Download Chapter 19: Eukaryotic Genomes: Organization

Chapter 19: Eukaryotic Genomes: Organization, Regulation, and Evolution
Key Concepts
19.1 Chromatin structure is based on successive levels of DNA packing
19.2 Gene expression can be regulated at any stag, but the key step is transcription
19.3 Cancer results from genetic changes that affect cell cycle control
19.4 Eukaryotic genomes can have many noncoding DNA sequences in addition to genes
19.5 Duplications, rearrangements, and mutations of DNA contribute to genome
evolution
Interactive Questions
19.1
List the multiple levels of packing in a metaphase chromosome in order of increasing
complexity.
Nucleosomes (10-nm fiber); 30-nm fiber; looped domains (300-nm fiber); coiling
and folding of looped domains into highly condensed metaphase chromosome.
19.2
a. Give an example of highly methylated and inactive DNA common in mammalian cells.
Barr body-compacted X chromosome in cells of female.
b. Would histone tail deacetylation increase or decrease the transcription of a gene
located in that nucleosome?
Histonetail deacetylation would decrease transcription because it would make genes
in the nucleosome less accessible.
19.3
Label the components of this diagram of how enhancers, mediator proteins, and
transcription factors facilitate formation of a transcription initiation complex.
a. distal control elements in enhancer
b. activators
c. DNA-bending protein
d. promoter
e. mediator proteins
f. transcription factors
g. TATA box
h. RNA polymerase
19.4
a. The untranslated regions (UTR) at both the 5’ and 3’ ends of an mRNA may contribute
to regulation of gene expression. Describe their different effects.
Regulatory proteins may bind to sequences in the 5’ UTR and block attachment of
ribosomes, thus decreasing gene expression. Sequences in the 3’ UTR may affect the
length of time an mRNA remains intact, thus either increasing or decreasing gene
expression.
b. Does the action of microRNAs increase or decrease gene expression? Explain.
These small, single-stranded RNA molecules (miRNAs) join with a complex of
proteins and act to decrease gene expression by base-pairing with target mRNA and
either blocking translation or degrading the mRNA.
19.5 These diagrams represent signaling pathways that stimulate (top diagram) or inhibit
(bottom) the cell cycle. Describe the numbered steps and then explain the effect of
mutations that make a hyperactive Ras protein (top) or a defective p53 transcription
factor (bottom).
Cell-cycle simulating pathway involving Ras: (1) and (2) growth factor binds with
receptor. (3) G protein Ras is activated, and (4) sets off protein kinase cascade. (5)
Transcription factor is activated that turns on gene. (6) Prtein produced that
stimulates cell cycle. Mutation to the Ras gene may crate a hyperactive Ras protein
that signals without binding of growth factor.
Cell-cycle inhibiting pathway involving p53: (1) Damage to DNA signals (2) protein
kinase cascade that (3) activates p53. This transcription factor turns on gene for (4)
protein that inhibits cell cycle so that damaged DNA does not replicate. A mutation
may result in a missing or defective p53 transcription factor. The protein that
inhibits the cell cycle would not be produced.
19.6
Match the letter of the description and fill in the percentage (listed below) for each type
of DNA sequences found in the human genome.
1. Exons & RNA-coding
D protein and RNA-coding sequences
1.5%
2. Introns & regulatory
F DNA related to gene expression
24%
3. Transposable elements and related repetitive sequences
B multiple copies of moveable sequences
44%
4. Simple sequence repeats
A satellite DNA in centromeres and telomeres
3%
5. Large-segment duplications
E multiple copies of large sequences
5%
6. Unique noncoding DNA
C gene fragments, nonfunctional genes
15%
19.7
Lysozyme and α-lacalbumin have similar sequences but different functions. Both genes
are found in mammals, but birds have only the gene for lysozyme. What does this
observation suggest about the evolution of these genes?
The lysozyme gene, which codes for a bacterial infection-fighting enzyme, was
present in the last common ancestor of birds and mammals. After their lineages
split, the gene underwent a duplication event in the mammalian lineage, and a cop
of the lysozyme gene evolved into a gene coding for a protein involved in milk
production.
Structure Your Knowledge
1. Fill in the table below to help you organize the major mechanisms that can regulate the
expression of eukaryotic genes.
