DNA, RNA, Genes, Chromosomes, and the Code of Life

Young Astronomers Blog, Volume 29, Number 8.

Recently, a large rover named Perseverance landed on the planet Mars. Perseverance is searching for signs that Mars had life, or at least the conditions for life, sometime in the distant past. Fundamental to life is something called DNA.

We have also been dealing with a pandemic caused by the SARS-CoV-2 virus, which can produce a disease called COVID-19. A virus is a germ made up of genetic material (DNA or RNA). It takes over the body’s cells and uses them to replicate. The first two vaccines available in the United States use genetic material (mRNA) to fight off the COVID-19 virus.

Given all this, I thought it would be interesting to understand a bit about DNA and RNA.

Proteins and Amino Acids

Proteins make up a large portion of our cells and form the basis for much of a cell’s structure and function. Proteins are composed of “polypeptide chains” of amino acids, which are bonded together using what are called “peptide bonds”. Each amino acid has a common structure consisting of a central carbon/hydrogen, a carboxyl group (COOH), an amino group (NH₂), and a variable “R” group that defines the specific amino acid.

While there are only twenty unique amino acids that bond together to create proteins, there are thousands of different proteins found in our cells. Proteins can be classified based on their function (cell structure, transportation of other molecules, enzymes to enhance chemical reactions, or communication/coordination of cell activities). They are also classified based on their structure.

1. Primary: sequence of amino acids
2. Secondary: “a or b fold”
3. Tertiary: 3D shape
4. Quaternary: linking of multiple amino acid chains

DNA and RNA

Different forms of RNA construct amino acids (and proteins) from our DNA. Therefore, our starting point for all this is the extremely important molecule found in all living things, Deoxyribonucleic Acid (DNA). DNA contains the instructions that tell our cells how to function. A similar molecule Ribonucleic Acid (RNA) carries instructions from the DNA in a cell’s nucleus to the rest of the cell and is used to create amino acids and proteins.

DNA is a long string of smaller molecules called nucleotides. Each nucleotide is composed of three parts.

• (Nitrogen) Base molecules create the genetic code found in all living things. DNA has four distinct base molecules; cytosine (C₄H₅N₃O), guanine (C₅H₅N₅O), adenine (C₅H₅N₅), and thymine (C₅H₆N₂O₂).
• The sugar deoxyribose (C₅H₁₀O₄) is found in the backbone of DNA.
• A phosphorus group (PO₄) attaches to the sugar molecules in the backbone.

The base molecules link together in pairs forming DNA into a double helix. Cytosine (C) always pairs with guanine (G), and adenine (A) always pairs with thymine (T).

RNA has a similar structure. However, the base molecules are singular, and its backbone is built from the sugar ribose (C₅H₁₀O₅). It also contains the base molecule uracil (C₄H₄N₂O₂) rather than thymine. There are different types of RNA.

• mRNA (messenger RNA) is the molecule that carries information from the cell’s DNA.
• tRNA (transfer RNA) translates the mRNA information into amino acids.
• rRNA (ribosomal RNA) is a component of ribosomes where the transfer takes place.

Genes

Individual nucleotides are strung together into long complex DNA molecules. This sequence of base pairs is the code of life. Subsections of the DNA molecules, called genes, define various traits or characteristics and provide instructions to our cells. A complete set of genes is found in every cell, but only certain ones are “turned on” depending on the cell’s function. Humans have around twenty to thirty thousand genes. A single gene can have a few thousand to a million or so base pairs.

Genes have been cataloged and assigned symbols. For example, the gene OCA2 plays a role in determining the color of one’s eyes. Genes, however, are only a small portion of the overall DNA molecules and the three billion base pairs in the human genome. The remaining sections of “uncoded DNA” are not completely understood but appear to play a role in how DNA is processed within the cell.

Transcription and Translation

Our genes (sequences of genetic code) are copied from DNA molecules to mRNA molecules through a process called transcription. During the process, thymine (T) is converted into uracil (U). The resulting mRNA molecule is a sequence of several three-letter codes (codons).

