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Eukaryotic Genomes

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Each Cell

-          Genes are expressed during interphase meaning that this is when they are transcribed and translated.

-          Cells must constantly turn genes on and off in response to signals from their external and internal environments.

-          Gene expression must also be controlled for cellular differentiation (the specificity of cells for different functions).

-          Highly specialized cells only express a tiny fraction f their genes.

-          The enzymes that transcribe DNA must find the right genes at the right time or serious imbalances and diseases can arise.

-          Gene activity is regulated by DNA-binding proteins that may interact with other proteins.  Usually, it is the transcription that is specifically controlled.

 

The Structural Organization of Chromatin

-          Eukaryotic chromatin consists of DNA that is complexed with a large amount of protein.

-          During interphase, the chromatin fibers are highly extended and tangled.

-          During mitosis, these strands coil and fold up to form a number of short, thick discrete chromosomes.

-          Eukaryotic chromosomes contain a great deal of DNA

 

Nucleosomes

-          Histones are responsible for the first level of DNA packing in chromatin. 

-          The amount of histones is equal to the amount of DNA present.

-          Histones are highly positive and are attracted to the highly negative DNA.

-          There are five types of histones.

-          Unfolded chromatin looks like beads on a string.  Each bead is a nucleosome which is the basic unit of DNA packing.

-          The nucleosome consists of DNA wound around a protein core composed of two molecules of each histone (H2A, H2B, H3, and H4

-          H1 may be attached to the outside of the bead.

 

Higher Levels of DNA Packing

-          With the aid of H1, the beaded string can coil tightly to make a cylinder of 30nm in diameter.  This is known as the 30nm chromatin fiber.

-          This 30nm chromatin fiber the forms loops called looped domains which are attached to a nonhistone protein scaffold.

-          The looped domains then coil and fold on themselves.

-          Chromatin during interphase is in the 30nm chromatin fiber.

-          Some think that the interphase chromatin is attached to a nuclear scaffolding that helps organize areas of active transcription.

-          Even during interphase portions of certain chromosomes are dense and is referred to as heterochromatin.

-          Euchromatin is true uncondensed chromatin.

-          Heterochromatin is not transcribed.

 

Noncoding Sequences and Gene Duplications

-          In eukaryotic genomes, most of the DNA does not encode protein or RNA.

-          Certain sequences may be present in multiple copies and coding sequences may be interrupted by long stretches of noncoding DNA called introns.

 

Repetitive Sequences

-          Approximately 10% to 25% of the total DNA is made up of short sequences repeated in series of thousands of times.

-          The nucleotide compositions of highly repetitive sequences are often different enough to have a different density.

-          Satellite DNA is DNA that can be separated by ultracentrifugation because it appears as a “satellite” band separated from the rest of the DNA.

-          Most of the satellite DNA is located at the tips and at the centromeres.

-          Satellite sequences are important at the ends of chromosomes called the telemetries.

-          Telemetries are repeating sequences at the ends of each chromosome to prevent the shortening of the chromosomes during replication. 

-          Telemetries periodically restores this sequence to the ends of the DNA molecule.

-          Many of the repeating sequences are transposons. 

-          These transposons are generally regarded as nonfunctional but have been associated with a number of diseases like elephant man’s disease and a number of different forms of cancer.

-          Normally, these are repeating sequences but mutations can take place which causes malfunctions.  These malfunctions include fragile X syndrome and Huntington’s disease.

 

Multigene Families

-          DNA sequences that code for proteins or RNA (genes) are usually present as unique sequences or single copies in the genome.

-           But, some genes are represented by more than one copy and others resemble each other in nucleotide sequence. 

-          A collection of identical or very similar genes I called a multigene family.

-          The members of a multigene family may be clustered or dispersed in the genome.

-          Some exist as multiple identical genes and are clustered together.

-          Multigene families usually consist of genes for RNA products like those for ribosomal RNA.

-          They are repeated in series and enable the cell to produce millions of ribosomes.

-          An example of nonidentical genes are those the code for the alpha and beta polypeptide in hemoglobin.

-          One family is found on chromosome 16 and codes for the alpha globulin while another family on chromosome 11 codes for beta globulin.

-          The different versions are expressed at different times during development.

-          Families of genes arise from one gene by tandem gene duplication and results from mistakes made in DNA replication and recombination.

-          Families of nonidentical genes arise from mutations that accumulate in duplicated genes over a long period of time.

-          The existence of DNA segments called pseudogenes is evidence of this.

-          Pseudogenes have sequences very similar to functional genes but lack the sites for gene expression.

-          Significant amounts of noncoding DNA are found within genes as introns.

 

The Control of Gene Expression

-          One function of packaging DNA is putting a great deal of information into a small area. 

-          This packaging is not random; the physical state of DNA within and around a gene is important in helping control which regions are available for transcription.

-          Thus, condensed heterochromatin is not expressed and location relative to scaffold attachment sites and Nucleosomes can determine whether a specific gene is expressed.

-          Being available does not ensure that a gene will be expressed.

-          Cells must be able to alter gene expression in response to changing environments, external signals or new demands following differentiation.

-          These genes must also be tightly regulated.

 

Organization of a Typical Eukaryotic Gene

-          Eukaryotic DNA that makes up a gene is typically organized as enhancer sequences, promoters, exons, introns, and the poly A addition site.  This information is the transcribed with the introns left out to form mRNA.  The mRNA is then translated into a polypeptide segment.

-          The difference between this and a prokaryotic cell is the presence of introns. The introns are removed during RNA processing.  The processing of the RNA also includes the poly a tale at the 3’ end and the GTP cap at the 5’ end.

-          Another feature is the presence of other non-coding control sequences.  Some located in close proximity to the promoter.  These genes are called enhancers and have an influence on transcription of the associated gene.

 

Transcriptional Control

-          RNA synthesis begins with an RNA polymerase enzyme acting at a promoter with numerous proteins called transcription factors.

-          Once the appropriate initiation complex forms, the polymerase moves on the DNA template producing a strand of RNA.

-          Transcription factors and enhancer sites play an important role in control of gene expression.

-          Transcription is probably enhanced when a loop in the DNA brings the transcription factor attached to the enhancer in contact with the transcription factor and polymerase at the promoter region.

-          The control of transcription depends on regulatory proteins that bind selectively to DNA and to other proteins.

-          Hundreds have been discovered.

-          Each domain (structural region) that binds to DNA is made of one of three types.

 

Posttranscriptional control

-          Transcription alone does not make gene expression.

-          The expression is measured in types and amounts of functional proteins.

-          Gene expression may be blocked or stimulated at any posttranscriptional step.

 

RNA Processing and Export

-          A cell must process initial transcripts before they may act as mRNA, tRNA or rRNA.

-          An mRNA transcript must receive a 5’ cap and a poly-A tail and the introns must be removed and the exons spliced back together.

-          These mRNAs are transported out of the nucleus through nuclear pores and usually have proteins attached.

-          In the cytoplasm, the mRNA interacts with a number of proteins and may be associated with ribosomes to undergo translation.

-          Each step represents a possibility for control.