Molecular Biology

What Biomolecules

DNA (Deoxyribonucleic Acid): DNA is a molecule that carries the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms. It consists of two long strands that coil around each other to form a double helix. Each strand is made up of nucleotides, which are the building blocks of DNA. A nucleotide comprises three components: Phosphate Group: Provides the backbone structure of DNA. Deoxyribose Sugar: A five-carbon sugar molecule that links the nucleotides together. Nitrogenous Base: Adenine (A), Thymine (T), Cytosine (C), and Guanine (G) are the four nitrogenous bases found in DNA. They pair specifically—A with T and C with G—forming complementary base pairs. The sequence of these base pairs along the DNA strand encodes genetic information. This information is transcribed into RNA for protein synthesis. RNA (Ribonucleic Acid): RNA is a molecule similar to DNA, but with a few key differences. It plays various roles in coding, decoding, regulation, and expression of genes. There are several types of RNA, each serving a distinct function: Messenger RNA (mRNA): mRNA carries genetic information from the DNA in the nucleus of a cell to the cytoplasm, where proteins are synthesized. This process is called transcription. Transfer RNA (tRNA): tRNA is responsible for transferring amino acids to the ribosome during protein synthesis. It reads the mRNA sequence and matches it with the corresponding amino acid, ensuring that proteins are built accurately. Ribosomal RNA (rRNA): rRNA is a structural component of ribosomes, which are the cellular machinery responsible for protein synthesis. It helps in the binding of mRNA and tRNA during translation. Transcription and Translation: The process of converting DNA into RNA (specifically mRNA) is called transcription. During transcription, an enzyme called RNA polymerase binds to a specific region of DNA and unwinds the double helix. It then builds an mRNA molecule by using one of the DNA strands as a template. The mRNA carries the genetic code from the DNA to the ribosome. Translation is the process where mRNA is decoded to build a specific protein. It occurs at the ribosome. The sequence of nucleotides in the mRNA is read in groups of three, called codons. Each codon codes for a specific amino acid or signifies the start or stop of protein synthesis. tRNA brings the corresponding amino acids to the ribosome based on the mRNA codons, forming a polypeptide chain, which folds into a functional protein. In summary, DNA holds the genetic blueprint of an organism, while RNA helps in translating that information into functional proteins essential for various biological processes. Their collaboration is fundamental to the existence and functioning of all living organisms.

Structure and Properties of Proteins

Proteins are macromolecules made up of linear polymers of amino acids. Proteins are most
abundant molecules of living system and have high molecular weights. Proteins play very
important functions in the cell such as enzyme catalysis, in immune response, transport and
storage of molecules, in transmission of nerve impulse, control growth and differentiation,
provide mechanical support, etc. Proteins are made up of carbon, hydrogen, oxygen and
nitrogen and in some cases sulfur and phosphorus.

Classification of amino acids

Classification of amino acids according to the polarities of R group is the most common way of classification. According to this classification there are five types of amino acids.

1. Non polar aliphatic amino acids This group contains seven amino acids. Four amino acids glycine, alanine, valine, leucine and isoleucine have are R groups of aliphatic hydrocarbon (Figure 4). Methionine, one of the two sulfur containing amino acids has a slightly non polar thiol ether side chain. Proline has a cyclic secondary amino (imino) group

Figure No 2

2. Amino acids with aromatic R groups
Three amino acids namely phenylalanine, tyrosine and tryptophan have aromatic side chain that makes them slightly non polar (hydrophobic) and hence participate in hydrophobic interactions (Figure 5). Tyrosine and tryptophan are relatively more polar than phenylalanine due to presence of –OH group in tyrosine and the nitrogen atom in the indole ring of tryptophan. The

. Amino acids with polar, uncharged R groups

The amino acids that belong to this class are serine, threonine, cycteine, asparagine and glutamine (Figure 6). The R groups of these amino acids are polar (hydrophilic) and therefore they are more soluble in water. Polarity in these amino acids is because they contain functional groups like -OH (serine and threonine), -CONH2 (glutamine and asparagine), -SH (cysteine).