Level of Control
Examples
Chromatin structure
DNA packing into nucleosomes; histone
tail acetylation increases, whereas
deacetylation and methylation of tails
decreases transcription; methylation of
DNA may be involved in long-term
inactivation of genes
Transcriptional regulation
Transcription factors (activators) bind with
enhancers, then interact with mediator
proteins and promoter regions to form
transcription initiation complex; repressors
can inhibit transcription; steroid hormones
or other chemical messages may bind with
receptor proteins, producing transcription
factors
Post-transcriptional regulation
RNA processing (alternative splicing, 5’
cap and poly-A tail added); mRNA
degradation by shortening of poly-A tail;
removal of 5’ cap, ad miRNA targeting
Translational regulation
Repressor proteins may prevent ribosome
binding so mRNA can be stockpiled
(awaiting fertilization in ovum); activation
of initiation factors
Post-translational regulation
Protein processing by cleavage or
modification; transport to target location;
selective degradation by proteosomes of
proteins marked with ubiquitin
2.
a. What are proto-oncogenes? How do they become oncogenes?
Proto-oncogenes are key genes that control cellular growth and division. When such
genes mutate to form a more active product, become amplified (multiple copies), or
have changes in their normal control mechanisms, they may become oncogenes and
produces the uncontrolled ell division that leads to formation of a tumor.
b. What is the role of tumor-suppressor genes in the development of cancer?
Tumor-suppressor genes code for proteins that regulate cell division. Loss or
mutation of both alleles of a tumor-suppressor gene may allow tumors to develop.
Usually mutations or other changes must occur both in oncogenes and in several
suppressor genes for cancer to develop.
3.
a. Describe a retrotransposon
Retrotransposons are transposable elements that move about a genome as an RNA
intermediate, which is converted back into DNA intermediate, which is converted
back into DNA by reverse transcriptase, coded for by the retrotransposon.
b. How do transposable elements contribute to genome evolution?
By moving copies of themselves around the genome, retrotransposons provide
locations for recombination between different chromosomes. They may also
transport genes or exons to new locations and interrupt coding or regulatory
sequences.
Multiple Choice
1. The control of gene expression is more complex in eukaryotic cells because
b. gene expression differentiates specialized cells. p359, p362
2. Histones are
a. small, positively charged proteins that bind tightly to DNA. p360
3. Heterochromatin
e. is all of the above. p360
4. DNA methylation of cytosine residues
b. may be a mechanism of exogenic inheritances when methylation patterns are
repeated in daughter cells. p364
5. Which of the following appears to be attached to the nuclear lamina in a precise and
organized fashion?
d. enhancer regions of actively transcribed genes. p
6. Which of the following is not true of enhancers?
e. They are located within the promoter, and when complexed with a steroid or
other small molecule, they release an inhibitory protein and thus make DNA more
accessible to RNA polymerase. p365
7. Which of the following is not an example of the control of gene expression that occurs
after transcription?
c. alternative RNA splicing before mRNA exits from the nucleus p368
8. Pseudogenes are
d. sequences of DNA that are similar to real genes but lack regulatory sequences
necessary for gene expression. p378
9. Which of the following might a proto-oncogene code for?
c. receptor proteins for growth factors p371
10. A gene can develop into an oncogene when it
e. does any of the above p371
11. What is the main reason that prokaryotic genes average 1,000 nucleotide base pairs
whereas human genes average about 27,000 base pairs?
d. Prokaryotic gees do not have introns; human genes have many.
12. A tumor-suppressor gene could cause the onset of cancer if
e. both a and d have happened.
13. What is apoptosis?
a. a cell suicide program that may be initiated by p53 protein in response to DNA
damage
14. Which of the following would you expect to find as part of a receptor protein that
binds with a steroid hormone?
b. a domain that binds to DNA and protein-binding domains
15. A eukaryotic gene typically has all of th following associated with it except
b. an operator
16. What are proteasomes?
d. enormous protein complexes that degrade unneeded proteins in the cell
17 Tissue plasminogen activator (TPA) is a protein with three types of domains. One of
each of these types is found in the protein’s epidermal growth factor, fibronectin, and
plasminogen. What is a likely explanation for this?
c. The gene for TPA arose by several instances of exon shuffling from the other
three genes.
18. Which of the following would most likely account for a family history of colorectal
cancer?
e. inheritance of one mutated APC allele that regulates cell adhesion and migration
19. Which of the following best describes what pseudogenes and introns have in
common?
c. They are not expressed—they do not produce a functional product.
20. How is the coordinated transcription of genes involved in the same pathway
regulated?
e. The gees have the same combination of control elements in the enhancer that bind
with the particular activators present in the cell.