Biochemical Concepts - AP Biology

The tails of phospholipids are hydrocarbons and are thus hydrophobic so they point towards the interior of the membrane to avoid contact with the aqueous solutions of the cytoplasm and the extracellular fluid.

The heads of phospholipids are hydrophilic and so they will face the exterior of the cell membrane in order to interact with the aqueous environments of the extracellular fluid and the cytosol. The hydrophobic tails will face the interior of the membrane to avoid water contact.

Lipids are mostly made up of hydrocarbons, which makes them nonpolar and thus, hydrophobic. Glycogen is a type of carbohydrate; it is the storage form of glucose in animals. Amino acids are the monomeric units of polypeptides.

Because lipids are made mostly of hydrocarbons, they are nonpolar and thus hydrophobic, which means they avoid contact with water. The root "hydro" refers to water and the root "phobic" refers to fear. Hence hydrophobic means "water fearing". Hydrophilic on the other hand means "water loving" and is used to describe polar molecules.

Lipids are a large class of hydrocarbon-based molecules that includes waxes, steroids, phospholipids and fats. Lipids are hydrophobic and have functions in energy storage, providing support to the cell/organism, cell signaling, and make up the majority of the cell membrane.

A phospholipid has two fatty acid chains and a phosphate group attached to glycerol. By replacing the phosphate group of a phospholipid with another fatty acid, the result is a glycerol with three fatty acid chains which makes it a fat (triglyceride). Saturated fatty acids are single chains of fatty acids, the resulting molecule has three fatty acids, which each could be saturated or unsaturated. Steroids have structures that consist of four fused carbon rings.

Starch is a carbohydrate. Specifically, it is a polysaccharide carbohydrate used in plants. The enzyme amylase breaks down starch in the mouth and small intestine, where it can is absorbed as monosaccharides and disaccharides.

Cholesterol is a type of steroid, which is a lipid. Amino acids are part of proteins. Cellulose and disaccharides are examples of carbohydrates.

Saturated fatty acids contain the maximum number of hydrogens on their hydrocarbon tails. These molecules form long, straight chains that can be very densely packed. By contrast, unsaturated fatty acids, do not contain the maximum number of hydrogens on their hydrocarbon tails, and thus have "kinks" in their tails. This does not allow for dense packing and storage of unsaturated fatty acids, and thus make them easier to burn.

Hemoglobin is the protein in red blood cells that binds and transports oxygen to the body tissues. It contains an iron core, and each hemoglobin molecule can bind up to four oxygen molecules.

Cholesterol is class of lipids known as steroids. All steroids have four fused carbon rings in their structures. Fats, fatty acids and phospholipid do not contain any ring structures. Fatty acids are components of both fats and phospholipids and are long chains of hydrocarbons. Phospholipids contain two fatty acids attached to a polar head and a phosphate group.

All of these affect protein function and give rise to the many functions of proteins. The order in which the individual residues (amino acids) are bonded contributes to the overall shape of a protein due to interactions between each amino acid side chain. This order matters so that the proper side chains can interact. The secondary structure of a protein consists of alpha helices and beta pleated sheets. Both of which play widely different roles structurally in cells. The quaternary structure categorizes interactions between different subunits of protein. Several subunits come together to perform a function they otherwise could not.

The different properties of the amino acid side chains are perhaps the most important aspect of protein function. Some are hydrophobic which are found in the centers of proteins (when the protein is globular). Others are hydrophilic and are found on the exterior of proteins. Yet are others are protonated or unprotonated in certain pH ranges. All of these give rise to incredibly diverse protein functions. As an example, there are pores in cell membranes called aquaporins that resemble hollow barrels or cylinders. These barrels are beta pleated sheets and the interior (the hole the membrane) is coated with hydrophilic amino acids while the exterior (which is hidden in the lipid bilayer of the cell membrane) consists of hydrophobic amino acids.

Hydrogen bonds form between electronegative atoms such as nitrogen and hydrogen atoms on their complementary bases between the DNA backbones. Adenine and thymine make two hydrogen bonds, while cytosine and guanine made three hydrogen bonds. Phosphodiester bonds keep the DNA backbone bonded together. Ionic and covalent bonds are too strong to bond the two antiparallel strands together since the strands must be separated during DNA synthesis. Hydrogen bonds are the perfect bond since they are weak individually, but collectively very strong.

Promoters help the transcription machinery and associated proteins (like DNA helicase) find the correct spot to start transcription and facilitate opening of the DNA. When transcription takes place, DNA helicase must open up or "unzip" the double helix. Te fewer the hydrogen bonds the easier it is for DNA to be denatured. Adenine and thymine only have two hydrogen bonds between them, while cytosine and guanine have 3. Thymine and adenine are the best candidates for promoter sequences based on their fewer number of hydrogen bonds which is evidenced by a common promoter sequence called "TATA box".

Fat is made up of glycerol and fatty acids. Specifically, a fat is composed of three fatty acids chains—composed of 16 or 18 carbon atoms in length—connected to a glycerol by way of an ester linkage.

Glycerol is composed of an alcohol attached to three carbons each bearing a hydroxyl group.

A saturated fatty acid has no double bonds between the carbon atoms making up the tail of the fatty acid. This lack of double bonding allows for as many hydrogen atoms as possible to be bonded to the carbon skeleton, thus the fatty acid is said to be saturated with hydrogen atoms.

An unsaturated fatty acid has one or more double bonds in its hydrocarbon tail. These double bonds are formed by the removal of hydrogen atoms from the carbon tail, resulting in a kink in the tail. As such, they are not fully saturated with hydrogen atoms. Cholesterol is a type of lipid that contains four hydrocarbon rings in its structure. Hydrogenated fatty acids are unnatural saturated fatty acids that are modified for their physical properties.

A triacylglycerol (also called commonly referred to as a fat or a triglyceride) is composed of three fatty acid chains linked to glycerol via an ester linkage. The fatty acids can be the same or two or three different types. Steroids are derived from cholesterol, a molecule that contains four hydrocarbon rings attached together. Phospholipids only have two fatty acid tails linked to a glycerol head and a phosphate group.