Genomes in Prokaryotes and Eukaryotes

8/8/2019 Genomes in Prokaryotes and Eukaryotes

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GENOMES IN PROKARYOTES AND

EUKARYOTES.

DR KITYAMUWESI RICHARD

MDENT(ORAL AND MAXILLO-FACIALSURGERY)



GENOMES

Genome is the total genetic information of an

organism.

For most organisms, it is the complete DNAsequence.

For RNA viruses, the genome is the complete

RNA sequence, since their genetic information

is encoded in RNA.



THE GENOMES OF PROMINENT

ORGANISMS.ORGANISM GENOME SIZE (Mb) GENE NUMBER

Hepatitis B virus 0.0032 4

HIV-1 Virus 0.0092 9

E.Coli 4.6 4437

S.cerevisiae(yeast) 12 6300

D.melanogaster(fruit fly) 137 14000

Homo sapiens(human) 3000 20000-30000

1 Mb = 1 million base pairs (for double-stranded DNA or RNA) or 1 million bases (forsingle-stranded DNA or RNA).



GENOMES IN EUKARYOTIC CELLS.

Nuclear DNA

Mitochondrial DNA



NUCLEAR DNA

Consists of chromosomes which are

essentially molecules of DNA.

DNA is a polymer of nucleotides. Genes are located on chromosomes.

Higher organisms have duplicate copies of

each gene hence are called diploid. Diploid cells have two copies of each

chromosome.





DNA STRUCTURE

In a solution with higher salt

concentrations or with alcohol

added, the DNA structure maychange to an A form, which is still

right-handed, but every 2.3 nm

makes a turn and there are 11 base

pairs per turn.



DNA STRUCTURE

Another DNA structure is called the Z form because

its bases seem to zigzag. Z DNA is left-handed. One

turn spans 4.6 nm, comprising 12 base pairs. The

DNA molecule with alternating G-C sequences inalcohol or high salt solution tends to have such

structure

DNA exists in a super coiled state largely due to the

action of the enzymes gyrases and topoisomerases .

This is for efficient packing during cell division and in

order to control of expression of parts of the

genome.



THE NORMAL RIGHT-HANDED "DOUBLE HELIX"

STRUCTURE OF DNA, ALSO KNOWN AS THE B FORM.



CHROMATIN

Chromatin is the substance which becomes visible chromosomes during prophase of celldivision. Its basic unit is nucleosome,

composed of 146 bp DNA and eight histoneproteins. The structure of chromatin is dynamically changing, at least in part, depending on the need of transcription.

At other times, the chromatin is less condensed, with some regions in a "Beads-On-a-String" conformation.



CHROMATIN

The 30 nm chromatin fiber is associated withscaffold proteins (notably topoisomerase II) to formloops. Each loop contains about 75 kb DNA. Scaffold

proteins are attached to DNA at specific regions called scaffold attachment regions (SARs), which arerich in adenine and thymine.

The chromatin fiber and associated scaffold proteins coil into a helical structure which may be observed as a chromosome. G bands are rich in A-T nucleotidepairs while R bands are rich in G-C nucleotide pairs.



STRUCTURE OF CHROMATIN



STRUCTURE OF NUCLEOSOMES

Histones are the proteins closelyresponsible for the structure of chromatin and play important roles in

the regulation of gene expression. Fivetypes of histones have been identified:H1 (or H5), H2A, H2B, H3 and H4.

H1 and its

homologous

protein H5 areLinker histones they stabilize the solenoidstructure of chromatin.



STRUCTURE OF NUCLEOSOMES

The other four types of histones associate withDNA to form nucleosomes. H1 (or H5) has about 220 residues. Other types of histones are

smaller, each consisting of 100-150 residues. Each nucleosome consists of 146 bp DNA and 8

histones: two copies for each of H2A, H2B, H3and H4. The DNA is wrapped around thehistone core, making nearly two turns pernucleosome.



3-D STRUCTURE OF A NUCLEOSOME



GENERAL ORGANISATION OF DNA

SEQUENCE



DNA STRUCTURE

A typical DNA molecule consists of genes,pseudogenes and extragenic region.

Pseudogenes are nonfunctional genes. They

often originate from mutation of duplicatedgenes .

Because duplicated genes have several copies, the organism can still survive even if a couple of them become nonfunctional.

Only the exons encode a functional peptide orRNA. The coding region accounts for about 3% of the total DNA in a human cell.



GENES

A gene is a unit of genetic information thatprovides instruction for a particular propertyof an organism.

It includes the entire nucleotide sequencenecessary for the expression of its product(peptide or RNA).

Each gene may exist in alternative forms calledalleles.

A gene is the fundamental unit of heredity.



GENE STRUCTURE.



GENE STRUCTURE.

A gene sequence may be divided intoregulatory and transcriptional regions.

The regulatory region could be near or far

from the transcriptional region.

