You may need to shop for a new brain after this chapter

Transcription

1 You may need to shop for a new brain after this chapter

2 Introduction Gene expression in eukaryotes vs. prokaryotes. First, the eukaryotic genome is much larger. Second, different eukaryotic cells in multicellular organisms use different genes; prokaryotic cells are the whole organism. Skin cells use different genes than bone cells.

3 1. Most of your DNA is a bunch of repeated nucleotides that don t code for proteins. In eukaryotes, most of the DNA (about 95% in humans) does not code for protein or RNA. Some noncoding regions are regulatory sequences. Others are introns. Finally, more of it consists of repetitive DNA, present in many copies. We used to call it junk DNA, not thinking it had any function. Now we know better (which means you need to know more ).

4 Scary but neat fact: A good bit, maybe up to 30%, of your DNA has actually been put into your genome by viruses that invaded the cells of your ancestors. Remember that your mitochondrial DNA is of prokaryotic origin, so we are composites of many different organisms. This is part of what it means to be human.

5 In mammals, about 10-15% of the genome is satellite DNA. These sequences (up to 10 base pairs) are repeated up to several hundred thousand times, but the number differs in each individual, which is the basis for modern DNA testing. Table 19.1 top

6 A number of genetic disorders are caused by abnormally long stretches of repeated nucleotide triplets within the affected gene. Huntington s disease, another neurological syndrome, occurs due to repeats of CAG that are translated into a protein with a long string of glutamines. The severity of the disease is correlated with the number of repeats; more repeats = worse symptoms. Watch how these repeats come about.

7 Much of the satellite DNA is at telomeres and centromeres. The telomeres protect genes from being lost as the DNA shortens with each round of replication.

8 2. Gene families have evolved by duplication of ancestral genes Multigene families are a collection of identical or very similar genes. These likely evolved from a single ancestral gene.

9 a. Multiple copies of alleles or genes (gene duplication) may provide new phenotypes A heterozygote may be a more advantageous genotype than a homozygote under particular conditions, since with two different alleles, the organism has two forms of proteins that may provide functional resilience in response to environmental stresses. 2. Gene duplication creates a situation in which one copy of the gene maintains its original function, while the duplicate may evolve a new function. To demonstrate student understanding of this concept, make sure you can explain: The antifreeze gene in fish

10 Identical genes: many are the genes for RNA products or those for histone proteins. For example, the three largest rrna molecules are encoded in a single transcription unit that is repeated hundreds to thousands of times. So you don t have two genes of each type!!

11 Fig. 19.2

12 Non-identical genes have diverged since their initial duplication event. The classic example is the two related families of globin genes, (alpha) and (beta), of hemoglobin.

13 Fig. 19.3

14 The different versions of each globin subunit are expressed at different times in development. What advantage could it be for a fetus to have different hemoglobin than their mom? Some genes are not used anymore. These pseudogenes are probably left over from a distant ancestor in which they were active. They are called fossil genes.

15 Rearrangement of the loci of genes in somatic cells may have a powerful effect on gene expression. Transposons are genes that can move from one location to another within the genome. Up to 50% of the corn genome and 10% of the human genome are transposons, or jumping genes If one jumps into a coding sequence of another gene, it can prevent normal gene function as seen in the pigment of this morning glory leaf. Fig. 19.4

16 Major rearrangements occur during immune system differentiation. B lymphocytes produce immunoglobins, or antibodies. Each differentiated cell makes a different antibody.

17 Fig. 19.6

18 How does a cell know which gene to use at any particular time? This is what is known as gene regulation, right? And now here is how it is done in eukaryotic cells

19 Here s an old summary of the switches that can, in some way, turn the effect of a gene on or off. Fig. 19.7

20 How DNA is packed with proteins is one way that gene expression is regulated. Densely packed areas are inactive (can t unzip). Loosely packed areas can be transcribed. This is one way a gene is turned on or off.

21 Histone proteins positively charged amino acids bind tightly to negatively charged DNA. Five types of histones. Unfolded chromatin has the appearance of beads on a string, a nucleosome, two loops of DNA around a core of 8 histone proteins.

22 Histones leave the DNA only transiently during DNA replication. They stay with the DNA during transcription. By changing shape and position, nucleosomes allow RNAsynthesizing polymerases to move along the DNA.

23 The beaded string coils to form the 30-nm chromatin fiber. This fiber forms looped domains attached to a scaffold of nonhistone proteins.

24 The looped domains coil and fold to produce the metaphase chromosome. Fig. 19.1

25 Interphase chromosomes have areas that remain highly condensed, heterochromatin, and less compacted areas, euchromatin. Let s look at animation Here s a really cool one And a song

26 Now here is some brand new (2012) info on how this coiling can regulate genes Or maybe here. Skip this if short on time.

