sau 21 Flashcards
Explain generating genetic variation
Mutation within a gene: An existing gene can be modified by a mutation that changes a single nucleotide or deletes or duplicates one or more nucleotides. These mutations can alter the splicing of a gene’s RNA transcript or change the stability, activity, location, or interactions of its encoded protein or RNA product.
Mutation within regulatory DNA sequences: When and where a gene is expressed can be affected by a mutation in the stretches of DNA sequence that regulate the gene’s activity. For examle, humans and fish have a large number of genes in common, but changes in the regulation of those shared genes underlie many of the differences between those species.
Gene duplication and divergence: An existing gene, or even a sholw genome, can be duplicated. As the cell containing this duplication, and its progeny, continue to divide, the original DNA sequence and the duplicate sequence can acquire different mutations and thereby assume new functions and patterns of expression.
Exon shuffling: Two or more existing genes can be broken and rejoined to make a hybrid gene containing DNA segments that originally belonged to separate genes. In eukaryotes, such breaking and rejoining often occurs within the long intron sequences, which do not encode protein. Because these intron sequences are removed by RNA splicing, the breaking and joining do not have to be precise to produce a functional gene.
Transcription of mobile genetic elements: Specialized DNA sequences that can move from one chromosomal location to another can alter the activity or regulation of a gene; they can also promote gene duplication, exon shuffling, and other genome rearrangements.
Horizontal gene transfer: A piece of DNA can be passed from the genome of one cell to that of another - even to that of another species. This process, which is rare amone eukaryotes but common among bacteria, differs from the usual “vertical” transfer of genetic information from parent to progeny.
Explain how in sexually reproducing organisms, only changes to the germ line are passed on to progeny
For bacteria and unicellular organisms that reproduce asexually, the inheritance of genetic information is fairly straightforward. Each individual duplicates its genome and donates one copy to each daughter cell when the individal divides in two.
For a mulitcellular organism that reproduces sexually, the family connections are considerably more complex. Although individual cells within that organism divide, only the specialized reproductive cells - the gametes - carry a copy of its genome to the next generation of organisms. All the other cells of the body - the somatic cells - are doomed to die without leaving evolutionary descendants of their own.
In a sense, somtaic ells exist only to support the germ-line cell lineage that gives rise to the gametes.
Explain how point mutations are cause by failures of the normal mechanisms for copying and repairing DNA
Changes that affect a single nucleotide pair are called point mutations. These typically arise from rare erros in DNA replication or repair.
The point mutation rate has been determined directly in expperiments with bacteria such as E. coli. Under laboratory conditions, E. coli divides about once every 20-25 minutes; in less than a day, a single E. coli can produce more descendants than there are humans on Earth - enough to provide a good change for almost any conceivable point mutation to occur. Such experiments have revealed that the overall point mutation frequency in E. coli is abou 3 changes for each 1010 nucleotide pairs replicated. With a genome size of 4.6 million nucleotide pairs, this mutation rate means that approximately 99.99% of the time, the two daughter cells produced in a round of cell division will inherit exactly the same genome sequence of the parent E.coli cell; mutant cells are therefore produced only rarely.
Point mutations can destroy a gene’s activity of - very rarely - improve it. More often, however, they do neither of these things. At many sites in the genome, a point mutation has absolutely no effect on the organism’s appearance, viability, or ability to reproduce. Such neutral mutations often fall in regions of the gene where the DNA sequence is unimportant, including most of an intron’s sequence. In cases where they occur within an exon, neutral mutations can change the third position of a codon such that the amino acid it specifies is unchanged - or is so similar that the protein’s function is unaffected.
Expalin why mutations can also change the regulation of a gene
Point mutations that lie outside the coding sequences of genes can sometimes affect regulatroy DNA sequences - elements that control the timing, location, and level of gene expression. For example, a small number of people are resistant to malaria because of a point mutation that affects the expression of a cell-surface receptor to which the malaria parasite Plasmodium vivax binds. The mutation prevents the receptor from being produced in red blood cells, rendering the individuals who carry this mutation immune to malarial infection.
