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Cytoplasm: The part of a cell that contains the Cytosol and small structures excluding the Cell nucleus; Mitochondria; and large Vacuoles. (Glick, Glossary of Biochemistry and Molecular Biology, 1990)

What is Gene Expression?

JoVE 10797

Gene expression is the process in which DNA directs the synthesis of functional products, such as proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino acids, a mediator is required to convert the information that is encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription takes place in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and transported into the cytoplasm where it serves as a template for protein synthesis during translation. In prokaryotes, which lack a nucleus, the processes of transcription and translation occur at the same location and almost simultaneously since the newly-formed mRNA is susceptible to rapid degradation. Every cell of an organism contains the same DNA, and consequently the same set of genes. However, not all genes in a cell are “turned on” or use to synthesize proteins. A gene is said to be “expressed” when the protein it encodes is produced by the cell. Gen

 Core: Biology

Organization of Genes

JoVE 10786

The genomes of eukaryotes can be structured in several functional categories. A strand of DNA is comprised of genes and intergenic regions. Genes themselves consist of protein-coding exons and non-coding introns. Introns are excised once the sequence is transcribed to mRNA, leaving only exons to code for proteins.

In eukaryotic genomes, genes are separated by large stretches of DNA that do not code for proteins. However, these intergenic regions carry important elements that regulate gene activity, for instance, the promoter where transcription starts, and enhancers and silencers that fine-tune gene expression. Sometimes these binding sites can be located far away from the associated gene. As researchers investigated the process of gene transcription in eukaryotes, they realized that the final mRNA that codes for a protein is shorter than the DNA it is derived from. This difference in length is due to a process called splicing. Once pre-mRNA has been transcribed from DNA in the nucleus, splicing immediately removes introns and joins exons together. The result is protein-coding mRNA that moves to the cytoplasm and is translated into protein. One of the largest human genes, DMD, is over two million base pairs long. This gene encodes the muscle protein dystrophin. Mutations in DMD cause muscular dystrophy, a disorder characteri

 Core: Biology

Anatomy of Chloroplasts

JoVE 10750

Green algae and plants, including green stems and unripe fruit, harbor chloroplasts—the vital organelles where photosynthesis takes place. In plants, the highest density of chloroplasts is found in the mesophyll cells of leaves.

A double membrane surrounds chloroplasts. The outer membrane faces the cytoplasm of the plant cell on one side and the intermembrane space of the chloroplast on the other. The inner membrane separates the narrow intermembrane space from the aqueous interior of the chloroplast, called the stroma. Within the stroma, another set of membranes form disk-shaped compartments—known as thylakoids. The interior of a thylakoid is called the thylakoid lumen. In most plant species, the thylakoids are interconnected and form stacks called grana. Embedded in the thylakoid membranes are multi-protein light-harvesting (or antenna) complexes. These complexes consist of proteins and pigments, such as chlorophyll, that capture light energy to perform the light-dependent reactions of photosynthesis. These processes release oxygen and produce chemical energy in the form of ATP and NADPH. The second part of photosynthesis—the Calvin cycle—is light-independent and takes place in the stroma of the chloroplast. The Calvin cycle captures CO2 and uses the ATP and NADPH to ultimately produce sugar.

 Core: Biology

The Citric Acid Cycle

JoVE 10741

The citric acid cycle, also known as the Krebs cycle or TCA cycle, consists of several energy-generating reactions that yield one ATP molecule, three NADH molecules, one FADH2 molecule, and two CO2 molecules.

Acetyl CoA is the point-of-entry into the citric acid cycle, which occurs in the inner membrane (i.e., matrix) of mitochondria in eukaryotic cells or the cytoplasm of prokaryotic cells. Prior to the citric acid cycle, pyruvate oxidation produced two acetyl CoA molecules per glucose molecule. Hence, the citric acid cycle runs twice per glucose molecule. The citric acid cycle can be partitioned into eight steps, each yielding different molecules (italicized below). With the help of catalyzing enzymes, one acetyl CoA (2-carbon) reacts with oxaloacetic acid (4-carbon), forming the 6-carbon molecule citrate. Next, citrate is converted into one of its isomers, isocitrate, through a two-part process in which water is removed and added. The third step yields α-ketoglutarate (5-carbon) from oxidized isocitrate. This process releases CO2 and reduces NAD+ to NADH. The fourth step forms the unstable compound succinyl CoA from α-ketoglutarate, a process that also releases CO2 and reduces NAD+ to NADH. The fifth

