# Biochemistry/Membranes and Lipids

Biochemistry

## Membranes And Lipids

All cells, from simple prokaryotic bacteria to complex multicellular organisms are surrounded by a membrane. The membrane acts as a selective barrier, letting some substances into the cell and preventing other substances from entering. The membrane also actively transports substances between the inside and outside of the cell, using cellular energy to do so. This is important in regulating the concentration of many substances which must be maintained within strict limits. The cell also contains membrane bound compartments, where the membrane acts as a barrier for the separation of different environments, like lysosomes which have a high pH that would be toxic to the rest of the cell. This chapter is about the chemical composition of the membrane and how this creates the functionality of the membrane.

## The Lipid Bilayer

The first person to link lipids with the cell membrane may have been Charles Ernest Overton, who was studying heredity in plants. Part of his studies involved studying which substances absorbed into plant cells most quickly. After characterizing a large number of substances, he came up with the idea that cell membranes were composed of something similar to the lipids found in vegetable oils, and that substances are absorbed into the cells by dissolving through the membrane.
The next big step came when Gorter and Grendel extracted the lipids from red blood cells and compared the surface area of the lipids spread out on water compared to the surface area of the red blood cells. They found the lipid surface area was twice that of the red blood cells, and concluded that the lipids must be arranged in a layer two lipid molecules thick. This is what biologists now call the lipid bilayer, and to understand the construction of the bilayer, we need to understand the lipids themselves.

### Fatty Acids

A fatty acid is simply a linear carbon chain with a carboxylic acid group at one end.
Fatty acids usually have between 14 and 24 carbon atoms and may have one or more double bonds. These double bonds are almost always in the cis configuration.
Fatty acids have both common names and systematic names. The systematic name is based on the alkane or alkene with the same number of carbon atoms, with the final e of the hydrocarbon replaced with oic acid. For example Laurate (Figure x) is a fatty acid with 12 carbon atoms and no double bonds, so the systematic name is dodecanoic acid, and the ionized form is dodecanoate. (saturated fatty acid table) If there are double bonds, the location is marked with the symbol Δ with a superscript number indicating the location of the double bond and preceded by cis or trans to indicate configuration (but almost invariably cis in natural fatty acids). Carbon atoms are counted from the carboxyl end, as in Figure x, so a dodecenoate acid with a cis double bond between carbon atoms 9 and 10 would be: cis-Δ$^9$-dodecenoate.
The number 2, 3 and last carbon atom are called the α, β and ω atoms, respectively.
One common shorthand for describing fatty acids is based on the fact that multiple double bonds are placed three bonds apart. This allows the acid to be described by the length of its carbon chain, number of double bonds, and location of the final double bond, relative to the ω carbon. Under this system, for instance, Docosahexaenoic Acid (DHA),a very important constituent of membranes in the brain and eyes, can by listed as 22:6 ω-3. This corresponds to: 22 carbons and 6 double bonds, of which the final double bond is at ω-3. This is equivalent to 22:6 Δ$^{4,7,10,13,16,19}$, or, in its full IUPAC form, cis-docosa - 4, 7, 10, 13, 16, 19 - hexaenoic acid.

### Phosphoglycerides

Phosphoglycerides are composed of a glycerol back bone with substituents in the following arrangements:
* Hydroxyl #1 of glycerol is usually esterified to a saturated fatty acid
* Hydroxyl #2 of glycerol is usually esterified to an unsaturated fatty acid
* Hydroxyl #3 of glycerol is esterified to a phosphate group
The simplest phosphoglyceride is phosphatidate (picture). Other phosphoglycerides can be made when a group with a hydroxyl is esterified to the phosphate group of phosphatidate. There are four common substituents for phosphatidate. Serine, ethanolamine and choline are structurally similar, while inositol is different:
When the fatty acid esterified to hydroxyl #2 is a cis- configured polyunsaturated fatty acid (i.e. one with more than one double bond), it tends to curl, and thus prevents the molecules from packing so closely together in a membrane. This makes the membrane more flexible.

