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Eukaryotic Cells: Cells of the higher organisms, containing a true nucleus bounded by a nuclear membrane.

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: Cell Structure and Function

Cell Structure- Concept

JoVE 10587


Cells represent the most basic biological units of all organisms, whether it be simple, single-celled organisms like bacteria, or large, multicellular organisms like elephants and giant redwood trees. In the mid 19th century, the Cell Theory was proposed to define a cell, which states:

Every living organism is made up of one or more cells.
The cells…

 Lab Bio

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: Cell Structure and Function

Prokaryotic Cells

JoVE 10690

Prokaryotes are small unicellular organisms in the domains Archaea and Bacteria. Bacteria include many common organisms such as Salmonella and Escherichia coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.

Like eukaryotic cells, all prokaryotic cells are surrounded by a plasma membrane and have DNA that contains the genetic instructions, cytoplasm that fills the interior of the cell, and ribosomes that synthesize proteins. However, unlike eukaryotic cells, prokaryotes lack a nucleus or other membrane-bound intracellular organelles. Their cellular components generally float freely within the cytoplasm, although their DNA—usually consisting of a single, circular chromosome—is clustered within a region called the nucleoid. Inside the cytoplasm, many prokaryotes have small circular pieces of DNA called plasmids. These are distinct from the chromosomal DNA in the nucleoid and tend to have just a few genes—such as genes for antibiotic resistance. Plasmids are self-replicating and can be transmitted between prokaryotes. Most prokaryotes have a cell wall made of peptidoglycan that lies outside of their plasma membrane, which physically protects the cell and helps it maintain osmotic pressure in different environments. Many prokaryotes also have a sticky capsule layer that covers

 Core: Cell Structure and Function

Cell Size

JoVE 10688

The size of cells varies widely among and within organisms. For instance, the smallest bacteria are 0.1 micrometers (μm) in diameter—about a thousand times smaller than many eukaryotic cells. Most other bacteria are larger than these tiny ones—between 1-10 μm—but they still tend to be smaller than most eukaryotic cells, which typically range from 10-100 μm.

Larger is not necessarily better when it comes to cells. For instance, cells need to take in nutrients and water through diffusion. The plasma membrane surrounding cells limits the rate at which these materials are exchanged. Smaller cells tend to have a higher surface area to volume ratio than larger cells. That is because changes in volume are not linear to changes in surface area. When a sphere increases in size, the volume grows proportional to the cube of its radius (r3), while its surface area grows proportional to only the square of its radius (r2). Therefore, smaller cells have relatively more surface area compared to their volume than larger cells of the same shape. A larger surface area means more area of the plasma membrane where materials can pass into and out of the cell. Substances also need to travel within cells. Hence the rate of diffusion may limit processes in large cells. Prokaryotes are often small and divide before they face limitat

 Core: Cell Structure and Function

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: Cell Structure and Function

Replication in Eukaryotes

JoVE 10789

In eukaryotic cells, DNA replication is highly conserved and tightly regulated. Multiple linear chromosomes must be duplicated with high fidelity before cell division, so there are many proteins that fill specialized roles in the replication process. Replication occurs in three phases: initiation, elongation, and termination, and ends with two complete sets of chromosomes in the nucleus.

Eukaryotic replication follows many of the same principles as prokaryotic DNA replication, but because the genome is much larger and the chromosomes are linear rather than circular, the process requires more proteins and has a few key differences. Replication occurs simultaneously at multiple origins of replication along each chromosome. Initiator proteins recognize and bind to the origin, recruiting helicase to unwind the DNA double helix. At each point of origin, two replication forks form. Primase then adds short RNA primers to the single strands of DNA, which serve as a starting point for DNA polymerase to bind and begin copying the sequence. DNA can only be synthesized in the 5’ to 3’ direction, so replication of both strands from a single replication fork proceeds in two different directions. The leading strand is synthesized continuously, while the lagging strand is synthesized in short stretches 100-200 base pairs in length, called Okazaki fragments. Once the bu

 Core: DNA Structure and Function

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


JoVE 10761

The cell cycle occurs over approximately 24 hours (in a typical human cell) and in two distinct stages: interphase, which includes three phases of the cell cycle (G1, S, and G2), and mitosis (M). During interphase, which takes up about 95 percent of the duration of the eukaryotic cell cycle, cells grow and replicate their DNA in preparation for mitosis.

