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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)

Positive Regulator Molecules

JoVE 10763

To consistently produce healthy cells, the cell cycle—the process that generates daughter cells—must be precisely regulated.

Internal regulatory checkpoints ensure that a cell’s size, energy reserves, and DNA quality and completeness are sufficient to advance through the cell cycle. At these checkpoints, positive and negative regulators promote or inhibit a cell’s continuation through the cell cycle. Positive regulators include two protein groups that allow cells to pass through regulatory checkpoints: cyclins and cyclin-dependent kinases (CDKs). These proteins are present in eukaryotes, ranging from yeast to humans. Cyclins can be categorized as G1, G1/S, S, or M cyclins based on the cell cycle phase or transition they are most involved in. Generally, levels of a given cyclin are low during most of the cell cycle but abruptly increase at the checkpoint they most contribute to (G1 cyclins are an exception, as they are required throughout the cell cycle). The cyclin is then degraded by enzymes in the cytoplasm and its levels decline. Meanwhile, cyclins needed for the next checkpoints accumulate. To regulate the cell cycle, cyclins must be bound to a Cyclin-dependent kinase (CDK)—a type of enzyme that attaches a phosphate group to modify the activity of a target protein.

 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

Tonicity in Plants

JoVE 10703

Tonicity describes the capacity of a cell to lose or gain water. It depends on the quantity of solute that does not penetrate the membrane. Tonicity delimits the magnitude and direction of osmosis and results in three possible scenarios that alter the volume of a cell: hypertonicity, hypotonicity, and isotonicity. Due to differences in structure and physiology, tonicity of plant cells is different from that of animal cells in some scenarios. Unlike animal cells, plants thrive when there is more water in their surrounding extracellular environment compared to their cytoplasmic interior. In hypotonic environments, water enters the cell via osmosis and causes it to swell because there is a higher concentration of solutes inside plant cells than outside. The force, that is generated when an influx of water causes the plasma membrane to push against the cell wall, is called turgor pressure. In contrast to animal cells, plant cells have rigid cell walls that limit the osmosis-induced expansion of the plasma membrane. By limiting expansion, the cell wall prevents the cell from bursting and causes plants to stiffen (i.e., become turgid). Turgidity allows plants to hold themselves upright instead of wilting. Plants wilt if they cannot take up sufficient water. In such a scenario, their extracellular surrounding becomes hypertonic, causing water to leave the

 Core: Biology

The Nucleus

JoVE 10691

The nucleus is a membrane-bound organelle that contains a eukaryotic organism’s genetic instructions in the form of chromosomal DNA. This is distinct from the DNA in mitochondria or chloroplasts that carry out functions specific to those organelles. While some cells—such as red blood cells—do not have a nucleus, and others—such as skeletal muscle cells—have multiple nuclei, most eukaryotic cells have a single nucleus. The DNA in the nucleus is wrapped around proteins such as histones, creating a DNA-protein complex called chromatin. When cells are not dividing—that is, when they are in the interphase part of their cell cycle—the chromatin is organized diffusely. This allows easy access to the DNA during the transcription process when messenger RNA (mRNA) is synthesized based on the DNA code. When a eukaryotic cell is about to divide, the chromatin condenses tightly into distinct, linear chromosomes. Humans have 46 chromosomes in total. Chromatin is particularly concentrated in a region of the nucleus called the nucleolus. The nucleolus is important for the production of ribosomes, which translate mRNA into protein. In the nucleolus, ribosomal RNA is synthesized and combined with proteins to create ribosomal subunits, which later form functioning ribosomes in the cytoplasm of the cell. The interior of t

 Core: Biology

Bacterial Transformation- Concept

JoVE 10573

Background

In early 20th century, pneumonia was accountable for a large portion of infectious disease deaths1. In order to develop an effective vaccine against pneumonia, Frederick Griffith set out to study two different strains of the Streptococcus pneumoniae: a non-virulent strain with a rough appearance (R-strain) and a virulent strain with a smooth appearance…

 Lab Bio

Water and Mineral Acquisition

JoVE 11096

Specialized tissues in plant roots have evolved to capture water, minerals, and some ions from the soil. Roots exhibit a variety of branching patterns that facilitate this process. The outermost root cells have specialized structures called root hairs that increase the root surface, thus increasing soil contact. Water can passively cross into roots, as the concentration of water in the soil is higher than that of the root tissue. Minerals, in contrast, are actively transported into root cells. Soil has a negative charge, so positive ions tend to remain attached to soil particles. To circumvent this, roots pump carbon dioxide into the soil, which spontaneously breaks down, releasing positively charged protons (H+) into the soil. These protons displace soil-associated positively charged ions that are available to be pumped into the root tissue, a process called cation exchange. Negatively charged anions exploit the tendency of H+ ions to diffuse down their concentration gradient and back into root cells using co-transport: ions like Cl- are cotransported into the root tissue in association with H+ ions. Molecules can travel into the core of the root tissue, called the stele, by two routes. Apoplastic transport is the movement of molecules in the spaces created between the continuous cell walls of neighboring cells and their corr

 Core: Biology

pre-mRNA processing

JoVE 11003

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA, to distinguish it from mature mRNA.

Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it. This 5’ cap helps the cell distinguish mRNA from other types of RNA in the cell and plays a role in subsequent translation. During or shortly after transcription, a large complex called the spliceosome cuts out various parts of the pre-mRNA transcript, rejoining the remaining sequences. RNA sequences that remain in the transcript are called “exons” (expressed sequences) while portions removed are called “introns”. Interestingly, a single RNA segment can be an exon in one cell type and an intron in another. Similarly, a single cell can contain multiple variants of a gene transcript that has been alternatively spliced, enabling the production of multiple proteins from a single gene. When transcription is completed, an enzyme adds approximately 30-200 adenine nucleotides to the 3’ end of the pre-mRNA molecule. This poly-A tail protects the mRNA f

 Core: Biology

Cleavage and Blastulation

JoVE 10908

After a large-single-celled zygote is produced via fertilization, the process of cleavage occurs while zygotes travel through the uterine tube. Cleavage is a mitotic cell division that does not result in growth. With each round of successive cell division, daughter cells get increasingly smaller.

At the beginning of embryogenesis, maternal mRNAs control development. However, by the eight-cell stage of cleavage, embryonic genes become activated in a process called zygotic genome activation (ZGA). As a result, maternal mRNAs get degraded, and ZGA causes a transition from maternal to zygotic genetic control of developing an embryo. Although maternal mRNAs get degraded, previously translated proteins may remain in the embryo through later stages of development. Cleavage patterns vary between organisms depending on the presence and distribution of egg yolk amongst other factors. For example, mammals have a holoblastic rotational cleavage pattern. They are holoblastic because they have sparse, but evenly distributed yolk and therefore end up with a cleavage furrow that extends through the entire embryo as opposed to being meroblastic where the cleavage furrow does not extend through the yolk-dense portion of the cytoplasm. At the onset of cleavage, rotational cleavage begins when the zygote first divides to form two smaller daughter cells called blas

 Core: Biology

Intracellular Hormone Receptors

JoVE 10876

Lipid-soluble hormones diffuse across the plasma and nuclear membrane of target cells to bind to their specific intracellular receptors. These receptors act as transcription factors that regulate gene expression and protein synthesis in the target cell

Based on their mode of action, intracellular hormone receptors are classified as Type I or Type II receptors. Type I receptors, including steroid hormone receptors such as the androgen receptor, are present in the cytoplasm. Hormone binding transports the hormone-receptor complex to the nucleus, where it binds to regulatory DNA sequences called hormone response elements and activates gene transcription. Type II receptors, such as the thyroid hormone receptor, are bound to their DNA response elements within the nucleus even in the absence of hormone. In this state, the receptor acts as an active repressor of transcription. However, upon hormone binding, the receptor-hormone complex activates transcription of thyroid hormone-inducible genes.

 Core: Biology

Cross-bridge Cycle

JoVE 10870

As muscle contracts, the overlap between the thin and thick filaments increases, decreasing the length of the sarcomere—the contractile unit of the muscle—using energy in the form of ATP. At the molecular level, this is a cyclic, multistep process that involves binding and hydrolysis of ATP, and movement of actin by myosin.

When ATP, that is attached to the myosin head, is hydrolyzed to ADP, myosin moves into a high energy state bound to actin, creating a cross-bridge. When ADP is released, the myosin head moves to a low energy state, moving actin toward the center of the sarcomere. Binding of a new ATP molecule dissociates myosin from actin. When this ATP is hydrolyzed, the myosin head will bind to actin, this time on a portion of actin closer to the end of the sarcomere. Regulatory proteins troponin and tropomyosin, along with calcium, work together to control the myosin-actin interaction. When troponin binds to calcium, tropomyosin is moved away from the myosin-binding site on actin, allowing myosin and actin to interact and muscle contraction to occur. As a regulator of muscle contraction, calcium concentration is very closely controlled in muscle fibers. Muscle fibers are in close contact with motor neurons. Action potentials in motor neurons cause the release of the neurotransmitter acetylcholine in the vicinity of muscle fibers. This ge

 Core: Biology
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