DNA, RNA, and Protein Synthesis

DNA and RNA are both nucleic acids, long chains built from repeating units called nucleotides. Every nucleotide has three parts: a sugar, a phosphate group, and a nitrogen base. The two nucleic acids differ in their sugar, in one of their bases, and in how many strands they have.

DNA is a double helix, two strands twisted around each other like a spiral ladder. The two sides of the ladder are a backbone of alternating sugar and phosphate groups. The rungs are pairs of nitrogen bases reaching across from one strand to the other, held together by hydrogen bonds. The two strands run in opposite directions, which biologists call antiparallel: one strand runs 5' to 3' while its partner runs 3' to 5'.

Base pairing follows strict rules. Adenine (A) always pairs with thymine (T), and cytosine (C) always pairs with guanine (G). A larger two-ring base (a purine, A or G) always pairs with a smaller one-ring base (a pyrimidine, T or C), which keeps the ladder an even width all the way down.

Before a cell divides, it must copy all of its DNA so each new cell receives a complete set. This copying is called replication, and in a cell with a nucleus it happens in the nucleus. Replication is semiconservative, meaning each new double helix keeps one original strand and one brand new strand. The original strand acts as a template, a pattern used to build its partner.

The central dogma of molecular biology describes the one-way flow of genetic information in a cell: DNA to RNA to protein. A gene, a segment of DNA, is first copied into RNA during transcription. That RNA message is then read to build a protein during translation. Proteins do most of the work in a cell, so a gene shapes a trait by specifying a protein.

In transcription, the enzyme RNA polymerase copies one gene from DNA into a strand of messenger RNA (mRNA). RNA polymerase unwinds a small section of the DNA, reads one strand as a template, and links RNA nucleotides into a complementary strand. Only one of the two DNA strands is used as the template for a given gene.

The base pairing rule is almost the same as in DNA, with one change. RNA has no thymine, so wherever the DNA template has adenine, the new RNA strand gets uracil instead of thymine.

In translation, the ribosome reads the mRNA and builds a protein. The mRNA is read three bases at a time. Each three-base group is a codon, and each codon calls for one specific amino acid. Transfer RNA (tRNA) molecules bring the matching amino acids, and the ribosome links them into a growing chain. That finished chain of amino acids folds into a protein.

With four possible bases read three at a time, there are 4 × 4 × 4 = 64 possible codons. These 64 codons specify the 20 amino acids used to build proteins, so the code has backups. Most amino acids are called for by more than one codon.

A mutation is a change in the DNA base sequence. Because DNA codes for proteins, a mutation can change a protein for better, for worse, or not at all. Swapping one base for another is a point mutation. Inserting or deleting a base shifts how every later codon is read, a frameshift, which usually damages the protein more severely because everything downstream is misread.

Using dna-strands.txt and the rules stated at the top of the file: 1. Strand 2 is given as a template strand, 3' to 5'. Write out the mRNA sequence transcribed from it, 5' to 3'. 2. List Strand 1's mRNA codons in order, and state which one is the stop codon. 3. Counting the amino acid coded by the start codon and not counting the stop codon, how many amino acids are in the protein made from Strand 3? 4. Do the same amino-acid count for all three strands. Which strand produces the longest protein? 5. Strand 1 is given as a coding (sense) strand, 5' to 3'. Using DNA base pairing, write out its DNA template strand.