Following each period of mitosis and cytokinesis, eukaryotic cells enter interphase, during which they grow and replicate their DNA in preparation for the next mitotic division. During the G1 (gap 1) phase, cells grow continuously and prepare for DNA replication. During this phase, cells are metabolically active and copy essential organelles and biochemical molecules, such as proteins. In the subsequent S (synthesis) phase of interphase, cells duplicate their nuclear DNA, which remains packaged in semi-condensed chromatin. During the S phase, cells also duplicate the centrosome, a microtubule-organizing structure that forms the mitotic spindle apparatus. The mitotic spindle separates chromosomes during mitosis. In the G2 (gap 2) phase, which follows DNA synthesis, cells continue to grow and synthesize proteins and organelles to prepare for mitosis. In human cells, the G1 phase spans approximately 11 hours, the S phase takes about

 Core: Cell Cycle and Division

What is the Cell Cycle?

JoVE 10757

The cell cycle refers to the sequence of events occurring throughout a typical cell’s life. In eukaryotic cells, the somatic cell cycle has two stages: interphase and the mitotic phase. During interphase, the cell grows, performs its basic metabolic functions, copies its DNA, and prepares for mitotic cell division. Then, during mitosis and cytokinesis, the cell divides its nuclear and cytoplasmic materials, respectively. This generates two daughter cells that are identical to the original parent cell. The cell cycle is essential for the growth of the organism, replacement of damaged cells, and regeneration of aged cells. Cancer is the result of uncontrolled cell division sparked by a gene mutation. There are three major checkpoints in the eukaryotic cell cycle. At each checkpoint, the progression to the next cell cycle stage can be halted until conditions are more favorable. The G1 checkpoint is the first of these, where a cell’s size, energy, nutrients, DNA quality, and other external factors are evaluated. If the cell is deemed inadequate, it does not continue to the S phase of interphase. The G2 checkpoint is the second checkpoint. Here, the cell ensures that all of the DNA has been replicated and is not damaged before entering mitosis. If any DNA damage is detected that cannot be repaired, the cell may undergo apoptosis, or

 Core: Cell Cycle and Division

Binary Fission

JoVE 10759

Fission is the division of a single entity into two or more parts, which regenerate into separate entities that resemble the original. Organisms in the Archaea and Bacteria domains reproduce using binary fission, in which a parent cell splits into two parts that can each grow to the size of the original parent cell. This asexual method of reproduction produces cells that are all genetically identical. Though its speed varies among species, binary fission is generally rapid and can yield staggering growth. In the amount of time it takes bacterial cells to undergo binary fission, the number of cells in the bacterial culture doubles. Thus, this period is the doubling time. For example, Escherichia coli cells typically divide every 20 minutes. Bacterial growth, however, is limited by factors including nutrient and space availability. Thus, binary fission occurs at much lower rates in bacterial cultures that have encountered a growth-limiting factor (i.e., entered a stationary growth phase). In addition to organisms in the Archaea and Bacteria domains, some organelles in eukaryotic cells also reproduce via binary fission. Mitochondria, for example, divide by prokaryotic binary fission. This process requires the division of mitochondrial proteins and DNA.

