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Cytosol: Intracellular fluid from the cytoplasm after removal of Organelles and other insoluble cytoplasmic components.

Cytoplasm

JoVE 10967

The cytoplasm consists of organelles, an aqueous solution called the cytosol, and a framework of protein scaffolds called the cytoskeleton. The cytosol is a rich broth of ions, small organic molecules such as glucose, and macromolecules such as proteins. Several cellular processes including protein synthesis occur in the cytoplasm.

The composition of the cytosol promotes protein folding such that hydrophobic amino acid side chains are oriented away from the aqueous solution and towards the protein core. However, cellular stressors such as aging and changes in pH, temperature, or osmolarity cause protein misfolding. Misfolded proteins may aggregate to form insoluble deposits in the cytoplasm. Insoluble protein aggregates are implicated in neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. The eukaryotic cytoskeleton consists of three types of filamentous proteins: microtubules, microfilaments, and intermediate filaments. Microtubules–the largest type of filament–are made up of the protein tubulin. Microtubules are dynamic structures that can grow or shrink by adding or removing tubulin molecules from the ends of their strands. They provide structural stability and provide tracks for the transport of proteins and vesicles within the cell. In addition, microtu

 Core: Biology

The Apoplast and Symplast

JoVE 11106

Plant growth depends on its ability to take up water and dissolved minerals from the soil. The root system of every plant is equipped with the necessary tissues to facilitate the entry of water and solutes. The plant tissues involved in the transport of water and minerals have two major compartments - the apoplast and the symplast. The apoplast includes everything outside the plasma membrane of living cells and consists of cell walls, extracellular spaces, xylem, phloem, and tracheids. The symplast, in contrast, consists of the entire cytosol of all living plant cells and the plasmodesmata - which are the cytoplasmic channels interconnecting the cells. There are several potential pathways for molecules to move through the plant tissues: The apoplastic, symplastic, or transmembrane pathways. The apoplastic pathway involves the movement of water and dissolved minerals along cell walls and extracellular spaces. In the symplastic route, water and solutes move along the cytosol. Once in this pathway, materials need to cross the plasma membrane when moving from cell to neighboring cell, and they do this via the plasmodesmata. Alternatively, in the transmembrane route, the dissolved minerals and water move from cell to cell by crossing the cell wall to exit one cell and enter the next. These three pathways are not mutually exclusive, and some solutes may use more than on

 Core: Biology

Eukaryotic Compartmentalization

JoVE 10689

One of the distinguishing features of eukaryotic cells is that they contain membrane-bound organelles—such as the nucleus and mitochondria—that carry out particular functions. Since biological membranes are only permeable to a small number of substances, the membrane around an organelle creates a compartment with controlled conditions inside. These microenvironments are often distinct from the environment of the surrounding cytosol and are tailored to the specific functions of the organelle. For example, lysosomes—organelles in animal cells that digest molecules and cellular debris—maintain an environment that is more acidic than the surrounding cytosol, because its enzymes require a lower pH to catalyze reactions. Similarly, pH is regulated within mitochondria, which helps them carry out their function of producing energy. Additionally, some proteins require an oxidative environment for proper folding and processing, but the cytosol is generally reductive. Therefore, these proteins are produced by ribosomes in the endoplasmic reticulum (ER), which maintains the necessary environment. Proteins are often then transported within the cell through membrane-bound vesicles. The genetic material of eukaryotic cells is compartmentalized within the nucleus, which is surrounded by a double membrane called the nuclear envelope. Sma

 Core: Biology

Endoplasmic Reticulum

JoVE 10969

The Endoplasmic Reticulum (ER) in eukaryotic cells is a substantial network of interconnected membranes with diverse functions, from calcium storage to biomolecule synthesis. A primary component of the endomembrane system, the ER manufactures phospholipids critical for membrane function throughout the cell. Additionally, the two distinct regions of the ER specialize in the manufacture of specific lipids and proteins. The rough ER is characterized by the presence of microscopically-visible ribosomes on its surface. As a ribosome begins translation of an mRNA in the cytosol, the presence of a signal sequence directs the ribosome to the surface of the rough ER. A receptor in the membrane of the ER recognizes this sequence and facilitates the entry of the growing polypeptide into the ER lumen through a transmembrane protein complex. With the assistance of chaperones, nascent proteins fold and undergo other functional modifications, including glycosylation, disulfide bond formation, and oligomerization. Properly folded and modified proteins are then packaged into vesicles to be shipped to the Golgi apparatus and other locations in the cell. Chaperones identify improperly folded proteins and facilitate degradation in the cytosol by proteasomes. Lacking ribosomes, the smooth ER is the cellular location of lipid and steroid synthesis, cellular detoxification,

 Core: Biology

What is Glycolysis?