Point mutations in regulatory DNA sequences also have a role in our ability to digest lactose, the main sugar in milk. Our earliest ancestors were lactose intolerant, because the enzyme that breaks down lactose - called lactase - was made only during infancy. Adults, who were no longer exposed to breast milk from domesticated cattle some 10,000 years ago, variant genes - the product of random mutation - enabled those who carried the variation to continue to express lactase as adults, and thus advantage of nutrition provided by cow’s milk. People who retain the ability to digest milk as adults contain a point mutation in the regulatory DNA sequence of the lactase gene, allowing it to be efficiently transcribed throughout life.
Explain how DNA duplication give rise to families of related genes
Gene duplication is perhaps the most important mechanism for generating new genes from old ones. Once a gene has been duplicated, each of the two copies is free to accumulate mutations - as long as whatever activities the original gene may have had are not lost. Over times, as mutations continue to accumulate in the descendants of the origina cell in which gene duplication occured, some of these genetic changes allow one of the gene copies to perform a different function. By repreated rounds of this process of gene duplication and divergence over many millions of years, one gene can give rise to a whole family of genes, each with a specialized function, within a single genome.
Many gene duplications are believed to be generated by homologous recombination. Homologous recombination provides an important mechanism for mending a broken double helix; it allows an intact chromosome to be used as a template to repair a damaged sequence on its homolog. But homologous recombination can also catalyze crossovers in which two chromosomes are broken and joined up to produce hybrid chromosomes. Crossovers take place only between regions of chromosomes that have nearly identical DNA sequences; for this reason, they usually occur between homologous chromosomes and generate hybrid chromosomes in which the order of genes is exactly the same as on the original chromosomes. This process occurs extensively during meiosis.
On rare occasions, a crossover can occur between a pair of short DNA sequences - identical or very similar - that fall on either side of a gene. If these short sequences are not aligned properly during recombination, a lopsided exchange of genetic information can occur. Such unequal crossovers can generate one chromosome that has an extra copy of the gene and another with no copy; this shorter chromosome will eventually be lost.
Once a gene has been duplicated in this way, extra copies of the gene can be added by the same mechanism. As a result, entire sets of closely related genes, arranged in series, are commonly found in genomes.
Show how Changes in regulatory DNA sequences can have dramatic
consequences for the development of an organism.
Explain how duplication and divergence produced the globin gene family
The simplest globin protein has a single polypeptide chain of about 150 amino acids, and is found in many marine worms, insects, and primitive fish. Like our hemoglobin, this protein transports oxygen molecules throughout the animal’s body. The oxygen-carrying protein in the blood of adult mammals and most other vertebrates, however, is more complex; it is composed of four globin chains of two distinct types - α globin and β globin. The four oxygen-binding sies in the α2β2 molecule interact, allowing allosteric change in the molecule as it binds and releases oxygen. This structural shift enables the four-chain hemoglobin molecule to efficiently take up and release four oxygen molecules in an all-or-none fashion, a feat not possible for the single-chain version.
The α- and β-globin genes are the result of a gene duplication that occured early in vertebrate evolution. Genome analysis suggest that one of our distant ancestors had a single globin gene. But about 500 million years ago, a gene duplication followed by an accumulation of different mutations in each gene copy is thought to have given rise to two slightly different globin genes, one encoding α-globin, the other encoding β-globin. Stilll later, as the different mammals began diverging from their common ancestor, the β-globin gene underwent its own duplication and divergence to give rise a second β-like globin gene that is expressed specifically in the fetus. The resulting fetal hemoglobin molecule has a higher affinity for oxygen compared with adult hemoglobin, a property that helps transfer oxygen from mother to fetus.
