Name Sec.. Score. 1. (4) Describe reasons why carbon is the atom of choice for macromolecules?

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1 Name Sec.. Score. Purpose The clear understanding of the principles of Organic Chemistry leads to a stronger foundation in being able to explain the processes found in biology. Completing this assignment will assist you in developing these skills and clarify the Course Content Learning Outcome number 3 for this course and the Campus Wide Outcome of Critical Thinking. Task Working in groups of two to four and armed with the definitions just provided in lecture, a textbook, the Chemistry Power Point presentation, or another reliable source answer the following questions about Organic Chemistry (Chapter 2). Be creative in how you approach and answer each question. Remember in science there are no correct answers but rather explanations of phenomena. This assignment will be due????? (Exact date will be given in class). Criteria This assignment is worth 60 points total. The possible points for each question is in parenthesis after the question number. A complete answer to each question will involve being cognizant of Organic Chemistry principles. Topics such as the importance of carbon as the atom used to build organic molecules, the categories of organic molecules to include the atoms in each organic molecules, the types of molecules in each category, special characteristics of each category or organic molecule, and the biological usefulness of each category of organic molecules. Clear answers will have each particle of an atom labeled clearly, descriptions and definitions are clear and concise, and will contain enough detail that anyone reading your answer could potentially draw the same conclusions that you have by answering the questions. These websites maybe helpful to your understanding: (4) Describe reasons why carbon is the atom of choice for macromolecules? Carbon is the atom of choice for organic molecules for the following reasons: 1) it is a relatively small atom, 2) it can form four non-polar covalent bonds with four other atoms or bond to other molecules, 3) when bonded to four other atoms the base carbon always forms a tetrahedron shape (think of a camera on a tripod with the adjusting knob below the camera being the central carbon) 4) it can bond to other carbon atoms in single, double, or triple non-polar covalent bonds, 5) carbons can be strung together to form chains of carbon (if all the carbons are bonded with hydrogens we call the molecule a hydrocarbon) with each individual carbon in the chain bonded to other atoms or molecules which can give the chain different properties, 6) the chains can be branched or folded into various shapes (like ringed structures) that relate to function of the large macromolecule. 2. (4) Define a functional group (see the figure of functional groups in your text) and explain how when they are attached to a base carbon atom chain how they yield different properties to the chain? A functional group is a group of atoms bonded together in a particular unit which can be attached to a carbon backbone (carbon chain). Once attached, the functional group can make the Biology& Class Assignment 3

2 chain react differently to other molecules or other carbon chains. For instance, if you had a carbon chain that is 2 carbons in length with 6 hydrogen s attached to the chain it would be a molecule called ethane, if you removed one of the end hydrogen s of ethane and replaced it with an OH group (hydroxyl functional group) you would make a gas into an alcohol called ethanol (This fact is important to remember. WHY?). Other functional groups give the base chain acidic properties (add an OOH in place of the OH below), basic properties (add an NH 2 in place of the OH below), buffering properties, or can make the chain act as a polar molecule. This is cool because now the chain can be used to perform various functions by simply changing the functional group. H H H H H C C H H C C OH H H H H Ethane Ethanol Look at the table below for other functional groups and note their properties: Biology& Class Assignment 3

3 3. (4) Explain the difference between a linear vs. a monomer vs. a polymer molecule and tell which of the following molecules: carbohydrates, lipids, proteins, or nucleic acids are polymers or linear? A linear molecule is simply a straight chain of carbon atoms bonded to carbon atoms as the backbone with hydrogens or other functional groups attached to each carbon to fill the octet pattern of each carbon atom in the chain, but that chain is not added to another chain to make the molecule functional. A monomer is like a Lego building block, whereas a polymer is like a Lego house. One Lego block does not build a house, but by combining the blocks you can put together a house. This is the pattern for the macromolecules called carbohydrates, proteins, and nucleic acids. Carbohydrates are chains of units called monosaccharides (sugar block ), proteins are chains of amino acids, and nucleic acids are chains of nucleotides. Lipids do not have monomers at all but are rather simply linear chains of carbon molecules of varying lengths, except in the category of the lipids called steroids. In steroids the chains are formed into ring structures with various functional groups attached to the rings at different locations to change the function of the steroid (think estrogen vs. testosterone). 4. (12) Provide the following information to describe the characteristics of a Carbohydrate. Name the atoms found in a carbohydrate. The atoms found in a carbohydrate are Carbon, Hydrogen, and Oxygen in a ratio of CH 2 O. How are these atoms arranged to build a carbohydrate? The atoms are laid down with the carbons forming a linear backbone chain with each carbon having a hydrogen and oxygen plus hydrogen (hydroxyl group) attached like H-C-OH or OH-C- H fashion. The pattern alternates from carbon to carbon down the linear chain. Attached to the first or second carbon is a carbonyl functional group (double bonded O to the C). This group then binds to the fifth carbon in the chain to form a ring structure called a monosaccharide. Explain the differences between a monosaccharides, disaccharides and polysaccharides by their structure and naming the various types. A monosaccharide (glucose, fructose, ribose, galactose and some others we did not mention) is considered to be the monomer for the carbohydrate family of organic molecules because they are attached to other monosaccharides to build longer chains. The primary disaccharides we talked about were sucrose (combining a glu. and a fru.), lactose (a gala. and a glu.), and maltose (a glu. and a glu.). Where would each of these disaccharides be found in nature? If we continue to string together glucose monomers we can make long polymers or polysaccharide of starch (storage form of glucose in plants), glycogen (glucose storage form in animals), cellulose (a structural saccharide in cell walls of plants), or chitin (a glucose monomer with an amino group replacing the OH group on the #2 carbon and then this monomer interacts with another chain of saccharides via the amino groups to form a very rigid molecule found in the exoskeleton of insects or crustaceans). The carbon atoms are numbered from the position of the oxygen in the ring structure of the monosaccharide with the carbon to the right of the oxygen being designated the #1 carbon and then numbered around the ring as shown on the figure on the next page. Biology& Class Assignment 3

