Digital World Biology



Investigating biochemicals with molecular modelsBackgroundMany large biomolecules fall into four major groups: lipids, carbohydrates, nucleic acids, and proteins. We will examine molecular models and uncover features that can be used for to characterize new biomolecules.MaterialsNote: You will need an Internet connection to download the collection of molecules. 1. Touch the question mark icon in Molecule World to open the information section.2. Touch “View Structure Collections” to access Digital World Biology structure collections. 3. Choose the Biochemicals collection.4. Touch “biochemicals.mwc” to select this collection.5. Choose “open in Molecule World” to download and open the collection in Molecule World.Skills Before starting, it may be helpful to practice the following skills in Molecule World:1. Touch “Biochemicals” to open the collection. Open any structure by touching the name.2. Touch the atom icon to view the drawing styles. Touch the name to change the style.A ball and stick drawing style shows atoms as balls and covalent bonds as sticks.The spacefill drawing style shows the size of the electron cloud for each atom. 3. Touch the palette icon to see the color key and identify atoms in a structure.NomenclatureFatty acids are a type of lipid. Carbohydrates are polymers of smaller sugar molecules like monosaccharides or polysaccharides. Amino acids are subunits of proteins. Proteins are also called peptides. Nucleotides are subunits of nucleic acids like RNA or DNA.Learning Objectives:1. Identify the kinds of atoms that are found in each type of molecule (fatty acids, carbohydrates, nucleotides / nucleic acids, or amino acids / proteins.2. Identify features that can be used to identify whether a molecule might be a fatty acid, carbohydrate, amino acid (or protein), or nucleotide (or nucleic acid).Assessment:1. Examine the structures of the unknown molecules and determine which ones are fatty acids, carbohydrates, nucleotides (or nucleic acids), or amino acids (or proteins).2. Identify features that can be used to identify each type of molecule.Part I. Match each structure with its categoryFor each structure in the collection: look at the description and the information at the top of the viewer window to identify where the structure belongs in the table below. Write or type the name in the appropriate table cell. CarbohydratesNucleotides / Nucleic AcidsFatty acidsAmino Acids / ProteinsPart II. Identify the atoms in each type of structure1. Identify the types of atoms in each structure and record their names in the appropriate part of the table below.CarbohydratesNucleotides (or Nucleic Acids)Fatty acidsAmino acids (or Proteins)Note: if you have a protein, touch the Show/Hide button and show all atoms to see all the different kinds of elements2. Pick a carbohydrate structure and count the number of oxygens and the number of carbons. Do the same thing for a fatty acid structure. Calculate the ratio of carbons to oxygen. Record your data in the table below.Structure TypeStructure nameNumber of CarbonsNumber of OxygensRatio (C:O)Fatty acidCarbohydrateA. Which kind of molecule has a higher carbon to oxygen ratio?B. Is this true for other pairs of fatty acids and carbohydrates? You can do this same kind of analysis with one or more pairs of structures to test this.Part III. Analyze your results, draw conclusions, and make predictionsUse your data from part II to answer the questions below.1. If you looked at a new structure, what kind of element(s) would suggest that it might be an amino acid?2. If you looked at a new structure, what kind of element(s) would tell that it might be a nucleotide?3. How would you tell the difference between:- an amino acid and a nucleotide?- an amino acid and a protein?- a nucleotide and a nucleic acid?4. How would you determine if you might be looking at a carbohydrate or a fatty acid?5. How would you tell the difference between a carbohydrate and a fatty acid?Part IV. Biochemical unknownsRecord the category for each of the four unknown biomolecules.Unknown numberType of molecule (Fatty acid, carbohydrate, nucleic acid, proteinHow did you identify this unknown?12345678 ................
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