The Eukaryotic Genome and Its Expression
The Eukaryotic Genome and Its Expression
The Eukaryotic Genome
Repetitive Sequences in the Eukaryotic Genome
The Structures of Protein-Coding Genes
RNA Processing
Posttranscriptional Regulation
Translational and ________ Regulation
The Eukaryotic Genome
Eukaryotic genomes are larger than those of prokaryotes.
Eukaryotic genomes have more ________ sequences and more regulatory proteins
that bind to them.
Much of eukaryotic DNA is noncoding.
Eukaryotes have multiple chromosomes.
In eukaryotes, transcription and translation are physically separated.
The Eukaryotic Genome
The genome of the yeast Saccharomyces cerevisiae has has been sequenced and
5,600 genes found.
By means of gene annotation, around 70 percent have been assigned probable
roles.
Yeast has become an important model for eukaryotic cells.
The proportions of the yeast genome coding for specific metabolic roles have
been determined.
The Eukaryotic Genome
Both E. coli (a prokaryote) and yeast (a eukaryote) use about the same number
of genes for cell survival.
Yeast has many more genes for protein targeting.
Eukaryotes require a greater number of genes because of the ________ of the
cells, confirming that eukaryote cells are structurally more complex than
prokaryote cells.
The Eukaryotic Genome
Genes for other types of proteins that are present in eukaryotes but have no
homologs in prokaryotes include:
§ Genes encoding histones
§ Genes encoding cytoskeletal and motor proteins such as actin and tubulin
§ Genes encoding cyclin-dependent kinases that control cell division
§ Genes encoding proteins involved in the ________ of RNA
The Eukaryotic Genome
Caenorhabditis elegans, a small nematode, has become a model for multicellular
organisms.
The genome of C. elegans has been sequenced and contains about 19,000
protein-coding genes.
About 3,000 genes in the worm have homologs in yeast. These genes are the ones
considered essential to all eukaryotes.
Many of the remaining 16,000 genes perform roles related to______________
The Eukaryotic Genome
Drosophila melanogaster is much larger than C. elegans, having 10 times more
cells, but the genome has fewer protein-coding genes than C. elegans.
C. elegans has more copies of related genes than Drosophila does.
About half of the fly genes have mammalian homologs.
The fly genome contains 177 genes whose sequences are known to be directly
involved in human diseases, such as cancer.
The roles of such genes are often more easily studied in the fly than in
humans.
The Eukaryotic Genome
The puffer fish, Fugu rubripes, has a very compact genome consisting of about
30,000 genes.
The human genome has about _____________ number of genes in eight times the
amount of DNA.
The human and puffer fish genomes have many similar genes; the puffer fish
genome is an "abridged" version of the human genome.
Repetitive DNA sequences, which make up 40 percent of the human genome, are
present in much smaller proportions in the puffer fish genome.
The Eukaryotic Genome
The thale cress, Arabidopsis thaliana, has a small genome and is a model
organism for study by plant biologists.
The DNA sequence contains about 26,000 protein-coding genes, many of which are
duplicates of other genes.
Many of these genes have homologs in the fruit fly and roundworm, suggesting
that plants and animals have a common ancestor.
Arabidopsis also has genes unique to plants, such as those for cell walls and
photosynthesis.
The Eukaryotic Genome
Rice, Oryza sativa, has many genes similar to Arabidopsis.
The genomes of different subspecies of rice have been sequenced, and each has
particular genes that make it unique.
Analyses of these genes will lead to improvements in this and other grain
crops.
Repetitive Sequences in the Eukaryotic Genome
Three types of highly repetitive sequences are found in eukaryotes:
§ Satellites are 5 to 50 bp long, repeated side by side up to a million times.
§ Minisatellites are 12 to 100 bp long and repeated several thousand times.
Individuals in a population can vary in the number of copies.
§ Microsatellites are 1 to 5 bp and present in 10 to 50 copies per cluster. They
are scattered all over the genome.
Repetitive Sequences in the Eukaryotic Genome
Telomeres are moderately repetitive sequences at the end of the chromosomes.
They are not transcribed into RNA.
However, some moderately repetitive DNA sequences code for tRNAs and rRNAs.
The genome has multiple copies of these coding regions so that tRNAs and mRNAs
can be produced in amounts needed by most cells.