In a process called translation, the mRNA molecule is “sandwiched” between the “large subunit” and “small subunit” of a ribosome, which is built from rRNA molecules. A specific three letter tRNA code (anticodon) is matched to each mRNA codon and a corresponding amino acid is added to an amino acid polypeptide chain. This process continues for all three letter mRNA codons that were transcribed from the original DNA gene. Eventually, the complete polypeptide chain of amino acids becomes a protein.

The mapping from codons to amino acids is unambiguous, but redundant (degenerate). There are a total of 61 unique codons associated with twenty specific amino acids. For example, codons GGU, GGC, GGA, and GGG translate into the amino acid glycine. In addition to the 61, there are three codons (UAA, UAG, and UGA) placed at the end of the mRNA sequence that represent the stop command. They tell the process to stop the translation when the sequence is done, and the protein is complete.

Because there are more codons than amino acids, there are only 31 distinct tRNA anticodons. Anticodons bond with codons in a way similar to the base pair bonding in DNA. Cytosine (C) bonds with guanine (G) and adenine (A) bonds with uracil (U). However, these strict rules hold only for the first two nucleoids. The third paring can “wobble” – it does not have to be exact. In this case, guanine (G) can bond with uracil (U).

Also, a fifth anticodon inosine (I) can bond with uracil (U), adenine (A), or cytosine (C). Inosine is formed from the base hypoxanthine (C₅H₄N₄O) and ribose, and sometimes is referred to as hypoxanthine (I) rather than inosine (I). For example, codons GGU, GGC, and GGA can all bond with a single tRNA anticodon (CCI). In all three cases, the amino acid glycine results.

Chromosomes

A complete DNA molecule is found in a chromosome. Each chromosome contains a unique DNA molecule with a few thousand genes. Chromosomes come in pairs and each chromosome pair holds a different DNA molecule with a different set of genes. For example, the OCA2 gene is found on the 15^th chromosome pair. Humans have 23 pairs of chromosomes for a total of 46 chromosomes. One chromosome in each pair comes from the father and the other from the mother. Each of the two chromosomes in a pair has the same DNA molecule and set of genes, although specific “alleles” might differ (e.g., brown eyes vs. blue eyes). The exception is the 23^rd pair, where females have two X chromosomes and males have a X and Y chromosome.

Cell Division (Mitosis and Meiosis)

When cells divide through a process called mitosis, the chromosomes duplicate, creating a copy for each of the new cells. Within the chromosomes, the DNA molecules unwind and split apart. Each of the nucleotides pair up with a new base molecule and two complete DNA molecules are formed. As the cell divides, one DNA molecule goes with each new cell.

During reproduction, a process called meiosis takes place. First, the cells for each parent divide. In this case, the chromosomes “crossover” and intermingle creating chromosomes with a mix of DNA from both chromosome pairs. After a few more steps, four cells are created, each with a single set of 23 chromosomes (haploid cells). Later, a cell from the father and one from the mother combine resulting in a cell with the full 46 chromosomes (diploid cell). In this case, the chromosomes are again paired up with one of each pair coming from the father and the other from the mother.

Heredity

Your chromosomes (genes and DNA) determine your heredity traits. Everyone receives two genes for each trait, one from your father and one from your mother. Each of the different versions is called an “allele”. Some traits (and genes) are dominate alleles (you only need one of the two for a particular trait), other traits are recessive alleles (you need both for the trait). Gene pairs that are the same are called homozygous. Gene pairs that are different are called heterozygous.

As an example, let’s consider the gene for eye color, although, this is a simplified example. There are actually several genes that determine eye color. Let B be the allele for brown eyes (dominate) and b the allele for blue eyes (recessive). Below are the eye color options shown in a “Punnett Square”, where the father could provide B or b (across the top) and the mother could provide B or b (down the column on the left). Their children would have some combination of BB, Bb or bb. Because B is dominate, combinations BB and Bb result in brown eyes. Only the combination bb results in blue eyes.