Cell

∞ generated and posted on 2016.01.24 ∞

Cells are the basic, fundamental, functional units of all living things.

This chapter provides an overview of basic biology from the perspective of human biology. This part, section 1, considers in particular cell biology, that is, the biology of the functioning of individual cells of the body.

This page contains the following terms: Cells, Plasma membrane, Selective permeability, Enzyme, Structural protein, Membrane protein, Membrane transport, Cytoplasm, Organelle, Cell nucleus, Mitochondria, Extracellular matrix, Extracellular fluid, Interstitial fluid, Cellular differentiation.



Cell

Membrane-enclosed, basic, replicable unit of living things.
Cells are the basic units of bodies. Tissues consist of multiple cells along with materials that are produced and then released by cells. The specialized functions of tissues are a product of specialized functions associated with individual cells. When an organism grows it is its cells that are increasing in number. When an organism develops, it is its cells that are moving about and becoming specialized. When cancers occur it is cells that are misbehaving. And when an organism reproduces, it is done via the production of specialized cells (gametes) that combine with another specialized cell (also a gamete) that in turn generates another specialized cell (a zygote). The zygote then goes through multiple rounds of cell division (reproduction of cells), specialization (cellular differentiation), with cells moving about as well as selectively dying, ultimately to produce you and me.


Links to terms of possible interest: Animal cell, Cell division, Cell nucleus, Centrosome, Chromatin, Cilia, Cytoskeleton, Endoplasmic reticulum, Flagellum, Golgi apparatus, Membrane, Microtubules, Mitochondrion, Organelles, Plasma membrane, Ribosome, Tissues, Transport vesicle, Zygote

The above video provides a quick history lesson on the origin of what is known as cell theory.

The above video provides a very, very basic, metaphorical idea of what a cell is all about.

The above video provides an introduction to cell biology and cell theory.

The above video is a bit overwhelming, though mostly accurate; beware however inappropriate use of "cell wall" in places when "cell membrane" would be more appropriate as well as the story of the origin of mitochondria, which happened well before there were any animals on Earth!

The above video provides amazing computer-generated graphics of the inner workings of eukaryotic cells.

This video introduces cells from a somewhat physiological perspective. It gets a few things incorrect, however. For example, "binary fusion" is actually "binary fission" and Robert Hooke invented the word "cell" because the plant cell remnants he found in cork, a plant product, reminded him of monestary "cells" which monks live in rather than of prison "cells". But all told this is a decent general introduction to what cells are all about.

Above provides a silly song that starts a bit(?) dry but does improves.



Plasma membrane

Fluid mosaic lipid bilayer that surrounds a cell, separating the cytoplasm on the inside from the extracellular environment on the outside.
The plasma membrane, also known as the cytoplasmic membrane, not only is crucial to the functioning of cells, including separating the inside of cells from the outside of cells, but also is crucial to a number of processes that are necessary for the functioning of bodies. This includes the conduction of nerve impulses, the absorption of nutrients from our intestines, and the insulation of our nerve cells in the form myelin sheaths. A great deal of hormonal communication within bodies involves transduction of a signal (as initiated by the hormone) across the plasma membrane to create a signal inside of a cell, that then tells that cell what now to do.


Links to terms of possible interest: Cytoplasm, Cytoplasmic membrane, Cytoskeleton, Fluid mosaic membrane, Glycoprotein, Lipid bilayer, Peripheral membrane protein, Phospholipid, Plasma membrane, Polysaccharide, Transmembrane protein

The above video provides a good introduction including to lipid bilayers and transport proteins.

Though there is some overlap with a subsequent video by the same person on membrane transport, the above video nonetheless is a nice introduction to the concept of cell membranes.

The above video provides a nice discussion of what cell membranes are all about including in terms of their context.

The above video starts by providing a short overview of various parts of the cell but then considers particularly mechanisms of movement of substances across membranes, such as the plasma membrane; emphasis particularly is on passive transport including especially the process of osmosis.

The above video provides further introduction the plasma membrane/lipid bilayer.

