Molecular Basis of Inheritance: common doubts, answered
The questions students ask most often about Molecular Basis of Inheritance, each with a short answer. For the full chapter, read the Molecular Basis of Inheritance notes.
The DNA: structure of polynucleotides
Read this section in the notes →What is the difference between a nucleoside and a nucleotide?
A nucleoside is a nitrogenous base joined to a pentose sugar, while a nucleotide is a nucleoside with a phosphate group added. In DNA the sugar is deoxyribose, and in RNA it is ribose. Nucleotides link through phosphodiester bonds to make a polynucleotide chain.
How is DNA different from RNA?
DNA has deoxyribose sugar, the base thymine and is usually double stranded, whereas RNA has ribose sugar, the base uracil in place of thymine and is usually single stranded. The 2′-OH group of ribose also makes RNA more reactive, which is why DNA is the more stable genetic material.
The double helix and central dogma
Read this section in the notes →How many hydrogen bonds join A with T and G with C?
Adenine pairs with thymine through two hydrogen bonds, and guanine pairs with cytosine through three. In each pair a two-ring purine faces a one-ring pyrimidine, which keeps the distance between the two strands nearly the same all along the helix. This complementary pairing explains Chargaff's rule that A equals T and G equals C in double-stranded DNA.
What does the central dogma state?
The central dogma states that genetic information flows from DNA to RNA to protein: DNA is transcribed to mRNA, and mRNA is translated to protein. In some viruses the flow can go from RNA to DNA by reverse transcription, as in retroviruses. So the direction is not absolute in all organisms.
Packaging of the DNA helix
Read this section in the notes →How is a long DNA molecule packed inside a small nucleus?
DNA wraps around a histone octamer to form a nucleosome, which carries about 200 base pairs. The nucleosomes make a beads-on-string structure of chromatin, which folds further into higher-order structures with the help of non-histone chromosomal proteins. The positively charged histones, rich in lysine and arginine, grip the negatively charged DNA.
What is the difference between euchromatin and heterochromatin?
Euchromatin is loosely packed and stains light, and it is transcriptionally active. Heterochromatin is densely packed and stains dark, and it is generally transcriptionally inactive. So genes in euchromatin can be copied into RNA, while those in heterochromatin are largely silent.
The search for genetic material
Read this section in the notes →What did Griffith's experiment show?
Griffith's experiment showed that some transforming principle from dead virulent S-type bacteria could change live harmless R-type bacteria into virulent ones. Mice injected with a mix of heat-killed S cells and live R cells died. He did not identify what the principle was, and later workers showed it was DNA.
Why did Hershey and Chase use radioactive phosphorus and sulphur?
DNA contains phosphorus but no sulphur, whereas protein contains sulphur but almost no phosphorus, so each could label one molecule alone. After infection, radioactive phosphorus (³²P) was found inside bacteria while sulphur (³⁵S) stayed in the outer coats. This proved that DNA, and not protein, is the genetic material of the virus.
Properties of genetic material and the RNA world
Read this section in the notes →Why is DNA a better genetic material than RNA?
DNA is chemically and structurally more stable because its sugar lacks the 2′-OH group, and thymine in place of uracil adds further stability. RNA is reactive and so unstable, though it can act as an enzyme and as genetic material, which supports the idea of an early RNA world. DNA therefore stores information better over time.
Replication
Read this section in the notes →What did the Meselson and Stahl experiment prove?
It proved that DNA replication is semiconservative. They grew E. coli in heavy nitrogen (¹⁵N) and then shifted it to ¹⁴N. After one generation (20 minutes) all DNA was hybrid, and after the second (40 minutes) half was hybrid and half light. CsCl density gradient centrifugation separated these.
Why is one strand of DNA made continuously and the other in pieces?
DNA polymerase can add nucleotides only in the 5′ to 3′ direction. On the template running 3′ to 5′ the new strand is built continuously, but on the template running 5′ to 3′ the new strand is made in short fragments, each synthesised 5′ to 3′. These fragments are later joined by DNA ligase.
What does it mean that DNA replication is semiconservative?
It means each new DNA double helix contains one old parental strand and one newly made strand. The parent strands separate and each acts as a template for its complementary strand. So half of the original molecule is conserved in each daughter, as the Meselson and Stahl experiment demonstrated.
Transcription
Read this section in the notes →What is the difference between the template strand and the coding strand?
The template strand has 3′ to 5′ polarity, and RNA polymerase reads it to make RNA. The coding strand, with 5′ to 3′ polarity, is not read but has the same sequence as the RNA, except that it has T where RNA has U. So the mRNA looks like the coding strand.
What are the roles of sigma and rho factors in bacteria?
The sigma factor helps RNA polymerase to recognise the promoter and start transcription, while the rho factor helps it to terminate. Together with the core enzyme the sigma factor forms the holoenzyme. Both are accessory proteins, so the polymerase alone cannot start or stop at the proper sites.
How is eukaryotic mRNA processed after transcription?
The primary transcript, hnRNA, undergoes three changes. Introns are removed and exons joined by splicing, a cap of methyl guanosine triphosphate is added at the 5′ end, and a tail of 200 to 300 adenylate residues is added at the 3′ end. The finished mRNA is then exported to the cytoplasm. Bacteria do not do this.
The genetic code and mutations
Read this section in the notes →What does it mean to say the genetic code is degenerate?
Degenerate means that most amino acids are specified by more than one codon, for example phenylalanine by UUU and UUC. It does not mean that one codon codes for several amino acids, since each codon codes for one amino acid only (or a stop). The code is also triplet, nearly universal and without punctuation.
How many codons are there and what are the start and stop codons?
There are 64 codons, of which 61 code for amino acids and 3 are stop codons: UAA, UAG and UGA. AUG is the start codon and also codes for methionine. The stop codons do not specify any amino acid, and so they terminate the polypeptide chain.
tRNA and translation
Read this section in the notes →Why is tRNA called the adapter molecule?
Because it reads the codon on the mRNA through its anticodon loop and carries the matching amino acid at its other end. It thus links the nucleotide language of mRNA to the amino acid language of proteins. The amino acid attaches to the 3′ CCA end, and there is a separate tRNA for each amino acid.
Regulation of gene expression: the lac operon
Read this section in the notes →How does the lac operon switch on in the presence of lactose?
Lactose, or its derivative allolactose, acts as the inducer and binds to the repressor, which then cannot bind the operator. RNA polymerase can now transcribe the structural genes z, y and a, making β-galactosidase, permease and transacetylase. When lactose is absent the repressor binds to the operator and blocks transcription.
What do the genes z, y and a in the lac operon code for?
The z gene codes for β-galactosidase, which splits lactose into glucose and galactose. The y gene codes for permease, which increases the permeability of the cell to lactose. The a gene codes for transacetylase. The i gene is separate and codes for the repressor protein.
Human Genome Project
Read this section in the notes →What are the main findings of the Human Genome Project?
The sequenced human genome is about 3 billion base pairs long and holds roughly 30,000 genes. Under 2 per cent codes for proteins, and large parts are repeated sequences. Chromosome 1 carries the most genes and the Y chromosome the fewest. Scientists also located about 1.4 million single nucleotide polymorphisms, single-base variations between people.
DNA fingerprinting
Read this section in the notes →On what principle does DNA fingerprinting work?
It works on the fact that the repetitive, non-coding VNTR sequences differ in number among individuals, although the rest of the genome is almost the same. DNA is cut, separated by electrophoresis, blotted and hybridised with a labelled probe to show the pattern. Only identical twins share the same pattern.
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