Pattern Matching
Time		This exercise takes approximately 6 hours.
Objectives			Once you have completed this knowledge mapping exercise, you should be able to:
		1.	Have a deeper understanding of organic molecules.
		2.	Be able to identify masked concepts based upon their relations to other concepts.
		3.	Know how to organize and construct a semantic network.
		4.	Be able to name the four major classes of organic molecules and to describe their key features.
		5.	Appreciate that in biology small differences in structure lead to large differences in function -- as in, for example, the structures of testosterone and estradiol, which produce male or female secondary sex characteristics.
Exercise 1		Understanding the Links
		1.	You can do this exercise alone or in groups of three or four students each. Use lined paper for your work and have one or more biology texts on hand for reference.
		2.	Your primary goal is to put all your ideas about organic molecules together in a coherent and well-organized way. You need to be clear about the relations between various ideas, and as you clarify your understanding of these linkages, you will find yourself developing a better understanding of the entire topic.
		3.	Your secondary goal is to systematically build your knowledge organization skills.
To Do		4.	You will begin by working your ideas out with paper and pencil. Table 1 shows all the relations we used to construct a network of ideas about organic molecules. Thoughtfully define each relation and give an example of how to use it. Compare your definitions with those created by other members of your group and resolve any differences.
		Table 1. Relations Useful for Describing Organic Molecules ASYMMETRIC RELATIONS produces produced by has type type of has characteristic characteristic of has subunit subunit of has example example of provides energy transport with provides energy transport in includes included in has component component of definition of has definition has part part of provides provided by gains phosphate to form loses phosphate to form site of occurs at site input to has input has kind kind of SYMMETRIC RELATIONS same as   contrasts with   pairs with   converted into   combines with   in dynamic equilibrium with
Exercise 2		Describing Proteins
To Do		1.	Table 2 summarizes key ideas about proteins. Organize these ideas on paper. Table 2. Key Ideas about Proteins PROTEINS Ideas Ideas Descriptors/Parts alanine amine group amino acid arginine asparagine aspartic acid carboxyl group cysteine glutamic acid glutamine glycine histidine isoleucine leucine lysine methionine -N-C-C- backbone phenylalanine proline protein serine threonine tryptophan tyrosine valine carbon carrier protein CHNOS complex folding enzyme hydrogen length 15 - 4000 aa linear chain of aa nitrogen oxygen structural protein sulfur toxin * Basic building blocks are bold and key macromolecules are in italics.
		2.	If you already know how to do this, go ahead without our help. Otherwise, follow our suggestions below. Feel free to add additional concepts and descriptors as you wish. Try not to add any new relations. There are two main ideas to describe here, protein and amino acid. Table 3. Describing a Protein Relation # of Related Concepts has subunit one idea has part 6 descriptors has characteristic 3 descriptors has type 5 descriptors Table 4. Describing an Amino Acid Relation # of Related Concepts has part 3 ideas has kind 20 ideas
Exercise 3		Describing Carbohydrates
To Do		1.	Key ideas about carbohydrates are summarized in Table 5. Use the same principles as above for describing carbohydrates, using the relations systematically and consistently. There are fewer ideas here, but the descriptions may be richer. Add any general information that you know about each idea. Table 5. Key Ideas about Carbohydrates* Ideas Descriptors/Parts carbohydrate cellulose disaccharide fructose glucose glycogen monosaccharide polysaccharide ribose saccharide starch sucrose sugar table sugar 3-carbon sugar 5-carbon sugar 6-carbon sugar carbon CHO complex hydrocarbons cross linked easily digestible hydrogen indigestible by most insoluble long chain hydrocarbons long chain sugars oxygen ring structure sugar straight chain sugar two glucose molecules * Basic building blocks are bold and key macromolecules are in italics.
Exercise 4		Describing Lipids
To Do		1.	Organize your knowledge about lipids in the same manner, using all the concepts in Table 6 and any additional knowledge that you are able to bring in (where are lipids found?, what do they do in the body?, etc.). Table 6. Key Ideas for Describing Lipids* Ideas Ideas Descriptors/Parts cholesterol estradiol fat fatty acid glycerol hormone lipid oil oleic acid palmitic acid phosphate head phospholipid progesterone stearic acid steroid testosterone wax 1/more double C=C bond 2/more double C=C bonds all C-C bonds are single carbon CHO hydrogen mono-unsaturated multi-ring structures one double C=C bond oxygen poly-unsaturated saturated solid at room temp unsaturated * Basic building blocks are bold and key macromolecules are in italics.
Exercise 5		Describing Nucleic Acids
		1.	Because nucleic acids are composed of subunits that have three different parts, and because those parts differ in RNA and DNA, and because the subunits add and lose phosphates, your description of nucleic acids will be more complex than those of the other three groups of organic molecules.
