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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

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CHAPTER 24 Genes and Chromosomes

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CHAPTER 24Genes 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

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 Central Dogma of Molecular Biology

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”


How does genes function?Central Dogma: DNA to RNA to Protein.


Genes and Chromosomes

  • What is gene?

    • One gene-one enzyme.

    • One gene-one protein (polypeptide).

    • Genes are segments of DNA that code for polypeptides and RNAs.

  • What is chromosome?

    Chromosome consists of one covalently connected DNA molecule and associated proteins

    • Viral genomic DNA may be associated with capsid proteins

    • Prokaryotic DNA is associated with proteins in the nucleoid

    • Eukaryotic DNA is organized with proteins into a complex called the chromatin


DNA is a Very Large Macromolecule

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


T2 phage


The sizes of E. coli cell and its DNA


DNA from a lysed E. coli cell


DNA, Chromosomes, Genes, and Complexity

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


Eukaryotic genomes have several sequence components

  • Nonrepetitive DNA: the complexity of the slow component corresponds with its physical size, i.e., unique sequences.

  • Moderately repetitive DNA:.component with a Cot1/2of 10-2 and that of nonrepetitive DNA. Contains families of sequences that are not exactly the same, but are related. The complexity is made up of a variety of individual sequences, each much shorter, whose total length together comes to the putative complexity. Usually dispersed throughout the genome.

  • Highly repetitive DNA: component which reassociates before a Cot1/2of 10-2. Usually forms discrete clusters.


Types of sequences in the human genome


Composition of the Human Genome

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)


Some Bacterial Genomes Also Contain 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


Transposons

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.


Eukaryotic Chromosomes


Important Structural Elements of the Eukaryotic Chromosome

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.


Telomeres and Cellular Aging

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)


How is DNA packed in the chromosomes

  • DNA Supercoiling.

  • Proteins assisted packaging (nucleosomes)


DNA Supercoiling

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


Supercoils


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.


Intertwining of the two strands

  • Nodes = ss crossing on 2D projection.

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

Bacterial topoisomerase

inhibitors

Type I topoisomerase

inhibitors


Human Type II topoisomerase inhibitors


DNA damages are produced by topoisomerase inhibitors

  • Most topoisomerase inhibitors act by blocking the last step of the topoisomerase reaction, the resealing of the DNA strand breaks. Therefore, these inhibitors will produce single-strand or double-strand DNA breaks in the DNA.


Plectonemic supercoiling


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.


Chromatin assembly


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

SMC Proteins


Model for the effect of condensins on DNA supercoiling


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