Structural Biochemistry/Chemistry of important organic molecules in Biochemistry

Amino AcidEdit

Amino acids are the building blocks of proteins. an amino acid consists of alpha carbon, which linked to an amino group, a carboxylic acid group, a hydrogen atom and a distinctive R group.these R groups varying in size, shape, charge, hydrogen bonding capacities, hydrophobic characterand chemical reactivity; these characteristics give rise to their distinctive properties and activities.For all proteins, only L isomer( S configuration) are constituents of proteins. Amino acid exists as dipolar ions(zwitterions)in neutral solution. amino acid has both amine group and carboxylic acid group,so it has an acid and base on different ends. in the dipolar form, the amino group is protonated and carboxylgroup is deprotonated. Besides proteins synthesis, amino acid also has other functions such as metabolic intermediates and neurotransmitters.


Nucleic acids DNA and RNA are macromolecules that are composed of monomer units called nucleotide. A single nucleotide is formatted with sugar, phosphate, and a base. These three components create nucleotide which can link up into a linear formation. There are many aspects to nucleotides. First, the sugar group in the DNA monomer is called deoxyribose where the 2’ carbon atom of the sugar doesn’t have a oxygen group. The sugar group of nucleotide is the reason for the phosphodiester bridges because it can be esterified to a phosphate group, specifically the 3’ hydroxyl group of the sugar. On the other hand, the RNA monomer is composed of same components with exception to the sugar group and the base. First, unlike DNA, RNA’s sugar group has a hydroxyl group attached to the 2’ end of the carbon ring. DNA contains bases called purines and pyrimidines. There are three purine bases: purine, adenine, and guanine while there are four pyrimidines: pyrimidine, cytosine, uracil, and thymine. In RNA specifically, thymine is absent while uracil is present. Same goes for DNA, absence of uracil and presence of thymine.


As one of the four major classes of molecules in biochemistry, carbohydrates include small sugar molecules such as table sugar to large polysaccharides such as starch in potatoes. Carbohydrates make up the majority of the organic matter on Earth and are an important source of energy, fuel and metabolic intermediates. It also play an important role in the structure of RNA, DNA and major structural components of the cell wall in living organisms. Furthermore, it can be bonded to the proteins and lipids, playing a role in cell to cell communication.


Monosaccharide is carbohydrate monomer. The name is derived from Greek word "mono"-single and "saccharide"-sugar. The simplest forms of carbohydrates are also known as aldehydes and ketones. It has one or more hydroxyl groups as well as a carbonyl group. The smallest possible monosaccharide is called trioses for it contains three carbons. A sugar containing four carbons is called tetrose. A sugar containing five carbons is called pentose. Many names for sugars end in the suffix -ose. Furthermore, there are two possible stereoisomer, D and L. D and L are designated by the absolute configuration of the asymmetric carbon atom farthest from the aldehyde or keto group.

Fischer projection of D-Aldoses that contains three, four, five, and six carbons. The Numbers shown in blue represents the ordering of the carbon atoms while the numbers in red represents the asymmetric carbon for each Aldose.
Fischer projection of D-Ketoses that contains three, four, five, and six carbons. The Numbers shown in blue represents the ordering of the carbon atoms while the numbers in red represents the asymmetric carbon for each Ketose.

The dominant forms of the monosaccharide are not an open chains, but ring forms because they are energetically stable. The formation of ring structure is possible because of the fact that aldehyde can react with an alcohol to form hemiacetal. Hemiacetal’s 2-carbon atom can react with either C-6 hydroxyl group or C-5 hydroxyl group to form five or six membered ring.


Glycosidic bonds between two monosaccharides allow linkage into disaccharide. During the linkage, one monosaccharide gives up a hydroxyl group while the other monosaccharide gives up a hydrogen. This reaction is known as dehydration reaction. There are three most abundant disaccharides called sucrose, lactose, and maltose. Sucrose is also known as table sugar. It's often found in plants and can be obtained from sugar canes and beets. An anomeric carbon of glucose and fructose are joined together into this disaccharide. The configuration of the glycosidic linkage for glucose is alpha and beta for fructose. Moreover, sucrose is not a reducing sugar because both of the components of monosaccharide are not converted into aldehyde or ketone. Maltose is made by linking two glucoses together by dehydration reaction. Lactose on the other hand is joined by glucose and galactose which are both beta configuration.


Oligosaccharide is composed of linkage of multiple monosaccharides called polysaccharides. Polysaccharide is an important source of energy storage and plays a role in maintaining the structural integrity of an organism. When the polymers of the oligosaccharides are all the same, then it’s called homopolymers. The most common type of homopolymer is called glycogen, which is a storage form of glucose. Glycogen is large and branches as it is linked by alpha-1, 4-glycosidic bond and alpha-1, 6-glycosidic bonds. Cellulose is another form of polysaccharide and unlike glycogen, it is found in plants. Cellulose play an important part in structural reinforcement and is the most abundant organic compound found in the biosphere. The unbranched polymer form is in beta configuration, beta-1, 4-linkage. The beta configuration allows cellulose to organize itself into long straight chain. Fibrils can be formed through parallel interaction between the chains. In the other hand, the alpha configuration leads to a hollow helix instead of the straight chain, specifically alpha-1, 4 linkages. Even though animals cannot digest cellulose, it is important component of dietary fiber, which decreases exposure of toxin to the animals.


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