 Core: Biology

Yeast Signaling

JoVE 10714

Yeasts are single-celled organisms, but unlike bacteria, they are eukaryotes—cells that have a nucleus. Cell signaling in yeast is similar to signaling in other eukaryotic cells. A ligand, such as a protein or a small molecule outside the yeast cell, attaches to a receptor on the cell surface. The binding stimulates second-messenger kinases (enzymes that phosphorylate specific substrates) to activate or inactivate transcription factors that regulate gene expression. Many of the yeast intracellular signaling cascades have similar counterparts in Homo sapiens, making yeast a convenient model for studying intracellular signaling in humans. Yeasts are members of the fungus kingdom. They use signaling for various functions, especially for reproduction. Yeasts can undergo “sexual” reproduction using mating pheromones, which are peptides—short chains of amino acids. Yeast colonies consist of both diploid and haploid cells. Both types of cells can undergo mitosis, but only diploid cells can undergo meiosis. When diploid cells undergo meiosis, the four resulting haploid cells, called spores, are not identical. In fact, the division of one diploid cell into four spores creates two “sexes” of yeast cells, each two cells of the type MAT-a and MAT-alpha. MAT-a cells secrete mating

 Core: Biology

Mitochondria

JoVE 10694

Mitochondria and peroxisomes are organelles that are the primary sites of oxygen usage in eukaryotic cells. Mitochondria carry out cellular respiration—the process that converts energy from food into ATP—the primary form of energy used by cells. Peroxisomes carry out a variety of functions, primarily breaking down different substances such as fatty acids.

Peroxisomes contain up to 50 enzymes and are surrounded by a single membrane. They carry out oxidative reactions that break down molecules and produce hydrogen peroxide (H2O2) as a by-product. H2O2 is toxic to cells, but the peroxisome contains an enzyme—catalase—that converts H2O2 into harmless water and oxygen. In addition, catalase uses H2O2 to break down alcohol in the liver into aldehyde and water. However, since H2O2 is produced in very low quantities in the body, other enzymes primarily degrade alcohol. A critical function of the peroxisome is to break down fatty acids in a process called β oxidation. The resulting product—acetyl-CoA—is released into the cytosol and can travel to the mitochondria, where it is used to produce ATP. In mammalian cells, the mitochondria also carry out β oxidation, as well as using products from the catabolism o

 Core: Biology

What are Cells?

JoVE 10687

Cells are the foundational level of organization of life. An organism may be unicellular, as with prokaryotes and most eukaryotic protists, or multicellular where the functions of an organism are divided into different collections of specialized cells. In multicellular eukaryotes, cells are the building blocks of complex structures and can have various forms and functions.

Cells are the building blocks of all living organisms, whether it is a single cell that forms the entire organism (e.g., a bacterium) or trillions of them (e.g., humans). No matter what organism a cell is a part of, they share specific characteristics. A living cell has a plasma membrane, a bilayer of lipids, which separates the watery solution inside the cell, also called cytoplasm, from the outside of the cell. Furthermore, a living cell can replicate itself, which requires that it possess genetic information encoded in DNA. DNA can be localized to a particular area of the cell, as in the nucleoid of a prokaryotic cell, or it can be contained inside another membrane, such as the nucleus of eukaryotes. Eukaryote means "true nucleus." The word prokaryote, hence, implies that the cell is from a group which arose before membrane-bound nuclei appeared in the history of life. Prokaryotic cells lack internal membranes. In contrast, eukaryotes have internal membran

 Core: Biology

Cell Division- Concept

JoVE 10571

Cell division is fundamental to all living organisms and required for growth and development. As an essential means of reproduction for all living things, cell division allows organisms to transfer their genetic material to their offspring. For a unicellular organism, cellular division generates a completely new organism. For multicellular organisms, cellular division produces new cells for…

 Lab Bio

Annexin V and Propidium Iodide Labeling

JoVE 5650

Staining with annexin V and propidium iodide (PI) provides researchers with a way to identify different types of cell death—either necrosis or apoptosis. This technique relies on two components. The first, annexin V, is a protein that binds certain phospholipids called phosphatidylserines, which normally occur only in the inner, cytoplasm-facing leaflet of a…

 Cell Biology

Cell-surface Biotinylation Assay

JoVE 5647

A cell can regulate the amount of particular proteins on its cell membrane through endocytosis, following which cell surface proteins are effectively sequestered in the cytoplasm. Once within a cell, these surface proteins can be either destroyed or “recycled” back to the membrane. The cell surface biotinylation assay provides researchers with a way to study…

 Cell Biology
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