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Cellular Biology    →   Cell Structure    →   Introduction    →    ©
Protoplasm

Protoplasm is the fluid within plant and animal cells. The protoplasm surrounding the nucleus is known as the cytoplasm. The protoplasm within the nucleus is the nucleoplasm. The protoplasm is mostly water, and its average elemental composition is:

Oxygen ………………….. .75 +
Carbon ………………….. .10 +
Hydrogen ………………….. .10
Nitrogen ………………….. .02 +
Sulfur ………………….. .002
Phosphorous ………………….. .003
Potassium ………………….. .003
Chlorine ………………….. .001
Sodium
Calcium
Magnesium
Etc.		 ………………….. < .001
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Cellular Structural Features

Most cells are between 10 and 100 micrometers. 1 micrometer is 10,000 angstrom units.

Structural Features of All Cells
Chromosome The chromosome is cDNA in prokaryotes. For eukaryotes, there are two categories: introns and exons. Introns are the noncoding regions of DNA. The chromosome is stored within the nucleus. The chromosome is divided into supercoiling domains (10-100 kb) and macrodomains (800-1000 kb). House-keeping genes essential for biosynthesis.
Cytoplasm The cytoplasm contains salt, sugar, RNA, DNA, amino acids, ribosomes, and protein. It is made of 75% Oxygen, 10% Carbon, 10% Hydrogen, 2% Nitrogen, .2% Sulfure, .3% Phosphorous, .3% Potassium, .1% Chlorine. In prokaryotes, there is not a nucleus; therefore, transcription and translation occur in the cytoplasm.
Cell Membrane The cytoplasmic Membrane is a permeable phospholipid bilayer. It is non-covalent, flexible, 8nm thick and as viscous as light-grade oil. To strengthen it are rigid planar molecules: sterols for eukaryotes and hopanoids for prokaryotes. It consists of glycerol, phosphate and fatty acids. Cations like Magnesium and Calcium stabilize the negatively charged phosphates. Primary function is to control movement of materials from one place to another. Hydrophobic bonds occur between nonpolar groups in water. The lipid Bilayer contains a strongly polar phosphate- or sugar-containing head of each molecule associating with water and nonpolar alkyl tails of the fatty acyl groups aggregating by hydrophobic interactions.
Membrane Proteins

Membrane proteins are proteins embedded in the lipid bilayer.

Integral Integral membrane proteins cannot be released from a membrane without breaking covalent bonds or disrupting the lipid bilayer. Some anchored to lipid bilayer by covalent linkage to a lipid, usually a fatty acyl group, prenyl, or a phospholipid.
Peripheral Peripheral membrane proteins face either internally or externally, but not both. They are bound noncovalently to integral membrane components (such as lipids or proteins). They can be removed by treatments milder than required to remove integral membran proteins.
Transmembrane Integral Transmembrane integral membrane proteins extend across the lipid bilayer. Most have α-helical 2° structure. Some transmembrane integral membrane proteins form ion channels across the membrane, some are active transport or facilitated diffusion carriers, and others are receptor for growth factors or hormones. Many have unknown function. They oftentimes have restricted mobility due to interaction with the cytoskeleton.

Structural Features of All Eukaryotes
Mitochondria
Nuclear Envelope
Nucleolus
Nucleus
Smooth ER
Rough ER
Golgi Complex
Secretory Vesicles
Peroxisomes
Cytoskeleton (cytoskeletal fibers)
Cell Wall

Structural Features of Animal Eukaryotes
Microvilli
Lysosomes

Structural Features of Plant Eukaryotes
Plant
Cell Wall
Vacuole
Chloroplast
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Surface Area to Volume Ratio

The surface area to volume ratio restricts cell size. Large cells have less surface relative to a small cells. Large cells produce more waste, but have proportionately less surface area through which to expel that waste. This means that waste will build up inside the cell and kill the cell. In addition, large cells need more nutrients, but have proportionately less surface area through which nutrients can diffuse. This means that large cells get proportionately less nutrients and can starve to death.

  • Large cells: Low surface area to volume ratio
  • Small cells: High surface area to volume ratio.