And yet more discussion of lipid bilayers, this time in terms of the diversity of lipid biochemical structures, which is worth delving into only if this sort of things excites you!



Selective permeability

Ability to allow the movement of some substances but not of others, particularly across membranes.
Selective permeability is crucial to the functioning of plasma membranes and therefore of cells as well as numerous other aspects of bodies. Selective permeability means that cells have a means by which they can control what substances can and cannot enter into their cytoplasms. The result is a distinction between the chemistry that is found inside of cells and that which is found outside of cells. Cells thus can do interesting chemical manipulations, such as produce substances needed by the rest of the body (e.g., glucose), and also can either leave alone or instead concentrate substances outside of their cells relative to the insides of cells (or vice versa) to create, for example, chemical gradients across their membranes. These chemical gradients are crucial, for example, in nerve conduction or muscle contraction. Basement membranes, which are tissue membranes (versus lipid bilayers), also serve as selectively permeable barriers.


Links to terms of possible interest: CO2, Drugs, Glucose, Hydrophilic, Hydrophobic, Lipid bilayer, O2, Polar compounds, Proteins, Selective permeability, Sodium ion, Starches, Transport proteins, Urea, Water

The above video provides a very simplistic though still more or less correct perspective on what selective permeability means to cells.

The above video provides a nice overview of what cell membranes are all about, including in terms of their selective permeability.



Enzyme

Protein-based catalyst.
Catalysts are the means by which chemical reactions may be speeded up without our having to add excessive amounts of heat to the reactions to force them to go forward. Because cells and bodies possess catalysts in the form of enzymes, they instead are able to allow necessary chemical reactions to proceed at the relatively low temperatures of bodies. In addition, because of the high specificity of enzymes, the only reactions that can occur within bodies are those for which active enzymes exist that are specific to catalyzing those reactions.

It is our body's possession or lack of possession of certain enzymes that determines much of what our bodies are capable of doing as well as how it is that specialized cells in fact are specialized for what they do. In addition, our bodies can turn on and off many functions by turning the activity of specific enzymes on and off, or instead by turning the production of certain enzymes on and off. It is as though you need a specific key to do each sort of task that the body or individual cells perform. You would only be able to do those tasks for which you have specific keys, and the more of certain type of key you have then the faster you could do that specific task. In our bodies, enzymes are those keys.


Links to terms of possible interest: Active site, Catalysts, Chemical reactions, Enzyme, Product, Substrate

The above video presents the basics of what membranes as well as selective permeability are all about.

The above video provides a short introduction to enzyme basics.

The above video provides a basic introduction to what catalysts are all about.



Structural protein

Specialized amino-acid based polymers within cells and bodies that provide important functions other than participating in chemical reactions.
Structural proteins thus are proteins that are not enzymes. They often form fibers either within or between cells. Differences in the types of proteins that make up these fibers give rise to different functions and abilities. An important structural protein that is found outside of the cells of animals is the protein collagen which makes up collagen fibers. Also important outside of cells is a protein called elastin. Elastin, as the name implies, is a somewhat elastic structural protein. Inside of cells are various members of what are known as a cell's cytoskeleton. Structural proteins give form as well as strength to cells and tissues.


Links to terms of possible interest: Amino acid, Chemical reactions, Enzymes, Gene expression, Polymers, Proteins, Structural proteins



Membrane protein

Amino acid-based polymeric substance that is found in association with lipid bilayers.
Key to a great deal of the selectivity displayed by selectively permeable membranes are membrane proteins. These provide various functions involved in membrane transport, i.e., the movement of materials that otherwise are unable to cross the lipid bilayers that otherwise make up much of the structure of membranes. Membrane proteins in addition are involved in cell-to-cell contact, which provides various functions including fusing cells together (thus making it more difficult to mechanically rip tissues apart), providing water-tight junctions (such as keep the digesting food found inside of our intestines from leaking through our intestine walls), and facilitating cell-to-cell communication (which is especially important in immune-system functioning).

