capacity.

Chloroplasts

These plant organelles have their own DNA like mitochondria. They are normally larger than mitochondria though and they also have a three membrane system.

Thylakoid

A thylakoid is a membrane-bound compartment inside chloroplasts and cyanobacteria. They are the site of the light-dependent reactions of photosynthesis. Thylakoids consist of a thylakoid membrane surrounding a thylakoid lumen. Chloroplast thylakoids frequently form stacks of disks referred to as grana (singular: granum). Grana are connected by intergrana or stroma thylakoids, which join granum stacks together as a single functional compartment.

Stroma

Stroma (fluid), the fluid in between grana, where carbohydrate formation reactions occur in the chloroplasts of plant cells photosynthesizing

Glycosaminoglycans (GAG's)

Also known as mucopolysaccharides these are long unbranched polysaccharides consisting of a repeating disaccharide unit. The repeating unit consists of a hexose (six-carbon sugar) or a hexuronic acid, linked to a hexosamine (six-carbon sugar containing nitrogen). These are the major component of the 'gel' found in the extracellular matrix of tissue. They are negatively charged and thus attract ions, especially sodium which aids diffusion of water in to the tissue, giving tissue it's compression resistance.

Extracellular Matrix

This matrix is secreted by cells and laid down externally and it's properties vary enormously depending on it's chemical composition and which tissue is being examined. In some cells it acts as cement or scaffolding. In plants it can be associated with individual cells.

Elastin

An flexible protein found in the extra cellular matrix of blood vessels.

Collagen

A strong protein which can provide strength and/or flexibility found in animal tissue.

Connective Tissue

The name often given to tissue that contain a large proportion of extracellular matrix. In this tissues the cells that are secreting the materials are often quite far from each other.

Gap junction

A specialised type of cell junction, an example of which is the smooth muscle of the intestine. The gap's allow for effective transmission of molecules and electrical activity between the cells.

Tight junctions

These cell junctions are linked very closely and prevent movement of membrane proteins, in the skin for example or in the role mainting the polarity of the cells of the intestine.

Cytoskeleton

A system of specialised long filament like proteins found in the cytosol of eukaryote cells which forms the constantly changing 'scaffolding'. They have many roles such as movement of motile cells, transport of organelles around the cell and intracellular movement of chromosomes during mitosis.

Microfilaments

Also known as actin filaments,one of three protein sub units that make up the eukaryote cytoskeleton. Found in highest concentration around the edges of the cell just below the cell membrane, they tend to form bundles. Actin polymers have the ability to disassemble and re-assemble meaning they are particulary useful for cell locomotion and in the microvilli of absorptive epithelial cells.

Tubulin

The protein of which the microtubules of the eukaryote cytoskeleton are formed.

Microtubules

Hollow tubes composed of thirteen parallel filaments of polymerized tubulin, measuring about 25 nm in external diameter. Part of the cytoskeleton of ALL eukaryote cells radiating from the centrosome in the nucleas towards the edges of the cell. They are very unstable and are constantly disassembling and reassembling so most do not reach the cell cortex. These tubules play a crucial role in cell organisation, movement of organelles and the reorganization of chormosomes in to daughter cells during mitosis.

Gel Filtration

This form of filtration chromatography seprarates proteins, peptides, and oligonucleotides on the basis of size. Molecules move through a bed of porous beads, diffusing into the beads to greater or lesser degrees. Smaller molecules diffuse further into the pores of the beads and therefore move through the bed more slowly, while larger molecules enter less or not at all and thus move through the bed more quickly. Both molecular weight and three-dimensional shape contribute to the degree of retention. This technique may be used for analysis of molecular size, for separations of components in a mixture, or for salt removal or buffer exchange from a preparation of macromolecules.

Gel Electrophoresis

In simple terms: This is a procedure which enables the sorting of molecules based on size and charge. Using an electric field, molecules (such as DNA) can be made to move through a gel made of agar. The molecules being sorted are dispensed into a well in the gel material. The gel is placed in an electrophoresis chamber, which is then connected to a power source. When the electric current is applied, the larger molecules move more slowly through the gel while the smaller molecules move faster. The different sized molecules form distinct bands on the gel.

SDS-PAGE

SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis, is a technique widely used in biochemistry, forensics, genetics and molecular biology to separate proteins according to their electrophoretic mobility (a function of length of polypeptide chain or molecular weight). SDS gel electrophoresis of samples that have identical charge per unit mass due to binding of SDS results in fractionation by size. This method can be used to separate all types, even those that are not water soluble.

