From DNA to Protein
From DNA to Protein
DNA directs the cell’s activities by telling it what proteins to make and when. These proteins form structural elements in the cell and regulate the production of other cell products. By controlling protein synthesis, DNA is hugely important in directing life.
Protein synthesis is a two-step process. DNA resides in the nucleus, but proteins are made in the cytoplasm. The cell copies the information held in DNA onto RNA molecules in a process called transcription. Proteins are synthesized at the ribosomes from the codes in RNA in a process called translation.
Before getting into the way that the information on DNA can be transcribed and then translated into protein, we have to spend some time studying the major players in the process: DNA and RNA.
DNA and the Genetic Code
The sequence of nucleotides in DNA makes up a code that controls the functions of the cell by telling it what proteins to produce. Cells need to be able to produce 20 different amino acids in order to produce all the proteins necessary to function. DNA, however, has only four nitrogen bases. How can these four bases code for the 20 amino acids? If adenine, thymine, guanine, and cytosine each coded for one particular amino acid, DNA would only be able to code for four amino acids. If two bases were used to specify an amino acid, there would only be room to code for 16 () different amino acids.
In order to be able to code for 20 amino acids, it is necessary to use three bases (which offer a total of 64 coding combinations) to code for each amino acid. These triplets of nucleotides that make up a single coding group are called codons or genes. Two examples of codons are CAG, which codes for the amino acid glutamine, and CGA, which codes for arginine.
Codons are always read in a non-overlapping sequence. This means that any one nucleotide can only be a part of one codon. Given the code AUGCA, AUG could be a codon for the amino acid methionine, with CA starting a new codon. Alternatively, GCA could be a codon specifying alanine, while the initial AU was the last two letters of a previous codon. But AUG and GCA cannot both be codons at the same time.
Degeneracy of the Genetic Code
There are 64 codons but only 20 amino acids. What happens to the other 44 coding possibilities? It happens that some of the different codons call for the same amino acid. The genetic code is said to be degenerate because of its redundancy.
Experiments have shown that there are also three stop codons, which signal when a protein is fully formed, and one start codon, which signals the beginning of an amino acid sequence.
Mutations of the Genetic Code
Since the sequence of nucleotides in DNA determines the order of amino acids in proteins, a change or error in the DNA sequence can affect a protein’s function. These errors or changes in the DNA sequence are called mutations.
There are two basic types of mutations: substitution mutations and frameshift mutations.
Substitution Mutation
A substitution mutation occurs when a single nucleotide is replaced by a different nucleotide. The effects of substitution mutations can vary. Certain mutations might have no effect at all: these are called silent mutations. For instance, because the genetic code is degenerate, if the particular codon GAA becomes GAG, it will still code for the amino acid glutamate and the function of the cell will not change. Other substitution mutations can drastically affect cellular and organismal function. Sickle-cell anemia, which cripples human red blood cells, is caused by a substitution mutation. A person will suffer from sickle-cell anemia if he has the amino acid valine in his hemoglobin rather than glutamic acid. The codon for valine is GUA or GUG, while the codon for glutamic acid is GAA or GAG. A simple substitution of A for U results in the disease.
Frameshift Mutation
A frameshift mutation occurs when a nucleotide is wrongly inserted or deleted from a codon. Both types of frameshifts usually have debilitating or lethal effects. An insertion or deletion will affect every codon in a particular genetic sequence by throwing the entire three-by-three codon structure out of whack. For example, if the A in the GAU were to be deleted, the code:
GAU GAC UCC GCU AGG
would become:
GUG ACU CCG CUA GG
and code for an entirely different set of amino acids in translation. The results of such mutations on an organism are usually catastrophic.
The only sort of frameshift mutation that might not have dire effects is one in which an entire codon is inserted or deleted. This will result in the gain or loss of one amino acid but will not affect surrounding codons.
Chromosomes
Even the tiniest cells contain meters upon meters of DNA. With the aid of special proteins called histones, this DNA is coiled into an entangled fibrous mass called chromatin. When it comes time for the cell to replicate (a process covered later in this chapter), these masses gather into a number of discrete compact structures called chromosomes.
In eukaryotes, the chromosomes are located in the nucleus of the cell. Prokaryotes don’t have a nucleus: their DNA is located in a single chromosome that is joined together in a ring. This ring chromosome is found in the cytoplasm. In this chapter, when we talk about chromosomes, we will be referring to eukaryotic chromosomes.
Different eukaryotes have varying numbers of chromosomes. Humans, for example, have 46 chromosomes arranged in 23 pairs. (Dogs have 78 chromosomes in 39 pairs. A larger number of chromosomes is not a sign of greater biological sophistication.) The total number of distinct chromosomes in a cell is the cell’s diploid number.
The cells in a human body that are not passed down to offspring, called somatic cells, contain chromosomes in two closely related sets—one set of 23 each from a person’s mother and father—making up a total of 46 chromosomes. These sets pair up, and the pairs are known as homologous chromosomes. Each homologous pair consists of one maternal and one paternal chromosome. The haploid number of a cell refers to half of the total number of chromosomes in a cell (half the diploid number), or the number of homologous pairs in somatic cells.
In humans and other higher animals, only the sex cells that are passed on to offspring have the haploid number of chromosomes. These sex cells are also called gametes.
RNA
Ribonucleic acid (RNA) helps DNA turn stored genetic messages into proteins. As discussed in the Biochemistry chapter, RNA monomers (nucleotides) are similar to those of DNA, but with three crucial differences:
  • DNA’s five-carbon sugar is deoxyribose. RNA nucleotides contain a slightly different sugar, called ribose.
  • RNA uses the nitrogenous base uracil in place of DNA’s thymine.
  • The RNA molecule takes the form of a single helix—half a spiral ladder—as compared with the double helix structure of DNA.
Two different types of RNA play important roles in protein synthesis. During transcription, DNA is copied to make messenger RNA (mRNA), which then leaves the nucleus to bring its still encoded information to the ribosomes in the cytoplasm. In order to use the information contained in the transcribed mRNA to make a protein, a second type of RNA is used. Transfer RNA (tRNA) moves amino acids to the site of protein synthesis at the ribosome according to the code specified by the mRNA strand. There are many different tRNAs, each of which bond to a different amino acid and the mRNA sequence corresponding to that amino acid.
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