Ruth Sundeen. Lesson 9 Part 1. Help Your Students Learn. Greetings and felicitations from Mrs. Ruth!

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1 Ruth Sundeen Lesson 9 Part 1 Help Your Students Learn Ages: Eighth grade to high school senior Topics: Protein Synthesis Enzymes Experiment to demonstrate fragility of enzymes Greetings and felicitations from Mrs. Ruth! Hold on to your hat! We re not finished with some important, but complicated material. In this lesson, we are going to discuss what proteins are, how they re made, a kind of protein called an enzyme, how all this relates to DNA and what genes are and how they make up who we are. Obviously, this is too much material for one lesson, so we re going to take several lessons to cover these ideas a little bite at a time. Let s start with a discussion of proteins and how they re made. Proteins are molecules that make up almost every living thing around us. They are built of components called amino acids which are held together by a chemical bond called a peptide bond. When a particular sequence of amino acids joins together in a three-dimensional molecule, they make up a particular protein. Look at it like this: PROTEIN amino acid peptide bond amino acid

2 There are approximately 20 amino acids that make up life as we currently know it, and each individual protein is made up of many more than two amino acids; in fact, proteins are made up of sequences of hundreds to thousands of amino acids uniquely linked together by peptide bonds. Think of a protein as a long strand of amino acids linked together in something like a pearl necklace, all joined together by peptide bonds, and the long strand of amino acids folds up into a three-dimensional molecule called a protein. Although you won t have to learn this entire list of amino acids (and their abbreviations) unless you take biochemistry in college, I d like you to at least see the list once. It will give you an appreciation for the staggering number of possibilities that these 20 amino acids can link in, creating a huge amount of variety and uniqueness in nature. Here we go: Alanine (Ala) Asparagine or Aspartic acid (Asx) Cysteine (Cys) Aspartic acid (Asp) Glutamic acid (Glu) Phenylalanine (Phe) Glycine (Gly) Histidine (His) Isoleucine (Ile) Lysine (Lys) Leucine (Leu) Methionine (Met) Asparagine (Asn) Proline (Pro) Glutamine (Gln) Arginine (Arg) Serine (Ser) Threonine (Thr) Valine (Val) Tryptophan (Trp) Tyrosine (Tyr) Glutamine or glutamic acid (Glx) The simplest protein that we know of is called ribonuclease. It is made up of a sequence of 124 amino acids and can be drawn as a string of pearls, with each pearl being a particular amino acid. It begins with the sequence: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg and ends with the sequence Tyr-Val-Pro-Val-His-Phe-Asp-Gly-Ser-Val. One of the very largest proteins is Titan and contains the same 20 amino acids, but in a unique sequence of 27,000 to 33,000. The study of proteins becomes extremely important when we see that evolutionists try to tell us that when all life began, a set of circumstances occurred that caused amino acids to link up and form the first proteins and all life eventually developed from those original proteins. As you can see from what I ve just told you, the probability of even the simplest protein randomly occurring is statistically impossible. There is just too much complexity for it to have happened randomly; it must have been designed that way. Why is it important to learn about proteins and how they re made? Because proteins make up genes which contain the genetic information that is passed from parent to offspring. Remember when I told you that most of the time, the DNA in the nucleus of the cell is in a resting phase called interphase, and is uncondensed. Although it s uncondensed, it is still in the shape of a double helix. It s basically two long, twisted strands joined together by chemical units called nucleotides. There are four nucleotides on a DNA strand: cytosine, guanine, thymine and adenine. Cytosine always binds to guanine; thymine binds to adenine; they are always paired together in a DNA strand and are held together by a hydrogen bond and this is

3 called hydrogen bonding (indicated below by: ). It s strong enough to hold the nucleotides together, but weak enough to easily unwind. DNA double helix G A Hydrogen bond C T When it s time for the DNA to reproduce a particular protein, the section of the double helix containing the sequence for a particular protein unwinds and the hydrogen bonds break, although the nucleotides are still attached to the individual DNA strand. A single strand of a copying mechanism called RNA then comes alongside the DNA strand and makes a negative (like a photograph negative) of the sequence on the DNA strand. This is called transcription and the RNA that did the transcribing is called messenger RNA (mrna). It now carries a message in a sequence of three nucleotides that will tell the ribosome which protein to make. This sequence of 3-nucleotides is called a codon. In other words, the mrna just transcribed the information from the DNA and now carries the instructions to the ribosome for building a particular protein. There is one main difference between the DNA strand and the RNA copy: the adenine on the DNA strand is now paired to a nucleotide called uracil (U) in place of thymine. In other words, wherever there is an A on the DNA strand, you will always have a U on the RNA strand in place of a thymine. Let me show you: DNA (double helix) Transcription DNA RNA copy (hydrogen bonds break) takes place T A T A A T A U (replaces T) G C G C C G C G

4 Let s look at what is inside the ribosome when the mrna arrives with the protein sequence. Let s say we have the following 3-nucleotide sequence on the mrna: GAU CCA GCU ACU [Note: You ll notice that since both strands are RNA, there are no thymines.] Ribosome mrna G A U C C A G C U A C U Codon trna C U A G G U C G A U G A Anticodon STOP leucine glycine arginine The 3-nucleotide sequence on the trna strand is called the anticodon and each one is carrying a particular amino acid. The nucleotides on the mrna strand attract their counterparts on the trna strand. The amino acids then line up in a particular sequence to make the specific protein called for. The process of coding for a particular protein is called translation. The amino acids are being translated into particular proteins. You don t have to know this for the quiz, but let me quickly tell you the following information: CUA codes for the amino acid leucine. GGU codes for the amino acid glycine. CGA codes for the amino acid arginine. UGA is one of the codes (called a stop codon) that tells the ribosome that the protein is finished, to break off at that point, and fold the newly-made protein into a 3-dimensional molecule that will now be transferred to the appropriate location. It is important to note that an amino acid can be ordered by several different codons. GCU, GCC, GCA and GCG all call for the amino acid alanine. UCU, UCC, UCA and UCG all call for the amino acid serine. So you can have several different codon sequences that call for a particular amino acid, but each codon can only call for one amino acid. As I told you above, each protein calls for a specific, unique sequence of amino acids, and the simplest one is made up of a sequence of 124 amino acids. The section of DNA from which the particular code for the proteins originated are called genes, and they produce what we call traits. Traits are things like hair color, eye color, skin type, etc. Genes also contain segments, called introns and exons, that were once thought to be junk DNA, but scientists have relatively recently discovered that they do, indeed, have a very important function, but this process is too complicated to discuss here.