Two Dimensional PAGE

Also known as 2-D electrophoresis, begins with 1-D electrophoresis but then separates the molecules by a second property in a direction 90 degrees from the first. In 1-D electrophoresis, proteins (or other molecules) are separated in one dimension, so that all the proteins/molecules will lie along a lane but that the molecules are spread out across a 2-D gel. Because it is unlikely that two molecules will be similar in two distinct properties, molecules are more effectively separated in 2-D electrophoresis than in 1-D electrophoresis.

Western Blotting

This protein seperation technique (sometimes called the protein immunoblot) is a widely used analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract. It uses gel electrophoresis to separate native or denatured proteins by the length of the polypeptide (denaturing conditions) or by the 3-D structure of the protein (native/ non-denaturing conditions). The proteins are then transferred to a membrane (typically nitrocellulose or PVDF), where they are probed (detected) using antibodies specific to the target protein.

There are now many reagent companies that specialize in providing antibodies (both monoclonal and polyclonal antibodies) against tens of thousands of different proteins. Commercial antibodies can be expensive, although the unbound antibody can be reused between experiments. This method is used in the fields of molecular biology, biochemistry, immunogenetics and other molecular biology disciplines.

Tertiary Structure

In biochemistry and molecular biology, this structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[6] Proteins and nucleic acids are capable of diverse functions ranging from molecular recognition to catalysis. Such functions require a precise three-dimensional tertiary structure. While such structures are diverse and seemingly complex, they are composed of recurring, easily recognizable tertiary structure motifs that serve as molecular building blocks. Tertiary structure is considered to be largely determined by the biomolecule's primary structure, or the sequence of amino acids or nucleotides of which it is composed. Efforts to predict tertiary structure from the primary structure are known generally as structure prediction.

Primary Structure

This is the name given to the sequence of amino acid monomer units, or residues of which a compound is composed.

Alpha carbon

The carbon bonded to the carboxyl group in an amino acid.

R Group

This is the group which varies in proteins and can be any of twenty amino acids, the polarity of this Group dictates how a protein will behave in certain pH conditions. This explains why enzymes require a certain pH to function.

Peptide Bond

This bond occurs when the amino group from one protein joins with the carboxyl group of another, forming a dipeptide.

Dipeptide

A protein formed by two amino acids linked by a peptide bond,

Amino Terminus

The name by which the -NH₂ free end of a peptide is known.

Carboxyl Terminus

The name by which the -COOH (carboxyl) free end of a peptide is known.

Peptide

Small chains of amino acids.

Mr

Shorthand for molecular mass.

Hydrophobic residues/amino acid

Amino acids which are non polar and are repelled by water example are Alanine, Valine, Leucine, Isoleucine, Proline, Methionine, Phenylalanine, Tryptophan and Cystine. Hydrophbicity is also affected by pH levels in some cases.

Hydrophillic residues/amino acid

Amino acids which are polar and are attracted to water examples are Glutamine, Serine,Theronine, Histodine, Lysine. Hydrophbicity is also affected by pH levels in some cases.

Polar

Pertaining to a compound exhibiting polarity or dipole moment, that is a compound bearing a partial positive charge on one side and a partial negative charge on the other.

Non Polar

Molecule which has no separation of charge, so no positive or negative poles are formed.

α Helix

A common motif in the secondary structure of proteins, the alpha helix (α-helix) is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier (i+4 \rightarrow i hydrogen bonding). This secondary structure is also sometimes called a classic Pauling-Corey-Branson alpha helix . Among types of local structure in proteins, the α-helix is the most regular and the most predictable from sequence, as well as the most prevalent.

β sheet

The β sheet (also β-pleated sheet) is the second form of regular secondary structure in proteins, only somewhat less common than alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A beta strand (also β strand) is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an almost fully extended conformation. The higher-level association of β sheets has been implicated in formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimer's disease.

Zymogens

A zymogen (or proenzyme) is an inactive enzyme precursor. A zymogen requires a biochemical change (such as a hydrolysis reaction revealing the active site, or changing the configuration to reveal the active site) for it to become an active enzyme. The biochemical change usually occurs in a lysosome where a specific part of the precursor enzyme is cleaved in order to activate it. The amino acid chain that is released upon activation is called the activation peptide.
The pancreas secretes zymogens partly to prevent the enzymes from digesting proteins in the cells in which they are synthesised. Fungi also secrete digestive enzymes into the environment as zymogens. The external environment has a different pH than inside the fungal cell and this changes the zymogen's structure into an active enzyme.

Proteolyisis

This process is the directed degradation (digestion) of proteins which fail to fold correctly by cellular enzymes called proteases or by intramolecular digestion.

Proteasomes

Proteasomes are very large protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm.The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into amino acids and used in synthesizing new proteins. Proteins to be destroyed are labelled by ubiquitin.

