RAVEN 9/e

CHAPTER 18: GENOMICS

WHERE DOES IT ALL FIT IN?

Chapter 18 blends the earlier coverage of genetics with Chapter 17 to discuss the topic of genomics. As with Chapter 17, Chapter 18 gives the instructors many opportunities to ask students critical thinking questions about applications of genetics knowledge. Chapter 18 builds upon coverage from Chapters 15 and 17. The structure of DNA and protein synthesis should be briefly revisited before covering the genomics information in Chapter 18.

SYNOPSIS

A genome, all the genetic information of an individual, can be characterized in different ways. In the past, genomes where characterized by genetic maps, or linkage maps, representing the positional relationship of genes on chromosomes. Currently, physical maps are being constructed of many species representing the positional relationship of DNA sequences on a particular chromosome. With the results of the current genome projects, entire genomes are being sequenced and assembled in proper order, similarly to the pieces of a jigsaw puzzle. The participation of large numbers of researchers and the advances in DNA technology, such as automated sequencers, have been crucial to researchers' ability to compile complete or almost complete genome sequences.

One of the more surprising findings of the Human Genome project is the actual number of genes a complex organism actually have. Comparing the genomes of several organisms, researchers have found that number of genes does not necessarily correlate with complexity of the organism. With genome sequences now available, researchers are attempting to locate genes within the genome by located coding sequences. By applying the knowledge of gene expression, transcription and translation, researchers can identify regions that appear to code for start and stop codons. These regions are known as open reading frames. Interestingly, evidence seems to indicate that alternative splicing patterns in humans seems to allow for complexity of proteins. The complexity of proteins is due to different patterns of intron splicing following transcription and not from addition of genes. Four classes of protein-encoding genes have been identified in eukaryotic genomes: single-copy genes, segmental duplications, multigene families, and tandem clusters. Also, it seems that a large portion of eukaryotic genomes are actually non-coding regions.

The vast amounts of information provided by the genome projects have given rise to new fields of science, particularly genomics. The study of genomes has several applications. These include determining the minimal genome to support a cell, investigating proteins more fully and the use of comparative genomics to answer evolutionary questions. Functional genomics is a field that attempts to determine the function of the vast number of proteins an organism can produce. Proteomics, yet another field that has been bolstered by the genome projects, is the study of the proteome, all the proteins coded for by the genome.

The information provided by the genome projects has opened many areas of research, both in theoretical science, but also in applied science. Information learned from the genome projects has the potential to improve pharmaceuticals, agriculture and diagnostic tools. But, with this information come many questions. How will society use the information? Will it be used for purposes of screening and possibly discrimination of some individuals? Will it alter the way we view certain behavioral traits?

LEARNING OUTCOMES

  • Distinguish between a genetic map and a physical map.
  • Explain how genetic and physical maps can be linked.
  • Characterize the main hurdle to sequencing an entire genome and how it has been overcome.
  • Differentiate between clone-by-clone sequencing and shotgun sequencing.
  • Describe the classes of DNA found in a genome.
  • Explain what a SNP is and why SNPs are helpful in characterizing genomes.
  • Describe the advances that have come from comparative genomics.
  • Distinguish between genomics and proteomics.
  • List ways in which genomics could be applied to infectious disease research.
  • Explain how genomics could enhance crop production and nutritional yield.
  • Evaluate the issues of genome ownership and privacy.

COMMON STUDENT MISCONCEPTIONS

There is ample evidence in the educational literature that student misconceptions of information will inhibit the learning of concepts related to the misinformation. The following concepts covered in Chapter 18 are commonly the subject of student misconceptions. This information on “bioliteracy” was collected from faculty and the science education literature.

  • Students believe that all genes program for proteins
  • Students do not distinguish between the DNA of prokaryotes and eukaryotes
  • Students believe that phenotype can be fully by knowing the genotype
  • Students do not take into account the presence of exon information in genomic DNA
  • Students do not fully understand the role of genetics and environment on determining observable variation in organisms
  • Students believe that genes for one characteristic are all located on the same chromosome
  • Students do not distinguish genomics from proteomics
  • Students believe that all mutations are deleterious.

INSTUCTIONAL STRATEGY

The area of genomics is so vast and new that many professional scientists are completely sure of all the applications or terminology, for that matter, of this field of science. Considering the number of anagrams that have been introduced in previous chapters, the addition of STS, YAC, BAC, etc. can be confusing for many students. I try to reinforce the function of these by explaining the meaning behind the anagram when used.

One of the wonderful applications of the area of genomics and recombinant DNA technology in teaching, is you have a chance to demonstrate what we can do with previous biological knowledge. By understanding how genes are expressed, how proteins are encoded in the DNA, researchers have the ability to located possible open reading frames. Also, with the apparent prevalence of alternative splicing in eukaryotes, there is still so much we have to learn. It is an exciting area of science.

Applications of the information provided by the genome projects are revealed so often that many students may hear these new "discoveries" on the news. This is one chapter that requires constant updating of information for presentation. Access the genome websites or science news websites for new updates on medical or agricultural applications.

HIGHER LEVEL ASSESSMENT

Higher level assessment measures a student’s ability to use terms and concepts learned from the lecture and the textbook. A complete understanding of biology content provides students with the tools to synthesize new hypotheses and knowledge using the facts they have learned. The following table provides examples of assessing a student’s ability to apply, analyze, synthesize, and evaluate information from Chapter 18.

