CHAPTER 24 Genes and Chromosomes. Organization of information in chromosomes DNA supercoiling Structure of the chromosome. Key topics : . Management and Expression of Genetic Information. Previous chapters dealt with
Organization of information in chromosomes
Structure of the chromosome
Previous chapters dealt with
metabolic pathways, in which the chemical structures of small molecules were modified by enzymes
signal transduction pathways, in which interactions of ligands with receptor proteins caused physiological responses
The following chapters deal with
information pathways, in which genetic information stored as the nucleotide sequence is maintained and expressed
The discovery of double-helical structure of DNA in 1953 laid a foundation to thinking of biomolecules as carriers of information
It was well understood by 1950 that proteins play roles of catalysts but their role in information transfer was unclear
Francis Crick proposed in 1956 that “Once information has got into a protein it can’t get out again”
The Central Dogma was proposed by Francis Crick at the time when there was little evidence to support it, hence the “dogma”
Chromosome consists of one covalently connected DNA molecule and associated proteins
The linear dimensions of DNA are much bigger than the virions or cells that contain them
Bacteriophages T2 and T4 are about 0.2 m long and 0.1 m wide
Fully extended T4 DNA double helix is about 60 m long
DNA in the virion or cell is organized into compact forms, typically via coiling and association with proteins
The Size and Sequence of DNA Molecules in Bacteria and their viruses
Bacteria(E. coli) 4,639,221 1.7 mm 0.002 mm
The sizes of E. coli cell and its DNA
DNA from a lysed E. coli cell
Note that despite the trends in the previous table, neither the total length of DNA, nor the number of chromosomes correlates strongly with the perceived complexity of the organisms
Amphibians have much more DNA than humans
Dogs and coyotes have 78 chromosomes in the diploid cell
Plants have more genes than humans
The correlation between complexity and genome size is poor because most of eukaryotic DNA is non-coding
Recent experimental work by Craig Venter suggests that a minimal living organisms could get by with less than 400 genes
DNA content and C-value paradox
Notice that only a small fraction (1.5 %) of the total genome encodes for proteins
The biological significance of non-coding sequences is not all clear
Some DNA regions directly participate in the regulation of gene expression (promoters, termination signals, etc)
Some DNA encodes for small regulatory RNA with poorly understood functions
Some DNA may be junk (pieces of unwanted genes, remnants of viral infections
Many eukaryotic genes contain intervening sequences (introns)
It was thought until 1993 that introns are exclusive feature of eukaryotic genes
About 25% of sequenced bacterial genomes show presence of introns
Introns in bacterial chromosome do not interrupt protein-coding sequences; they interrupt mainly tRNA sequences
Introns in phage genomes within bacteria interrupt protein-coding sequences
Many bacterial introns encode for catalytic RNA molecules that have ability to insert and reverse transcribe themselves into the genomic DNA
DNA sequence is not completely static
Some sequences, called transposons, can move around within the genome of a single cell
The ends of transposons contain terminal repeats that hybridize with the complementary regions of the target DNA during insertion
To be covered in Ch. 25.
Telomeres cap the ends of linear chromosomes and are needed for successful cell division
Centromere functions in cell division; that’s where the two daughter chromosomes are held together during mitosis (i.e. after DNA replication but before cell division)
Centromere: Mitotic segregation of chromosomes. Simple-sequence DNA is located at centromere in higher eukaryotes.
Telomere: At ends of chromosomes. (TTAGGG)n in human.
In many tissues, telomeres are shortened after each round of replication (end-replication problem of linear DNA); the cellular DNA ages
Normal human cells divide about 52 times before losing ability to divide again (Hayflick limit)
DNA in the cell must be organized to allow:
Packing of large DNA molecules within the cells
Access of proteins to read the information in DNA sequence
There are several levels of organization, one of which is the supercoiling of the double-stranded DNA helix
Supercoiling of DNA can only occur in closed-circular DNA or linear DNA where the ends are fixed.
Underwinding produces negative supercoils, wheres overwinding produces positive supercoils.
Negative and positive supercoils .
Topoisomerases catalyze changes in the linking number of DNA.
Supercoiling induced by separating the strands of duplex DNA (eg., during DNA replication)
Relaxed and supercoiled plasmid DNAs
Negative supercoils facilitate separation of DNA strands (may facilitate transcription)
Topology of cccDNA is defined by: Lk = Tw + Wr, where Lk is the linking number, Tw is twist and Wr is writhe.
Right-handed crossing = +1/2
Left-handed crossing = -1/2
Lk = number of times one strand winds around the
other on 2D projection.
One linking number = 2 nodes.
Promotion of cruciform structures by DNA underwinding
Mechanism of Type I topoisomerase action
Proposed mechanism of Type II topoisomerase action
Topoisomerases are Targets for Antibiotics and Anti-cancer Drugs
Type I topoisomerase
Human Type II topoisomerase inhibitors
DNA Compaction Requires Solenoidal Supercoiling, not plectonemic supercoiling.
Changes in chromosome structure during the cell cycle
Protein-assisted Packaging of DNA
Nucleosomes are the fundamental organizational units of eukaryotic chromatin
Each nucleosome has a histone core wrapped by DNA (146 bps) in a left-handed solenoidal supercoil about 1.8 times. The linker DNA is about 54 bps in length.
DNA wrapped around a nucleosome core
Histones are small, basic protein. The histone core in nucleosomes contains two copies each of H2A, H2B, H3 and H4. Histone H1 binds to linker DNA.
Nucleosomes are packed into successively higher-order structures
The 30 nm fiber, a higher-order organization of nucleosomes.
A partially unraveled human chromosome, revealing numerous loops of DNA attached to scaffold.
Higher order of folding is not yet understood. Certain regions of DNA are associated with a nuclear scaffold. The scaffold associated regions are separated by loops of DNA with 20 to 100 kb long.
Model of DNA compaction in eukaryotic chromosomes
Condensed chromosome are maintained by SMC proteins
Model for the effect of condensins on DNA supercoiling