Ubiquitin

A small regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. Among other functions, it directs protein recycling.It can be attached to proteins and label them for destruction. This protein tag directs proteins to the proteasome, which is a large protein complex in the cell that degrades and recycles unneeded proteins. This discovery won the Nobel Prize for chemistry in 2004.
The tags can also direct proteins to other locations in the cell, where they control other protein and cell mechanisms.

Post-translation modification

This is the chemical modification of a protein after its translation. It is one of the later steps in protein biosynthesis, and thus gene expression, for many proteins.A protein (also called a polypeptide) is a chain of amino acids. During protein synthesis, 20 different amino acids can be incorporated to become a protein. After translation, the posttranslational modification of amino acids extends the range of functions of the protein by attaching it to other biochemical functional groups (such as acetate, phosphate, various lipids and carbohydrates), changing the chemical nature of an amino acid (e.g. citrullination), or making structural changes (e.g. formation of disulfide bridges).Also, enzymes may remove amino acids from the amino end of the protein, or cut the peptide chain in the middle. For instance, the peptide hormone insulin is cut twice after disulfide bonds are formed, and a propeptide is removed from the middle of the chain; the resulting protein consists of two polypeptide chains connected by disulfide bonds. Also, most nascent polypeptides start with the amino acid methionine because the "start" codon on mRNA also codes for this amino acid. This amino acid is usually taken off during post-translational modification.Other modifications, like phosphorylation, are part of common mechanisms for controlling the behavior of a protein, for instance activating or inactivating an enzyme.

Enzyme Substrate Complex

A non-covalent complex composed of a substrate bound to the active site of the enzyme

Substrate

In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate(s). In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or more products, which are then released from the active site. The active site is now free to accept another substrate molecule. In the case of more than one substrate, these may bind in a particular order to the active site, before reacting together to produce products.

Substrate specificity

A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. An ezyme can only react upon the substrate with which it locks.

Enzyme Assay

A technique used to measure the rate of activity of an enzyme by measuring the products expected of the enzyme activity, for example CO₂.

Km

The point on a rectangular hyperbola which is half the value of the Vmax. It indicates the affinity of an enzyme and substrate a high value means low affinity and a low value means high affinity (the enzyme substrate locks more securely and takes longer to seperate and release products).

Vmax

The point on a hyperbolic plot/during an enzyme assay at which the maximum rate of substrate to product conversion is reached and the line begins to level out. This is often used to indicate the maximum rate of enzyme activity, however it is only approximate as the plot line never completely levels out.

Michaelis-Menton equation

This equation can be used if a range of [S] values is known, to plot a line.
E + S ↔ ES → E + P

Hofstee-Eadie plot

A plot used to obtain a more accurate indication of Km and Vmax. Simplified - v/[S] so the figures used to plot the original hyperbolic rectangle are used dviding the enzyme byt hte substrate. These new figures are then plotted on along the horizontal axis and a best fit line drawn along them. The point at which the line crosses the vertical axis is the Vmax, the point at which it crosses the horizontal axis is the Km.

pH Optima

The optimum pH in which an enzyme is most active, this is normally related to the normal environment of the enzyme, for example Pepsin has a pH optima of around 2, ideal for the acidic environment of the vertebrate stomach.

Cofactors

Other conditions required by enzymes in order for them to perform their roles. For example metal ions (Mg²⁺ + K⁺) or coenzymes such as NDP, ATP or ADP. They cannot be made in the body of mammals and must be derived from vitamins in the diet.

Enzyme Inhibition

An important control mechanism in metabolism, this is also the route of effect used by many drugs and also of many toxins.

Irreversible Inhibitors

Usually not of biological origins, these act by forming strong covalent bonds with the enzyme, poisoning them. The bond is so strong it is irreversible and example of this would be heavy metal toxicity.

Reversible Inhibitors

This inhibition can be relieved by the removal of the inhibitor from the enzyme solution due to weak reversible interactions they form with the enzyme.

Competitive Inhibitor

This form of inhibitor is very similar in structure to the substrate and can thus form an enzyme inhibitor complex which prevents the enzyme substrate complex from forming. It is theorised that the higher concentration of substrate to that of inhibitor the lower the rate of inhibitor interaction thus allowing Vmax to be obtained.

Non Competitive Inhibitor

These inhibitors do not appear to have the same structure as substrate, it therefor binds at a different site on the enzyme and the ES complex can still form. It does however hinder the catylitic action of the enzyme and the end product is never produced.

Induced Fit

The term used to describe the effect of a substrate on the active site of an enzyme on binding. This suggests that the active site and substrate are not an exact fit but the actual binding of the substrate induces a change in the structure of the active site.