 Core: Cell Cycle and Division

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 are present 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 contrib

 Core: Classical and Modern Genetics

The Central Dogma

JoVE 10798

The central dogma of biology states that information encoded in the DNA is transferred to messenger RNA (mRNA), which then directs the synthesis of protein. The set of instructions that enable the mRNA nucleotide sequence to be decoded into amino acids is called the genetic code. The universal nature of this genetic code has spurred advances in scientific research, agriculture, and medicine. In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is directly converted into its encoded protein. Two crucial discoveries in eukaryotic cells challenged this theory: First, protein production does not take place in the nucleus. Second, DNA is not present outside the nucleus. These findings sparked the search for an intermediary molecule that connects DNA with protein production. This intermediary molecule, found in both the nucleus and the cytoplasm, and associated with protein production, is RNA. During transcription, RNA is synthesized in the nucleus, using DNA as a template. The newly-synthesized RNA is similar in sequence to the DNA strand, except thymidine in DNA is replaced by uracil i

 Core: Gene Expression

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: Cell Signaling

What is Cell Signaling?

JoVE 10985

Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.

Cells respond to many types of information, often through receptor proteins positioned on the membrane. For example, skin cells respond to and transmit touch information, while photoreceptors in the retina can detect light. Most cells, however, have evolved to respond to chemical signals, including hormones, neurotransmitters, and many other types of signaling molecules. Cells can even coordinate different responses elicited by the same signaling molecule. Typically, cell signaling involves three steps: (1) reception of the signal, (2) signal transduction, and (3) a response. In most signal reception, a membrane-impermeable molecule, or ligand, causes a change in a membrane receptor; however, some signaling molecules, such as hormones, can traverse the membrane to reach their internal receptors. The membrane receptor can then send this signal to intracellular messengers, which transduces the message into a cellular response. This intracellular response may include a change transcription, translation, protein activation, or many

 Core: Cell Signaling


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: Cell Structure and Function

Mitosis and Cytokinesis

JoVE 10762

In eukaryotic cells, the cell's cycle—the division cycle—is divided into distinct, coordinated cellular processes that include cell growth, DNA replication/chromosome duplication, chromosome distribution to daughter cells, and finally, cell division. The cell cycle is tightly regulated by its regulatory systems as well as extracellular signals that affect cell proliferation. The processes of the cell cycle occur over approximately 24 hours (in typical human cells) and in two major distinguishable stages. The first stage is DNA replication, during the S phase of interphase. The second stage is the mitotic (M) phase, which involves the separation of the duplicated chromosomes into two new nuclei (mitosis) and cytoplasmic division (cytokinesis). The two phases are separated by intervals (G1 and G2 gaps), during which the cell prepares for replication and division. Mitosis can be divided into five distinct stages—prophase, prometaphase, metaphase, anaphase, and telophase. Cytokinesis, which begins during anaphase or telophase (depending on the cell), is part of the M phase, but not part of mitosis. As the cell enters mitosis, its replicated chromosomes begin to condense and become visible as threadlike structures with the aid of proteins known as condensins. The mitotic spindle apparatus b

 Core: Cell Cycle and Division

Levels of Organization

JoVE 10648

Biological organization is the classification of biological structures, ranging from atoms at the bottom of the hierarchy to the Earth’s biosphere. Each level of the hierarchy represents an increase in complexity that builds upon the previous level.

The most basic levels include atoms, molecules, and biomolecules. Atoms, the smallest unit of ordinary matter, are composed of a nucleus and electrons. Molecules comprise two or more atoms held together by chemical bonds, most commonly covalent, ionic, or metallic bonds. Biomolecules are molecules found in living organisms, including proteins, nucleic acids, lipids, and carbohydrates. Biomolecules are often polymers—large molecules that are created from smaller, repeating units. For instance, proteins are composed of amino acids, and nucleic acids are composed of nucleotides. Biomolecules can be endogenous or exogenous. Endogenous means that the biomolecule is produced inside a living organism. Biomolecules can also be consumed; for example, a cow gets carbohydrates from digesting grass (exogenous), but the grass must produce the carbohydrates through photosynthesis (endogenous). The next hierarchical level comprises subcellular structures called organelles. Organelles are made up of biomolecules and compartmentalize eukaryotic cells. Organelle means “little organ” as

 Core: Scientific Inquiry


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, microtubules play a

 Core: Cell Structure and Function

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, ca

 Core: Cell Structure and Function

Detection of Bacteriophages in Environmental Samples

JoVE 10190

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Author: Alex Wassimi

Viruses are a unique group of biological entities that infect both eukaryotic and prokaryotic organisms. They are obligate parasites that have no metabolic capacity, and in order to replicate, rely on host metabolism…

 Environmental Microbiology


JoVE 10692

Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.

