DNA Structure, Function, and Amino Acid Properties
DNA: Structure and Function
DNA is a linear polymer composed of a pentose, a phosphate, and a nitrogenous base, which can be A, T, C, or G.
Primary Structure
The primary structure is the sequence of nucleotides linked by phosphodiester bonds. These links are established between the phosphate radical located in the 5′ carbon of one nucleotide and the OH radical in the 3′ carbon of the next nucleotide. A DNA strand has two free ends: the 5′ phosphate and the 3′ attached to a hydroxyl. These chains of nucleotides differ from each other in size, composition, and base sequence, indicating the order of ATCG. The order in which DNA nucleotides are linked is crucial when a protein is synthesized. The genetic information contained in a specific portion of the DNA molecule carries the information needed to join amino acids in a particular order, constituting the primary structure of a protein, which in turn determines its three-dimensional structure and the function it exerts in the cell.
Secondary Structure (Form B)
The secondary structure was established in 1953 by Watson and Crick. It was already known that DNA was formed by a nucleotide structure with known dimensions linked by phosphodiester bonds. Watson and Crick used the work of other researchers as a basis for discovering the structure of DNA.
- The DNA molecule is long, stiff, and not folded.
- In the molecule, small details are repeated every 0.34 nm and 3.4 nm.
- The base composition varies, but for the same species, the content and the ratio of purine bases equals pyrimidine bases.
Watson and Crick Model
Watson and Crick proposed a model that was consistent with this data, allowing us to understand the functioning of DNA, which reads:
- The DNA double helix is 2 nm in diameter, formed by two polynucleotide chains coiled around an imaginary axis, where the nitrogenous bases are inside, and the planes of their rings are parallel to each other and perpendicular to the axis of the double helix.
- The coiling is right-handed and plectonemic, meaning that to separate the two strands, it is necessary to unroll them.
- Each pair of nucleotides is separated from the next by 0.34 nm, and each turn of the double helix is formed by 10 pairs of nucleotides, resulting in a length of 3.40 nm per turn of the helix.
- The polynucleotide chains are antiparallel and complementary, meaning there is a correspondence between the nitrogenous bases.
DNA Form A
Obtained from the secondary structure when the humidity of the environment is reduced to 75%, it is never found in physiological conditions. This is a double helix that rotates clockwise. Base pairs are tilted 20° to the axis, measure 2.3 nm, and have 11 base pairs per turn.
Z Form of DNA
It is longer and narrower than form B since it measures 3.8 nm and has 12 base pairs per turn of the helix. The two polynucleotide chains are coiled to form a zigzag, besides turning counterclockwise. This zigzag shape is due to the large presence of cytosine and guanine. It is believed that this structure of DNA is involved in the processes of expression of the genetic message.
Biological Function of DNA
DNA is the store of genetic information and the molecule responsible for transmitting to offspring the necessary instructions for building all the proteins present in a living being. To do so, it has the ability to make copies of itself through replication, which is based on the complementarity between the bases of the two strands of DNA.
In prokaryotes, there is a circular DNA molecule called the bacterial chromosome. It sometimes contains small plasmids. In eukaryotes, the DNA is inside the nucleus, forming linear molecules associated with basic proteins. This set forms a fiber that is called chromatin. When the cell divides, chromosomes are formed. In viruses, DNA can take several forms because they contain a single molecule that can be single or double-stranded.
Amino Acids
Amino acids are simple, low molecular weight organic compounds that join together to form proteins. Chemically, they are composed of C, H, O, and N. They are characterized by having in their molecule a carboxyl group, an amino group, and a side chain, all linked together by covalent bonds to a central carbon atom. There are 20 amino acids that are the building blocks of proteins. However, there are some 150 amino acids that are found in cells and tissues but are not part of proteins (non-protein amino acids).
Acid-Base Properties
When amino acids are in an aqueous solution, they are zwitterions or in hybrid form. Any amino acid can behave as an acid and a base; these are called amphoteric substances. When a molecule has zero net charge, it is at its isoelectric point. If an amino acid has an isoelectric point of 6.1, the net charge is zero when the pH is 6.1. Amino acids and proteins behave as buffer substances.
Peptide Bond
A covalent bond between the amino (-NH2) group of one amino acid and the carboxyl (-COOH) group of another amino acid. Peptides and proteins are formed by the joining of amino acids by peptide bonds, forming dipeptides (2 amino acids), tripeptides (3 amino acids), and oligopeptides (up to 50 amino acids). The peptide bond involves the loss of one molecule of water and the formation of a covalent CO-NH bond. It is actually a substituted amide bond. We can continue adding amino acids to the peptide, but always at the COOH-terminal.
Peptide Bond Features
The peptide bond is a covalent bond shorter than most other C-N bonds. It has some double bond character, which prevents it from spinning freely. The four atoms of the peptide bond and the two central carbon atoms are located in the same plane, with fixed distances and angles. The only bonds that can rotate, albeit with limitations, are the C-C and N-C bonds.