Allosteric Regulation

The form of enzyme regulation brought about when an effector molecule binds to an enzyme at it's allosteric site, thus bringing about changes in it's conformation and therefor effecting it's ability to function. This form of regulation is immediately effective and also immediately reversible.

Feedback inhibition of regulatory enzymes

This is the mechanism by which the activity of an enzyme is allosterically effected by the later products in the catalytic pathway, thus preventing over production of the product. So the penultimate product of the enzyme also acts as the effector molecule at the enzyme allosteric site.

Allosteric Inhibitor

A product produced later in a catalytic pathway which inhibits the activity of enxymes earlier in the catalytic pathway.

Allosteric Activator

These effectors are often products of an earlier step in a catalytic pathway, they act to increase the activity of an enzyme at a time of high substrate availability.

Cooperativity

This is the concept that allosteric enzymes have multiple active sites and that binding of a bustrate to one of these active sites changes the conformation of the other sites making ES binding more likely. This gives the enzyme greater sensitivity to change allowing better responsiveness to changes in substrate availability.

Allosteric enzymes

Five key characteristics (of this enzyme)
1.Larger, multi-subunit proteins consisting generally of two different subunits eg. catalytic and regulatory.
2. Substrates bind cooperatively to active sites on catalytic subunits.
3. A plot of v against s produces an S shaped sigmoid curve.
4. Effectors for these enzymes can be inhibiting or activating and their binding can also produce sigmoid curves.
5. Feedback inhibition can occur- the end product of the enzymes pathway can inhibit enzyme activity.

Reversible covalent modification

This process involves the reversible addition of a small chemical group (e.g phosphate, acetyl) to the side chain of a particular amino acid residue. The most common example of this modification is protein phosphorolation. This process plays a major role in cell functioning.

Plasmalemma

The name by which the cell membrane of a plant is sometimes known.

Spherical Micelle

The most stable structure for an aggregate of single tailed amphipathic liquid molecules e.g detergent in water.

Amphipathic Lipids

These lipids are molecules that are mostly lipid-like (hydrophobic) in structure, but at one end have a region that is polar or ionic (hydrophilic). The hydrophilic region is usually referred to as the head group, and the lipid portion is known as the tail(s). Cell membranes typically consist of three separate classes of lipids of this type. These include phospholipids, glycolipids, and steroids.

Liposomes

The structure formed by two tailed lipids when mixed with water, it consists of a spherical bilayer withthe hydrophobic tails pointing inwards and the hydrophillic heads pointing outwards in close contact with each other and the water.

FRAP (Fluorescence recovery after photobleaching)

An optical technique capable of quantifying the two dimensional lateral diffusion of a molecularly thin film containing fluorescently labeled probes, or to examine single cells. This technique is very useful in biological studies of cell membrane diffusion and protein binding. In addition, surface deposition of a fluorescing phospholipid bilayer (or monolayer) allows the characterization of hydrophilic (or hydrophobic) surfaces in terms of surface structure and free energy. Similar, though less well known, techniques have been developed to investigate the 3-dimensional diffusion and binding of molecules inside the cell; they are also referred to as FRAP.

Phospholipids

Phospholipids are a class of lipids and are a major component of all cell membranes as they can form lipid bilayers. Most phospholipids contain a diglyceride, a phosphate group, and a simple organic molecule such as choline; one exception to this rule is sphingomyelin, which is derived from sphingosine instead of glycerol. The first phospholipid identified as such in biological tissues was lecithin, or phosphatidylcholine, in the egg yolk, by Theodore Nicolas Gobley, a French chemist and pharmacist, in 1847. The structure of the a phospholipid molecule consists of hydrophobic tails and hydrophilic heads, it also consists of cholesterol molecules which are found in-between the spaces of the phospholipid.

Lipopolysaccharides

Abbreviated as(LPS), also known as lipoglycans, are large molecules consisting of a lipid and a polysaccharide joined by a covalent bond; they are found in the outer membrane of Gram-negative bacteria, act as endotoxins and elicit strong immune responses in animals.

Sphingolipids

A class of lipids containing a backbone of sphingoid bases, a set of aliphatic amino alcohols that includes sphingosine. They were discovered in brain extracts in the 1870s and were named for the mythological Sphinx because of their enigmatic nature. These compounds play important roles in signal transmission and cell recognition. Sphingolipidoses, or disorders of sphingolipid metabolism, have particular impact on neural tissue. A sphingolipid with an R group consisting of a hydrogen atom only is a ceramide. Other common R groups include phosphocholine, yielding a sphingomyelin, and various sugar monomers or dimers, yielding cerebrosides and globosides, respectively. Cerebrosides and globosides are collectively known as glycosphingolipids.