Ribosomes are composed of ribosomal RNA (rRNA) and proteins. Ribosomes are not surrounded by a membrane (i.e., despite their specific cell function, they are not an organelle). In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome production. Within the nucleolus, rRNA is combined with proteins that are imported from the cytoplasm. The assembly produces two subunits of a ribosome—the large and small subunits. These subunits then leave the nucleus through pores in the nuclear envelope. Each one large and small subunit bind to each other once mRNA binds to a site on the small subunit at the start of the translation process. This step forms a functional ribosome. Ribosomes may assemble in the cytosol—called free ribosomes—or while attached to the outside of the nuclear envelope or endoplasmic reticulum—called bound ribosomes. Generally, free ribosomes synthesize proteins used in the cytoplasm, while bound ribosomes synthesize proteins that are inserted into membranes, packaged into org

 Core: Cell Structure and Function

DNA Isolation and Restriction Enzyme Analysis- Concept

JoVE 10628

The revelation of DNA as the hereditary molecule in all organisms has led to enormous scientific and medical breakthroughs and significantly enhanced our understanding of ourselves and other organisms. DNA isolation and profiling have been the fundamental first steps for many of the advancements in the past century; from identification of gene function, to revolutions of agriculture and…

 Lab Bio


JoVE 10693

There are three types of cytoskeletal structures in eukaryotic cells—microfilaments, intermediate filaments, and microtubules. With a diameter of about 25 nm, microtubules are the thickest of these fibers. Microtubules carry out a variety of functions that include cell structure and support, transport of organelles, cell motility (movement), and the separation of chromosomes during cell division. Microtubules are hollow tubes whose walls are made up of globular tubulin proteins. Each tubulin molecule is a heterodimer, consisting of a subunit of α-tubulin and a subunit of β-tubulin. The dimers are arranged in linear rows called protofilaments. A microtubule usually consists of 13 protofilaments, arranged side by side, wrapped around the hollow core. Because of this arrangement, microtubules are polar, meaning that they have different ends. The plus end has β-tubulin exposed, and the minus end has α-tubulin exposed. Microtubules can rapidly assemble—grow in length through polymerization of tubulin molecules—and disassemble. The two ends behave differently in this regard. The plus end is typically the fast-growing end or the end where tubulin is added, and the minus end is the slow-growing end or the end where tubulin dissociates—depending on the situation. This process of dynamic instability, where microtu

 Core: Cell Structure and Function

Electron Transport Chains

JoVE 10742

The final stage of cellular respiration is oxidative phosphorylation, which consists of (1) an electron transport chain and (2) chemiosmosis.

The electron transport chain is a set of proteins and other organic molecules found in the inner membrane of mitochondria in eukaryotic cells and the plasma membrane of prokaryotic cells. The electron transport chain has two primary functions: it produces a proton gradient—storing energy that can be used to create ATP during chemiosmosis—and generates electron carriers, such as NAD+ and FAD, that are used in glycolysis and the citric acid cycle. Generally, molecules of the electron transport chain are organized into four complexes (I-IV). The molecules pass electrons to one another through multiple redox reactions, moving electrons from higher to lower energy levels through the transport chain. These reactions release energy that the complexes use to pump H+ across the inner membrane (from the matrix into the intermembrane space). This forms a proton gradient across the inner membrane. NADH and FADH2 are reduced electron carriers produced during earlier cellular respiration phases. NADH can directly input electrons into complex I, which uses the released energy to pump protons into the intermembrane space. FADH2 inputs electrons into complex II, the only co

 Core: Cellular Respiration

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: Cellular Respiration

Electrophoretic Mobility Shift Assay (EMSA)

JoVE 5694

The electrophoretic mobility shift assay (EMSA) is a biochemical procedure used to elucidate binding between proteins and nucleic acids. In this assay a radiolabeled nucleic acid and test protein are mixed. Binding is determined via gel electrophoresis which separates components based on mass, charge, and conformation.