Subsequent rounds of duplication and divergenxe in both the α- and
β-globin genes gave rise to additional members of these families. Each of these duplicated genes has been modified by point mutations that affet the properties of the final hemoglobin molecules, and by changes in regulatory DNA sequences that determine when - and how strongly - each gene is expressed. As a result, each globin differs slightly in its ability to bind and release oxygen and in the stage of development during which it is expressed.
In addition to these specialized globin genes, there are several duplicated DNA sequences in the α- and β-globin gene clusters that are not functional genes. They are similar in DAN sequence to the funtional globin genes, but they have been disabled by the accumulation of many inactivating mutations. The existence of such pseudogenes makes it clear that not every DNA duplication leads to a new functional gene. In fact, most gene duplication events are unsuccesful in that one copy is gradually inactivated by mutation.
Show how repeated rounds of duplication and mutation generated the globin gene family in humans
Explain how whole-genome duplications have shaped the evolutionary history of many species
Almost every gene in the genomes of the vertebrates exists in multiple versions, suggesting that, rather than single gens being duplicated in a piecemeal fashion, the whole vertebrate genome was long ago duplicated in one fell swoop. Early in vertebrate evolution, it appears that the entire genome actually underwent duplication twice in succession, giving rise to four copies of every gene.
Explain how novel genes can be created by exon shuffling
Many proteins are composed of smaller functional domains. In eukaryotes, each of these protein domains is usually encoded by a separate exon, which is surrounded by long strecthes of noncoding introns. This organization of eukaryotic genes can facilitate the evolution of new proteins by allowing exons from one gene to be added to another - a process called exon shuffling.
Such duplication and movement of exons is promoted by the same type of revombination that gives rise to gene duplications. In this case, recombination occurs within the introns that surround the exons.
If the introns in question are from two different genes, this recombination can generate a hybrid gene that includes complete exons from both. The results of such exon shuffling are seen in many present-day proteins, which contain patchwork of many different protein domains.
Explain how the evolution of genomes has been profoundly influences by mobile genetic elements.
Mobile genetic elements - DNA sequences that can move from one chromosomal location to another - are an important source of genomic change and have profoundly affected the structure of modern genomes. These parasitic DNA sequences can colonize a genome and the spread within it. In the process, they can disrupte the function or alter the regulation of existing genes; sometimes they even create novel genes through fusions between mobile sequences and segments of existing genes.
The insertion of a mobile genetic element into coding sequence of a gene or into its regulatory DNA sequence can cause the “spontaneous” mutations that are observed in many of today’s organisms. Mobile genetic elements can severely disrupt a gene’s activity if they land directly within its coding sequence. Such an insertion mutation destroys the gene’s capacity to encode a useful protein - as if the case for anuber of mutations that cause hemophilia in humans, for example.
The activity of mobile genetic elements can also change the way existing genes are regulated. An insertion of an element into a regulatory DNA sequence, for instance, will often have a striking effect on where of when genes are expressed. Many mobile genetic elements carry DNA sequences that are recognized by specific transcription regulators; if these elements insert themselves near a gene, that gene can be brought under the control of these transcription regulators; thereby changing the gene’s expression pattern. Thus, mobile genetic elements can be a major source of developmental changes.
Finally, mobile genetic elements provide opportunities for genome rearrangements by serving as targets of homologous recombination. For example, the duplications that gave rise to the β-globin gene cluster are thought to have occured by crossovers between the abundant mobile genetic elements sprinkled throughout the humane genome.
Explain how genes can be exchanged between organisms by horizontal gene transfer
Genes and other portions of genomes can also be exchanged between individuals of different species. This mechanism of horizontal gene transfer is rare amon eukaryotes but common among bacteria, which can exchange DNA by the process of conjugation.