Triacylglycerols

Also known as triglyceride (TG, triacylglycerol, TAG, or triacylglyceride)an ester derived from glycerol and three fatty acids.It is the main constituent of vegetable oil and animal fats.

Oligonucleotide

A short polymer of 2 to twenty nucleotides. Derived from the Greek word Oligo, meaning few or little.

Nucleotide

The basic building block of nucleic acids, such as DNA and RNA. It is an organic compound made up of nitrogenous base, a sugar, and a phosphate group.

cis-unsaturated fatty acid

A cis configuration means that adjacent hydrogen atoms are on the same side of the double bond. The rigidity of the double bond freezes its conformation and, in the case of the cis isomer, causes the chain to bend and restricts the conformational freedom of the fatty acid. The more double bonds the chain has in the cis configuration, the less flexibility it has. When a chain has many cis bonds, it becomes quite curved in its most accessible conformations. For example, oleic acid, with one double bond, has a "kink" in it, whereas linoleic acid, with two double bonds, has a more pronounced bend. Alpha-linolenic acid, with three double bonds, favors a hooked shape. The effect of this is that, in restricted environments, such as when fatty acids are part of a phospholipid in a lipid bilayer, or triglycerides in lipid droplets, cis bonds limit the ability of fatty acids to be closely packed, and therefore could affect the melting temperature of the membrane or of the fat.

Fatty Acid

A carboxylic acid with a long unbranched aliphatic tail (chain), which is either saturated or unsaturated. Most naturally occurring fatty acids have a chain of an even number of carbon atoms, from 4 to 28. Fatty acids are usually derived from triglycerides or phospholipids. When they are not attached to other molecules, they are known as "free" fatty acids. Fatty acids are important sources of fuel because, metabolized, they yield large quantities of ATP. Many cell types can use either glucose or fatty acids for this purpose. In particular, heart and skeletal muscle prefer fatty acids. The brain cannot use fatty acids as a source of fuel; it relies on glucose or ketone bodies.

Saturated fatty acids

Saturated fatty acids are long-chain carboxylic acids that usually have between 12 and 24 carbon atoms and have no double bonds. Thus, saturated fatty acids are saturated with hydrogen (since double bonds reduce the number of hydrogens on each carbon). Because saturated fatty acids have only single bonds, each carbon atom within the chain has 2 hydrogen atoms (except for the omega carbon at the end that has 3 hydrogens).

Cholesterol

A waxy steroid of fat that is produced in the liver or intestines. It is used to produce hormones and cell membranes and is transported in the blood plasma of all mammals. It is an essential structural component of mammalian cell membranes and is required to establish proper membrane permeability and fluidity.It causes areas of rigidity in the membrane due to the interaction of its four fused ring sections with the hydrophobic tails of surrounding lipids.In addition, cholesterol is an important component for the manufacture of bile acids, steroid hormones, and vitamin D. Cholesterol is the principal sterol synthesized by animals; however, small quantities can be synthesized in other eukaryotes such as plants and fungi. It is almost completely absent among prokaryotes including bacteria. Although cholesterol is important and necessary for mammals, high levels of cholesterol in the blood can damage arteries and are potentially linked to diseases such as those associated with the cardiovascular system (heart disease).

Integral membrane proteins

Proteins which span the width of the cell membrane, protruding on the apical and basal surface.

Peripheral membrane proteins

Proteins found in the cell membrane which attached to only one side of the membrane.

Multipass integral membrane protein

An integral protein which has a polypeptide change which loops back across the membrane several times.

Spectrin

A membrane protein that cross links actin filaments.

Anchoring Junction

Junctions present in many types of animal tissue which serve to hold the constituentcells to each other and to the surrounding extra cellular matrix. They all have a common general structure consisting of transmembrane protein molecules known as cadhedrins.

Cadherin

Cadherins (named for "calcium-dependent adhesion") are a class of type-1 transmembrane proteins. They play important roles in cell adhesion, ensuring that cells within tissues are bound together. They are dependent on calcium (Ca2+) ions to function, hence their name. The extra cellular domains on cadherins interact with their counterparts in other cell membranes and their intracellular domains interact intracellular proteins. The intracellular proteins are then bound to cytoskeleton intermediate filaments known as keratin.

Adherens Junctions

These junctions function in the same way as anchoring junctions, linking intercellular cytoskeletons using cadherin. Unlike the anchoring junctions these junctions use the actin filaments not the intermediate filaments to secure the cells.

Plasmodesmata

Membrane lined gap junctions which cross cell walls in plants.

Connexon

A multisubunit protein which holds gap junctions together in animal cells.