This video shows the concepts of EMSA and a general procedure, …


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 fr

 Core: Gene Expression

The Colonization of Land

JoVE 11016

Changes in the environment of the early Earth drove the evolution of organisms. As prokaryotic organisms in the oceans began to photosynthesize, they produced oxygen. Eventually, oxygen saturated the oceans and entered the air, resulting in an increase in atmospheric oxygen concentration, known as the oxygen revolution approximately 2.3 billion years ago. Therefore, organisms that could use oxygen for cellular respiration had an advantage. More than 1.5 years ago, eukaryotic cells and multicellular organisms also began to appear. Initially, all of these species were restricted to the oceans of Earth. The first organisms to live on land were photosynthetic prokaryotes that inhabited moist environments near ocean shores. Despite the lack of water, terrestrial environments offered an abundance of sunlight and carbon dioxide for photosynthesis. Around 500 million years ago, the ancestors of nowadays plants were able to colonize drier environments, but they required adaptations to prevent dehydration. They developed methods for reproduction that did not depend on water and protected their embryos from drying out. These early plants furthermore evolved a vascular system that included roots to acquire water and nutrients and a shoot to obtain sunlight and carbon dioxide. Plants and fungi appear to have colonized land at the same time. Their coevolution onto land

 Core: Evolutionary History

Golgi Apparatus

JoVE 10970

As they leave the Endoplasmic Reticulum (ER), properly folded and assembled proteins are selectively packaged into vesicles. These vesicles are transported by microtubule-based motor proteins and fuse together to form vesicular tubular clusters, subsequently arriving at the Golgi apparatus, a eukaryotic endomembrane organelle that often has a distinctive ribbon-like appearance.

The Golgi apparatus is a major sorting and dispatch station for the products of the ER. Newly arriving vesicles enter the cis face of the Golgi—the side facing the ER—and are transported through a collection of pancake-shaped, membrane-enclosed cisternae. Each cisterna contains unique compositions of enzymes and performs specific protein modifications. As proteins progress through the cis Golgi network, some are phosphorylated and undergo removal of certain carbohydrate modifications that were added in the ER. Proteins then move through the medial cisterna, where they may be glycosylated to form glycoproteins. After modification in the trans cisterna, proteins are given tags that define their cellular destination. Depending on the molecular tags, proteins are packaged into vesicles and trafficked to particular cellular locations, including the lysosome and plasma membrane. Specific markers on the membranes of these vesicles allow them to dock

 Core: Cell Structure and Function

Photosynthesis- Concept

JoVE 10565


Almost all living organisms on Earth depend on photosynthesis, which is the process that converts sunlight energy into a simple sugar called glucose. This molecule can be used as a short-term energy source or to build more complex carbohydrates like starches for long-term energy storage. Autotrophs are organisms that capture light energy using photosynthesis. Also known …

 Lab Bio

Cell Structure - Prep Student

JoVE 10631

Visualizing Onion and Cheek Cells
Immediately before the experiment, wash and peel onion bulbs for the class.
Remove the entire brown outer skin and cut the onion in half with a knife. Pull apart the layers of the onion. The thin, nearly transparent film layers within the onion will be used by the students.
Place the onion film into a Petri…