4 Explain how each type of carbohydrate named in the previous answer is used by a biological organism. Most carbohydrates function as an energy releasing molecule to provide energy for other cellular functions in living organisms, but some of the glucose can be used for structural purposes as well (antigens (labels) on cell surfaces, cellulose in cell walls, or chitin in exoskeletons). 5. (12) Provide the following information to describe the characteristics of a Lipid. Name the atoms found in a lipid. The atoms found in a lipid are Carbon, Hydrogen, and Oxygen but the ratio is not as balanced as the carbohydrates because lipids have less oxygen, making these molecules immiscible (will not mix or dissolve) in H 2 O. How are these atoms arranged to build a lipid? The atoms are arranged in a linear fashion to form molecules called neutral fats, phospholipids, or rings in steroids. Explain the differences between a neutral fat, a phospholipid, and a steroid by their structure. A neutral fat consists of essentially two different molecules. A glycerol (a 3C alcohol) forms the backbone to which long carbon chains (fatty acids) are attached to the OH group of each C of the glycerol. If only one fatty acid is attached to the glycerol the whole molecule is called a monoglyceride, two a diglyceride, or three a triglyceride. The fatty acids have chains of carbon atoms with hydrogen atoms attached. The fatty acid chains differ because of the length of the carbon chain (fewer than 6 carbons to longer than 22 carbons in the chains) and the number of hydrogen s attached to each carbon. If two hydrogen s are attached to each carbon in the chain and three hydrogens on the end carbon, then it is a saturated fatty acid or if two carbons in sequence are doubly bonded and have only one hydrogen attached to each carbon on either side of the double bond then it is an unsaturated fatty acid. The unsaturation between neighboring carbons causes a slight bend in the chain. If the hydrogen s across the double bond have the hydrogen s on the same side of the chain it is called a cis orientation or on opposite sides of the chain it is called a trans orientation. Neutral fats can also be classified as being either essential (meaning you have to ingest these) or non-essential (you have the gene technology to build these from other neutral fats). Biology& Class Assignment 3

5 A phospholipid has a similar appearance to the neutral fat except that one of the fatty acids is removed and replaced by a polar phosphate group and one of the fatty acids attached to the glycerol is always unsaturated while the other is saturated. This structure leaves the overall molecule with a polar head of the phospholipid (hydrophilic and can interact with water or loves water) and the non-polar fatty acid tails (hydrophobic and cannot interact with water or hates water). Steroids are ringed structures of four fatty acids chains linked together. On the outside of the rings various functional groups can be attached to give different properties or structure to the rings and therefore different functions (think about estrogen vs. testosterone effects on a body). Please see your textbook or internet for images of these molecules. Explain how each type of lipid named in the previous answer is used by a biological organism. The neutral fats have a variety of functions ranging from being used as insulation barriers, padding for delicate internal organs, building blocks for other organic molecules, or as a back-up energy source when carbohydrates are lacking (usually not a problem in our society). The phospholipids are used to build cellular barriers called membranes. Steroids are used to change the fluidity of cellular membranes or act as a building block to make a number of hormones by changing the types of functional groups attached to the steroid backbone. 6. (12) Provide the following information to describe the characteristics of a Protein. Name the atoms found in a protein. The atoms found in a protein are Carbon, Hydrogen, Oxygen, Nitrogen, and sometimes Sulfur. How are these atoms arranged to build a protein? These atoms are arranged into a monomer called an amino acid (see a in picture below) that has an amino functional group added to a central carbon on one end and a carboxylic acid functional group added to the other end. The other bonds of the central carbon are occupied by a hydrogen atom on one side and a variable group (can be a variety of attachments ranging from one single hydrogen atom to a large multi-molecular structure) on the other side (see b below). Biology& Class Assignment 3