Glycophorin

Negatively charged membrane glycoprotein which help to prevent red blood cells from sticking together through the actions of sialic acid sugar which is attached to it's extracellular domain .

N-CAMS/Neural Cell Adehesion Molecules

Membrane glycoproteins with an extracellular region made up of several domains. They are involved in the formation of intercellular junctions in neural tissue and unlike cadherins are not calcium dependant. As with cadherins they have sialic acid sugar components giving the cell membrane a negative charge discouragin inter cell adhesion.

Sialic Acid

A generic term for the N- or O-substituted derivatives of neuraminic acid, a monosaccharide with a nine-carbon backbone. It is the sugar present on cadherins and N-CAMS which gives them their negative charge. It is also the name for the most common member of this group, N-acetylneuraminic acid (Neu5Ac or NANA). Sialic acids are found widely distributed in animal tissues and to a lesser extent in other species ranging from plants and fungi to yeasts and bacteria, mostly in glycoproteins and gangliosides. The amino group generally bears either an acetyl or glycolyl group but other modifications have been described. The hydroxyl substituents may vary considerably: acetyl, lactyl, methyl, sulfate, and phosphate groups have been found.

Passive diffusion

This route of diffusion requires no assistance from membrane proteins or other sources. Non polar molecules such as oxygen and steroids pass easily through the lipid bilayer of the cell membrane as they are lipid soluble. Some small polar molecules, such as water, can also pass through the membrane via this route.

Carrier Protein

A membrane protein, involved in passive and active transport, that binds to a solute molecule or ion and releases it on the other side of the membrane. An example of this is the glucose carrier protein in mammalian cells which responds only to glucose and not other sugars and moves glucose down a concentration gradient from the outside to the inside of the cell.

Facilitated diffusion

Also known as facilitated transport or passive-mediated transport) is a process of passive transport, facilitated by integral proteins. Facilitated diffusion is the spontaneous passage of molecules or ions across a biological membrane passing through specific transmembrane integral proteins in response to messages received or changes in extracellular conditions. It works along the concentration gradient and does not require any energy.

Active transport

This form of transport is the movement of a substance against its concentration gradient (from low to high concentration). In all cells, this is usually concerned with accumulating high concentrations of molecules that the cell needs, such as ions, glucose, and amino acids. If the process uses chemical energy, such as from adenosine triphosphate (ATP), it is termed primary active transport. Secondary active transport involves the use of an electrochemical gradient. Active transport uses energy, unlike passive transport, which does not use any type of energy. Active transport is a good example of a process for which cells require energy. Examples of active transport include the uptake of glucose in the intestines in humans and the uptake of mineral ions into root hair cells of plants.

Ficks Law

These laws of diffusion describe diffusion and can be used to solve for the diffusion coefficient, D. They were derived by Adolf Fick in the year 1855.The equation relates the difference (Ch-Cl) between the higher, Ch, and the lower Cl, concentrations of the substance, the area (A) and the thickness (x)of the membrane and a constant (D), called the diffusion coefficient, the value of which depends on the nature of the diffusing substance (e.g polarity, size, temperature etc).

Membrane potential

Also known as transmembrane potential this is the difference in voltage (also called electrical potential) between the interior and exterior of a cell. The membrane potential arises from the interactions of ion channels and ion pumps embedded in the membrane, which produce different concentrations of electrically charged ions on the intracellular and extracellular sides of the membrane. This enhances the passage of positive ions and impedes the entry of negative ions via the cell membrane.

Sodium Pump

This pump is involved in active transport and is responsible for cells containing relatively high concentrations of potassium ions but low concentrations of sodium ions. It moves these two ions in opposite directions across the plasma membrane. This was investigated by following the passage of radioactively labeled ions across the plasma membrane of certain cells. It was found that the concentrations of sodium and potassium ions on the two other sides of the membrane are interdependent, suggesting that the same carrier transports both ions. It is now known that the carrier is an ATP-ase and that it pumps three sodium ions out of the cell for every two potassium ions pumped in.

Primary active transport

This type of transport is also called direct active transport, directly uses energy to transport molecules across a membrane.
Most of the enzymes that perform this type of transport are transmembrane ATPases. A primary ATPase universal to all cellular life is the sodium-potassium pump, which helps to maintain the cell potential. Other sources of energy for Primary active transport are redox energy and photon energy (light). An example of primary active transport using Redox energy is the mitochondrial electron transport chain that uses the reduction energy of NADH to move protons across the inner mitochondrial membrane against their concentration gradient. An example of primary active transport using light energy are the proteins involved in photosynthesis that use the energy of photons to create a proton gradient across the thylakoid membrane and also to create reduction power in the form of NADPH.

