Download Chromosomes in prokaryotes

Lecture 4. Genome
Genome - the complete set of chromosomes inherited from a single parent; the
complete DNA component of an individual.
A chromosome
The DNA molecule may be circular or linear, and can be composed of 10,000 to
1,000,000,000 base pairs. Typically eukaryotic cells have large linear
chromosomes and prokaryotic cells have smaller circular chromosomes.
In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed
structure called chromatin. Chromosomes may exist as either duplicated or
unduplicated—unduplicated chromosome is linear DNA molecule, whereas
duplicated chromosome contains two copies of DNA joined by a centromere.
In prokaryotes DNA is usually arranged as a circle, which is tightly coiled in,
sometimes accompanied by smaller, circular DNA molecules called plasmids. The
small circular DNA molecules are also found in mitochondria and chloroplasts,
reflecting their bacterial origins.
The simplest genomes are found in viruses: these DNA or RNA molecules are
short linear or circular that often lack structural proteins.
Eukaryotic Chromosome Structure
Eukaryotic chromosomes consist of condensed DNA and associated proteins called
histones and non-histons. DNA-protein complex is named chromatin. The fundamental
unit of chromatin is the nucleosome
Histones are basic proteins that form the nucleosomes. The nucleosomes are then
arranged in a coiled pattern to produce a chromatin fiber. This fiber is further compacted
with non-histones by looping to produce looped domains. The looped domains are
coiled and compacted to produce chromosomes.
Nucleosome Structure of Chromosomes
Nucleosome - simplest packaging structure of eukaryotic chromosomes; the
nucleosome consists of about 200 bp of DNA wrapped around a histones. 146 bp DNA
is wrapped around an octamer that contains two copies of histone proteins H2A, H2B,
H3 and H4. The remaining bases link to the next nucleosome; this structure causes
negative super coiling.
The 30 nm fiber is the next level of organization of the chromatin. This appears to
be a solenoid structure with about six nucleosomes per turn. The stability of this
structure requires the presence of histone H1.
Fig 6. The levels of organization of the chromatin: the nucleosomes’ chain.
Chromatin structure. The final level of packaging is characterized by the 700 nm
structure seen in the metaphase chromosome. This appears to be the result of
extensive looping of the DNA in the chromosome.
Chromatin - the unit of analysis of the chromosome. Heterochromatin is DNA that is
coiled and condensed. In this state, it is not transcribed. Euchromatin is less condensed
chromatin, it is transcribed.
During the process of cell division, the DNA becomes tightly coiled, forming structures
called chromosomes. They are doubled after replication in S phase and consist of two
chromatids joining together be the centromere.
Centromeres and Telomeres
Centromeres and telomeres are two essential features of all eukaryotic chromosomes.
Centromeres are required for the segregation of the chromosomes during cell division.
Telomeres - the region of DNA at the end of linear eukaryotic chromosome; required for
the replication and stability of the chromosome. The telomeric DNA has
heterochromatin and contains direct tandemly repeated sequences (e.g., TTAGGG).
Classes of Eukaryotic DNA Sequences
Coding and Non Coding DNA Sequences
Less than 5% of eukaryotic DNA codes for proteins. Approximately 1.5% of human DNA
codes for protein. The function of the remaining DNA is not known but perhaps much of
it has no function.
Essential Conserved Non Coding DNA Sequences
These DNA sequences do not code for proteins and include: 1) promoters (sites that
bind RNA polymerases), 2) regulatory elements (enhancers, silencers, and locus control
regions LCRs) that bind regulatory proteins, 3) the origin of replication (sites that bind
the DNA replication complex), 4) the centromeric and the telomeric DNA.
Analysis of DNA Sequences in Eukaryotic Genomes
The technique that is used to determine the sequence complexity of any genome
involves the denaturation and renaturation of DNA. DNA is denatured by heating which
melts the H-bonds and renders the DNA single-stranded. If the DNA is allowed to cool
slowly, sequences that are complementary will find each other and eventually base pair
again (DNA renaturates or reanneals).
Genomes that contain different classes of sequences reanneal in a different manner.
The first sequences to reanneal are the highly repetitive sequences because so many
copies of them exist in the genome. The second portion of the genome to reanneal is
the middle repetitive DNA, and the final portion to reanneal is the single copy DNA.
Classes of Eukaryotic DNA Sequences
Single copy sequences




Found once or a few times in the genome
Reanneal very slowly
The sequences which encode functional genes fall into this class
The genes have exons and introns
Repeated DNA sequences are found more than once in the genome of the species.
Middle repetitive Sequences (DNA)



Found from 10 to 1000 times in the genome
Examples include rRNA, tRNA genes and histones genes
Middle repetitive DNA can vary from 100-300 bp to 5000 bp and can be
dispersed throughout the genome (they are named SINES and LINES).
Highly Repetitive Sequences
10-25% of eukaryotic DNA consists of sequences of 5 to 10 nucleotides repeated
100,000 to 1,000,000 times. They are minisatellites and microsatellites DNA.