6 The twenty or so amino acids can be categorized generally into two groups: essential or nonessential. The essential amino acids (probably eight) must be ingested in the diet of all animals, fungi, protozoans, and most prokaryotes, whereas the non-essential amino acids can be built by these organisms from precursor molecules like fatty acids or other molecules. Amino acids can also be categorized based on their overall chemical makeup. They can be categorized as being polar, non-polar, acidic, or basic, (Aside: Why don t plants, alga, and cyanobacteria have essential amino acids?) Explain the differences between the various levels of organization (primary, secondary, tertiary, and quaternary) found in a protein. The primary (1 o ) level of protein organization is simply the sequence of amino acids linked together by a non-polar covalent bond called a peptide bond to form a chain called a polypeptide or protein. The variable groups of the individual monomeric amino acids will determine the final shape of the polymeric chain. If all the side groups are of the same size and have the same chemical properties the chain should be fairly straight but with the variability of the shapes of the variable groups the chain can be curved (sort of twisted or bent) where amino acids in one position can interact with amino acids in another position to form hydrogen bonds. These hydrogen bonds between different amino acids form the basis of the secondary (2 o ) level of protein organization. This organization is described as being either in an alpha ( ) helix shape or a beta ( ) pleated sheet shape. Further bending of the chain brings the variable side groups between different amino acids of the chain in close proximity where the side groups can interact or form R-group to R-group interactions. This again locks the protein into a designated shape (Conformation) (Aside: Where does one find the information to put the amino acids into the correct sequence?) called the tertiary (3 o ) level of protein orientation. Finally, some protein chains must be combined with other protein chains to become functional. This is called the quaternary (4 o ) level of protein orientation and is held together by H-bonds, polar interactions, and other bonding forces. Biology& Class Assignment 3

7 For proteins to become functional, they must be folded into a specific shape or conformation (based on the levels above). Once folded the protein will remain in this state of function until it is placed into a situation where the homeostasis of the protein is disturbed. A number of conditions can alter the shape of a protein such as ph changes, temperature changes, chemical changes, or others. If these changes are temporary the protein may return to its functional conformation, if the change is permanent then the protein is said to have been denatured and then the protein would have to be rebuilt from scratch. (Aside: Can you eat denatured protein and still receive some benefit?) So a proteins conformation is dependent on its primary structure or amino acid sequence. Explain how proteins are used in a biological organism and what is meant by conformation and denaturation of a protein. Proteins are the most functionally varied group of all the organic molecules. Their functions range from being contractile, to storage, to defensive, to signal molecules, to transporter, to structural, and enzymatic. 7. (12) Provide the following information to describe the characteristics of a Nucleic Acid. Name the atoms found in a nucleic acid. The atoms found in nucleic acids are Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus. How are these atoms arranged to build a nucleic acid? These atoms are arranged into a monomer called a nucleotide (see a. below) that has different molecules in its structure. All nucleotides have a ribose sugar as the organizational base, with a phosphate group bonded to its #5 carbon (hanging to the side of the 4 th carbon position of the ring) of the sugar, and a nitrogenous base bonded to its #1 carbon. The sugar can be either a Ribose (in RNA) or a Deoxyribose (in DNA and has lost an oxygen fro the #2 carbon) and the bases can be guanine (G), cytosine (C), thymine (T) (only found in DNA), Adenine (A), or Uracil (U) (only found in RNA). Nucleic acids come in two forms Deoxyribose Nucleic Acid (DNA) or Ribose Nucleic Acid (RNA). To build either DNA or RNA the nucleotide monomers are linked by non-polar covalent bonds together to form the polymeric DNA or RNA which vary from each other in concentration within a Biology& Class Assignment 3

8 cell based on the answer to the last question in this series. The strands of DNA are held together by hydrogen bonds (3 between A and T and 2 between G and C) Explain the differences between Deoxyribose Nuclei Acid and Ribose Nucleic Acid. DNA RNA Strand# double singular Bases A, T, G, & C A, U, G, & C Sugars Deoxyribose Ribose Size Huge Portion copied from DNA Location Eukaryotes have in nucleus Both in the nucleus and cytoplasm Types One Three (mrna, rrna, & trna Why do we not consider prokaryotes in terms of location of their DNA versus RNA? Explain how nucleic acids are used in a biological organism. These molecules function as information storage (DNA) and retrieval molecules (RNA). The DNA (storage) houses the original plans or directions to build the products which make-up the organism, while the RNA (retrieval) is a copy of those plans which are read to actually build the products used to form the organism. In eukaryotes the strategy of keeping the DNA inside a double membrane bound nucleus allows for hopefully the maximum protection against having the original plans (DNA) being altered. Damage to the DNA sequence can happen when copying the DNA to direct the building of product (making RNA), when the cell is replicating its DNA during cellular division, or being changed due to some outside force like chemicals or radiation causing damage to the base sequences. If the RNA is built correctly but later damaged the original directions remain intact inside the eukaryotic nucleus and the damaged RNA can be dismantled and then by reading the DNA (correct directions) the correct RNA can be rebuilt to make functional product. Cool. Biology& Class Assignment 3