Cellular Biology Chapter 9

10. Which of the following is true of a retrovirus, but NOT of the Alu retrotransposon? A) It requires cellular enzymes to make copies. true for Alu B) It can be inserted into the genome. true for retrotrans and alu C) It can be excised and moved to a new location in the genome. D) All (A-C) are true.

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Mobile genetic elements

-Also called: jumping genes and transponsons -found in virtually all cells -their DNA make up almost 1/2 of the human genome -can insert into any region of the genome -most lack ability to leave the cell -classified according to the mechanism by which they move or transpose -typically encodes specialized enzyme: transposase -some carry anti-biotic resistance genes -They relocate and occasionally rearrange the DNA sequences of the genome in which they are embedded -most ge occasionally rearrange the DNA sequences -move exons from one gene to another

3. List the components of a typical transposon (Mobile agents)

-Move from one chromosomal location to another -important source of genomic change -profoundly affected the structure of modern genomes -parasitic DNA sequences that can colonize a genome and then spread within it -disrupt gene activity -changes the way genes are regulated

14. Viral genomes___.

Can be made of DNA Can be made of RNA. Can be either double-stranded or single-stranded.

12. HIV is a human retrovirus that integrates into the host cell's genome and will eventually replicate, produce viral proteins, and ultimately escape from the host cell. Which of the following proteins is not encoded in the HIV genome? A) Reverse transcriptase. B) Envelope protein. C) RNA polymerase. D) Capsid protein

RNA polymerase.

11. Which of the following DNA sequences is NOT commonly carried on a DNA-only transposon? A) Transposase gene. B) Reverse transcriptase gene. C ) Recognition site for transposase.

Recognition site for transposase.

16. Which of the following statements about retroviruses is false? A) Retroviruses are packaged with a few molecules of reverse transcriptase in each virus particle. B) Retroviruses use the host-genome integrase enzyme to create the provirus. C) The production of viral RNAs can occur long after the initial infection of the host cell by the retrovirus. D) Viral RNAs are translated by host-cell ribosomes to produce the proteins required for the production of viral particles.

Retroviruses use the host-genome integrase enzyme to create the provirus.

Retrotransposons

Transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA.

15. Viruses reproduce inside a host cell because_______. A) viruses package DNA from the host-cell genome into the virus particle. B) viruses need host-cell reverse transcriptase to convert its RNA into DNA. C) viruses use host-cell ribosomes to produce viral coat proteins. D) all viruses must insert their genomes into the host-cell genome in order to be replicated.

all viruses must insert their genomes into the host-cell genome in order to be replicated.

Transposons are classified by

the mechanism by which they move or transpose bacteria---> DNA-only transposon

6. Outline the steps involved in the integration and replication of retrovirus

1. Single-stranded RNA genome of the retrovirus enters a cell 2. reverse transcriptase brought with it makes complementary DNA strand to form a DNA/RNA hybrid double helix 3. RNA strand is removed and reverse transcriptase now synthesizes a complementary DNA strand to produce: a DNA double helix. 4. this dna is inserted (integrated) into a randomly selected site in the host genome by integrase enzyme 5. in the integrated state, virus is latent (each time host cell divides) it passes on a copy of the integrated viral genome (provirus) to its progeny cells 6. copying of the integrated viral DNA into RNA by a host-cell RNA polymerase which produces large numbers of single-stranded RNAs identical to the original infecting genome Viral RNAs are then translated by the host-cell ribosomes to produce the viral shell proteins, envelope proteins, and reverse transcriptase

The most common mobile genetic elements in bacteria (DNA-only transposons) move by

1. in cut-and-paste transposition 2. in replicative transposition

21. Fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. 0.5 1.5 3 4 9 23 30 50 75 The human genome has ~3 × 10__________ nucleotide pairs that make up the sequence of __________ sets of chromosomes. This sequence encodes approximately 1.9 × 10 __________ protein-coding genes and about 5 × 10__________ non-protein-coding genes, which include structural catalytic, and regulatory RNAs. Approximately __________% of the human genome is made up of high-copy repetitive elements, while the percentage of DNA sequence in protein-coding exons is __________%.