JoVE 10737

Cells make energy by breaking down macromolecules. Cellular respiration is the biochemical process that converts “food energy” (from the chemical bonds of macromolecules) into chemical energy in the form of adenosine triphosphate (ATP). The first step of this tightly regulated and intricate process is glycolysis. The word glycolysis originates from Latin glyco (sugar) and lysis (breakdown). Glycolysis serves two main intracellular functions: generate ATP and intermediate metabolites to feed into other pathways. The glycolytic pathway converts one hexose (six-carbon carbohydrate such as glucose), into two triose molecules (three-carbon carbohydrate) such as pyruvate, and a net of two molecules of ATP (four produced, two consumed) and two molecules of nicotinamide adenine dinucleotide (NADH). Did you know that glycolysis was the first biochemical pathway discovered? In the mid-1800s, Louis Pasteur determined that microorganisms cause the breakdown of glucose in the absence of oxygen (fermentation). In 1897, Eduard Buchner found that fermentation reactions can still be carried out in cell-free yeast extracts, achieved by breaking open the cell and collecting the cytoplasm which contains the soluble molecules and organelles. Shortly thereafter in 1905, Arthur Harden and William Young discovered that the rate of fermentation decreases wit

 Core: Biology

The Fluid Mosaic Model

JoVE 10698

The fluid mosaic model was first proposed as a visual representation of research observations. The model comprises the composition and dynamics of membranes and serves as a foundation for future membrane-related studies. The model depicts the structure of the plasma membrane with a variety of components, which include phospholipids, proteins, and carbohydrates. These integral molecules are loosely bound, defining the cell’s border and providing fluidity for optimal function. The most abundant component of the fluid mosaic model is lipids. Lipids include both phospholipids and cholesterols. Phospholipids are amphipathic, having both hydrophobic and hydrophilic parts. They consist of a hydrophilic—water-loving—head, and two hydrophobic—water-fearing—fatty acid tails. Phospholipids spontaneously form a lipid bilayer that separates the inside of the cell from the outside. The lipid bilayer consists of the hydrophobic tails facing inward and the hydrophilic heads facing the aqueous environment inside and outside the cell. Cholesterols are a class of steroids that play a role in regulating membrane fluidity and flexibility. Membrane fluidity facilitates the transport of specific molecules and ions across the plasma membrane. The second major component of the mosaic is proteins. Proteins can differentially associate with the li

 Core: Biology

ATP Yield

JoVE 11008

Cellular respiration produces 30-32 ATP molecules per glucose molecule. Although most of the ATP results from oxidative phosphorylation and the electron transport chain (ETC), 4 ATP are gained beforehand (2 from glycolysis and 2 from the citric acid cycle).

The ETC is embedded in the inner mitochondrial membrane and comprises four main protein complexes and an ATP synthase. NADH and FADH2 pass electrons to these complexes, which in turn pump protons into the intermembrane space. This distribution of protons generates a concentration gradient across the membrane. The gradient drives the production of ATP when protons flow back into the mitochondrial matrix via the ATP synthase. For every 2 input electrons that NADH passes into complex I, complexes I and III each pump 4 protons and complex IV pumps 2 protons, totaling 10 protons. Complex II is not involved in the electron chain initiated by NADH. FADH2, however, passes 2 electrons to complex II, so a total of 6 protons are pumped per FADH2; 4 protons via complex III and 2 via complex IV. Four protons are needed to synthesize 1 ATP. Since 10 protons are pumped for every NADH, 1 NADH yields 2.5 (10/4) ATP. Six protons are pumped for every FADH2, so 1 FADH2 yields 1.5 (6/4) ATP. Cellular respiration produces a maximum of 10 NADH and 2 FADH2

 Core: Biology

Energy-requiring Steps of Glycolysis

JoVE 10738

Glucose is the source of nearly all energy used by organisms. The first step of converting glucose into usable energy is called glycolysis. Glycolysis occurs in the cytosol of the cell over two phases: an energy-requiring phase and an energy-releasing phase. Over the first three steps, glucose is converted into different forms and attaches to two phosphate groups donated by two ATP molecules, resulting in an unstable sugar. In the next two stages, the unstable sugar splits into two sugar isomers which are either converted or used directly in the next phase of glycolysis. First, glucose receives a phosphate group from ATP converting it into a more reactive form (glucose 6-phosphate). Because glucose attached to the negatively-charged phosphate cannot cross the hydrophobic cell membrane, the addition of a phosphate group also traps glucose inside the cell. Next, the more reactive form of glucose is converted into one of its isomers, fructose 6-phosphate, which is required for subsequent energy-requiring steps of glycolysis. Fructose 6-phosphate then receives a phosphate group from a second ATP molecule. This converts fructose 6-phosphate into fructose 1,6-bisphosphate, an unstable sugar. This unstable sugar splits into two distinct three-carbon sugar isomers, glyceraldehyde 3-phosphate and DHAP. Glyceraldehyde 3-phosphate can be directly use

 Core: Biology

Secondary Active Transport

JoVE 10707

One example of how cells use the energy contained in electrochemical gradients is demonstrated by glucose transport into cells. The ion vital to this process is sodium (Na+), which is typically present in higher concentrations extracellularly than in the cytosol. Such a concentration difference is due, in part, to the action of an enzyme “pump” embedded in the cellular membrane that actively expels Na+ from a cell. Importantly, as this pump contributes to the high concentration of positively-charged Na+ outside a cell, it also helps to make this environment “more positive” than the intracellular region. As a result, both the chemical and electrical gradients of Na+ point towards the inside of a cell, and the electrochemical gradient is similarly directed inwards. Sodium-glucose cotransporters (SGLTs) exploit the energy stored in this electrochemical gradient. These proteins, primarily located in the membranes of intestinal or kidney cells, help in the absorption of glucose from the lumen of these organs into the bloodstream. In order to function, both an extracellular glucose molecule and two Na+ must bind to the SGLT. As Na+ migrates into a cell through the transporter, it travels with its electrochemical gradient, expelling energy that the protein uses to move glucose ins

 Core: Biology
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