Membrane proteins also serves as receptors for molecules found outside of cells, which is crucial to communication between nerve cells across what are known as synapses as well as for the functioning of numerous hormones which attach to the outside of cells (via membrane proteins) rather than entering into cells to modify cell functioning. Whether or not a cell is able to participate in these various activities is dependent on what types of membrane proteins they possess. As cells specialize they are modified in terms of what proteins they produce and therefore possess, including in terms of what membrane proteins they possess.


Links to terms of possible interest: Amino acid, Hydrophobic, Hydrophobic R groups, Integral membrane protein, Lipid bilayer, Lipid-anchored membrane protein, Membrane lipids, Membrane protein, Membrane transport, Monotopic integral membrane protein, Multi-span integral membrane protein, Peripheral membrane protein, Polymer, Selectively permeable membranes, Single-span integral membrane protein

The above video provides a nice introduction to the concept of membrane proteins; note that when the narrator says "sequencing the amino acids" what is really mean is sequencing the gene that encodes the membrane protein and then deducing the amino acid sequence from the gene nucleotide sequence.

The above video continues the previous, but goes somewhat deeper into the biochemistry.



Membrane transport

Movement of materials such as into and out of cells.
Membrane transport can occur either with or without ongoing input of energy (passive transport versus active transport) and either requires or does not require protein facilitation (simple diffusion versus facilitated transport). In this way certain substances can simply accumulate within or otherwise be released from cells, other substances may be acquired by cells but only if they possess the necessary type of transport protein, and yet other substances may be actively pumped into or out of cells. For some substances more than one of these transport processes may apply.


Links to terms of possible interest: Active transport, Against a concentration gradient, Facilitated diffusion, Facilitated transport, Lipid bilayer, Membrane, Membrane transport Membrane transport protein, Passive transport Protein facilitation Simple diffusion Transport protein

The above video considers the two basic types of membrane transport proteins, channel proteins and carrier proteins.

The above video is a good introduction to transport across membranes. Note though that he gets the conclusion to the "U tube" experiment wrong, that is, the sugar concentrations will not be the same but instead higher on the left and lower on the right. Can you tell me why that would be? There are also issues associated with the description of the last step of phagocytosis during which what is known as "antigen presentation" is hinted at (i.e., in terms of reference to movement to the nucleus).

The above video considers the differences as well as similarities between diffusion, passive diffusion, facilitated diffusion (which is not simple diffusion) and simple diffusion (which is not facilitated diffusion) though is presented at a slightly more sophisticated level than the previous videos covering this subject.

The above video is equivalent to the previous but takes the subject that much further, focusing on facilitated diffusion as well as active transport.



Cytoplasm

The liquid volume of a cell that is found immediately interior to the plasma membrane.
A key aspect of what cells are, are that they possess a cytoplasm that is surrounded by a plasma membrane (a.k.a., cytoplasmic membrane). Numerous chemical reactions take place within these cytoplasms, including the all-important production (translation) of cell proteins. In addition, the cell nucleus and other cell organelles are found suspended within the cell's cytoplasm. The cytoplasm in turn can be differentiated into fluid components, called cytosol, along with larger material suspected in the cytosol, such as cytoskeleton.


Links to terms of possible interest: Cell, Cell nucleus, Cytoplasm, Cytosol, Eukaryote, Nucleus, Organelle, Plasma membrane, Prokaryote

The above is a pretty cool if a bit old a video. It is, however, about a bit more than "just" cytoplasm. Note, though, that they get the movement of proteins from the rough endoplasmic reticulum to the Golgi apparatus totally wrong…



Organelle

Multi-molecular, including multi-protein, sub-cellular machine.
Cells within bodies not only contribute to the functioning of the body as a whole but must also take care of their own functioning so that they can metabolize, continue to exist, and replicate to make new cells. The cells within our bodies are notable, as eukaryotic cells, for possessing numerous large components that are suspended within their cytoplasms. These sub-cellular components literally are biochemical machines found within cells that possess specialized functions that are necessary for ongoing cell survival as well as cell contribution to body functioning. The cell's ribosomes for example are required for both production of cell proteins and production of any proteins that are secreted out of the cell into the body at large, with the latter including the enzymes that we use to digest our food.