Genetic exchanges are currently responsible for the rise of new and potentially dangerous strains of drug-resistant bacteria. Genes that confer resistance to antibiotics are readily transferred from species to species, providing the recipient bacteirum with an enormous selective advantage in evading the anitmicrobial compounds that constitute modern medicine’s frontline attack against bacterial infection. As a result, many antibiotics are no longer effective against the common bacterial infections for which they were originally used; as an example, most strains of Neisseria gonorrhoeae, the bacterium that causes gonorrhea, are now resistant to penicilin, which is therefore no longer the primary drug used to treat this disease.
Explain how genetic changes that provide a selective advantage are likely to be preserved
Evolution is commonly thought of as progressive, but at the molecular level the process is random. Consider the fate of a point mutation that occurs in a germ-line cell. On rare occasions, the mutation might cause a change for better. But most often it will either have no consequence or cause serious damage. Mutations of the first type will tend to be perpetuated, becuase the orgaism that inherits them will have an increased likelihood of reproducing itself. Mutations that are deleterious will usually be lost. And mutations that are selectively neutral may or may not persist, depending on factors such as the size of the population, or whether the individual carrying the neutral mutation also harbors a favorable mutation located nearby. Through endless repetition of such cycles of mutation and natural selection - a molecular change and the develop new ways to exploit the environment - to outcompete others and reproduce succesfully
Explain how related organisms have genomes that are similar in organization as well as sequence
For species that are closely related, it is often most informative to focus on selectively neurtral mutations. Because they accumulate steadily at a rate that is unconstrained by selection pressures.
Explain why functionally important genome regions show up as islands of conserved DNA sequence
Show how Ancestral gene sequences
can be reconstructed by comparing
closely related present-day species.
Show how Accumulated mutations have
resulted in considerable divergence in the
nucleotide sequences of the human and
the mouse genomes.
show how Comparison of nucleotide sequences from many different vertebrates reveals regions of high conservation.
Explain how sequence conservation allows us to trace even the most distant evolutionary relationships
Show The tree of life has three major divisions.
Explain how mobile genetic elements encode the components they need for movement
Mobile genetic elements, also called transposons, are typically classified according to the mechanism by which they move or transpose. In bacteria, the most common mobile genetic elements are the DNA-only transposons. The element moves from one place to another as a piece of DNA, as opposed to being converted into an RNA intermediate - which is the case for another type of mobile element. Bacteria contain many different DNA-only transposons. Some move to the target site using a simple cut-and-paste mechanism, whereby the element is simply excised from the genome and inserted into a different site. Other DNA-only transposons replicate before transposing; in this case, the new copy of the transposon inserts into a second chromosomal site, while the original copy remians intact at its previous location.
Each mobile genetic element typically encodes a specialized enzyme, called a transposase, that mediates its movement. These enzymes recognize and act on unique DNA sequences that are present on the mobile genetic elements that code for the transposase. Many mobile genetic elements, carry antibiotic-resistance genes, which have contributed greatly to the widespread dissemination of antibiotic resistance in bacterial populations.
In addition to relocating themselves, mobile genetic elements occassionally rearrange the DNA sequences of the genome in which they are embedded. For example, if two mobile genetic elements that are recognized by the same transposase integrate into neighboring regions of the same chromosome, the DNA between them can be accidentally excised and inserted into a different gene or chromosome. In eukaryotic genomes, such accidental transposition provides a pathway for generating novel genes, both by altering gene expression and by duplicating existing genes.
Explain how the human genome contains two major families of transposale sequences
A large part of our DNA is not entirely our own. Nearly half of the human genome is made up of mobile genetic elements. Some of these elements have moved from place to place within the human genome using the cut-and-paste mechanism. However, most have moved not as DNA, but via an RNA intermediate. These retrotransposons appear to be unique to eukaryotes.
One abundant human retrotransposon, the L1 element (sometimes refered to as LINE-1, a long interspersed nuclear element), is transcribed into RNA by a host cell’s RNA polymerase. A double-stranded DNA copy of this RNA is then made using an enzyme called reverse transcriptase, an unusual DNA polymerase that can use RNA as a template. The reverse transcriptase is encoded by the L1 element itself. The DNA copy of the element is then free to reintegrate into another site in the genome.
