Chapter 1 - Organisation, Structure and Function of Genetic Material

Subtopics - Chromosomes, Nucleic acids & other Genetic elements

Bacterial Chromosomes
The bacterial chromosome is found in a region of the cell called the nucleoid. The cytoplasm is enclosed by a plasma membrane that regulates the uptake of nutrients and excretion of waste products. Outside the plasma membrane is a rigid wall. The nucleoid is not bounded by membrane so the DNA is in direct contact with the cytoplasm Bacterial chromosomal DNA is usually a circular molecule that is a few million nucleotides in length Escherichia coli ~ 4.6 million base pairs Haemophilus influenzae ~ 1.8 million base pairs A typical bacterial chromosome contains a few thousand different genes Structural gene sequences (encoding proteins) are the majority; the nontranscribed DNA between adjacent genes are intergenic regions.

Bacterial Chromosomes
A few hundred nucleotides in length Most, but not all, bacterial species contain circular chromosomal DNA. A typical chromosome is a few million base pairs in length. Origin of replication

Several thousand different genes are interspersed throughout the chromosome. The short regions between adjacent genes are called intergenic regions.
One origin of replication is required to initiate DNA replication.

Genes Intergenic regions Repetitive sequences

These play roles in DNA folding, DNA replication, gene regulation, and genetic recombination

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Bacterial Chromosomes
To fit within the bacterial cell, the chromosomal DNA must be compacted about a 1000-fold. The first way is by formation of loop domains. The number of loops varies according to the size of the bacterial chromosome and the species. Example an E. coli has 50-100 with 40,000 to 80,000 bp of DNA in each loop

The looped structure compacts the chromosome about 10-fold

Loop domains

DNAbinding proteins

Looped chromosomal DNA with associated proteins

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10 bp per turn

Plates preventing DNA ends from rotating freely

360 left-handed turn (underwinding)

360 right-handed turn (overwinding)

Both overwinding and underwinding can induce supercoiling

12.5 bp per turn (not a stable structure)

10 bp per turn plus 1 negative supercoil

8.3 bp per turn (not a stable structure)

10 bp per turn plus 1 positive supercoil

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The second way of compacting the bacterial chromosome is by DNA supercoiling.

Supercoiling

Looped and supercoiled DNA Looped chromosomal DNA

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Nucleic acids
Bacterial DNA has the same composition and general structure as that from multicellular organisms, including human beings. Views about the role of DNA in inheritance changed in the late 1940's and early 1950's. An analysis of DNA from many sources lead to Erwin Chargaff finding that the composition of DNA to be species specific.

In addition, he found that the amount of adenine (A) always equaled the amount of thymine (T), and the amount of guanine (G) always equaled the amount of cytosine (C), regardless of the DNA source.
In the following table, the ratio of (A+T) to (C+G) varied from 2.70 to 0.35 were shown. The last two organisms are bacteria.

Nucleic acids
Two monocyclic bases are classified as pyrimidines and the two bicyclic bases are purines. Each has at least one N-H site at which an organic substituent may be attached.

Bacterial DNA has the same composition and general structure as that from multicellular organisms, including human beings. Views about the role of DNA in inheritance changed in the late 1940's and early 1950's. An analysis of DNA from many sources lead to Erwin Chargaff finding that the composition of DNA to be species specific. He also found that the amount of adenine (A) always equaled the amount of thymine (T), and the amount of guanine (G) always equaled the amount of cytosine (C), regardless of the DNA source.

In the following table, the ratio of (A+T) to (C+G) varied from 2.70 to 0.35 were shown. The last two organisms are bacteria.

Nucleic acids
Nucleoside Base Distribution in DNA
Base Composition (mole %) Organism A 30.9 28.8 31.3 36.9 G 19.9 20.5 18.7 14.0 T 29.4 29.2 32.9 36.3 C 19.8 21.5 17.1 12.8 Base Ratios A/T 1.05 1.02 0.95 1.01 G/C 1.00 0.95 1.09 1.09 Ratio (A+T)/(G+C) 1.52 1.38 1.79 2.70

Human Chicken Yeast Clostridium perfringens Sarcina lutea

13.4

37.1

12.4

37.1

1.08

1.00

0.35

Nucleic acids
The polymeric structure of DNA may be described in terms of monomeric units of increasing complexity. Condensation polymerisation of these leads to the DNA formulation outlined below. A 5'- monophosphate ester, called a nucleotide may be drawn as a single monomer unit, shown in the shaded box to the right.

Names of DNA Base Derivatives Base Nucleoside 5'-Nucleotide 2'-Deoxyadenosine-5'monophosphate 2'-Deoxycytidine-5'monophosphate 2'-Deoxyguanosine-5'monophosphate

Adenine
Cytosine Guanine Thymine

2'-Deoxyadenosine
2'-Deoxycytidine 2'-Deoxyguanosine 2'-Deoxythymidine

2'-Deoxythymidine-5'monophosphate

*Nucleic acids
Information is stored or encoded in the DNA polymer by the pattern in which the four nucleotides are arranged. To access this information the pattern must be "read" in a linear fashion, just as a bar code is read at a supermarket checkout. Because living organisms are extremely complex, a correspondingly large amount of information related to this complexity must be stored in the DNA. Consequently, the DNA itself must be very large. Even the single DNA molecule from an E. coli bacterium is found to have roughly a million nucleotide units in a polymer strand, and would reach a millimeter in length if stretched out. The nuclei of multicellular organisms incorporate chromosomes, which are composed of DNA combined with nuclear proteins called histones. The fruit fly has 8 chromosomes, humans have 46 and dogs 78 (note that the amount of DNA in a cell's nucleus does not correlate with the number of chromosomes).