4. Amino acids with positively charged (basic) R groups

In this class of amino acids R groups have positive charge at physiological pH (Figure 7). Lysine has a second primary amino group at the ε position on its aliphatic chain. Arginine has a positively charged guanidium group and histidine has an aromatic imidazole group.

5. Amino acids with negatively charged (acidic) R groups There are two amino acids having a negative charge at pH 7.0 (Figure 8). These are aspartate and glutamate; both contain a second -COOH group.

Primary Structure of Protein

The α-COOH of one amino acid links to α-NH2 group of another amino acid through a peptide bond (also called amide bond) to form linear polymer. Formation of a peptide bond from two amino acids is accompanied by the loss of water molecule. The equilibrium of this reaction lies on the side of the hydrolysis rather than synthesis. Hence the biosynthesis of peptide bond requires an input of free energy.
Depending on the number of amino acids composing a chain, the peptides may be termed as a dipeptide (containing two amino acids units), a tripeptide (containing three amino acid units). Peptides containing less than ten amino acid residues are called oligopeptide. Peptides containing more than ten residues are termed polypeptide. Each amino acid unit in polypeptide is called a residue.

Secondary structure of proteins

Secondary structure of proteins Folding of polypepeptide chain is possible because of the presence of hydrogen bond. A regular secondary structure occurs when each dihedral angle φ and ψ remains the same or nearly same throughout the segment. In 1951 Linus Pauling and Robert Corey proposed two types of periodic structures called α helix and β pleated sheet. α Helix Pauling and Corey observed that a polypeptide chain with planar peptide bonds would form a right handed helical structure by simple twists about the Cα–N and the Cα–C bonds. They called this helical structure as α helix. An α helix is a rod like structure. The inner part of helix is made up of the tightly coiled backbone and the side chains extend outward in the helix. The protruding side chains determine the interaction of α helix both with other parts of the folded protein chain and with other protein molecules. The helix is stabilized by hydrogen bonds between NH and CO groups of the main chain. The α helix contains 3.6 amino acids per turn of the helix and has a pitch of 5.4 Å (0.54 nm), thereby giving a rise per turn residue of 5.4/3.6=1.5 Å, which is the identity period of the helix. The value of rotational angles φ and ψ is -60° and -45° to -50°, respectively. The α helix can be right handed (clockwise) or left handed (counterclockwise). All known polypeptides contain right handed α helix. The occurrence of α helical content in proteins ranges widely. For example in ferritin, that helps storage of iron, has 75% of its amino acid residues form α helix. β pleated sheet The second type of periodic structure is β pleated sheet. In contrast to α helix β pleated sheet involve hydrogen bonds between groups from residues distant from each other in the linear sequence. In β sheets two or more strands widely separated in the protein sequence are arranged side by side, with hydrogen bonds between the strands. Based on the orientation of the strands β sheets are of two types. If strands run in the same direction they are called parallel β sheets; if strands run in opposite direction they are called antiparallel β sheets. In parallel arrangement the NH group is hydrogen bonded to the CO group of the one amino acid on the adjacent strand, whereas the CO group is hydrogen bonded to the NH group on the amino acids two residues farther along the chain. Tertiary structure of protein The overall three dimensional arrangement of all atoms in a protein is called as tertiary structure of protein. The amino acids that are far apart in polypeptide chain are in differenttypes of secondary structures may interact with each other to form completely folded structure of a protein. In tertiary structure there is an involvement of some additional bonds like disulfide, hydrogen, hydrophobic and ionic (Figure 10). This makes the protein globular in shape. The enzymes, transport protein, some peptide hormones and immunoglobulins are all globular in shape which is their tertiary structure. In these globular proteins the head group are located on the outer surface because of their hydrophilicity (water loving property) and non polar R groups are located interior where their interaction create a hydrophobic (water hating property) environment. The tertiary structure thus involves the folding of the helices of globular proteins.

Secondary Structure of protein

Tertiary Structure

Tertiary Structure: The overall three-dimensional shape of a protein molecule is the tertiary structure. The protein molecule will bend and twist in such a way as to achieve maximum stability or lowest energy state. Although the threedimensional shape of a protein may seem irregular and random, it is fashioned by many stabilizing forces due to bonding interactions between the side-chain groups of the amino acids.