Reanneal very rapidly
They do not transcribe
These sequences are found from 100,000 to 1 million times in the genome
These sequences are found in heterochromatin, centromeric and telomeric DNA
Tend to be arranged as a tandem repeats;
o ATTATA ATTATA ATTATA // ATTATA
Extra chromosomal DNA
Mitochondrial DNA
In animals the mitochondrial genome is typically a single circular chromosome and
mitochondrial DNA lacks introns; however, introns have been observed in mitochondrial
DNA of yeast and protists. There is a very high proportion of coding DNA and an
absence of repeats in mitochondrial genome. Not all proteins necessary for
mitochondrial function are encoded by the mitochondrial genome; most proteins are
coded by genes in the cell nucleus and are imported into the mitochondrion.
The human mitochondrial genome is a circular DNA molecule of about 16 000 bp. It
encodes 37 genes: 13 for subunits of respiratory complexes I, III, IV and V; 22 genes for
mitochondrial tRNA (for the 20 standard amino acids, plus an extra gene for leucine and
serine), and 2 for rRNA. One mitochondrion can contain two to ten copies of its DNA.
Genetic code in mitochondria
Mitochondrial genes use an alternative mitochondrial code. Many slight variants have
been discovered. Further, the AUA, AUC, and AUU codons are all start codons.
Replication and inheritance
Mitochondria divide by binary fission similar to bacterial cell division. In many singlecelled eukaryotes, their growth and division is linked to the cell cycle. In other
eukaryotes (in humans for example), mitochondria may replicate their DNA and divide in
response to the energy needs of the cell. When the energy needs of a cell are high,
mitochondria grow and divide. When the energy use is low, mitochondria become
inactive.
Mitochondria and the mitochondrial DNA are inherited down the female line, known as
maternal inheritance. This mode is seen in most organisms including humans.
Mitochondrial diseases
Damage and dysfunction in mitochondria is an important factor in a wide range of
human diseases. Mitochondrial disorders often present as neurological disorders, but
can manifest as myopathy, diabetes and multiple endocrinopathy.
Prokaryotes Genome
Chromosomes in prokaryotes
The chromosome of prokaryotes consists of a single circular double-stranded DNA. It is
not condensed into chromosomes as in eukaryotes.
Structure in sequences
There is a very high proportion of coding DNA and an absence of repeats in bacteria
genome. Bacteria typically have a single origin of replication. The genes in prokaryotes
are often organized in operons, and do not contain introns.
DNA packaging
Prokaryotes DNA is organized into a structure called the nucleoid. Histone-like proteins
associate with the bacterial chromosome. Prokaryotic chromosomes and plasmids are
supercoiled double-stranded DNA. The DNA must first be released into its relaxed state
for access for transcription, regulation, and replication. Bacterial chromosomes tend to
be tethered to the plasma membrane of the bacteria.
Extra chromosomal Prokaryotic DNA
Plasmids
A plasmid is an extra chromosomal circular and double-stranded DNA molecule which
is capable of replicating independently from the chromosomal DNA. Plasmids usually
occur in bacteria, but are sometimes found in eukaryotic organisms (e.g., in
Saccharomyces cerevisiae).
Plasmids are often associated with conjugation, a mechanism of gene transfer.
Plasmids may carry genes that provide resistance to naturally occurring antibiotics.
Plasmids are now being used to manipulate DNA and may be a tool for genetic
engineering techniques.
Types of plasmids





Fertility-F-plasmid which contain tra-genes (transfer). They are capable of
conjugation and help bacteria produce pili.
Resistance- R-plasmids, which contain genes that can build a resistance against
antibiotics or poisons.
Col-plasmids, which contain genes that determine the production of bacteriocins,
proteins that can kill other bacteria cells.
Degradative plasmids, which enable the digestion of unusual substances
(toluene or salicylic acid).
Virulence plasmids, which turn the bacterium into a pathogen (one that causes
disease).
Mobile genetic elements
Transposons and retrotransposons
Transposons are discrete segments of DNA capable of moving through the genome of
their host.
There are two types of transposons:
 Class I retrotransposons move via an RNA intermediate by using RNApolymerase and then reverse transcriptase to produce cDNA (copy DNA).
 Class II DNA transposons move via "cut-and-paste" mechanism by using of their
own enzyme transposase.
Fig.7. Transposon structure: transposons are discrete segments of DNA capable of
moving through the genome. Both sides of transposon flanking by inverted sequences
(IS). Gene for transposition codes for enzyme transposase. Structural genes often
codes for antibiotic resistance for bacteria cell.