Repetitive Sequences in the Eukaryotic Genome
In mammals there are four different rRNA molecules that make up the ribosome:
18S, 5.8S, 28S, and 5S.
The 18S, 5.8S, and 28S rRNAs are transcribed as a single precursor RNA, which
is twice the size of all three ultimate products.
There are 280 copies of sequences coding for the transcript located in
clusters on five different chromosomes.
Repetitive Sequences in the Eukaryotic Genome
Some moderately repetitive DNA sequences are transposons of which there are
four main types.
SINEs are short interspersed elements up to 500 bp long. They are transcribed
but not translated.
LINEs are long interspersed elements up to 7,000 bp long. Some are transcribed
and translated into proteins.
Retrotransposons, constituting about 17 percent of the human genome, also make
an RNA copy when they move.
DNA transposons do not use an RNA intermediate, but actually move to a new
spot without replicating.
Repetitive Sequences in the Eukaryotic Genome
Beneficial roles for transposons are unknown. They may be cellular parasites
that simply replicate themselves.
Insertion of a transposon into a functional gene can ________ it or alter its
transcription rate.
Insertions in a germ cell line can result in new mutations.
If insertion occurs in a somatic cell, cancer may result.
Transposition increases genetic variation by shuffling genetic material and
creating new genes.
Transposons may have played a role in the evolution of cell organelles.
The Structures of Protein-Coding Genes
Many protein-coding genes in eukaryotes are single-copy DNA sequences.
Unlike most prokaryotes, however, eukaryotes have genes with ________ internal
sequences.
Eukaryotes also form gene families with structurally and functionally related
"cousins" in the genome.
The Structures of Protein-Coding Genes
Genes have three types of noncoding sequences:
§ The promoter occurs at the beginning of the gene and is the site where RNA
polymerase begins transcription.
§ The terminator occurs at the end of the gene and signals the end of
transcription.
§ Noncoding sequences called ________ are interspersed with the coding regions,
called exons.
The Structures of Protein-Coding Genes
The entire sequence, including introns, is transcribed. The resulting RNA is
the primary transcript, or pre-mRNA.
The transcripts of the ________ are removed from the pre-RNA and the
transcripts of the exons are spliced together, resulting in mature mRNA.
Nucleic acid hybridization can be used to determine the location of introns in
DNA. This method was also used in the initial discovery of introns.
The Structures of Protein-Coding Genes
About half of all eukaryotic protein-coding genes have a single copy in the
haploid genome. The rest have multiple copies.
Pseudogenes (y) are inexact, ________ copies of genes, often found near the
functional copy.
The Structures of Protein-Coding Genes
Sometimes copies of genes are functional, but slightly different. A set of
duplicated or related genes is called a gene family.
DNA sequences in gene families vary, but as long as one member retains the
original DNA sequence, the other members can mutate without negative effects.
These extra genes provide material for evolution. If the mutated gene is
useful, it will be selected for in succeeding generations.
The Structures of Protein-Coding Genes
The gene family encoding the globins is an example.
Humans have three a-globins and five b-globins.
During development, different members of the b-globin gene family are
expressed at different times and in different tissues.
The Structures of Protein-Coding Genes
The globin gene family also includes nonfunctional pseudogenes.
These "black sheep" family members result from ________ that cause loss of
function.
As long as some members of a gene family are functional and pseudogenes are
not actively detrimental, there appears to be little selective pressure to
________ the pseudogenes.
RNA Processing
The first two steps of processing pre-mRNA take place in the nucleus:
The G cap, a modified GTP, is added to the 5’ end. It facilitates the binding
of mRNA to the ribosome and protects the mRNA from being ________ by
ribonucleases.
A poly A tail is added to the 3’ end. It is 100 to 300 residues of adenine
(poly A) in length.
RNA Processing
RNA splicing removes the introns and splices the exons together:
At the boundaries between introns and exons are consensus sequences.
A small ribonucleoprotein particle (snRNP) binds to the consensus sequence at
the 5’ exonintron boundary.
Another snRNP binds near the 3’ exonintron boundary.
Then other proteins bind, forming a large RNAprotein complex called a
spliceosome. This complex cuts the RNA, releases the introns, and joins the ends
of the exons.
