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Daily Newsletter
September 6, 2013 Carbohydrates, Lipids, and Nucleotides
Carbohydrates
While carbohydrates are mainly used as chemical energy storage, carbohydrates are also used as modifiers of proteins and in forming cellular receptors and anchors. One of your goals is to gain a good understanding of the structure of carbohydrates, and a little about their naming.A topic that will come up throughout the semester is how carbons are numbered in carbohydrates. This is important as we will find carbohydrates being components of monomers and when we move through the carbohydrate catabolism. The following image from Rensselaer Polytechnic Institute shows the linear form of glucose, and the two possible cyclic (pyranose ring) isomers.
Notice also, that when the ring was formed, there were differences in the groups coming off of carbon 1. These differences are important, and can influence how the sugar is metabolized. We say that these different forms are isomers (if you don't know what an isomer is, look it up and add the definition to your notebook).
One critical difference comes when linking two monosaccharides together to form disaccharides and polysaccharides. For instance (again from rpi.edu), here is maltose:
This is an α 1-4 glycosidic linkage. We have an α Maltose (look at carbon 1) bound from carbon 1 to carbon 4. Since the maltose on the left hand side is α at the 1 carbon, we form an α linkage. In comparison, look at cellobiose:
Cellobiose has a β 1-4 glycosidic linkage. The designation of β comes from the sugar unit that donates carbon 1 to the bond.So, what is the big deal? Maltose is digestible by humans, cellobiose is not. Just this slight isomeric difference changes the metabolism.
All carbohydrate monomers are connected through glycosidic linkages, whether it is a disaccharide, oligosaccharide or a polysaccharide. Make sure that you learn the different types of carbohydrates.
Lipids
Lipids are an odd group of biomolecules. Proteins, Carbohydrates and Nucleic Acids are all formed through polymerization reactions; they have monomeric units that join to make polymers. Lipids do not polymerize, and they have no monomers. Instead, Lipid is a word that defines a class of hydrophobic organic compounds found in living systems. There are a number of important groups of Lipids, such as the triglycerides, phospholipids and cholesterols. Today, we are going to concentrate on the triglycerides and the phospholipids.Both triglycerides and phospholipids possess a glycerol molecule and fatty acids.
Glycerol is a 3 carbon compound that we will see from time to time. It acts as the backbone or schaffold of the triglycerides and phospholipids. As you can see, on each carbon atom, there is a hydroxyl group (-OH). This hydroxyl group is where other molecules can bond. Another thing to note is that there is free rotation around the carbon atoms. When you take organic chemistry, you will learn more about free rotation, why it is important, and how it can affect a molecule. For now, just note that there can be free rotation.Fatty acids are long hydrocarbon chains with a carboxyl group (-COOH) at one end. To the left is a diagram of palmitic acid, a typical saturated fatty acid.
In this diagram, each angle on the line represents a carbon atom, and off of these carbon atoms are hydrogens. This is one of many ways that organic 
chemicals are depicted. Below the first depiction is a molecular model. Carbon atoms are in black, and the white balls are hydrogens. What you will begin to recognize in these diagrams is that there are only single bonds between the carbon atoms. This means that the maximum number of hydrogen atoms are attached to the fatty acid. In other words, they are saturated with hydrogen.In contrast, an unsaturated fatty acid does not have the maximum number of hydrogen atoms. This occurs when double bonds (two electrons from each carbon are shared) occur in the carbon chain. To the right is a diagram of oleic acid.
Note that there is a double bond in the carbon chain. Notice that the chain is bent, or kinked. This creates a very different structure for lipids that carry unsaturated fatty acids.As a general rule, saturated fatty acids are solid at room temperature, and unsaturated fatty acids are liquid in room temperature. But one thing is the same in both: the carbon chains are HYDROPHOBIC!
In a triglyceride, the carboxyl end of the fatty acid will react with the hydroxyl end of the glycerol.
As you can see in the diagram, the two molecules are joined together through an oxygen molecule. As with other biosynthetic reactions, this is a dehydration synthesis (water is released). The resulting bond, as noted in the diagram, is an ester bond. You will learn more about this bond in organic chemistry, so for now I just want you to remember the general look of it. Why is this so critical? Because not all living organisms make triglycerides and phospholipids this way. Member of domain Archaea use an ether bond.So, what is the difference between a triglyceride and a phospholipid?