To Do		2.	Put these ideas together as you have done above. We'll give you a few hints. You can skip them if you feel you don't need them.
		3.	Begin with identity using the 'same as' relation. For example, 'ATP' is the same as 'adenosine triphosphate' and 'DNA' is the same as 'deoxyribonucleic acid'. Match up all abbreviations in this way.
Table 7. Key Ideas for Describing Nucleic Acids* Ideas Ideas Descriptors/Parts adenine adenosine diphosphate adenosine monophosphate adenosine triphosphate ATP C-G base pair A-T base pair A-U base pair CTP cytidine diphosphate cytidine monophosphate cytidine triphosphate cytosine deoxyribonucleic acid deoxyribose diphosphate DNA DNA nitrogenous base DNA nucleotide GTP guanidine diphosphate guanine guanodine monophosphate guanodine triphosphate nitrogenous base nucleic acid nucleic acid synthesis nucleoside nucleoside diphosphate nucleoside monophosphate nucleoside triphosphate nucleotide ribose guanosine diphosphate ribonucleic acid RNA RNA nucleotide RNA nitrogenous base phosphate thymidine diphosphate thymidine monophosphate thymidine triphosphate thymine TTP uracil uridine diphosphate uridine monophosphate uridine triphosphate UTP -H on carbon 2 -OH on carbon 2 carbon CHNOP high energy bonds hydrogen nitrogen oxygen phosphorus * Basic building blocks are bold and key macromolecules are in italics.
		5.	Then do the conversions. For example, 'adenosine triphosphate' can be converted into 'adenosine diphosphate' which can be converted into 'adenosine monophosphate'. All five nitrogenous bases will have similar conversions.
		6.	Think about the whole/part relations. 'DNA' and 'RNA' each has subunit 'nucleotide'. Each 'nucleotide' pas part 'nucleoside' and 'phosphate'. Each 'nucleoside' has part 'nitrogenous base' and 'sugar' ('ribose' or 'deoxyribose'). This set of relations can be developed for each of the five bases (A, T, G, C, U).
		7.	Think about the type relations. There are two types of nucleic acids, five basic types of nucleotides, five types of nucleosides and five types of nitrogenous bases. Make all these connections.
		8.	Nucleic acids are composed of what atoms? Work out these relations.
		9.	Look at the descriptors. What concepts do they best describe?
Exercise 6		Big Ideas
		1.	Finally, think about the big ideas you will use to tie the entire network together (Table 8). When organizing your knowledge, you want to 'sew your ideas up the hierarchy' to one encompassing concept when possible. In this case, each of the four classes of molecules we have described is a type of 'organic molecule'. Work out the best linkages for each of the big ideas and any others you want to add. Table 8. Some Big Ideas BIG IDEAS animal atom biochemical reactions homeostasis inorganic molecule liquid living thing macromolecule matter metabolism molecule organic molecule plant amphipathic carbon-based CHNOPS contains 2/more atoms covalently bonded non-polar one end non-polar one end polar soluble water-hating
Exercise 7		Constructing Your Network of Ideas
To Do		1.	You have now completed your pre-planning. Your teacher will give you a semantic network called '1.6c Pattern Matching Exercise' which contains all the concepts and relations named in the tables above. Your task is to put these together by creating instances. In doing so, use the Down arrow for the Relation Dialog in the create an Instance dialog to select the desired relation ray, and let name completion help you enter each concept name. Doing this is work-efficient and will save many errors and confusions. Use all the concepts in the net, describe each idea well, use relations in a consistent and systematic manner, and try to optimize your net coherency and organization.
		2.	When done, submit your net to the teacher for review. Your teacher may want you to print it out as follows: a. About Net. Select Print from the File menu and you will get the Print Dialog Box as shown in Figure 1. Click once on the radial (round) button beside About Net in the first column. Click on Print.
Figure 1. Print Dialog Box
			b. Concepts, Alphabetical. Select Print from the File menu. Select Concepts and Text. The computer will automatically select Alphabetical and All. Select attached items, Header, Numbering, and Statistics. Click on the Print button. c. Relations, Creation Order. Select Print from the File menu. Select Relations, Text, Creation, and All. Select attached items, Header, Numbering, and Statistics. Click on the Print button. d. Concepts, Graphically. Select Print from the File menu. Select Concepts, Graphic, Compact Screen, Creation, and Concepts with 3 or more instances (not All). Select attached items, Header, Numbering, and Statistics. Click on six frames per page. Click on the Print button.
		3.	Staple the pages together in the order given, put the names of your group members on the front, and give them to your teacher for review and comment.