Bio 111 Study Guide Chapter 3 – Carbon and the Molecular Diversity of Life

BEFORE CLASS: Reading:

• Read the introduction and Concept 3.1 for some good background on organic chemistry. Pay attention to Figure 3.6. You’ll need to be able to recognize the functional groups and some of their properties.

• Most of the rest of the chapter focuses on the four major categories of macromolecules.

• There are several really important figures about proteins. Figure 3.17 shows examples of functions of proteins. We’ll go in more depth of each of these functions as the semester progresses, but get a general idea for now. For Figure 3.18, take a look at the R groups just to see the variety and their general properties. Figure 3.22 depicts one of the most important concepts in this chapter – the four levels of protein structure. Spend time studying it and reading the text.

• Concept 3.7 is about genomics and proteomics; it gives several interesting applications of these fields.

Definitions: organic molecule –

macromolecule –

hydrocarbons –

isomers – structural isomers – cis-trans isomers – enantiomers –

functional groups –

adenosine triphosphate (ATP) –

polymer –

monomer –

dehydration reaction –

hydrolysis –

carbohydrate –

monosaccharide –

disaccharide –

glycosidic linkage –

polysaccharide –

lipid –

fat –

fatty acid –

saturated fatty acid –

unsaturated fatty acid –

trans fat –

phospholipids –

steroids –

ester linkage –

polypeptide –

protein –

amino acid –

peptide bond –

α helix –

β pleated sheet –

hydrophobic interactions –

disulfide bridges –

denaturation –

gene –

nucleic acids (polynucleotides) –

nucleotides –

genomics –

proteomics –

Questions: 1. Name at least three carbon-based molecules that you know (specific names or general categories). 2. Write the molecular formula for each of the following functional groups:

Hydroxyl –

Carbonyl – Carboxyl – Amino –

Sulfhydryl – Phosphate – Methyl –

3. What are the four major classes of macromolecules in living organisms? 4. List the type(s) of bonding involved at each level of protein structure:

primary – secondary – tertiary – quaternary –

RET Gene Case Study: We will be examining a case study throughout this semester involving the RET gene and the protein it makes. We will talk about different aspects of the gene and protein as it becomes relevant to the content in class. In the most general terms, the RET gene codes for a receptor protein found in some cell membranes.

DURING CLASS: Organic Molecules Carbon atom – DRAW a carbon atom. (Atomic number is ____.) Isomers Structural – cis-trans – Enantiomers – Major Functional Groups Hydroxyl – Carbonyl –

Carboxyl – Amino – Sulfhydryl – Phosphate – Methyl – ATP (adenosine triphosphate) Macromolecules Polymer – Monomer – Dehydration reaction –

Hydrolysis – Animation – Polymers Carbohydrates Description – Functions – Monosaccharides – Disaccharides – Polysaccharides –

Lipids Description – Functions – Fatty Acids – Fats – Phospholipids – Steroids – Proteins Description – Functions – Amino Acids –

Polypeptide – Protein – Four Levels of Protein Structure: *Primary – *Secondary – *Tertiary – Quaternary –

RET Gene Case Study: The V804L mutation is the mutation in the RET gene that we’ll be studying in class. The name of the V804L mutation comes from the fact that it should be an amino acid Valine at codon position 804 but instead, it is a Leucine because of the mutation. 1. Look at the chemical structure of the amino acids valine and leucine in Figure 3.18. What differences are there? 2. With a leucine in the place where a valine should be, what effects on the protein’s structure do you think might happen? 3. Do you think this might be a mild, moderate, or severe mutation?

Protein Denaturation – Protein Folding – Nucleic Acids Description – Functions – Nucleotides – DNA Double Helix – Compare and contrast DNA and RNA in a Venn diagram. Genomics and Proteomics **Take Away Concept** All of these biological molecules play important roles in the basic functioning of each and every cell of a living organism.

AFTER CLASS: Questions/Problems: 1. Some scientists think that life elsewhere in the universe might be based on the element silicon, rather than carbon. Look at the electron distribution diagram for silicon in Figure 2.7 in your textbook. What properties does silicon share with carbon that would make silicon-based life more likely than neon-based life or aluminum-based life? Can you think of any problems or limitations with the idea of silicon-based life? 2. Explain why isomers are important to understand when working with living organisms. 3. Fill in the table below about the important functional groups in living organisms. 4. Draw a molecule of ATP, making sure to label the important parts.

Functional Group Molecular Formula

Names and Characteristics of Compounds Containing this Group

5. Draw a dehydration reaction that will form a peptide bond (use the shorthand way showing only necessary functional groups or atoms involved in the reaction). Label the peptide bond. 6. Draw how hydrolysis would affect a molecule of sucrose (use rings for the sugar monomers). Label them, and show the functional groups involved. 7. Fill in the table below.

8. What do all the examples of polysaccharides that we talked about in class have in common? What is the main thing that is different about them?

Organic Molecule

Building Block(s) Name of

Covalent Bond Function(s) Examples

Carbohydrates

Lipids

Proteins

Nucleic Acids

9. Fill in the blanks:

A. The group of macromolecules called ___________________ store genetic information.

B. In order for a cell to produce a triacylglycerol, it must have one molecule of ________________ and three _________________.

C. Sucrose is a disaccharide made of two monosaccharides: _______________ and ________________.

D. A group of molecules whose structure vary but all are hydrophobic are the _______________.

E. A protein may become ___________________ if its environment gets too acidic, too hot, or has a lot of ions in it.

10. Describe the four structural levels in the functional shape of a protein. 11. Label the three parts of this nucleotide. 12. The RET gene mutation in our case study alters or could alter which level(s) of protein structure? a. primary b. tertiary c. secondary d. all of the above e. primary and tertiary structures only