Recall the look of the glycerol, and note that there are three locations where an ester bond can be formed. In a triglyceride, a fatty acid will be bound to each of the carbon atoms by ester bonds. Tri- means three, so we have three fatty acids attached to the glycerol. The image to the right is an example of a triglyceride, and please note, you can have more than one type of fatty acid in a triglyceride.The phospholipid in contrast only has two fatty acids. The third binding location will be used for a "phosphate head". This head contains a phosphate group and usually a diglyceride and some small charged organic structure.
Phosphytidyl choline is a commonly studied phospholipid that uses choline as the charged organic structure. NOTE: both the phosphate group and the organic structure carry a charge. This phosphate head is charged, thus it is hydrophillic (water loving). The phospholipid contains non-polar, hydrophobic fatty acids (usually referred to as the tails) and a polar, charged, hydrophillic head. This molecule is both hydrophobic and hydrophillic. Amphiphathic is the word we use to describe a molecule with both hydrophobic and hydrophillic properties. A main use for the phospholipid is in biological membranes, as shown in the image to the right.Nucleic Acids
Nucleotide Structure: The following image from wikipedia's image gallery shows the basic structure of the nucleotide and the five nitrogenous bases.
There are five nitrogenous bases, divided into two categories: Purines and Pyrimidines. Notice that the purines are a composite of two ring structures, while the pyrimidines are a single ring structure. When you take organic chemistry and biochemistry, the importance and complexity of these ring structures will be further discussed. At present, just become aware of their respective shapes and sizes (and inclusion of nitrogen).
As with amino acids, the nucleotide contains a functional group: the nitrogenous base. Just like the side chain in an amino acid, the nitrogenous base will play an important part in the function of this biomolecule. The Sugar-Phosphate then becomes the backbone of the molecule (line the Amino-Chiral Carbon-Carboxyl of an amino acid). We will in later weeks that the sugar-phosphates of nucleotides will create the strands of DNA and RNA. The nitrogenous bases then playing an information role.
Base Complementarity:
The nucleic acids are referred to as informational biomolecules (biopolymers). This is because the sequence of nucleotides carries information on how to build RNA and Proteins. One of the central foundations of genetics (i.e., how it all works), is base complementarity. Here we are looking at the interactions between purines and pyrimidines:A links with T through 2 hydrogen bonds.
G links with C through 3 hydrogen bonds.
A to T G to C
U has the binding properties of T, but is only found in RNA.
T is never found in RNA, only DNA.
NOTE: base complementarity is a critical concept to remember. All genetic processes rely on base complementarity!
Directionality
When we get to genetics, we will be talking about the directionality of the nucleic acids. For example, we will talk about DNA being built from the 5' to 3'. This is in reference to the carbon atoms in the ribose or deoxyribose. The 5' holds a phosphate, while the 3' holds an open -OH (hydroxyl) group. This concept of directionality is critical, and you are warned to learn how it works, and what the terms represent.As with all biopolymers, monomers are added together through dehydration synthesis, and separation is through hydrolysis. When synthesis occurs, the 5' phosphate links to the 3' -OH, forming a phosphodiester bond.
Daily Challenge
The basics of biochemistry that you have learned this week will be expanded upon throughout the coming weeks. You will see further examples of proteins, carbohydrates, nucleic acids and lipids. Proteins, carbohydrates and nucleic acids have the ability to form complex polymers. Proteins and nucleic acids have their function determined by the sequence of monomers. Phospholipids can spontaneously form sealed spheres that create an inside vs. an outside. All life functions rest upon the diversity of these chemicals.Your challenge today is to reflect upon these biochemical. As mentioned, we will often return to these biochemical, and your goal is to start building mental models of what they are and how they interact. Draw out the structures, write out a full dehydration synthesis or hydrolysis. What factors cause proteins to fold, and why is it DNA forms into a helix? What would occur if you used saturated fatty acids in a phospholipid? What about non-saturated fatty acids? Take some time and really build an idea about each of these molecules, and appreciate the diversity. After spending time, write in the discussion forum your thoughts and ideas about these biochemicals.
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