5 We previously discussed the reproductive processes of mitosis and meiosis and I told you that when reproduction was triggered in a cell, the DNA condensed into X-shaped structures called chromosomes. Each of the stripes on the chromosomes are individual genes (traits). Now you know how those traits originated. Enzymes and the Lock & Key Theory The last topic we ll discuss in this part of the lesson is enzymes since they are complex proteins produced by all living organisms. Enzymes are what we call catalysts. Catalysts are substances that make a chemical reaction run faster, but do not get used up in the process. In other words, the amount of catalyst when you end is the same amount as when you started the reaction. Catalysts are extremely important to living things. Enzymes are proteins that are also catalysts. When a chemical process in an organism calls for an enzyme catalyst, you first must have something that will undergo the reaction. This something is called a substrate. This might be a disaccharide sugar (lactose, for example) that needs to be broken down into two monosaccharides (galactose and glucose) in order for your body to use it. This would be your key. Its chemical structure has a unique shape. Enzyme names end in ase, so if you see this suffix, you know you re dealing with an enzyme. It turns out that the enzyme lactase (the lock ) will break apart lactose into the monosaccharides galactose and glucose. The lactase enzyme lock has a shape in it into which the lactose key will fit. Once the key is in the lock (it has to match pretty closely), it completes the perfect fit, initiates a reaction that breaks lactose apart into its two monosaccharides (by adding water), and your body can now utilize them. Let s see what this might look like: Sucrose (galactose + glucose) is the key. Lactase is the lock. Galactose Glucose Water muscles in between the two monosaccharides that make up sucrose (key) and breaks them apart. If a person does not have an enzyme to break down a particular substance, it can cause all kinds of trouble. People who don t have lactase in their body have difficulty breaking down lactose in dairy products and are considered lactose intolerant.

6 It turns out that enzymes are extremely important in the everyday function of our bodies, but they are very fragile. To see how fragile enzymes are, let s do the following edible experiment with Jell-O. Experiment: How Fragile is an Enzyme? What we will see: How easily enzyme function can be destroyed Supplies for the experiment: Part of a fresh pineapple (It cannot be canned; it must be fresh) Blender Three small to medium cups (should hold 1 cup) Small box of Jell-O gelatin mix any flavor (generic brands are fine) Small pan Stove Refrigerator Measuring spoons Procedure: 1. Cut fresh pineapple to remove any skin (or purchase it already cut up, as long as it s fresh). Put several pieces in a blender and blend well so you end up with a thick, pulpy mixture of fresh pineapple. You need about one cup of this mixture. 2. Prepare the Jell-O as described in the directions on the box. 3. As you re boiling the water for the Jell-O, take a tablespoon of the thick, pulpy, fresh pineapple mixture and put it into one of the three small cups. Save that tablespoon for use with that cup only. Do not use that spoon with any other cup. Label the cup as room-temperature fresh pineapple. 4. Take the rest of the thick, pulpy pineapple mixture and pour it into the small pan. You will eventually heat it, but do not do that now. 5. When you have finished preparing the Jell-O up to the point where you stick it in the refrigerator, fill each of the three cups about one-third full. Stir the cup that has Jell-O and the thick, pulpy, fresh pineapple mixture with the tablespoon you saved in Step Take the pot of thick, pulpy pineapple mixture and heat it on high for five minutes. Keep stirring it constantly, in order to distribute the heat evenly. The thick, pulpy mixture may boil. That s fine; just keep stirring.

7 7. After five minutes of heat, take one tablespoon of the hot, pulpy mixture and pour it into one of the two cups that have only Jell-O in them. Use a different tablespoon than the one you used in Step 3. Stir vigorously. Label that cup as heated pineapple juice. Here s what your cups should look like: Jell-O only. Jell-O plus fresh, uncooked pineapple only. Jell-O plus cooked pineapple. 8. Put all three cups in the refrigerator and wait for the amount of time described on the Jell-O box. 9. Take the three cups of Jell-O out of the refrigerator and observe. What happened? Regular Jell-O with nothing added: Jell-O and fresh pineapple: Jell-O and heated pineapple: 10. Clean up your mess. You may eat the results of this experiment. Now that we have this information under our belt, we can discuss genetics and how traits are passed on to offspring. We ll start this discussion in the next part of our lesson. Now let s see how much you remember from this lesson.

8 Reflect and Recall 1. A protein is made up of a sequence of that are connected by. 2. There are approximately amino acids that we know about. 3. The simplest protein is called and it s made up of amino acids. 4. Name the four nucleotides on a DNA strand. [I want the word, not the abbreviation.] a. b. c. d. 5. What binds the nucleotides together in the double helix? 6. If the following is a DNA strand, write the RNA nucleotide (abbreviation) that binds to it. DNA: C G A T C T T C G G G A RNA: 7. Since every three nucleotides code for one amino acid, how many amino acids does the sequence in Question 6 code for? 8. What is the theory for enzyme action called? Theory

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