Gene Regulation and Genetic Code

Gene regulation and the genetic code explain how a cell reads its genes and when it switches them on. This page covers how the triplet code was proposed and deciphered by Gamow, Khorana, Nirenberg and Ochoa, the codon table and its six salient features, point and frameshift mutations, and tRNA as the adapter molecule. It then covers the levels of gene regulation and the lac operon of Jacob and Monod, with its repressor and inducer. NEET often asks codon features, stop codons and the lac genes under gene regulation and the genetic code.

1. The Genetic Code

• In replication and transcription, one nucleic acid is copied into another, so complementarity makes them easy to picture.
• Translation transfers information from a polymer of nucleotides to a polymer of amino acids.
• ★ Exam imp There is no complementarity between nucleotides and amino acids, and none can be drawn even in theory.
• Yet there was ample evidence that changes in nucleic acids (the genetic material) caused changes in the amino acids of proteins.
• This led to the proposal of a genetic code that directs the sequence of amino acids during protein synthesis.

1.1 Proposing and deciphering the code

• Proposing and deciphering the code was the most challenging task. It needed physicists, organic chemists, biochemists and geneticists.
• ★ Exam imp George Gamow, a physicist, argued that 4 bases must code for 20 amino acids, so each code word must be a combination of bases.
• He suggested that each code word, or codon, should be made of three nucleotides.
• This was a bold proposal, because the permutations give $4\times 4\times 4$ = 64 codons, many more than needed.

• Proving that the codon is a triplet was an even more daunting task.
• Har Gobind Khorana developed a chemical method to synthesise RNA molecules with defined combinations of bases (homopolymers and copolymers).
• Marshall Nirenberg's cell-free system for protein synthesis finally helped decipher the code.
• Severo Ochoa's enzyme (polynucleotide phosphorylase) also helped, by polymerising RNA with defined sequences without a template (enzymatic synthesis of RNA).
• Finally, a checker-board of the genetic code was prepared.

The codons for the amino acids

1.2 Salient features of the genetic code

1. The codon is a triplet. 61 codons code for amino acids and 3 do not code for any amino acid, so they work as stop codons.
2. Some amino acids are coded by more than one codon, so the code is degenerate.
3. The codon is read in mRNA in a contiguous fashion. There are no punctuations.
4. The code is nearly universal: from bacteria to humans, UUU codes for phenylalanine (Phe). Some exceptions are found in mitochondrial codons and in some protozoans.
5. AUG has dual functions: it codes for methionine (Met) and also acts as the initiator codon.
6. UAA, UAG and UGA are the stop (terminator) codons.

• The mRNA -AUG UUU UUC UUC UUU UUU UUC- codes for Met-Phe-Phe-Phe-Phe-Phe-Phe, since both UUU and UUC code for phenylalanine.
• Going the other way is harder. For Met-Phe-Phe-Phe-Phe-Phe-Phe, each Phe could be UUU or UUC, so many different mRNAs are possible.
• Reading forward always gives one answer, because each codon codes for only one amino acid; reading backward does not, because the code is degenerate.

2. Mutations and the Genetic Code

• The relationship between genes and DNA is best understood by studying mutations.
• Large deletions and rearrangements in a DNA segment are easy to understand: they may cause loss or gain of a gene, and so of a function.
• A point mutation is a change of a single base pair.
• ★ Exam imp A classic example is a single base pair change in the gene for the beta globin chain, which changes the amino acid glutamate to valine. This causes sickle cell anaemia.

2.1 Insertions and deletions: RAM HAS RED CAP

• Think of a sentence made of three-letter words, just like codons: RAM HAS RED CAP.

• ★ Exam imp Inserting or deleting one or two bases changes the reading frame from the point of change: these are frameshift insertion or deletion mutations.
• Inserting or deleting three bases, or a multiple of three, adds or removes one or more codons, and so one or more amino acids.
• In that case the reading frame stays unaltered from that point onwards.