Secondary active transport

In secondary active transport or co-transport, uses energy to transport molecules across a membrane; however, in contrast to primary active transport, there is no direct coupling of ATP; instead, the electrochemical potential difference created by pumping ions out of the cell is used.The two main forms of this are antiport and symport.

Antiport

In this form of secondary transport two species of ion or other solutes are pumped in opposite directions across a membrane. One of these species is allowed to flow from high to low concentration which yields the entropic energy to drive the transport of the other solute from a low concentration region to a high one. An example is the sodium-calcium exchanger or antiporter, which allows three sodium ions into the cell to transport one calcium out.

Symport

This form of secondary active transport uses the downhill movement of one solute species from high to low concentration to move another molecule uphill from low concentration to high concentration (against its electrochemical gradient). An example is the glucose symporter SGLT1, which co-transports one glucose (or galactose) molecule into the cell for every two sodium ions it imports into the cell. This symporter is located in the small intestines, trachea, heart, brain, testis, and prostate. It is also located in the S3 segment of the proximal tubule in each nephron in the kidneys. Its mechanism is exploited in glucose rehydration therapy and defects in SGLT1 prevent effective reabsorption of glucose, causing familial renal glucosuria.

Chemiosmotic Hypothesis

The hypothesis of the movement of ions across a selectively permeable membrane, down their electrochemical gradient, generates energy. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration.
An Ion gradient has potential energy and can be used to power chemical reactions when the ions pass through a channel.
Hydrogen ions (protons) will diffuse from an area of high proton concentration to an area of lower proton concentration. Peter Mitchell proposed that an electrochemical concentration gradient of protons across a membrane could be harnessed to make ATP. He linked this process to osmosis, the diffusion of water across a membrane, which is why it is called chemiosmosis.
ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

Homogenate

Cells are broken up by a homogeniser (blender). This releases the organelles from the cell. The resultant fluid is known as the homogenate, which is then filtered to remove any complete cells and large pieces of debris.

Chaperone Protein

In molecular biology, these are proteins that assist the non-covalent folding or unfolding and the assembly or disassembly of other macromolecular structures, but do not occur in these structures when the structures are performing their normal biological functions having completed the processes of folding and/or assembly. The common perception that they are concerned primarily with protein folding is incorrect. The first protein to be called a chaperone assists the assembly of nucleosomes from folded histones and DNA and such assembly chaperones, especially in the nucleus,are concerned with the assembly of folded subunits into oligomeric structures.

One major function of chaperones is to prevent both newly synthesised polypeptide chains and assembled subunits from aggregating into nonfunctional structures. It is for this reason that many chaperones, but by no means all, are also heat shock proteins because the tendency to aggregate increases as proteins are denatured by stress. However, 'steric chaperones' directly assist in the folding of specific proteins by providing essential steric information, e.g. prodomains of bacterial proteases, lipase-specific foldases, or chaperones in fimbrial adhesion systems.

Signal recognition particle

Also called SRP, this is an abundant, cytosolic, universally conserved ribonucleoprotein (protein-RNA complex) that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes.

Translation

The process of synthesizing amino acids based on the genetic DNA code, this involve ribosomes which are a complex of several RNA molecule and up to 50 proteins. The ribosome decodes the anti codon of the tTNA to the codon of the mRNA.

Nascent Chain

The name given to a growing polypeptide chain. Literally translated this word means beginning to exist or develop.

Biosynthetic-Secretory pathway

The first step of this protein synthesis pathway is the cotranslational targeting pathway, followed by the post translational modification of newly synthesized proteins in the ER and the Golgi beofre finally being either returned to the ER, forwarded on to other cell organelles or secreted from the cell by endocytosis.

Membrane Biogenesis

The production of new membrane material, whic takes place in the ER.

Nuclear pore complex

These complexes in the nuclear membrane allow the transport of water-soluble molecules across the nuclear envelope. This transport includes RNA and ribosomes moving from nucleus to the cytoplasm and proteins (such as DNA polymerase and lamins), carbohydrates, signal molecules and lipids moving into the nucleus. It is notable that the nuclear pore complex (NPC) can actively conduct 1000 translocations per complex per second. Although smaller molecules simply diffuse through the pores, larger molecules may be recognized by specific signal sequences and then be diffused with the help of nucleoporins into or out of the nucleus. This is known as the RAN cycle. Each of the eight protein subunits surrounding the actual pore (the outer ring) projects a spoke-shaped protein into the pore channel. The center of the pore often appears to contain a plug-like structure. It is yet unknown whether this corresponds to an actual plug or is merely cargo caught in transit.