The transcriptional region consists of exonsand introns.

Exons encode a peptide or functional RNA. Introns will be removed after transcription by

splicesomes and self-splicing.



ORGANELLE DNAS

Present within the mitochondria of

eukaryotes.

Present within the chloroplasts of plants. These are the main sites of ATP formation

during oxidative phosphorylation.



HUMAN MITOCHONDRIAL DNA

(eukaryotic cell)

Is much less than in the nuclear genome.

Is a double stranded circular molecule

containing 16,569 base pairs. Encodes for 13 protein subunits that are

associated with proteins encoded by nuclear

genes to form 4 enzyme complexes , 2 rRNAs

and 22 tRNAs needed for protein synthesis by

intramitochondrial ribosomes.



HUMAN MITOCHONDRIAL DNA

(eukaryotic cell)

There is no effective DNA

repair system in the

mitochondria hence mutations

occur.

Is maternal in origin.



Mitochondria Contain Multiple mtDNA

Molecules

Individual mitochondria are largeenough to be seen under the light

microscope and even themitochondrial DNA (mtDNA) can bedetected by fluorescence

microscopy. The mtDNA is located inthe interior of the mitochondrion, the region known as the matrix.



Mitochondria Contain Multiple mtDNA

Molecules

All the mitochondria in eukaryoticcells contain multiple mtDNA

molecules. Thus the total amount of mtDNA in a cell depends on thenumber of mitochondria, the size of

the mtDNA, and the number of mtDNA molecules permitochondrion





MITOCHONDRIAL GENES

All proteins encoded by mtDNA are synthesizedon mitochondrial ribosomes. All mitochondriallysynthesized polypeptides identified thus far (with

one possible exception) are not completeenzymes but subunits of multimeric complexes used in electron transport or ATP synthesis. Mostproteins localized in mitochondria, such as the

mitochondrial RNA and DNA polymerases, aresynthesized on cytoplasmic ribosomes and areimported into the organelle .



Products of Mitochondrial Genes Are

Not Exported

As far as is known, all RNA transcripts of

mtDNA and their translation products remain

in the mitochondrion, and all mtDNA-encoded

proteins are synthesized on mitochondrial

ribosomes. Mitochondria encode the rRNAs

that form mitochondrial ribosomes, although

all but one or two of the ribosomal proteins (depending on the species) are imported from

the cytosol.



Products of Mitochondrial Genes Are

Not Exported

Reflecting the bacterial ancestry of mitochondria, mitochondrial ribosomes resemble bacterialribosomes and differ from cytoplasmic ribosomesin their RNA and protein composition .

chloramphenicol blocks protein synthesis bybacterial and most mitochondrial ribosomes, butnot by cytoplasmic ribosomes. Conversely, cycloheximide inhibits protein synthesis by

eukaryotic cytoplasmic ribosomes but does notaffect protein synthesis by mitochondrialribosomes or bacterial ribosomes.



Mitochondrial Genetic Codes Differ

from the Standard Nuclear Code

The genetic code used in animal and fungal

mitochondria is different from the standard

code used in all prokaryotic and eukaryotic

nuclear genes; remarkably, the code even

differs in mitochondria from different species

Why and how this phenomenon happened

during evolution is mysterious.



Mitochondrial Genetic Codes Differ

from the Standard Nuclear Code

UGA, for example, is normally a stop codon,

but is read as tryptophan by human and

fungal mitochondrial translation systems;

however, in plant mitochondria, UGA is still a

stop codon. AGA and AGG, the standard

nuclear codons for arginine also code for

arginine in fungal and plant mtDNA, but theyare stop codons in mammalian mtDNA and

serine codons in Drosophila mtDNA.



DNA IN CHLOROPLASTS

In contrast to other eukaryotes, which contain asingle type of mtDNA, plants contain severaltypes of mtDNA that appear to recombine witheach other. Plant mtDNAs are much larger andmore variable in size than the mtDNAs of otherorganisms.. The mitochondrial rRNAs of plants are also considerably larger than those of othereukaryotes. The recent sequencing of one of the

smallest plant mtDNAs has revealed that long, noncoding regions and duplicated sequences arelargely responsible for the greater length of plantmtDNAs.



DNA IN CHLOROPLASTS

Differences in the size and coding capacity of mtDNA from various organisms most likely reflectthe movement of DNA between mitochondria

and the nucleus during evolution. Direct evidencefor this movement comes from the observationthat several proteins encoded by mtDNA in somespecies are encoded by nuclear DNA in others. It

thus appears that entire genes moved from themitochondrion to the nucleus, or vice versa, during evolution.