Links to terms of possible interest: Cell membrane, Cell organelles, Centriole, Cytoplasms, Cytoskeleton, Endoplasmic reticulum, Eukaryotic cells, Golgi apparatus, Lysosomes, Membrane-bound organelle, Mitochondria, Nucleus, Organelle, Ribosomes, Rough endoplasmic reticulum, Smooth endoplasmic reticulum, Vacuole

The above video provides a moderately detailed idea of what cell organelles as well as cytoplasm are all about.

Paul takes us slightly off topic but ultimately does a nice job in providing us with an overview of what cell organelles are all about.



Cell nucleus

Double-layered membrane-associated structure containing the chromosomes of eukaryotic organisms, part of the endomembrane system.
The cell nucleus is the center of the cell in that it harbors the cell's DNA. The DNA serves not only as the hereditary material that is passed from parent cell to daughter cell, as well as from parent to offspring during reproduction, but also the blueprint for the ongoing construction and functioning of a cell. Much of these latter functions involve production of what are known as gene products, which consist of either RNA products (products of transcription) or instead polypeptide and protein products (products of translation). It is these gene products that are directly responsible for cell and therefore body functioning, and different cells within a body differ in terms of what sorts of gene products those cells possess. Different cells in turn come to possess different gene products, such as different proteins, in the course of the specialization (cellular differentiation) during body development.


Links to terms of possible interest: Cell nucleus, Chromatin, Endomembrane system, Euchromatin, Eukaryotic organisms, Hereditary material, Heterochromatin, Inner membrane of the nucleus, Light microscope, Lumen, Nuclear membrane, Nuclear pore, Nucleolus, Outer membrane of the nucleus

The above video takes a nice and easy to take in overview of the cell nucleus.



Mitochondria

The site of cellular respiration in eukaryotic cells.
Cellular respiration is the means by which cells convert energy-rich nutrients, such as glucose or fat, into chemical energy that is directly usable by a cell, particularly as the molecule known as ATP. Part of the process of conversion of these nutrients into ATP, as occurs within the organelles known as mitochondria, is the use of what can be described as molecular oxygen, or O2, as also known as a final electron acceptor. In order for our cells to have a continuous as well as substantial supply of ATP they need an ongoing supply of this oxygen. The delivery of this oxygen requires hemoglobin, red blood cells (a.k.a., RBCs), capillaries, larger blood vessels, your heart, and your lungs, just to name a subset of the key players. The mitochondria also generate carbon dioxide or CO2. We literally breathe in to supply our mitochondria with oxygen and literally breathe out to relieve our bodies of this carbon dioxide.


Links to terms of possible interest: ATP Bacterial cell, Cellular respiration, Cristae junction, DNA, Energy, F0 complex, F1 complex, Inner membrane of the mitochondria, Intermembrane space, Matrix of the mitochondria, Mitochondria, Outer membrane of the mitochondria, Oxygen, Ribosomes

See above videos for some mention of mitochondria.

The above video is about oxygen, but also about cellular respiration, and therefore about mitochondria. If you want to learn why mitochondria are important, and for that matter why oxygen is important, then this is a good video to watch.

The above video on mitochondria is short though also pretty superficial; I haven't been able to identify a good alternative, however…

The above video doesn't say much about mitochondria but sure has pretty images.



Extracellular matrix

Material found between animal cells, supplying both cushioning to tissues and resistance to tearing.
The extracellular matrix consists of carbohydrates, proteins, and other not dissolved substances, all floating within an extracellular fluid. This material supplies various mechanical between-cell functions such as resisting compression and supplying the tensile strength necessary to hold together the multiple cells making up tissues. As can be seen on macroscopic scales, it is the extracellular matrix that makes up the bulk of cartilage, tendons, ligaments, and also bone. In addition is extracellular matrix that is found in much smaller but still significant amounts between individual cells, that is, as exists on microscopic scales.


