Unit 19: Chromosome and DNA — Short Questions

On the basis of centromere position, chromosomes are of four types: (1) Metacentric — centromere at the centre; (2) Sub-metacentric — centromere slightly away from the centre; (3) Acrocentric — centromere located near the end; (4) Telocentric — centromere located at the very end of the chromosome.

Chromatin fibre is a thicker, 30 nm-thick fibre formed by tight packing of nucleosomes. During condensation, the 11 nm nucleosome string coils again about its own axis in the early stages of cell division; the tightly packed, condensed nucleosomes thus produce the thicker chromatin fibre.

A gene is a short segment of DNA that encodes the amino acid sequence of a particular polypeptide; the whole DNA of a chromosome is not coding, only these specific short segments (genes) carry information for proteins. The fixed position/location of a gene on a chromosome is called its locus (plural: loci); on homologous chromosomes, the alternative forms of a gene (alleles) occupy the same locus.

DNA polymerase III is the main replication enzyme — it adds new complementary nucleotides to both template strands, building the leading and lagging strands. DNA polymerase I supports polymerase III by removing the RNA primers at the end of replication and filling the gaps with DNA nucleotides. DNA polymerase II is mainly involved in repairing DNA damage during the lifetime of the cell, rather than in normal replication.

The central dogma (proposed by Francis Crick) states that genetic information flows in one direction only: DNA → RNA → Protein. Information passes from genes (DNA) to an RNA copy (transcription), and the RNA copy then directs the assembly of a chain of amino acids into a protein (translation); once information has passed into protein, it never flows back.

Degeneracy of the genetic code means that more than one codon can specify the same amino acid. For example, the four codons AUG, GUG, UUG and CUG all code for methionine. This characteristic is important for mutation tolerance and evolutionary flexibility, since some nucleotide changes in a codon do not change the amino acid produced.

Common minor mutations in humans include: (1) Single nucleotide polymorphisms (SNPs) — change of a single nucleotide, e.g., causing lactose intolerance; (2) Insertions and deletions — e.g., a three-nucleotide deletion causing Cystic Fibrosis; (3) Silent mutations — nucleotide change that, due to degeneracy of the code, still codes for the same amino acid (e.g., GGC to GGU, both coding for glycine); (4) Missense mutations — change of one amino acid, e.g., the glutamic-acid-to-valine change causing sickle cell anaemia; (5) Nonsense mutations — creation of a premature stop codon, e.g., causing Duchenne Muscular Dystrophy.

Histones are small, positively charged proteins (H1, H2A, H2B, H3, H4) rich in arginine and lysine that bind to the negatively charged DNA. A nucleosome is the structural unit formed when about 146 nucleotides of DNA wrap twice around a histone octamer (two copies each of H2A, H2B, H3, H4); thus a histone is a protein molecule while a nucleosome is the DNA-histone complex built from histones.

Heterochromatin consists of the inactive, tightly condensed, darkly staining regions of chromatin. Euchromatin consists of the active, loosely packed, lightly staining regions of chromatin that are available for transcription.

In the conservative model, the parental double helix stays completely intact and a wholly new double helix is generated, so one daughter DNA has both old strands and the other has both new strands. In the semi-conservative model, the two parental strands separate and each acts as a template, so every daughter DNA has one parental strand and one newly made strand.

DNA helicase is the unwinding enzyme that breaks hydrogen bonds between base pairs at the origin, separating the two strands and forming the replication fork. DNA gyrase (a topoisomerase) acts ahead of the replication fork to remove/prevent the supercoiling that results from this unwinding.

DNA polymerase I removes RNA primers and fills the resulting gaps with DNA nucleotides during termination of replication, supporting polymerase III. DNA polymerase II is mainly involved in repairing DNA damage during the cell's lifetime rather than in normal replication.

The leading strand is synthesised continuously, in the same direction as the fork opening, from a single primer. The lagging strand is synthesised discontinuously, moving away from the fork, as short Okazaki fragments, each needing its own RNA primer, which are later joined by DNA ligase.

Transcription is the synthesis of a complementary RNA from a DNA template strand (DNA → RNA), carried out by RNA polymerase in the nucleus. Translation is the synthesis of a polypeptide using the codon sequence of mRNA (RNA → protein), carried out at the ribosome with the help of tRNA.

The genetic code is the whole set of rules — the complete series of three-nucleotide codons — by which DNA/mRNA sequences specify amino acids. A codon is a single unit of this code: one particular three-nucleotide sequence that specifies one amino acid (or a start/stop signal).

A codon is a three-nucleotide sequence on mRNA that specifies a particular amino acid. An anticodon is the complementary three-nucleotide sequence on tRNA that base-pairs with the mRNA codon during translation.

A gene is a specific segment of DNA that codes for a polypeptide and occupies a fixed locus on a chromosome. An allele is one of the alternative forms of the same gene occupying the same locus on homologous chromosomes, e.g., different alleles of the eye-colour gene.