Chloroplasts Contain Large Circular DNAs

Encoding More Than a Hundred Proteins

The structure of chloroplasts is similar in many

respects to that of mitochondria. Like mitochondria,

chloroplasts contain multiple copies of the organellar

DNA and ribosomes, which synthesize somechloroplast-encoded proteins using the standard

genetic code. Other chloroplast proteins are

fabricated on cytosolic ribosomes and are

incorporated into the organelle after translation. Chloroplast DNAs are circular molecules of 120,000

160,000 bp, depending on the species.



Chloroplasts Contain Large Circular

DNAs Encoding More Than a Hundred

Proteins Of the 120 genes in chloroplast DNA, about 60 are

involved in RNA transcription and translation, includinggenes for rRNAs, tRNAs, RNA polymerase subunits, andribosomal proteins. About 20 genes encode subunits of the chloroplast photosynthetic electron transportcomplexes and the F0F1 ATPase complex. Also encodedin the chloroplast genome is the larger of the twosubunits of ribulose 1,5-bisphosphate carboxylase,

which is involved in the fixation of carbon dioxideduring photosynthesis.

.



Chloroplasts Contain Large Circular

DNAs Encoding More Than a Hundred

Proteins Reflecting the endosymbiotic origin of

chloroplasts, some regions of chloroplast DNA arestrikingly similar to those of the DNA of present-

day bacteria. For instance, chloroplast DNAencodes four subunits of RNA polymerase thatare highly homologous to the subunits of E. coli

RNA polymerase. One segment of chloroplast

DNA encodes eight proteins that are homologous to eight E. coli ribosomal proteins; the order of these genes is the same in the two DNAs



MITOCHONDRIA-SUMMARY

Mitochondria and chloroplasts are believedto have evolved from bacteria that formed asymbiotic relationship with ancestral cells

containing a eukaryotic nucleus. Most of thegenes originally within these organelles havebeen transferred to the nuclear genome overevolutionary time, leaving different genes inthe organelle DNAs of different organisms.




mtDNAs are only 16 kb in length; they contain

no introns and very little noncoding DNA. Yeast

and plant mtDNAs are much longer. All mtDNAs

encode rRNAs, tRNAs, and some of the proteins involved in mitochondrial electron transport and

A TP synthesis.

Most mtDNA is inherited from egg cells ratherthan sperm, and mutations in mtDNA result in a

maternal cytoplasmic pattern of inheritance.




Mitochondrial ribosomes resemble bacterialribosomes in their structure, sensitivity tochloramphenicol, and resistance to cycloheximide.

The genetic code of animal and fungal mtDNAs differs from that of bacteria and the nuclear genomein that several codons encode alternative aminoacids or stop signals. The mitochondrial code differs

between different animals and fungi. Plantmitochondria appear to use the standard nuclearand bacterial genetic code.




Mutations in mtDNA can cause human

neuromuscular disorders, probably because of

the high demand for ATP in these tissues.

Patients generally have a mixture of wild-type

and mutant mtDNA in their cells

(heteroplasmy). The severity of the phenotype

is greater, the higher the fraction of mutantmtDNA.



PROKARYOTIC GENOMES

Single short circular chromosome present.

None or few structural proteins present.

Genomes augmented by plasmids DNA.

The chromosome has a single set of genes hence haploid save for those encoding for therRNA.

90% of the DNA encodes polypeptides orstable RNA,10% is used for controlling geneexpression or has a purely structural function.



PROKARYOTIC GENOMES

Have less junk DNA 10-15%(i.e.non coding

DNA that is probably largely remnants of

genes that have been lost during the course of

evolution).

Genome sizes range from 0.6-over 10mb pairs.

Domains of circular genome tend to be

pinched off the loop of supercoiled DNA to

form small supercoiled domains.



PROKARYOTIC GENOMES

Because the genomes are relatively small and

contained in one circular molecule,only one

replication initiation site known as the ori is

needed.This accounts for the quick division

rates in prokaryotes because the ori sequence

is regenerated first during replication

providing a new site for replication to begineven as the original round of replication is still

proceeding.



PROKARYOTIC GENOMES

Since prokaryotic chromosomes have no ends, the entire genome can be copied.

There are no telomeres in prokaryotic genomes.

Prokaryotic DNA is substantially less packedduring cell division than in eukaryotes.This is because:-

1. The genome is small.

2. There is no nuclear membrane.

3. The DNA is circular (has no loose ends).



PROKARYOTIC GENOMES.

In a prokaryotic genome, there is generally

only one copy of each gene, and thus the

dominant/recessive phenomenon does not

apply.

Each and every gene will be expressed,

making prokaryotes a much

better vehicle for developing new genes.

There is no interference from dominant

forms.



PROKARYOYIC GENOMES.

Disadvantageous forms of a gene are much less

likely to persist in a community of prokaryotes,

since a more advantageous dominant form of the

gene cannot cover for it.

This is but one reason why prokaryotes tend to

have much greater rates of change in their genomes than eukaryotes.

Documents

Genomes in Prokaryotes and Eukaryotes