9 23 -- --- 50% 1.5-2%

Retrovirus

An RNA virus that reproduces by transcribing its RNA into DNA and then inserting the DNA into a cellular chromosome; an important class of cancer-causing viruses. Found only in eukaryotic cells "rna as genetic information"

1. Explain how mobile genetic elements can alter the activity of regulation of a gene or promote gene duplication and exon shuffling

By rearranging the DNA sequences in which they are embedded. "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 alternating gene and by duplicating existing genes

Most common mobile genetic elements in bacteria

DNA-only transposons

Movement of DNA-only transposons

DNA-only transposons the element moves from one place to another as a piece of DNA.

9. Which of the following statements about mobile genetic elements is true?

During replicative transposition, the donor DNA will no longer have the mobile genetic element embedded in its sequence when transposition is complete.

purifying selection

Elimination of individuals carrying mutations that interfere with important functions.

17. Transposable elements litter the genomes of primates, and a few of them are still capable of moving to new regions of the genome. If a transposable element jumped into an important gene in one of your cells when you were a baby and caused a disease, is it likely that your child would also have the disease? Explain.

It is not likely that child would have the disease, because it is unlikely that the mutation is carried in the germ line. Probably the mutation occurred in a cell that gave rise to somatic cells and not germ cells. Only mutations in germ cells are passed on to progeny.

13. In humans and in chimpanzees, 99% of the Alu retrotransposons are in corresponding positions. Which of the following statements below is the most likely explanation for this similarity?

Most of the Alu sequences in the chimpanzee genome underwent duplication and divergence before humans and chimpanzees diverged

2. Explain how purifying selection leads to the conservation of functionally important DNA sequences and characterize the roles that these conserved sequences might play.

Negative selection or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilizing selection through the purging of deleterious genetic polymorphisms that arise through random mutations

19. Proteins required for growth, metabolism, and cell division are more highly conserved than those involved in development and in response to the environment. Explain. TRUE OR FALSE

TRUE. All organisms need to perform a similar basic set of fundamental functions, such as those for metabolism, protein synthesis, and DNA replication. Proteins involved in these functions are shared by descent, and their evolution is constrained. Different species and cells are likely to require different developmental paths and to encounter different environmental challenges, so the proteins involved in these processes will tend to be more variable. For example, bacteria do not undergo elaborate developmental programs and so lack many of the regulators of development found in

18. Most mutations and genome alterations have neutral consequences. Explain. TRUE OR FALSE

TRUE. Most genomic changes do not alter the amino acid sequence of proteins or the regulatory properties of genes. Even some mutations that cause minor alterations have little effect on protein function.

20. Some retrotransposons and retroviruses integrate preferentially into regions of the chromosome that are packaged in euchromatin and are also located outside the coding regions of genes that contain information for making a protein. Why might these mobile genetic elements have evolved this strategy?

The most evolutionarily successful mobile genetic elements are those that are best at reproducing themselves. To increase the number of copies of a particular element, the element must meet two criteria: (1) it must not kill its host, and (2) it must maximize its ability to continue reproducing. If an element inserts into the coding region of a gene, it might disable the gene and thereby confer a selective disadvantage in the reproduction or survival of its host. Thus, elements that devised a way to avoid insertion into coding regions were probably better able to increase their copy number throughout the human population. If an element inserts into a heterochromatic region of a chromosome, its genes may not be expressed and therefore it may become immobile. Elements that devised a way to direct insertion into euchromatin would be more likely to maintain mobility and thereby increase their copy number over time.

5. Explain how viruses differ from mobile genetic elements.

can escape from cells and move to other cells and organisms. are essentially small genomes enclosed by a protective protein coat must enter the cell and coopt its molecular machinery to express their genes, make proteins, and reproduce

transposase

enzyme which recognizes host DNA and cuts and glues transposons in and out of genome

8 . Differentiate between the amount of the human genome that codes for proteins versus the amount that consists of mobile genetic elements

human genome that codes for proteins: less than 2% mobile genetic elements: 1/2 of our genome

7. Assess how retroviruses and retrotranspospns are similar.

key feature of replication: -DNA is synthesized using RNA as a template -both use reverse transcriptase to convert RNA into DNA