The DNA from the smallest human chromosome is over ten times larger than E. coli DNA, and it has been estimated that the total DNA in a human cell would extend to 2 meters in length if unraveled. Since the nucleus is only about 5m in diameter, the chromosomal DNA must be packed tightly to fit in that small volume. In addition to its role as a stable informational library, chromosomal DNA must be structured or organized in such a way that the chemical machinery of the cell will have easy access to that information, in order to make important molecules such as polypeptides. Furthermore, accurate copies of the DNA code must be created as cells divide, with the replicated DNA molecules passed on to subsequent cell generations, as well as to progeny of the organism.

Plasmid
Plasmid is an extrachromosomal genetic element found in many bacterial strains. They are circular deoxyribonucleic acid (DNA) molecules that replicate independently of the bacterial chromosome. They are not essential for the bacterium but may confer a selective advantage. One class of plasmids, colicinogenic (or Col ) factors, determines the production of proteins called colicins, which have antibiotic activity and can kill other bacteria. Another class of plasmids, R factors, provides bacteria to be resistance to antibiotics. Some Col factors and R factors can transfer themselves from one cell to another and thus are capable of spreading rapidly through a bacterial population. A plasmid that is attached to the cell membrane or integrated into the bacterial chromosome is called an episome. Plasmids are extremely valuable tools in the fields of molecular biology and genetics, specifically in the area of genetic engineering. They play a critical role in such procedures as gene cloning, recombinant protein production (e.g., of human insulin) and gene therapy research

Plasmids are extremely valuable tools in the fields of molecular biology and genetics, specifically in the area of genetic engineering. They play a critical role in such procedures as gene cloning, recombinant protein production (e.g., of human insulin) and gene therapy research. In such procedures, a plasmid is cut at a specific site (or sites) using enzymes called restriction endonucleases. A foreign DNA element (such as the gene for insulin) is then spliced into the plasmid. The resulting circular structure, a recombinant DNA molecule, is then introduced into bacterial cells (a process called transformation). The autonomous replication of the plasmid within the bacterial cells makes it possible to produce large numbers of copies of the recombinant DNA molecule for experimental manipulation or commercial purposes (such as the production of large amounts of insulin).

Plasmid

Figure of a bacterium having chromosomal DNA and plasmids.

Figure shows two types of plasmid integration into a host bacteria: Nonintegrating plasmids replicate (top ), whereas episomes, integrate into the host chromosome (bottom).

Transposon
Transposoble genetic elements or transposons are genetic units that can move or be transposed within a genome. This will then disrupts genetic function and results in phenotypic variation. It can sometimes create or reverse mutations and thereby altering the cell's genomes size.

Transposon
Transposable elements were first studied in maize by Barbara McClintock a long time ago. But only in the early 1970swere the first observation of transposon at the molecular level was observed. Read more of transposons in the bacterial system. You can refer to Essentials of Genetics, 4 th edition, William S. Klug & Michael R. Cummings, 2002, Prentice Hall, Upper Saddle River, New Jersey 07458; pages 296-298.

Viral genome
A viral genome is the genetic material of the virus and termed the viral chromosome. The genome can be DNA or RNA; Single-stranded or double-stranded; Circular or linear. Viral genomes vary in size from a few thousand to more than a hundred thousand nucleotides During an infection process, mature viral particles need to be assembled.

Viruses with a simple structure may self-assemble. Genetic material and capsid proteins spontaneously bind to each other. Example: Tobacco mosaic virus

Viruses have nucleic acid that is surrounded by a capsid of proteins. For replication, viruses rely on their host cells or the cells they infect. Most viruses exhibit a limited host range. They typically infect only specific types of cells of one host species.

Viral genome
Complex viruses, such as T2 bacteriophages, undergo a process called directed assembly. Virus assembly requires proteins that are not part of the mature virus itself. The noncapsid proteins usually have two main functions :- To carry out the assembly process. To act as proteases that cleave viral capsid proteins. Single-stranded RNA molecule

Capsid protein

Capsid composed of 2,130 identical protein subunits

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Viral genome
Bacteriophages may also contain a sheath, base plate and tail fibers
General structure of viruses
Capsid (protein coat) Membrane

Nucleic acid

Spike proteins

(a) Nonenveloped virus

(b) Enveloped virus with spikes

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Chromosome Function Is Influenced by DNA Supercoiling

The chromosomal DNA in bacteria is negatively supercoiled. In E. coli, there is one negative supercoil per 40 turns of the double helix Negative supercoiling has two major effects:1. Helps in the compaction of the chromosome 2. Creates tension that may be released by DNA strand separation

Area of negative supercoiling Strand separation

Circular chromosome
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Two main enzymes control supercoiling in bacteria. 1. DNA gyrase (also termed DNA topoisomerase II) Introduces negative supercoils using energy from ATP It can also relax positive supercoils when they occur Can untangle intertwined DNA molecules
2. DNA topoisomerase I Relaxes negative supercoils The competing action of these two enzymes governs the overall supercoiling of bacterial DNA The ability of gyrase to introduce negative supercoils into DNA is crucial for bacteria to survive. Blocking the function of this enzyme is a way to cure or alleviate bacterial diseases Two main classes of drugs inhibit gyrase and other bacterial topoisomerases ; 1. Quinolones 2. Coumarins

These do not inhibit eukaryotic topoisomerases. An example of a quinolone is Ciprofloxacin (Cipro). Used in the treatment of anthrax and other diseases.

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