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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)

Non-nuclear Inheritance

JoVE 11007

Most DNA resides in the nucleus of a cell. However, some organelles in the cell cytoplasm⁠—such as chloroplasts and mitochondria⁠—also have their own DNA. These organelles replicate their DNA independently of the nuclear DNA of the cell in which they reside. Non-nuclear inheritance describes the inheritance of genes from structures other than the nucleus.

Mitochondria aresent in both plants and animal cells. They are regarded as the “powerhouses” of eukaryotic cells because they break down glucose to form energy that fuels cellular activity. Mitochondrial DNA consists of about 37 genes, and many of them contribute to this process, called oxidative phosphorylation. Chloroplasts are found in plants and algae and are the sites of photosynthesis. Photosynthesis allows these organisms to produce glucose from sunlight. Chloroplast DNA consists of about 100 genes, many of which are involved in photosynthesis. Unlike chromosomal DNA in the nucleus, chloroplast and mitochondrial DNA do not abide by the Mendelian assumption that half an organism’s genetic material comes from each parent. This is because sperm cells do not generally contribute mitochondrial or chloroplast DNA to zygotes during fertilization. While a sperm cell primarily contributes one haploid set of nuclear chromosomes to the zygote, an egg cell contribu

 Core: Biology

Genomic DNA in Prokaryotes

JoVE 10758

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance. Although bacterial genomes are much smaller than eukaryotic genomes, they vary considerably in size and gene content. One of the smallest known bacterial genomes is that of Mycoplasma genitalium, a sexually transmitted pathogen that causes urinary and genital tract infections in humans. The M. genitalium genome is 580,076 base pairs long and consists of 559 (476 coding and 83 noncoding) genes. On the other end of the spectrum lies a particular strain of Sorangium cellulosum, a soil-dwelling bacterium. The S. cellulosum genome is enormous for a bacterium at 14,782,125 base pairs long, encoding 11,599 genes. Before the discovery of antibiotics, minor injuries could turn deadly due to the inability to stop simple bacterial infections. The discovery of penicillin in 1928 ushered in the antibiotic era, characterized by revolutionizing medical treatments and an increase in life expectancy. Howe

 Core: Biology

What are Second Messengers?

JoVE 10720

Because many receptor binding ligands are hydrophilic, they do not cross the cell membrane and thus their message must be relayed to a second messenger on the inside. There are several second messenger pathways, each with their own way of relaying information. G-protein coupled receptors can activate both phosphoinositol and cyclic AMP (cAMP) second messenger pathways. The phosphoinositol path is active when the receptor induces phospholipase C to hydrolyze the phospholipid, phosphatidylinositol biphosphate (PIP2), into two second messengers: diacylglycerol (DAG) and inositol triphosphate (IP3). DAG remains near the cell membrane and activates protein kinase C (PKC). IP3 translocates to the endoplasmic reticulum (ER) and becomes the opening ligand for calcium ion channels on the ER membrane- releasing calcium into the cytoplasm. In the cAMP pathway, the activated receptor induces adenylate cyclase to produce multiple copies of cAMP from nearby adenosine triphosphate (ATP) molecules. cAMP can stimulate protein kinase A (PKA), open calcium ion channels, and initiate the enzyme- Exchange-protein activated by cAMP (Epac). Similar to cAMP, is cyclic guanosine monophosphate (cGMP). cGMP is synthesized from guanosine triphosphate (GTP) molecules when guanylyl cyclase is activated. As a second messenger, cGMP induces protein kinase G

 Core: Biology

Xylem and Transpiration-driven Transport of Resources

JoVE 11098

The xylem of vascular plants distributes water and dissolved minerals that are taken up by the roots to the rest of the plant. The cells that transport xylem sap are dead upon maturity, and the movement of xylem sap is a passive process.

Tracheids and vessel elements transport xylem sap

Tracheary elements are the transport cells of the xylem. They lack cytoplasm and organelles when they are mature and are considered part of the apoplast of the plant because they connect directly with the extracellular space. There are two types of tracheary elements: tracheids and vessel elements. Tracheids are elongated cells with lignified walls that contain small gaps called pits, which conduct xylem sap from one cell to the next in places where their walls overlap. Seedless vascular plants and most gymnosperms, or cone-bearing plants, have only tracheids, which are thought to have evolved before vessel elements. Vessel elements are wider lignified cells that stack vertically to form vessels. They are connected by perforation plates, specialized cell end structures that have spaces through which xylem sap can flow. The larger diameter and the more efficient structure of perforation plates means that vessels made up of vessel elements can move a much larger volume of sap. Most angiosperms, or flowering plants, have both tracheids a

 Core: Biology

Plant Cell Wall

JoVE 11084

The plant cell wall gives plant cells shape, support, and protection. As a cell matures, its cell wall specializes according to the cell type. For example, the parenchyma cells of leaves possess only a thin, primary cell wall.

Collenchyma and sclerenchyma cells, on the other hand, mainly occur in the outer layers of a plant's stems and leaves. These cells provide the plant with strength and support by either partially thickening their primary cell wall (i.e., collenchyma), or depositing a secondary cell wall (i.e., sclerenchyma). Altogether, the varying cell wall compositions determine the function of specific cells and tissues. Some plants, such as trees and grasses, deposit a secondary cell wall around mature cells. Secondary cell walls typically contain three distinct layers: the secondary wall layer 1 (S1) to the outside, the secondary wall layer 2 (S2) in the middle, and the innermost secondary wall layer 3 (S3). In each layer, the cellulose microfibrils are organized in different orientations. The S2 layer may make up to 75% of the cell wall. Regardless of composition, all plant cell walls have small holes, or pits, that allow for the transport of water, nutrients, and other molecules. In a pit, the middle lamella and primary cell wall merely form a thin membrane that separates adjacent cells.