L1 elements constitute about 15% of the human genome. Although most copes have been immobilized by the accumulation of deleterious, a few still retain the ability to transpose. Their movement can sometimes precipitate disease: for example, movement in the germline of an L1 element into the gene that encodes Factor VIII - a protein essential for proper blood clotting - caused hemophilia in a child with no family history of the disease.
Another type of retrotransposon, the Alu sequence, is present in about 1 million copies, making up about 10% of our genome. Alu elements do not encode their own reverse transcriptase and thus depend on enzymes already present in the cell to help them move.
Show how Transposons contain the components they need
for transposition.
Explain how viruses can move between cells and organisms
Viruses are mobile, but unlike the transposons, they can actually escape from cells and move to other cells and organisms. Viruses are essentially small genomes enclosed by a protective protein coat, and that they must enter a cell and coopt its molecular machinery to express their genes, make their proteins, and reproduce.
Viral reproduction is ofen lethal to the host cells; in many cases, the infected cell breaks open (lyses), releasing progeny viruses, which can then infect neighboring cells.
Most viruses that cause human disease have genomes made of either double-stranded DNA or single-stranded RNA. However, viral genomes composed of single-stranded DNA and double-stranded RNA are also known. The simplest viruses have a small genome, composed of as few as three genes, enclosed by a protein coat built from many copies of a single polypeptide chain. More complex viruses have larger genomes of up to several hundred genes, surrounded by an elaborate shell composed of many different proteins. The amount of genetic material that can be packaged inside a viral protein shell is limited. Because these shells are too small to encase the genes needed to encode the many enzymes and other proteins that are required to replicate, viruses must hijack their host’s biochemical machinery to reproduce themselves. A viral genome will typically encode both viral coat proteins and proteisn that help the virus to commandeer the host enzymes needed to replicate its genetic material.
Show how Viruses come in different
shapes and sizes.
Show how viruses commandeer the host cell’s molecular machinery to reproduce
Show how Infection by a retrovirus includes reverse transcription and integration of the viral genome into
the host cell’s DNA.
Show how The sequence of Chromosome 22 shows how human chromosomes are organized.
Explain how the nucleotide sequences of human genomes show how our genes are arranged
Less than 2% of the human genome codes for protein. Almost half of our DNA is made up of mobile genetic elements that have colonized our genome over evolutionary time. Because these elements have accumulated mutations, most can no longer move; rather, they are relics from an earlier evolutionary era when mobile genetic elements ran rampant through our genome.
Show how The bulk of the human
genome is made of repetitive nucleotide
sequences and other noncoding DNA.
Explain genome variation and how it contributes to our individuality
Single-base changes that are present in at least 1% of the population are called single-nucleotide polymorphisms (SNPs). These polymorphisms are simply points in the genome that differ in nucleotide sequence between one portion of the population and another - positions where, for example, more than 1% of the population has a G-C nucleotide pair, while the rest have an A-T.
Most of these SNPs are genetically silent, as they fall within noncritical regions of the genome. Such variations have no effect on how we look or how our cells function. This means that only a small subset of the variation we observe in our DNA is responsible for heritable differences from one human to the next.
Explain how dideoxy sequencing depends on the analysis of DNA chains terminated at every position
Dideoxy sequencing or sanger sequencing uses DNA polymerase, along with special chain-terminating nucleotides called dideoxyribonucleoside triphosphates, to make partial copies of the DNA fragment to be sequenced. Dideoxy sequencing reactions ultimately produce a collection of different DNA copies that terminate at every position in the original DNA sequence.
Show how Automated dideoxy
sequencing relies on a set of four
ddNTPs, each bearing a uniquely colored
fluorescent tag.
Show how Illumina sequencing
is based on the basic principles of
automated dideoxy sequencing.