Nuclear localization signal

Also known as a nuclear localisation sequence (NLS) this is an amino acid sequence which 'tags' a protein for import into the cell nucleus by nuclear transport. Typically, this signal consists of one or more short sequences of positively charged lysines or arginines exposed on the protein surface. Different nuclear localized proteins may share the same NLS. An NLS has the opposite function of a nuclear export signal, which targets proteins out of the nucleus.

Pinocytosis

Also known as "cell-drinking", "bulk-phase pinocytosis", "non-specific, non-absorptive pinocytosis", "fluid endocytosis" is a form of endocytosis in which small particles are brought into the cell - forming an invagination, and then suspended within small vesicles that subsequently fuse with lysosomes to hydrolyze, or to break down, the particles. This process requires a lot of energy via ATP. It is used primarily for the absorption of extracellular fluids (ECF), and, in contrast to phagocytosis, generates very small vesicles. Unlike receptor-mediated endocytosis, pinocytosis is nonspecific in the substances that it transports. The cell takes in surrounding fluids, including all solutes present. Pinocytosis also works as phagocytosis, the only difference being that phagocytosis is specific in the substances it transports. Phagocytosis actually engulfs whole particles, which are later broken down by enzymes, such as lysosomes, and absorbed into the cells. Pinocytosis, on the other hand, is when the cell engulfs already-dissolved or broken-down food.

Clathrin

This protein plays a major role in the formation of coated vesicles. It forms a triskelion shape composed of three clathrin heavy chains and three light chains. When the triskelia interact they form a polyhedral lattice that surrounds the vesicle. Coat-proteins, like clathrin, are used to build small vesicles in order to safely transport molecules between cells. The endocytosis and exocytosis of vesicles allows cells to transfer nutrients, to import signaling receptors, to mediate an immune response after sampling the extracellular world, and to clean up the cell debris left by tissue inflammation. On occasion, this mechanism also provides a pathway for raiding pathogens or toxins.

Early endosomes

This stage of endosome matures in several ways to form late endosomes.They consist of a dynamic tubular-vesicular network (vesicles up to 1 µm in diameter with connected tubules of approx. 50 nm diameter). Markers include RAB5 and RAB4, Transferrin and its receptor and EEA1. They become increasingly acidic mainly through the activity of the V-ATPase. Many molecules that are recycled are removed by concentration in the tubular regions of early endosomes. Loss of these tubules to recycling pathways means that late endosomes mostly lack tubules. They also increase in size due to the homotypic fusion of early endosomes into larger vesicles.

Autophagy

Also known as autophagocytosis,this is a catabolic process involving the degradation of a cell's own components through the lysosomal machinery. It is a tightly regulated process that plays a normal part in cell growth, development, and homeostasis, helping to maintain a balance between the synthesis, degradation, and subsequent recycling of cellular products. It is a major mechanism by which a starving cell reallocates nutrients from unnecessary processes to more-essential processes.

Receptor mediated endocytosis

RME, also called clathrin-dependent endocytosis, is a process by which cells internalize molecules (endocytosis) by the inward budding of plasma membrane vesicles containing proteins with receptor sites specific to the molecules being internalized.

Ligand

From the Latin ligandum, meaning binding, this is a substance that forms a complex with a biomolecule to serve a biological purpose. In a narrower sense, it is a signal triggering molecule, binding to a site on a target protein.
The binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and van der Waals forces. The docking (association) is usually reversible (dissociation). Actual irreversible covalent binding between a ligand and its target molecule is rare in biological systems. In contrast to the meaning in metalorganic and inorganic chemistry, it is irrelevant whether the ligand actually binds at a metal site, as is the case in hemoglobin.

Hydrolases

An enzyme that catalyzes the hydrolysis of a chemical bond. Systematic names of these enzymes are formed as "substrate hydrolase." However, common names are typically in the form "substratease." For example, a nuclease is a hydrolase that cleaves nucleic acids.

Caveolae

Latin for little caves, singular: caveola, which are a special type of lipid raft, are small (50-100 nanometer) invaginations of the plasma membrane in many vertebrate cell types, especially in endothelial cells and adipocytes.These flask-shaped structures are rich in proteins as well as lipids such as cholesterol and sphingolipids and have several functions in signal transduction.They are also believed to play a role in endocytosis, oncogenesis, and the uptake of pathogenic bacteria and certain viruses.They are one source of clathrin-independent endocytosis involved in turnover of adhesive complexes.

Caveolin

A transmembrane protein responsible for the formation of caveola.

SNARE hypothesis

The hypothesis that t- SNARE and v-SNARE proteins are embedded in vessicles to ensure that they only fuse with the correct destination organnele or membrane.

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