27 Now, here are the two hottest topics in biology first is the one related to coiling epigenetics! Watch this from NOVA Science Now This one for some detail (3 min.).

28 So without changing the DNA sequence, here are two ways to turn a gene on and off, and pass that along to your kids: DNA methylation is the attachment of methyl groups (-CH 3 ) to DNA bases after DNA synthesis. Usually C s followed by G s are methlylated. CpG islands, these stretches of CGCGCGCG are called. Inactive DNA is generally highly methylated. For example, the inactivated mammalian X chromosome in females is heavily methylated.

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31 Histones can be modified as well, this time by acetyl groups. Added to histone tails, acetyl groups will usually turn a gene on.

32 Using the original DNA strands as a template, methyl copying enzymes attach methyl tags to newly replicated DNA copies. One original DNA strand and one copy will be passed to each daughter cell. Gene regulatory proteins recruit enzymes that add or remove epigenetic tags such as methyl groups to the DNA. Epigenetic tags give the cell a way to "remember" long-term what its genes should be doing.

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36 And here s a simple look at how these changes are passed on

37 Let s see what role your diet plays

38 Both mom and dad need to eat well! A study in Sweden linked times of famine and plenty with effects on children. Moms pregnant during famine led to kids with higher rates of diabetes and heart disease when food was again abundant.

39 Now let s read and do Chapter 7 in survival of the sickest may scare you, but it is better to know!! If time, let s try some mouse licking!

40 Let s see where we are now. Fig. 19.7

41 Enduring understanding 3.B: Expression of genetic information involves cellular and molecular mechanisms. Essential knowledge 3.B.1: Gene regulation results in differential gene expression, leading to cell specialization. a. Both DNA regulatory sequences, regulatory genes, and small regulatory RNAs are involved in gene expression. Evidence of student learning is a demonstrated understanding of each of the following: 1. Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription. To demonstrate student understanding of this concept, make sure you can explain: i. Promoters ii. Terminators iii. Enhancers 2. A regulatory gene is a sequence of DNA encoding a regulatory protein or RNA.

42 Transcription factors Initiation of transcription is the most important and universally used control point in gene expression. A eukaryotic gene includes introns and exons, a promoter sequence, and a number of control elements. Each of these can act like an on-off switch, much like operons. Control elements bind transcription factors.

43 Fig. 19.8

44 Bending of DNA enables transcription factors bound to enhancers to contact the protein initiation complex at the promoter. This helps position the initiation complex on the promoter. See animation Here s a cool one And another 3.5 min Fig. 19.9

45 Mom s egg has many of the transcription factors needed to get us started So here s an early mother s day tribute: Y So, after transcription, how can things be controlled? Post-transcriptional regulation, you say?

46 Only rarely are eukaryotic genes organized like operons in prokaryotes. Genes coding for the enzymes of a metabolic pathway may be scattered over different chromosomes. Even if genes are on the same chromosome, each gene has its own promoter and is individually transcribed.

47 In alternative RNA splicing, different mrna molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns And Fig

48 Regulation may occur at any of these steps. For example, cystic fibrosis results from mutations in the genes for a chloride ion channel protein that prevents it from reaching the plasma membrane where it belongs. Review control of gene expression: mations.html# Here s the latest project on gene regulation, called ENCODE: ure=relmfu

49 1. Transcription factors bind to specific DNA sequences and/or other regulatory proteins. 2. Some of these transcription factors are activators (increase expression), while others are repressors (decrease expression). 3. The combination of transcription factors binding to the regulatory regions at any one time determines how much, if any, of the gene product will be produced. d. Gene regulation accounts for some of the phenotypic differences between organisms with similar genes.

50 Here s the latest on gene regulation, Part 2 Small bits of RNA, coded for by some of that junk DNA or maybe even RNA that was cut out as introns, can interfere with gene action, hence the term RNA interference, or RNA i. First this: 4 min. If time, watch from the DVD, NOVA Sc. Now. Now see the NY Times article.

51 Best sign of the weekend

52 sirna vs. mirna????? sirna comes from viruses, or from your local genetic engineer; mirna is made by your cells to regulate gene expression. They both shut down gene expression, either cutting up mrna or stopping translation like a roadblock. If time, watch here. 5:15

53 And so what if the protein is finally made? Watch here for some protein modification that can also cause something to happen or stop happening in a cell. :48 And now here for more on ubiquitin and proteasomes. 1:45

54 Ubiquitin a regulator of already made proteins. Ubiquitin is a small regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. It directs proteins to compartments in the cell, including the proteasome which destroys and recycles proteins. Ubiquitin can be attached to proteins and label them for destruction. This discovery won the Nobel Prize for chemistry in 2004.[1][2] Ubiquitin tags can also direct proteins to other locations in the cell, where they control other protein and cell mechanisms.

