Biology Unit 2, Structure of Life, Lab Activity 2-1

Transcription

1 Biology Unit 2, Structure of Life, Lab Activity 2-1 The primary biological molecules are composed of a surprisingly small variety of atoms. The vast majority of all organisms are composed simply of carbon (18% by mass), hydrogen (10%), oxygen (65%), and nitrogen (3%). It is not the variety of atoms that is important but the different ways in which they are covalently bonded to form molecules. Carbon forms the central structure for all biological molecules. Actually to qualify as organic a molecule must have carbon included in its structure. The carbon backbone can then branch out and make covalent bonds in a wide variety of configurations. In this lab you will model eight different biological molecules from the largest protein hemoglobin- to the smallest glucose. You will use both physical and computer based modeling techniques. The purpose is to provide you with mental images of these molecular structures as we explore their importance to living systems. Research Question How are the major biological molecules structured? What are their similaritiesand differences Materials computer Molecular modeling kit(s) Paper,scissors,tape Protocol Parts one and two (computer models) are to be completed individually. Part three (physical kit modeling) is to be completed individually, in pairs, or as a lab group and then checked by your teacher. Procedure 1. Locate jmol or jsmol (use jsmol if Java is giving difficulties) models of each of the organic molecules listed below. The best site is; the above site was used to write this exercise. Most of the questions in the lab are answered within this site. Another good site is;

2 especially if you are having browser trouble with Java. The second site might be a little more difficult to find answers to questions but works fine. You are not limited to these sites. Any search for the molecule you are looking for followed by 'jmol', or jsmol, in the search line should get you a number of usable sites showing 3D renderings of the models. Once you have a model you may move it around with your mouse. Right clicking on the model will produce a dropdown menu. From the dropdown menu select 'Style' to change the format of the model. If you want to view the model in stereo you select 'Style>Stereographic>Red+Cyan glasses'. Mr. Ballog will provide you with a pair of 3D glasses. Finally, if you are having trouble with the Java plugins you can search for static computer models of the molecules. They aren t as fun but work for the exercise. Find computer models of the following organic molecules; Glucose (a monosaccharide) Sucrose (a disaccharide) Amylose starch (a polysaccharide) Triacylglycerol (a lipid) Hemoglobin (a protein) Chlorophyll (a pigment) DNA (a nucleic acid) ATP/ADP (nucleotides) 2. Look at each molecule in order. Once you have looked at the structure of a particular molecule either draw (the hard way) or take a screen shot (a lot easier) of the molecule as a ball and stick model unless instructed otherwise. To view as a ball and stick model right click the model > Style>Ball and Stick. Before you take the screen shot be sure to change the model background to white by right clicking the mode>select Color> Background> White. If you take a screen shot paste the screen capture into a document so you can control the final print size. Answer the STOP questions for each molecule before you go to the next one (the answers are often right next to the model). 3. Once you have seen the computer model of one of these biological molecules you or your lab partner or group can build it using the model kits. If you do not have access to one of the kits you may cut atoms out of paper and tape them together to form the model. The larger molecules are the most challenging. When you get to the physical model of DNA there are links to paper origami DNA models on the Falcon Biology web site under lab links. The protein molecules may be modelled with pipe cleaners or garden ties. Show your completed models to your teacher so he can mark your lab packet as completed. If you are having trouble with one or more of the models then think of some other physical method to show its structure (This applies primarily to the hemoglobin molecule which is much too large to do with the ball and stick kits). Use your creative artistic spirit to model these molecules in any way that accurately represents their structure. Don't forget to get your teacher's 'stamp' of approval. Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 2 of 8

3 Data Glucose a monosaccharide Click on the Show the hydrogens to include the hydrogen atoms. Draw or capture the ball and stick form. 1) Why is glucose called a monosaccharide? 2) How many carbon atoms does glucose have? Sucrose a disaccharide Draw or capture the ball and stick form. 3) Why is sucrose called a disaccharide? 4) What atom holds the two monosaccharide rings together? Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 3 of 8

4 Amylose a polysaccharide Draw or capture the ball and stick form. Draw/capture the amylose. Compare amylose to glycogen (animal starch) to answer the stop question #6. 5) Why is amylose called a polysaccharides? 6) What is the main structural difference between amylose (plant starch) and glycogen (animal starch)? Triacylglycerol a lipid (fat) Draw or capture the ball and stick form. Select the Color button to highlight the components of a tricylglycerol 7) What are the two components of this fat molecule? 1 and 3 8) Why is this fat molecule unsaturated? Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 4 of 8

5 Hemoglobin a protein Select the ribbons box in the text for your capture (you probably don't want to draw this one). After you capture the entire protein select the heme box. The heme group captures oxygen in your blood. Go down the list 1-4 and click each option. Do not click the option at 5, instead change to a ball and stick view and capture this model. Ribbon View of protein Heme group bonded to oxygen 9) How many oxygen (O2) can one hemoglobin bind (careful, read the text next to the model)? 10) What atom is in the center of the heme group? What four atoms is the central atom covalently bonded to? This atom is the reason your blood is red! Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 5 of 8

6 Chlorophyll You will have to go to a different site to find this one. Try; Chlorophyll is listed under 'Other molecules of biological interest.' Draw or capture the ball and stick form (it comes up as default). 11) What atom is in the center of the chlorophyll ring structure? What four atoms is the central atom covalently bonded to? 12) What are two structural similarities shared by the heme in hemoglobin and chlorophyll? 1-2- DNA You can use the either of the recommended sites for this model. This is a great molecule to view and manipulate in 3D stereo. 13) What ring molecule alternates on the outside edges of DNA? 14) What four nucleotides make up the 'rungs' of the DNA ladder? Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 6 of 8

7 ATP/ADP Use the first site for these. They are listed under Nucleotides. First look at and capture ATP, then switch to ADP. ATP is the main energy carrier for our cells. ATP 15) How many phosphates are bonded in ATP? In ADP? 16) What other molecule in this exercise contained adenine? ADP Physical Models Molecule Checked Molecule Checked Glucose (I) Sugar Sucrose (P) Sugar Amylose starch (G) Triacylglycerol fat (G) Hemoglobin protein (P) Chlorophyll (G) DNA (I) ATP/ADP (P one eachpartner) I=individual P=lab partners(2) G=lab group(4) Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 7 of 8

8 Conclusion Be sure to read the first page of this lab before answering Conclusion questions. 1. What four elements make up the majority of your body? 1) 2) 3) 4) 2. Which element forms the central structure of all biological molecules? 3. What type of bond is typically formed between the atoms in biological molecules? 4. Which biological molecule is the largest? smallest? 5. Which molecule stores the most energy? 6. Which molecule works to transfer energy from food? 7. Which molecule contains genetic information? 8. List three ways all of these molecules are similar. 1) They all contain Carbon, Hydrogen, and Oxygen 2) 3) Extra Credit: Research the four different levels of protein structure. Draw each of the levels of protein structure and write a one paragraph description of each level. Attach the drawings and descriptions to this lab packet. (25 points extra) Unit2,Lab2-1,Biological Molecules2017.docx Text 2017 Greg Ballog Page 8 of 8