Transcriptional Regulation of Gene Expression
Each cell in a multicellular organism contains all the genes of the organism's
genome.
For normal development, the expression of genes must be regulated.
Regulation of gene expression can occur at many points during development.
Some mechanisms result in the selective transcription of specific genes.
Transcriptional Regulation of Gene Expression
With few exceptions, all cells in an organism have the same genes, but they
express them differently.
For example, both brain and liver cells transcribe "housekeeping" genes that
code for enzymes and other molecules essential to the survival of all cells.
However, liver cells transcribe some genes for ________ proteins, and brain
cells transcribe some genes for ________ proteins.
The difference in the production of proteins is due to differential
transcription.
Transcriptional Regulation of Gene Expression
Unlike prokaryotes, in which related genes are transcribed in units called
operons, eukaryotes tend to have ________ genes.
Eukaryotes have three different RNA polymerases:
§ RNA polymerase II transcribes protein-coding genes to mRNA.
§ RNA polymerase I transcribes rRNA coding sequences.
§ RNA polymerase III transcribes tRNA and small nuclear RNAs.
Transcriptional Regulation of Gene Expression
Most eukaryotic genes have other DNA sequences that regulate transcription.
In prokaryotes, a single peptide subunit can cause RNA polymerase to recognize
the promoter; in eukaryotes many different proteins are involved in initiating
transcription.
Transcriptional Regulation of Gene Expression
Transcription factors are regulatory proteins required for transcription in
eukaryotes.
RNA polymerase II does not bind until several other proteins, such as TFIID,
have already bound the proteinDNA complex.
Some DNA sequences, such as the TATA box, are common to most promoters; others
are unique to only a few genes.
Transcription factors play an important role in cell differentiation during
development.
Transcriptional Regulation of Gene Expression
In addition to the promoter, nearby regulator sequences also affect
transcription by binding regulator proteins that activate RNA polymerase.
Much farther away are enhancer regions, which bind activator proteins and
strongly stimulate the transcription complex.
Negative regulatory regions of DNA called silencers bind proteins called
repressors and turn off transcription. Thus they have the opposite effect of
enhancers.
Transcriptional Regulation of Gene Expression
In eukaryotes, genes on different chromosomes may require coordination.
Regulation of various genes can be coordinated if all have the same regulatory
sequences that bind to the same activators and regulators.
One example is the stress response element in plants.
Stress response elements near each of the scattered genes stimulate RNA
synthesis.
RNA then codes for proteins needed for water conservation.
Transcriptional Regulation of Gene Expression
Key to transcription regulation in eukaryotes is the binding of protein to
specific DNA sequences.
Proteins need to recognize and bind appropriate sites.
There are four different structural themes or motifs for proteinDNA
interactions:
§ Helix-turn-helix
§ Zinc finger
§ Leucine zipper
§ Helix-loop-helix
Transcriptional Regulation of Gene Expression
Other mechanisms that regulate transcription act on the structure of chromatin
and chromosomes.
The packaging of DNA by the nuclear proteins in chromatin can make DNA
physically inaccessible to RNA polymerase and associated components.
Transcriptional Regulation of Gene Expression
Nucleosomes inhibit initiation and elongation of transcription.
Nucleosomes are inactivated by two protein complexes in a process called
chromatin remodeling.
Nucleosome disaggregation occurs by ________ of amino groups on the histones,
and is associated with the activation of genes.
Nucleosomes reform by deacetylation of the amino groups, and is associated
with gene deactivation.
Transcriptional Regulation of Gene Expression
Two different kinds of ________ can be distinguished by staining the
interphase nucleus.
Euchromatin stains lightly. It contains DNA that is transcribed into mRNA.
Heterochromatin stains densely and is generally not transcribed. Any genes in
heterochromatin are thus inactivated.
Transcriptional Regulation of Gene Expression
Heterochromatin is in found in the ________ X chromosome of mammals.
One of the X chromosomes in each cell of a female is ________ early in
development.
The chromosome remains condensed and appears as a Barr body under the
microscope. Condensation physically prevents DNA from being transcribed.
Methylation of cytosine on DNA may be involved with the inactivation.
Transcriptional Regulation of Gene Expression
The inactive X has one gene that is only lightly methylated and
transcriptionally active, called Xist.