### Sphingolipids

Sphingolipids', have the same overall shape as phosphoglycerides but have different chemistry, using sphingosine in place of glycerol. Sphingosine has a long hydrocarbon tail similar to fatty acids attached to a structure that is similar to the amino acid serine. A fatty acid can attach to the amine group, and a "head" group can attach to a hydroxyl (see Figure x). Sphingolipids are named according to this head group:
* If there is no head group it is called a ceramide
* If the head group is phosphate and choline, it is called sphingomyelin
* If the head group is a sugar, it is called a glycosphingolipid (or a glycolipid)
The majority of sphingolipids are of the third type, glycosphingolipids. It is thought they have functions in cell recognition and protection in addition to their structural role in the membrane.
Sphingolipids are known to regulate activity in cells, such as immune responses, production of cells, and development of specialized cells. Although these are under the spatial and temporal control, it was recently discovered that sphingosine kinases will be focused on therapeutic effects on enzymes for people with cancer and other conditions.
* General structures of sphingolipids

### Formation Of The Bilayer

If we compare the structures of phosphoglycerides and sphingolipids, we see that they are very similar compounds. Each lipid has two long hydrophobic hydrocarbon "tails" and a single polar "head". Since the molecule has both polar and nonpolar moieties, it is said to be amphipathic. It is the amphipathic nature of these molecules that causes them to form bilayers, mediated by four forces:
* The hydrophobic effect- this causes the hydrophobic tails to come together. This is the strongest force driving the formation of the bilayer. It is a consequence of the increased entropy in water molecules when non polar substances are aggregated in water.
* Van der Waals forces between the hydrophobic tails.
* Electrostatic forces of the head groups.
* Hydrogen bonds between the head groups.
One possible structure that satisfies the above forces is called a micelle (pictures). This is common with free fatty acids, but not with most phosphoglycerides and sphingolipids because these groups have twice as many acyl chains per head than the fatty acid (picture), and it is difficult to pack them all into the center of the micelle. Phospholipids and sphingolipids more often form a bilayer in a sheet or a sphere (picture). This is the so called lipid bilayer.

### Lipid Motion
#### Studying Motion

NMR, ESR, X-Ray, Differential scanning calorimetry
FRAP is a good way to measure diffusion of receptors through a lipid membrane after tagging the protein of interest with a GFP construct

#### Intramolecular Motion

There are three basic kinds of motion within the lipid molecules: stretching between bonds, rotating between bonds, and wagging between bonds (?). [picture] 99% of motion within liquid crystal is due to rotation about carbon-carbon bonds. Unsaturated fatty acids of membrane lipids rotate more often. This is because of the packed arrangement of the lipid bilayer. When there is rotation about one bond, an adjacent bond rotates to compensate for steric clashes [pictures]. Since double bonds in fatty acids are nearly always cis, they introduce kinks in the fatty acid. When a bond adjacent to a double bond rotates, the other bond adjacent to the double bond also rotates, and the whole thing moves like an old fashioned bit and brace [pictures]. It takes more energy to rotate the double bonds closer to the head groups due to [angle thing picture]. Double bonds react with O2 readily and create poisons [more] bacteria have [cyclopropane picture].

#### Types of Membrane Protein Diffusion

Rotational
Lateral
Liquid crystal
Flip Flop

## Plasma Membrane Function
### Barrier

Interior of cell is separated from surrounding environment. to keep undesirable substances out keep desirable substances in intracellulat membranes:act to compartmentalize functions within eukaryotic cells(ex:mitochondria,chloroplast)

### Transport Regulation

The lipid membrane is impermeable to many essential nutrients to the cell, such as glucose. In order to get the proper nutrients into the cell protein transporters are constantly moving through the membrane. For the example of glucose, there are several isoforms of the glucose transporter, some of which are specific for only certain types of cells. One of the more interesting transporter is the water transporter: aquaporins. Even though water can get through the membrane, at times the cell needs more water than can be provided through diffusion.

### Cell Communication

Gap junctions are channels found between cells that allow for the cytoplasm to exchange between the cells. This is how very fast signalling can occur by cells close together.

### Cell Adhesion

Several classes of proteins are responsible for cells sticking together: Cadherins