Links to terms of possible interest: Carbohydrates, Collagen, Extracellular fluid, Extracellular matrix, Fibronectin, Integrin, Laminin, Proteins, Proteoglycan

The above video is relatively short but also a bit off topic from extracellular matrix specifically. The video also is pretty sophisticated in terms of the topics covered. Mostly, that is, this video just might overwhelm you, though it was the best that I could find on this topic…



Extracellular fluid

Nonsolid aspects of bodies that are found outside of cells and which are contained within the integumentary system.
The extracellular fluids – all as contained by the skin and mucous membranes – can be differentiated into that which makes up fluid portions of blood and lymph versus that which is found within tissues outside of these circulatory fluids. The latter is called interstitial fluid. All of these are distinct from whatever fluids may be found, for example, within the lumen of our alimentary canal, which technically are not found within our integumentary system but instead are separated from our body tissues via mucous membrane. Contrast as noted the large amount of fluid within our bodies that instead is found within our cells.


Links to terms of possible interest: Blood, Extracellular fluid, Homeostasis, Integumentary system, Interstitial fluid, Intracellular fluid, Mucous membrane, Plasma, Skin, Total body water

The above video provides a nice introduction to the concept of extracellular fluid, very much within the context of homeostasis. Remember that extracellular fluid includes both interstitial fluid and plasma. The video is a bit slow, however.



Interstitial fluid

Nonsolid aspects of bodies that are found outside of cells, within the integumentary system, and other than that making up blood and lymph.
Interstitial fluid is that which directly baths the majority of the plasma membranes of our cells. It is from the interstitial fluid that our cells obtain water, minerals, molecular oxygen, and various organic substances necessary for their ongoing functioning. It is to the interstitial fluid that cells deposit their wastes such carbon dioxide and nitrogenous waste. Movement of these substances generally occurs from and to the blood. Materials thus tend to move from the blood to the interstitial fluid and then to cells as well as from cells to the interstitial fluid and then to the blood. Hormones also generally move from the blood to the interstitial fluid to their target cells. Hormone-like paracrine substances, but contrast, function strictly within the interstitial fluid, serving as a means of local communication among adjacent cells.


Links to terms of possible interest: Blood, Cells, Interstitial fluid, Integumentary system, Intracellular fluid, Lymphatic system, Plasma, Vessels

The above video provides a nice, straightforward introduction to the concept of interstitial fluid, including how it remains in balance with blood. Keep in mind as you watch, however, that plasma of the blood contains a lot more protein than does interstitial fluid since these blood proteins do not normally flow out of the blood into the interstitial fluid.



Cellular differentiation

Cells making up the same organism having dissimilar functions and appearances despite being genetically identical.
It is the process of cellular differentiation that results in different cells within a body possessing different functions. Differentiation is a consequence of modification of what genes are expressed in different cells. This results in differences in terms of what gene products are present and therefore in differences in cell functioning. Different cells, for example, possess differences in either what hormones they can interact with or how they respond to those interactions. Different cells also possess different functions within tissues, and indeed different tissues possess different functions depending on their type. All of these differences are a consequence of cellular differentiation as that occurs within the course of the development of the bodies of organisms such as ourselves.


Links to terms of possible interest: Cells, Cellular differentiation, Development, Ectoderm, Embryonic development, Endoderm, Hormones, Mesoderm, Pluripotent stem cells, Primary germ layers, Stem cells

The above video follows the formation of intestinal epithelial cells.

The above video discusses cellular differentiation within the context animal development, which I should note is complicated stuff! Caution too as there is confusion in the video between the concepts of "gene" and "gene product" as well as between intracellular factors and extracellular factors (genes don't move from cell to cell during development, and even the movement of the products of genes between cells is much more complicated than you might think).

The above video goes into the basics of cells, tissues, and organs, but then looks into the question of how otherwise genetically identical cells can take on different morphologies and functions so as to become, for example, a muscle cell versus a nerve cell. Note the important reference to stem cells.


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