Application /
  • Have students predict the fragments of DNA produced on a section of the DNA sense strand sequence ACGTCGGATCCGGCCTAGC using the restriction enzyme HaeIII.
  • Have students explain.
  • Ask students to hypothesize how unexpected SNPs can effect the action of restriction enzymes on a sequence of DNA.

Analysis /
  • Have students to explain how proteomic analysis can give insights into the characteristics of genes that have not yet been sequenced.
  • Ask students to explain why genomics is not a predictor of how proteins interact in a cell.
  • Ask students to explain how introns interfere with the characterization of a gene based on the mRNA sequence determined by proteomic techniques.

Synthesis /
  • Ask students to find a way restriction enzymes can be used to determine the variability of exon base pair sequences in an organism.
  • Ask students to assess the value of conducting a genomic analysis of a 15,000 year old body found frozen in northern Alaska.
  • Ask students come up with a strategy in which proteins collected from a frozen ancient plant can be used to build a picture of its genomic information. .

Evaluation /
  • Ask students to evaluate the pros and cons of performing SNP analyses on all humans.
  • Ask students to explain the medical implications of knowing that humans and chimpanzees are 98% similar according to genomic analyses.
  • Ask student to debate the value of using genomics to determine the probability of a child living to a certain age.

VISUAL RESOURCES

Palindromes are words that exhibit two-fold rotational symmetry (bob, kook, deed). The phrase “a toyota” is a palindrome as is “a man, a plan, a canal, panama.” Search the web for thousands of examples, but start here:

Hopefully you will notice that the URL itself is a palindrome!

The scifi film “Gattaca” touches on future (or maybe not so future!) gene technology and the ethical implications of genetic control. Substantial information is available at the movie website

IN-CLASS CONCEPTUAL DEMONSTRATIONS

A. Genomic Videostreaming

Introduction

This demonstration provides up-to-date information about genomic applications called gene chips and microarrays. The demonstration uses an animated and narrated videostream to show students how gene chips and microarrays are used in genomics..

Materials

  • Computer with live access to Internet
  • Videostreaming software preinstralled
  • LCD projector attached to computer
  • Web browser with bookmark to Howard Hughs Genomics Videos at

Procedure & Inquiry

  1. Review the concept of genomics to the class.
  2. Tell students they will be viewing a genomic strategy called gene chips
  3. Show the Gene Chip Manufacturing Video
  4. Discuss the possible uses of gene chips with the class.
  5. Show the microarrayer in Action Video
  6. Discuss the possible uses of microarrays with the class.

B. Virtual Electrophoresis

Introduction

Electrophoresis is one of the fundamental techniques used in the genomic analysis of DNA. This accurate and simple to understand animation helps teach the principles of electrophoresis.

Materials

  • Computer with live access to Internet
  • LCD projector attached to computer University of Utah Virtual Electrophoresis website
  • Web browser with bookmark to :

Procedure & Inquiry

  1. Provide students with a brief introduction to electrophoresis
  2. Then go to the University of Utah Virtual Electrophoresis website.
  3. Click on the Forward icon to begin the animation.
  4. Take time to ask the students to review particular parts of the animation sequence before proceeding with the next step.
  5. At the end of the animation ask the students to explain how electrophoresis is useful in genomic studies.

LABORATORY IDEAS

Electrophoresis is one of the earliest tools of genomics analysis. The principles of electrophoresis are not always evident using an actual DNA or protein procedure. Plus, there are many variables that can lead students to poor results making it confusing to make conclusions. This virtual electrophoresis setup provides a user-friendly virtual hands-on laboratory activity for learning the principles of genomics.

  1. Introduce students to basic principles of electrophoresis as a genomics tool.
  2. Provide students with the following resources:
  3. Computer with Internet access
  4. Web browser bookmarked to
  5. New England BioLabs webstie showing restriction enzyme cutting points at
  6. Instruct students to use a drop-down window to select a plasmid to sequence using restriction enzymes and electrophoresis.
  7. Tell the students to predict the number and relative sizes of the fragments for the particular plasmid when mixed with the restriction enzymes provided in the animation.
  8. Then have the students load the samples. They should know to load the plasmid each of the different restriction enzymes provided and the molecular weight marker.
  9. They should then run the gel to completion.
  10. Have the students record whether their predictions were accurate.
  11. Have the students predict the molecular weights of the fragments based on the molecular weight marker.
  12. Have them repeat this procedure for each plasmid.

LEARNING THROUGH SERVICE

Service learning is a strategy of teaching, learning and reflective assessment that merges the academic curriculum with meaningful community service. As a teaching methodology, it falls under the category of experiential education. It is a way students can carry out volunteer projects in the community for public agencies, nonprofit agencies, civic groups, charitable organizations, and governmental organizations. It encourages critical thinking and reinforces many of the concepts learned in a course.

  1. Have students organize a human genomics forum for the community.
  2. Have students do an educational program for high school students using the Gene Almanac website at
  3. Have students do a simple electrophoresis demonstration for elementary school students.
  4. Have students do a genomics display at a local library.

ETYMOLOGY OF KEY TERMS

-ase enzyme (modern)

bio- life or relating to living organisms (from the Greek bios- mode oflife)

homeo- likeness; resemblance; similarity (from the Greek homoios- like)

para- beside; next to (from the Greek para- beside)

prote- of, or relating to, protein; first (from the Greek protos- first)

retro- backwards (from the Latin retro- back; to the rear)

transpose to change in form (from the Latin trans- across or through andponere- to place)