55 The ubiquitin (Ub)-proteasome pathway (UPP) of protein degradation. Lecker S H et al. JASN 2006;17: by American Society of Nephrology

56 Here s a summary of the switches that can, in some way, turn the effect of a gene on or off. What else do we need to add to this? Fig. 19.7

57 1. Cancer results from genetic changes that affect the cell cycle Cancer is a disease in which cells escape from the control methods that normally regulate cell growth and division. Cancer-causing genes, oncogenes, were initially discovered in retroviruses, but close counterparts, proto-oncogenes were found in other organisms.

58 The products of proto-oncogenes are proteins that stimulate normal cell growth and division. An oncogene arises from a genetic change that leads to an increase in the proto-oncogene s protein or the activity of each protein molecule, leading to uncontrolled cell division. So normal cell processes that cause mitosis to happen have a change occur that causes it to happen too much, like a car with a gas pedal that sticks. Let s look at one of the main ones, the Ras proto-oncogene.

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60 The Ras protein is talented A growth factor molecule hits the receptor and causes it to change shape. This causes the Ras protein to grab a GTP, change shape, and activate the Raf protein, leading to S phase DNA replication if enough of this happens. Ras is also an enzyme that changes GTP to GDP, shutting itself off, kind of like cruise control on a car. A common mutation to the Ras gene changes the 12 th amino acid, causing Ras to not change the GTP and shut off, so it keeps activating Raf, leading to mitosis. Cancer.

61 This is what the Ras gene did. Fig

62 Mutations to genes whose normal products inhibit cell division, tumor-suppressor genes, also contribute to cancer. Any decrease in the normal activity of a tumorsuppressor protein may contribute to cancer. So you have cancer go genes (oncogenes) and cancer stop genes (tumor suppressor genes).

63 2. Oncogene proteins and faulty tumorsuppressor proteins interfere with normal signaling pathways Mutations in the products of two key genes, the ras proto-oncogene, and the p53 tumor suppressor gene occur in 30% and 50% of human cancers respectively.

64 The p53 gene, named for its 53,000-dalton protein product, is often called the guardian angel of the genome. Damage to the cell s DNA acts as a signal that leads to expression of the p53 gene. Check out this. :25Then this. 1:00

65 Here s what P53 protein does When DNA damage is irreparable, the p53 protein can activate suicide genes whose protein products cause cell death by apoptosis (how does that work?). It also turns on the P21 gene which stops the cell cycle to give more time for DNA repair. It also turns on genes involved in DNA repair. It also activates mirna s that stop the cell cycle.

66 3. Multiple mutations underlie the development of cancer More than one somatic mutation is generally needed to produce a fullfledged cancer cell. If cancer results from an accumulation of mutations, then the longer we live, the more likely we are to develop cancer.

67 Colorectal cancer, with 135,000 new cases in the U.S. each year, illustrates a multi-step cancer path. The first sign is often a polyp, a small benign growth in the colon lining with fast dividing cells. Through gradual accumulation of mutations that activate oncogenes and knock out tumorsuppressor genes, the polyp can develop into a malignant tumor.

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69 In many malignant tumors, the gene for telomerase is activated, removing a natural limit on the number of times the cell can divide. Nitrosamines, from meat, especially when cooked on a barbecue and charred, can cause some of these mutations. So here is a call to be a vegetarian. 30 sec.

70 Viruses, especially retroviruses, play a role in about 15% of human cancer cases worldwide. These include some types of leukemia, liver cancer, and cancer of the cervix. Viruses promote cancer development by integrating their DNA into that of infected cells. By this process, a retrovirus may donate an oncogene to the cell. Alternatively, insertion of viral DNA may disrupt a tumor-suppressor gene or convert a protooncogene to an oncogene.

71 The fact that multiple genetic changes are required to produce a cancer cell helps explain the predispositions to cancer that run in some families. An individual inheriting an oncogene or a mutant allele of a tumor-suppressor gene will be one step closer to accumulating the necessary mutations for cancer to develop.

72 For example: About 15% of colorectal cancers involve inherited mutations, especially to DNA repair genes or to the tumor-suppressor gene APC. Between 5-10% of breast cancer cases, the 2 nd most common U.S. cancer, show an inherited predisposition. Mutations to one of two tumor-suppressor genes, BRCA1 and BRCA2, increases the risk of breast and ovarian cancer. Here s another genetic connection to cancer: VEGF And here s a Top 40 hit for sure. 2:11

73 HARD? I know. I saw this movie recently (it s an old one) and almost jumped up at this scene. The star player of an all girls professional baseball team during WWII decides to leave the team when her husband returns from the war. What Jimmy Duggins, former major league star played by Tom Hanks, says to her is almost word for word what I have said in the past to athletes and students. Let s watch. 1:49