Cell size is restricted by surface area to volume ratio. Cells become large only when they are able to expel their waste quickly, and obtain nutrients readily. There are some cells which at first seem to contradict this rule:

  • Neurons have axons which can be as long as 2 meters. They maintain a high surface area to volume ratio by making this axons extremely thin.
  • Some kelp, which can be as tall as 30 meters, are unicellular. They maintain a high surface area to volume ratio by staying extremely flat.
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Microbe Terminology
Colony Form Description
Pinpoint Smaller than 1 mm.
Circular A circle larger than 1 mm.
Irregular A non-circular shape.
Filamentous Resembling a bunch of strings.
Colony Elevation
Cushion figure of a cushion-shaped colony
Raised figure of a raise-shape colony
Flat figure of a flat-shaped colony
Raised Center figure of a raise-center-shaped colony
Colony Surface
Smooth Smooth colony surface.
Rough Rough colony surface.
Ringed A colony surface with rings.
Colony Texture
Amorphous A typical textureless colony.
Granular Chunky and sand-like.
Fluffy A fluffy texture, like bread or a smoothie.
Mucoid Runny, like mucous.
Colony Optics
Opaque Light does not penetrate the colony.
Translucent Light somewhat penetrates the colony.
Transparent Light can fully penetrate the colony.
Iridescent Colony is iridescent, like foil.
Cell Morphology
Cell Morphology Description
Coccus Sphere
Baccilus (Rod) Rod.
Spirilium Curved baccilus. Spirilium is also spelled spirrilium.
Spirochete Spiral.
Appendaged Bacteria possessing extensions as tubes or stalks.
Filamentous Bacteria which form long, thin cells or chains of cells.
Endospore Endospore nucleuses can be centered (central), at one end (terminal) or off-center (subterminal).
Flagella Peritrichous flagella are located all across the cell surface; polar flagella are located at one location.
Capsule Capsules have a thick polysaccharide layer surrounding the cell.
Biochemical Conditions
Environment Microbe
Very Cold Psychrophile
Cold Viable Psychrotolerant
25º-37º Mesophile
Hot Thermophile
Extremely Hot Hyperthermophile
pH < 5 Acidophile
5 < pH < 9 Neutrophile
pH > 9 Alkaliphile
Dies w/ O2 Obligate anaerobe
Dies w/o O2 Obligate aerobe
Viable w/ & w/o O2 Facultative aerobe
Viable w/o O2 Tolerant anerobe
High [NaCl] Halophile
Metabolism Microbe
Uses Unfixed Carbon Autotroph
Needs Fixed Carbon Prototroph
Ferments Lactose Coliform
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Lipid Bilayer

The lipid bilayer consists of phospholipids. Phospholipids consist of a nonpolar alkyl attached to a phosphate. The nonpolar alkyl resembles a tail. These nonpolar alkyls are hydrophobic, meaning they repel water. As a result, when phospholipids are mixed into water, the nonpolar alkyls will join together and the attached phosphates will have contact with water. The result looks like:

lipid bilayer figure

The head of each molecule associates with water, while nonpolar alkyl tails of fatty acyl groups aggregate hydrophobically.

Glycerophospholipids A glycerol is attached to 2 fatty acyl groups and one phosphate group. The phosphate may in turn be linked to further groups: ethanolamine (phosphatidyl etholamine), choline (phosphatidyl choline), serine (phosphatidyl serine) or inositol (phosphatidyl inositol).
Sphingolipids A sphingosine linked to 1 fatty acyl group. Sphingolipids are usually linked to a phosphate plus a choline (sphingomyelin), sugar (ceramides) or a complex oligosaccharide (gangliosides). Sphingolipids are absent in most prokaryotes, but are oftentimes present in the outer face of the eukaryotic plasma membrane.
Lysophospholipids Are phospholipids with 1 fatty acyl group removed. This promotes conversion of phospholipid bilayers into micelles, and may destabilize membranes. Substituting cis-unsaturated fatty acids decreases closeness of packing in the nonpolar layer. This increases fluidity and thereby increases movement of small polar molecules across the layer. Cholesterol reduces fluidity and penetration of small polar molecules.

In the fluid mosaic model, proteins are able to move freely around in the lipid bilayer.

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Fluid Mosaic Model

Some membrane proteins are able to move within the plane of the membrane, while other membrane proteins (particularly receptors) are restricted or can be clustered in response to stimuli. This model of membrane organization is called the fluid mosaic model because of the freedom of movement of lipids and some proteins in the membrane.

Integral Membrane Proteins Cannot be released from a membrane without breaking covalent bonds or disrupting the lipid bilayer.
Peripheral membrane proteins Attached to integral membrane components (lipids or proteins) by noncovalent bonds. Peripheral proteins may be removed from a membrane by milder treatments than those needed to remove integral membrane proteins.
Transmembrane integral
membrane proteins		 Contain at least one protein domain extended across the lipid bilayer. Most transmembrane domains adopt alpha helical secondary structure and consist primarily of amino acids with hydrophobic side chains. Some transmembrane integral membrane proteins form ion channels across the membrane; others are active transport or facilitated diffusion carriers; still others are receptors for growth factors or hormones.
Lipid Rafts Lipid rafts are mobile membrane microdomains (small parts of the membrane) which are rich in sphingomyelin, glycosphingolipids and cholesterol. They can contain membrane proteins.
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