 Lab Bio

An Introduction to Saccharomyces cerevisiae

JoVE 5081

Saccharomyces cerevisiae (commonly known as baker’s yeast) is a single-celled eukaryote that is frequently used in scientific research. S. cerevisiae is an attractive model organism due to the fact that its genome has been sequenced, its genetics are easily manipulated, and it is very easy to maintain in the lab. Because many yeast proteins are similar in sequence and function…

 Biology I

An Overview of Genetic Engineering

JoVE 5552

Genetic engineering – the process of purposefully altering an organism’s DNA – has been used to create powerful research tools and model organisms, and has also seen many agricultural applications. However, in order to engineer traits to tackle complex agricultural problems such as stress tolerance, or to realize the promise of gene therapy for treating…


What is Gene Expression?

JoVE 10797

Gene expression is the process in which DNA (i.e., a gene) 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 cel

 Core: Gene Expression

Transcription Factors

JoVE 10983

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of certain tissues or body parts without affecting the entire organism. An additional layer of complexity is added by transcription factors in eukaryotes exerting combinatorial control. That means input provided by several transcription factors synchronously regulate the expression of a single gene. The combination of several transcriptional activators and repressors enables a gene to be differentially regulated and adapt to a variety of environmental changes without the need for additional genes.

 Core: Gene Expression

An Overview of Epigenetics

JoVE 5549

Since the early days of genetics research, scientists have noted certain heritable phenotypic differences that are not due to differences in the nucleotide sequence of DNA. Current evidence suggests that these “epigenetic” phenomena might be controlled by a number of mechanisms, including the modification of DNA cytosine bases with methyl groups, the addition…


An Overview of Gene Expression

JoVE 5546

Gene expression is the complex process where a cell uses its genetic information to make functional products. This process is regulated at multiple stages, and any misregulation could lead to diseases such as cancer.

This video highlights important historical discoveries relating to gene expression, including the…


Plasmid Purification

JoVE 5062

Plasmid purification is a technique used to isolate and purify plasmid DNA from genomic DNA, proteins, ribosomes, and the bacterial cell wall. A plasmid is a small, circular, double-stranded DNA that is used as a carrier of specific DNA molecules. When introduced into a host organism via transformation, a plasmid will be replicated, creating numerous copies of the DNA fragment under…

 Basic Methods in Cellular and Molecular Biology

A Multi-well Format Polyacrylamide-based Assay for Studying the Effect of Extracellular Matrix Stiffness on the Bacterial Infection of Adherent Cells

1Department of Biochemistry, Stanford University School of Medicine, 2Department of Mechanical and Aerospace Engineering, University of California San Diego, 3Departments of Biochemistry, Microbiology and Immunology and Howard Hughes Medical Institute, Stanford University School of Medicine

JoVE 57361

 Immunology and Infection

Semi-automatic PD-L1 Characterization and Enumeration of Circulating Tumor Cells from Non-small Cell Lung Cancer Patients by Immunofluorescence

1Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, 2Circulating Cancer (CIRCAN) Program, Hospices Civils de Lyon Cancer Institute, 3University of Lyon, Claude Bernard University, Cancer Research Center of Lyon, 4Biolidics Limited, 5Institut de Pathologie Multisites des HCL-Site Sud, Hospices Civils de Lyon, 6Acute Respiratory Disease and Thoracic Oncology Department, Lyon Sud Hospital, Hospices Civils de Lyon Cancer Institute, 7EMR-3738 Therapeutic Targeting in Oncology, Lyon Sud Medical Faculty, Lyon 1 University

JoVE 59873

 Cancer Research

Photostimulation by Femtosecond Laser Activates Extracellular-signal-regulated Kinase (ERK) Signaling or Mitochondrial Events in Target Cells

1Department of Respiratory Medicine, Shanghai Sixth People's Hospital, School of Medicine, Shanghai Jiao Tong University, 2Ultrafast Laser Laboratory, College of Precision Instrument and Optoelectronics Engineering, Tianjin University, 3School of Biomedical Engineering, Shanghai Jiao Tong University

JoVE 59661

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