Chapter 19 Reading Quiz 1.What are the proteins called around which DNA winds? 2.What is the basic unit of DNA packing? 3.The attachment of methyl groups to DNA bases after DNA is synthesized is known as..? 4.What general effect does this process have on DNA? 5.What are “oncogenes”?

1. Compare the organization of prokaryotic and eukaryotic genomes. Prokaryotic Usually circular Smaller Found in the nucleoid region Less elaborately structured and folded Eukaryotic Complexed with a large amount of protein to form chromatin Highly extended and tangled during interphase Found in the nucleus

2. Describe the current model for progressive levels of DNA packing. Nucleosome  basic unit of DNA packing [formed from DNA wound around a protein core that consists of 2 copies each of the 4 types of histone (H2A, H2B, H3, H4)] A 5 th histone (H1) attaches near the bead when the chromatin undergoes the next level of packing 30 nm chromatin fiber  next level of packing; coil with 6 nucleosomes per turn the 30 nm chromatin forms looped domains, which are attached to a nonhistone protein scaffold (contains 20,000 – 100,000 base pairs) Looped domains attach to the inside of the nuclear envelope

3. Explain how histones influence folding in eukaryotic DNA. Histones  small proteins rich in basic amino acids that bind to DNA, forming chromatin Contain a high proportion of positively charged amino acids which bind tightly to the negatively charged DNA

4. Distinguish between heterochromatin and euchromatin. Heterochromatin Chromatin that remains highly condensed during interphase and is NOT actively transcribed Euchromatin Chromatin that is less condensed during interphase and IS actively transcribed Becomes highly condensed during mitosis

5. Describe where satellite DNA is found and what role it may play in the cell. Satellite DNA  highly repetitive DNA consisting of short unusual nucleotide sequences that are tandemly repeated 1000’s of times It is found at the tips of chromosomes and the centromere Its function is not known, perhaps it plays a structural role during chromosome replication and separation

6. Describe the role of telomeres in solving the end-replication problem with the lagging DNA strand. Telomere  series of short tandem repeats at the ends of eukaryotic chromosomes; prevents chromosomes from shortening with each replication cycle Telomerase  enzyme that periodically restores this repetitive sequence to the ends of DNA molecules

7. Using the genes for rRNA as an example, explain how multigene families of identical genes can be advantageous for a cell. Multigene family  a collection of genes that are similar or identical in sequence and presumably of common ancestral origin Include genes for the major rRNA molecules, huge tandem repeats of these genes enable cells to make millions of ribosomes during active protein synthesis

8. Using  -globin and  -globin genes as examples, describe how multigene families of nonidentical genes probably evolve, including the role of transposition. They arise over time from mutations that accumulate in duplicated genes Can be clustered on the same chromosome or scattered throughout the genome Original α & β genes evolved from duplication of a common ancestral globin gene Transposition separated the α globin and β globin families, so they exist on different chromosomes

9. Explain gene amplification. Gene amplification  the selective replication of certain genes that is a potent way of increasing expression of the rRNA genes, enabling more ribosomes to be made Selective gene loss  in certain tissues, genes are selectively lost and may be eliminated from certain cells

10. Describe the effects of transposons and retrotransposons. Transposons  jump and interrupt the normal functioning may increase or decrease production of one or more proteins - can carry a gene that can be activated when inserted downstream from an active promoter and vice versa Retrotransposons  transposable elements that move within a genome by means of an RNA intermediate, a transcript of the retrotransposon DNA - to insert it must be converted back to DNA by reverse transcriptase

11. Explain immunoglobin genes. Immunoglobin genes  genes that encode antibodies Basic immunoglobin molecule  consists of four polypeptide chains held by disulfide bridges - each chain has 2 regions: constant and variable - variable gives each antibody its unique function

12. Explain the chromatin modifications of DNA methylation, genomic imprinting, and histone acetylation. DNA methylation  the attachment of methyl groups (-CH 3 ) to DNA bases -Inactive DNA is usually highly methylated (adding methyl groups inactivates DNA) Genomic imprinting  where methylation permanently turns off either the maternal or paternal allele of certain genes at the start of development Histone acetylation  the attachment of acetyl groups (-COCH 3 ) to certain amino acids of histone proteins - transcription proteins have easier access to genes in acetylated regions of DNA

13. Explain the potential role that promoters and enhancers play in transcriptional control. Promoters Include the proximal control elements Produces a low rate of initiation with few RNA transcripts Unless  DNA sequences can improve the efficiency by binding additional transcription factors Enhancers The more distant control elements Bending of the DNA enables the transcription factors bound to enhancers to contact proteins of the transcription-initiation complex at the promoter

14. Compare the arrangement of coordinately controlled genes in prokaryotes and eukaryotes. Prokaryotic Prokaryotic genes that are turned on and off together are often clustered into operons which are transcribed into one mRNA molecule and translated together Eukaryotic Eukaryotic genes coding for enzymes of a metabolic pathway are often scattered over different chromosomes and are individually transcribed

15. Explain how eukaryotic genes can be coordinately expressed and give some examples of coordinate gene expression in eukaryotes. Associated with specific regulatory DNA sequences or enhancers that are recognized by a single type of transcription factor that activates or represses a group of genes in synchrony -heat shock response  series of proteins that help stabilize and repair -Steroid hormone action  steroids activate protein receptors which activate genes -Cellular differentiation  the genes produce particular sets of proteins which go on and off

16. Explain why the ability to rapidly degrade mRNA can be an adaptive advantage for prokaryotes. Prokaryotic mRNA molecules are degraded by enzymes after only a few minutes  thus bacteria can quickly alter patterns of protein synthesis in response to environmental changes

17. Describe the importance of mRNA degradation in eukaryotes, describe how it can be prevented. The longevity of a mRNA affects how much protein synthesis it directs; those that are viable longer can produce more of their protein Control mechanisms of gene expression can help prevent degradation

18. Explain how gene expression may be controlled at translation and post-translation. Translational  binding of translation repressor protein to the 5’ end of a particular mRNA can prevent ribosome attachment - translation of all mRNAs can be blocked by the inactivation of certain initiation factors Posttranslational  last level - many eukaryotic polypeptides must be modified or transported before becoming biologically active by adding phosphates, chemical groups, etc. - selective degradation of particular proteins and regulation of enzyme activity are also control mechanisms of gene expression

19. Describe the normal control mechanisms that limit cell growth and division. Proto-oncogenes  gene that normally codes for regulatory proteins controlling cell growth, division, and adhesion

20. Briefly describe the four mechanisms that can convert proto-oncogenes to oncogenes. 1.Movement of DNA within the genome  chromosomes have been broken and rejoined 2.Gene amplification  sometimes more copies of oncogenes are present in a cell than is normal 3.Point mutation  a slight change in the nucleotide sequence might produce a growth-stimulating protein that is more active or more resistant to degradation than the normal protein 4.Changes in tumor-suppressor genes that normally inhibit growth can promote cancer

21. Explain how changes in tumor-suppressor genes can be involved in transforming normal cells into cancerous cells. Frequency of mutation is close to 50% for the p53 tumor suppressor gene

22. Explain how oncogenes are involved in virus- induced cancers. Viruses might add oncogenes to cells, disrupt tumor-suppressor genes’ DNA, or convert proto-oncogenes to oncogenes