Introns are the non-coding regions of a gene/pre-mRNA that do not code for protein and are removed during splicing. Exons are the coding regions that are expressed/translated into protein, and after splicing the exons are joined together to form the mature mRNA.

The start codon (AUG) occurs at the beginning of the coding sequence of mRNA, specifies methionine, and initiates translation. Stop codons (UAA, UAG, UGA) occur at the end of mRNA, do not specify any amino acid, and terminate translation.

Sense codons are the 61 codons that each specify a particular amino acid. Non-sense (stop) codons are the three codons (UAA, UAG, UGA) that do not code for any amino acid and instead signal the termination of translation.

Repressor proteins bind to operator sequences near the promoter and block RNA polymerase, stopping or reducing transcription (negative regulation). Activator proteins bind to the operator and help RNA polymerase bind to the promoter, starting or increasing transcription (positive regulation).

Point mutations are small-scale changes involving one or a few nucleotides within a gene (substitution, insertion, deletion). Chromosomal mutations are large-scale changes involving the structure (deletion, duplication, inversion, translocation) or the number of whole chromosomes.

Down syndrome is caused by trisomy of autosome 21 (47 chromosomes, 2n+1), affects both males and females, and produces mental impairment, flat facial features, short neck/limbs, and heart defects. Klinefelter syndrome is caused by trisomy of the sex chromosomes (47, XXY), affects only males, and produces sterility with feminised body features such as breast growth and small testicles.

Klinefelter syndrome results from an extra X chromosome (47, XXY — trisomy) and affects males, causing sterility with some female characteristics. Turner syndrome results from the loss of one sex chromosome (45, XO — monosomy) and affects females, causing short stature, webbed neck, and infertility.

DNA replication occurs during the S-phase of interphase, when chromatin is in its relatively loose, uncoiled fine network form rather than the highly condensed chromosome structure seen at cell division — so the DNA is not buried inside a tightly packed coil at this stage. Even so, at the replication fork the unwinding enzyme helicase actively separates the two DNA strands by breaking the hydrogen bonds between base pairs; the nucleosomes just ahead of the fork are transiently displaced/opened to expose the bases, allowing the replication enzymes access to the template strands, and the histones are reassembled onto the two new daughter DNA double helices immediately behind the fork.

No. With four kinds of nucleotides, a two-letter (doublet) code would give only 4 × 4 = 16 possible combinations, which is not enough to uniquely specify all 20 amino acids used in proteins. Some amino acids could not be coded for at all, so the full diversity of proteins needed for complex structures and functions could not be built, and a complex organism like a human could not develop normally. This is exactly why Crick's group concluded the code must be a triplet (3-letter) code, since 4 × 4 × 4 = 64 combinations are more than enough to code for 20 amino acids.

If the gene coding for DNA polymerase III is itself mutated, the enzyme's proofreading ability may be reduced or lost. This would allow replication errors (mismatched nucleotides) to go uncorrected and accumulate in the DNA with every round of replication, producing far more point mutations than normal (a 'mutator' cell). These extra mutations could disrupt important genes, cause genomic instability, and significantly raise the risk of harmful effects such as non-functional proteins or diseases like cancer.

The mRNA transcribed directly from a eukaryotic gene (pre-mRNA) contains both coding exons and non-coding introns. Before it leaves the nucleus and enters the cytoplasm for translation, it undergoes splicing, during which the introns are cut out and only the exons are joined together to form the mature mRNA. Since the introns are removed, the mature mRNA that enters the cytoplasm is shorter than the original transcribed pre-mRNA.

Since the triplet genetic code specifies 20 amino acids, a living cell needs a minimum of 20 types of tRNA — one type of tRNA (with the matching anticodon) for each amino acid, delivered by one of the 20 corresponding aminoacyl-tRNA synthetase enzymes. (Because of degeneracy, several of the 61 sense codons code for the same amino acid, so in principle up to 61 distinct tRNA types, each matching one sense codon, could exist, but at least 20 are essential to translate all amino acids.)

After only one round of replication, the semi-conservative and dispersive models cannot be distinguished, because both predict that all the DNA will show a single band of intermediate density (one old strand + one new strand for semi-conservative; a uniform mix of old and new nucleotides in every strand for dispersive) — only the conservative model is ruled out at this stage, since it would have produced one fully heavy and one fully light band. A second round of replication was essential to tell the two remaining models apart: the semi-conservative model predicts that the DNA will now split into two distinct bands — one intermediate and one fully light (14N) — because each strand again acts as a separate template, while the dispersive model would still predict a single, continuously lighter intermediate band for all molecules (never a fully light band). Since the actual result after the second replication showed two bands, one intermediate and one light, Meselson and Stahl could conclusively confirm the semi-conservative model and rule out the dispersive model.