3. tRNA: the Adapter Molecule

• From the start, Francis Crick saw that something must read the code and link it to amino acids, because amino acids have no structural features to read the code themselves.
• He postulated an adapter molecule that would read the code on one side and bind a specific amino acid on the other.
• ★ Exam imp tRNA, then called sRNA (soluble RNA), was known before the genetic code was proposed. Its role as the adapter was assigned much later.
• tRNA has an anticodon loop, with bases complementary to the code.
• It also has an amino acid acceptor end, to which it binds an amino acid.
• tRNAs are specific for each amino acid.
• For initiation there is another specific tRNA, the initiator tRNA.
• ★ Exam imp There are no tRNAs for stop codons.
• Drawn on paper, the secondary structure of tRNA looks like a clover-leaf. Its actual structure is a compact molecule shaped like an inverted L.

4. Regulation of Gene Expression

• Regulation of gene expression is a broad term; it can occur at various levels.
• Gene expression results in a polypeptide, so it can be regulated at several steps.
• In eukaryotes, regulation can be exerted at four levels:

1. Transcriptional level: formation of the primary transcript.
2. Processing level: regulation of splicing.
3. Transport of mRNA from the nucleus to the cytoplasm.
4. Translational level.

• Genes in a cell are expressed to perform a particular function or a set of functions.
• Example: E. coli makes the enzyme beta-galactosidase to hydrolyse the disaccharide lactose into galactose and glucose, which it uses as a source of energy.
• If there is no lactose around, the bacteria no longer need to make beta-galactosidase.
• ★ Exam imp So, in simple terms, metabolic, physiological or environmental conditions regulate the expression of genes.
• The development and differentiation of an embryo into an adult also result from the coordinated regulation of several sets of genes.

4.1 Regulation in prokaryotes

• ★ Exam imp In prokaryotes, control of the rate of transcriptional initiation is the main site for controlling gene expression.
• The activity of RNA polymerase at a promoter is regulated by accessory proteins, which affect its ability to recognise start sites.
• These regulatory proteins can act positively (activators) or negatively (repressors).
• Access to promoter regions is often controlled by proteins that interact with sequences called operators.
• In most operons, the operator lies adjacent to the promoter, and in most cases it binds a repressor protein.
• Each operon has its own operator and repressor. The lac operator is present only in the lac operon and interacts only with the lac repressor.

5. The lac Operon

• ★ Exam imp The lac operon was worked out by the geneticist François Jacob and the biochemist Jacques Monod, the first to explain a transcriptionally regulated system.
• Here lac refers to lactose.
• In the lac operon, a polycistronic structural gene is regulated by a common promoter and regulatory genes.
• Such an arrangement is very common in bacteria and is called an operon. Examples: lac, trp, ara, his and val operons.
• The lac operon has one regulatory gene (the i gene) and three structural genes (z, y and a).
• The letter i does not stand for inducer; it comes from the word inhibitor.

• All three gene products of the lac operon are needed for the metabolism of lactose.
• In most other operons too, the genes are needed together in the same or a related metabolic pathway.

5.1 How lactose switches the operon on

1. Lactose is the substrate of beta-galactosidase, and it regulates the switching on and off of the operon. So it is called the inducer.
2. In the absence of a preferred carbon source such as glucose, lactose added to the medium is transported into the cells by permease.
3. A very low level of lac operon expression must be present all the time; otherwise lactose cannot enter the cells.
4. The repressor is synthesised all the time (constitutively) from the i gene.
5. Without inducer, the repressor binds the operator and prevents RNA polymerase from transcribing the operon.
6. With an inducer, such as lactose or allolactose, the repressor is inactivated by interacting with the inducer.
7. RNA polymerase then gets access to the promoter, and transcription of z, y and a proceeds.

• ★ Exam imp Regulation of the lac operon can be seen as regulation of enzyme synthesis by its substrate.
• Glucose or galactose cannot act as inducers for the lac operon.
• The operon stays on only as long as lactose is present. Once lactose is used up, the repressor is no longer inactivated, binds the operator again and switches the operon off.
• Regulation of the lac operon by the repressor is called negative regulation.
• The lac operon is also under positive regulation, but that is beyond the scope of this level.
• Transcription and translation are energetically very expensive, so they are tightly regulated, and regulation of transcription is the primary step.
• The lac operon is the prototype operon in bacteria: it codes for the genes of lactose metabolism and is regulated by the amount of lactose in the medium.

6. Exam Essentials

Pairs to Match