The molecular mechanisms of oxygen-sensing in human ductus arteriosus smooth muscle cells: A comprehensive transcriptome profile reveals a central role for mitochondria

 

DNA(Deoxyribonucleic Acid):

DNA, abbreviation of deoxyribonucleic acid, organic chemical of complex molecular structure that is found in all prokaryotic and eukaryotic cells and in many viruses. DNA codes genetic information for the transmission of inherited traits. The chemical DNA was first discovered in 1869, but its role in genetic inheritance was not demonstrated until 1943. In 1953 James Watson and Francis Crick, aided by the work of biophysicists Rosalind Franklin and Maurice Wilkins, determined that the structure of DNA is a double-helix polymer, a spiral consisting of two DNA strands wound around each other. The breakthrough led to significant advances in scientists’ understanding of DNA replication and hereditary control of cellular activities. Each strand of a DNA molecule is composed of a long chain of monomer nucleotides.

The nucleotides of DNA consist of a deoxyribose sugar molecule to which is attached a phosphate group and one of four nitrogenous bases: two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). The nucleotides are joined together by covalent bonds between the phosphate of one nucleotide and the sugar of the next, forming a phosphate-sugar backbone from which the nitrogenous bases protrude. One strand is held to another by hydrogen bonds between the bases; the sequencing of this bonding is specific—i.e., adenine bonds only with thymine, and cytosine only with guanine. The configuration of the DNA molecule is highly stable, allowing it to act as a template for the replication of new DNA molecules, as well as for the production (transcription) of the related RNA (ribonucleic acid) molecule. A segment of DNA that codes for the cell’s synthesis of a specific protein is called a gene.

DNA replicates by separating into two single strands, each of which serves as a template for a new strand. The new strands are copied by the same principle of hydrogen-bond pairing between bases that exists in the double helix. Two new double-stranded molecules of DNA are produced, each containing one of the original strands and one new strand. This “semiconservative” replication is the key to the stable inheritance of genetic traits.

Within a cell, DNA is organized into dense protein-DNA complexes called chromosomes. In

 eukaryotes, the chromosomes are located in the nucleus, although DNA also is found in mitochondria and chloroplasts. In prokaryotes, which do not have a membrane-bound nucleus, the DNA is found as a single circular chromosome in the cytoplasm. Some prokaryotes, such as bacteria, and a few eukaryotes have extrachromosomal DNA known as plasmids, which are autonomous, self-replicating genetic material. Plasmids have been used extensively in recombinant DNA technology to study gene expression.

RNA (Ribonucleic acid): 

Ribonucleic acid (RNA) is a molecule similar to DNA. Unlike DNA, RNA is single-stranded. An RNA strand has a backbone made of alternating sugar (ribose) and phosphate groups. Attached to each sugar is one of four bases--adenine (A), uracil (U), cytosine (C), or guanine (G). Different types of RNA exist in the cell: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). More recently, some small RNAs have been found to be involved in regulating gene expression.

Proteins:

Proteins are the end products of the decoding process that starts with the information in cellular DNA. As workhorses of the cell, proteins compose structural and motor elements in the cell, and they serve as the catalysts for virtually every biochemical reaction that occurs in living things. This incredible array of functions derives from a startlingly simple code that specifies a hugely diverse set of structures. The building blocks of proteins are amino acids, which are small organic molecules that consist of an alpha (central) carbon atom linked to an amino group, a carboxyl group, a hydrogen atom, and a variable component called a side chain (see below). Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a long chain. Peptide bonds are formed by a biochemical reaction that extracts a water molecule as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid. The linear sequence of amino acids within a protein is considered the primary structure of the protein.

Proteins fold into stable three‐dimensional shapes, or conformations, that are determined by their amino acid sequence. The complete structure of a protein can be described at four different levels of complexity: primary, secondary, tertiary, and quaternary structure.

The primary structure of a protein is the hierarchy’s basic level and is the particular linear sequence of amino acids comprising one polypeptide chain.

The secondary structure is the next level up from the primary structure and is the regular folding of regions into specific structural patterns within one polypeptide chain. Hydrogen bonds between the carbonyl oxygen and the peptide bond amide hydrogen are normally held together by secondary structures.

Tertiary structure is the next level up from the secondary structure and is the particular three-dimensional arrangement of all the amino acids in a single polypeptide chain. This structure is usually conformational, native, and active, and is held together by multiple noncovalent interactions.

Quaternary structure is the next ‘step up’ between two or more polypeptide chains from the tertiary structure and is the specific spatial arrangement and interactions.

Activity:

Read the following information carefully. Would you be able to add some more examples of biological data? Feel free to explore and include new examples on your own!

DNA - sequences; genes (start and stop nucleotide); position; homology for nucleotide sequence.

RNA - sequence; types; structure; gene expression; homology.

Proteins - amino acid sequence; structure (primary, secondary [beta sheets and alpha helices], tertiary [domains - small parts of the protein structure that have a specific function], quaternary [sometimes 2 or more small proteins bind to each other for a specific function]); function; similarity between the sequence/structural domains (homology)