 Core: Biology

Gap Junctions

JoVE 10986

Multicellular organisms employ a variety of ways for cells to communicate with each other. Gap junctions are specialized proteins that form pores between neighboring cells in animals, connecting the cytoplasm between the two, and allowing for the exchange of molecules and ions. They are found in a wide range of invertebrate and vertebrate species, mediate numerous functions including cell differentiation and development, and are associated with numerous human diseases, including cardiac and skin disorders. Vertebrate gap junctions are composed of transmembrane proteins called connexins (CX), and six connexins form a hemichannel called a connexon. Humans have at least 21 different forms of connexins that are expressed in almost all cell types. A connexon hemichannel is said to be homomeric when all six connexins are the same, and heteromeric when composed of different types. Most cells express more than one type of connexin. These can form functional connexon hemichannels or a full gap junction channel by pairing up with a counterpart on an adjacent cell. The gap junctions are considered homotypic when each connexon is the same, and heterotypic when they differ. Clusters called gap junction plaques often form where the channels are continually recycled and degraded at the center of the plaques and replaced at the periphery. Gap junctions allow th

 Core: Biology

Spermatogenesis

JoVE 10905

Spermatogenesis is the process by which haploid sperm cells are produced in the male testes. It starts with stem cells located close to the outer rim of seminiferous tubules. These spermatogonial stem cells divide asymmetrically to give rise to additional stem cells (meaning that these structures “self-renew”), as well as sperm progenitors, called spermatocytes. Importantly, this method of asymmetric mitotic division maintains a population of spermatogonial stem cells in the male reproductive tract, ensuring that sperm will continue to be produced throughout a man’s lifespan. As spermatogenesis proceeds, spermatocytes embark on meiosis, and each ultimately divides to form four sperm—each with only 23 chromosomes— that are expelled into the male reproductive tract. Interestingly, this is in contrast to oogenesis in women, during which only a single egg is generated for every progenitor cell. At the end of spermatogenesis, sperm demonstrate their characteristic shape: a “head” harboring minimal cytoplasm and a highly condensed nucleus, as well as a motile tail (flagellum). They are small cells, with no organelles such as ribosomes, ER or Golgi, but do have many mitochondria around the flagellum for power. Just below the head is the acrosomal vesicle which contains hydrolytic enzymes to penetrate the egg outer coat—th

 Core: Biology

Retrovirus Life Cycles

JoVE 10825

Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the retrovirus to replicate. New retroviral RNA is transported to the cytoplasm, where it is translated into proteins that assemble new retroviruses. Particular drugs have been developed to fight retroviral infections. These drugs target specific aspects of the life cycle. One class of antiretroviral drugs, fusion inhibitors, prevents the entry of the retrovirus into the host cell by inhibiting the fusion of the retrovirus with the host cell membrane. Another class of antiretrovirals, reverse transcriptase inhibitors, inhibits the reverse transcriptase enzymes that make DNA copies of the retroviral RNA genome. Reverse transcriptase inhibitors are competitive inhibitors; during the process of reverse transcription, the drug molecules are incorporated into the growing DNA strand instead of the usual DNA bases. Once incorporated, the drug molecules block further progress by the r

 Core: Biology

Lytic Cycle of Bacteriophages

JoVE 10823

Bacteriophages, also known as phages, are specialized viruses that infect bacteria. A key characteristic of phages is their distinctive “head-tail” morphology. A phage begins the infection process (i.e., lytic cycle) by attaching to the outside of a bacterial cell. Attachment is accomplished via proteins in the phage tail that bind to specific receptor proteins on the outer surface of the bacterium. The tail injects the phage’s DNA genome into the bacterial cytoplasm. In the lytic replication cycle, the phage uses the bacterium’s cellular machinery to make proteins that are critical for the phage’s replication and dispersal. Some of these proteins cause the host cell to take in water and burst, or lyse, after phage replication is complete, releasing hundreds of phages that can infect new bacterial cells. Since the early 20th century, researchers have recognized the potential value of lytic bacteriophages in combating bacterial infections in crops, humans, and agricultural animals. Because each type of phage can infect and lyse only specific types of bacteria, phages represent a highly specific form of anti-bacterial treatment. This quality stands in contrast to the familiar antibiotic drugs that we often take for bacterial infections, which are typically broad-spectrum treatments that kill both pathogenic and beneficial bacteria. The w

 Core: Biology

Reproductive Cloning

JoVE 10816

Reproductive cloning is the process of producing a genetically identical copy—a clone—of an entire organism. While clones can be produced by splitting an early embryo—similar to what happens naturally with identical twins—cloning of adult animals is usually done by a process called somatic cell nuclear transfer (SCNT).

In SCNT, an egg cell is taken from an animal and its nucleus is removed, creating an enucleated egg. Then a somatic cell—any cell that is not a sex cell—is taken from the animal to be cloned. The nucleus of the somatic cell is then transferred into the enucleated egg—either by direct injection or by fusion of the somatic cell to the egg using an electrical current. The egg now contains the nucleus, with the chromosomal DNA, of the animal to be cloned. It is stimulated to divide, forming an embryo, which is then implanted into the uterus of a surrogate mother. If all goes well, it develops normally and the clone is born. Although this process has been used to successfully clone many different types of animals—including sheep, cows, mules, rabbits, and dogs—its success rate is low, with only a small percentage of embryos surviving to birth. Cloned animals that survive to birth also appear to age and die prematurely. This is because their DNA comes from adult cells that have unde

 Core: Biology
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