The RNA transcribed from Xist is not an mRNA and remains in the nucleus.
It binds the X chromosome that transcribes it and triggers inactivation.
This RNA transcript is called interference RNA (RNAi).
Transcriptional Regulation of Gene Expression
Some gene expression is regulated by DNA rearrangement.
Saccharomyces cerevisiae has two mating types, a and a. All cells have alleles
for both types, but only one is expressed at at time.
The alleles have separate locations on the chromosomes, and are separate from
the MAT locus.
The mating type of a given yeast cell depends on which copy, a or a, exists at
the MAT site. Alleles at the MAT site can be moved in and out.
Transcriptional Regulation of Gene Expression
One cell can make more proteins than another cell by making more copies of a
gene, a process called gene amplification.
Mature frog and fish eggs have up to a trillion ribosomes, which are used for
massive protein synthesis following fertilization.
To make this number, ribosomal rRNA gene clusters are selectively amplified
and copied until there are a million copies in just one cell.
Later, after cell division begins, the number of copies returns to normal.
The mechanism for this selective amplification of a single gene is not clearly
understood.
Posttranscriptional Regulation
There are many ways in which gene expression can be regulated after
transcription.
Pre-mRNA can be processed in the nucleus by cutting and splicing.
The longevity of mRNA in the cytoplasm can also be regulated.
Posttranscriptional Regulation
Alternative splicing of a specific pre-mRNA can generate different proteins
from a single gene.
For example, cells in five different tissues splice the pre-mRNA for the
structural protein tropomyosin into five different mRNAs.
As a result, each of the five tissues in mammals (skeletal muscle, smooth
muscle, fibroblast, liver, and brain) has a different form of tropomyosin.
Posttranscriptional Regulation
RNA has no repair mechanisms.
Different mRNAs have different life spans, and the less time an mRNA spends in
the cytoplasm, the less of its protein can be translated.
Specific AU-rich nucleotide sequences within some mRNAs mark them for rapid
breakdown by a ribonuclease complex called the exosome.
Signaling molecules, such as growth factors, are made only when needed and
then break down rapidly.
Posttranscriptional Regulation
RNA ________ can be used to change the sequence of mRNA after transcription.
This editing can take place by either the insertion of nucleotides to the mRNA
sequence or the alteration of nucleotides in the mRNA.
Translational and Posttranslational Regulation
Proteins can regulate translation by binding to mRNA in the cytoplasm.
This is important for long-lived mRNAs. It prevents the production of
unnecessary proteins.
For example, cyclin, which stimulates the cell cycle, must be shut off after
it has done its job. If not, inappropriate cell division may lead to a tumor.
Translational and Posttranslational Regulation
The translation of mRNA can be regulated to control levels of certain
proteins.
1. Regulation by the G cap: An mRNA capped with an unmodified GTP is not
translated. These mRNAs can be stored and modified later when the proteins are
needed.
Translational and Posttranslational Regulation
2. Regulation of ferritin, an iron storage protein:
§ When excess iron is present, ferritin synthesis increases, but the amount of
ferritin mRNA remains constant.
§ When iron is low, a translational repressor protein binds to ferritin mRNA and
prevents translation.
§ When iron levels rise, excess iron binds to the repressor and alters its
structure, causing it to detach from the mRNA. Translation then proceeds.
Translational and Posttranslational Regulation
3. Regulation of hemoglobin:
§ Hemoglobin consists of four globin units and four heme pigments.
§ If globin synthesis does not equal heme synthesis, some heme stays free in the
cell.
§ Excess heme in the cell increases the rate of translation of globin mRNA by
removing a block to initiation of translation at the ribosome.
Translational and Posttranslational Regulation
Regulating the ________ of a protein is a way to control its actions.
Proteins identified for breakdown are often linked to the protein________
For a reward, be the first to come up and politely tell me what
common word is related to the underlined term below.
The proteinubiquitin complex then binds to a complex called a
proteasome, nicknamed the "molecular chamber of doom."
The protein is cleaved from the ubiquitin and three different proteases digest
it.
Overall, concentrations of proteins depend on rates of synthesis and rates of
digestion.
Animation 14.1 RNA Splicing
Animation 14.2 Initiation of Transcription