Exam #1 Review General Study Suggestions: 1) Begin by reviewing your lecture notes. If there is anything that you do not understand, make an appointment with me, attend office hours or review the content in your book. 2) Next, carefully review the questions that we discussed during lecture and the homework questions. **The exam questions will be similar to the homework questions! 3) Finally, go through this review as it may serve as a reminder of the overarching content of the exam. Format and composition: There will be 25 multiple choice questions. These are followed by 7 - 8 short answer, matching or fill-in-the-blank questions worth 10 points a piece. All students must answer #26 regarding Gram-positive and Gram-negative cell wall structure. Then, choose to answer any four of the remaining questions. Circle the questions that you would like to answer. Topics covered by these free response questions: - Application/implication of microbiology - Macromolecules - The cell membrane / transport - Vocabulary (macromolecules / cell components) - Basic cell structure and function The exam is worth 100 points. Your overall score will be determined in one of two ways depending on which leads to the highest overall total: 1) Multiple Choice Score * 2 + Free Response Score 2) Multiple Choice Score + Free Response Score * 1.5 All of the following is in your notes but here it is in review format: Microbiology is the study of life forms and agents that are too small to be seen with the unaided eye. Although humans utilized microorganisms to make bread and beer as early as 2100 B.C., it was not until 1673 that Antony van Leeuwenhoek, using a handcrafted microscope, viewed and thoroughly described these tiny organisms which he called “animalcules”. I. The origin of microorganisms (lecture #1) A. Scientists struggled for over a hundred years to reject the idea of spontaneous generation and support the idea that all forms of life arise from other living things of the same kind (biogenesis). Be familiar with all the scientists involved in this debate and understand their contributions. Practice: The idea of spontaneous generation postulated that a. organisms could evolve into the next generation of organisms. b. organisms could spontaneously combust. c. organisms could spontaneously arise from other living organisms. d. living organisms could arise from nonliving material. B. Review and understand Koch’s Postulates! II. Microbiology: Implications and Applications (lecture #1) A. Fixing nitrogen, replenishing oxygen and degradation (decomposition) are essential (vital) activities of microorganisms. B. Microorganisms also have a very big economic impact. Practice: Microorganisms are involved in a. Food production b. Food preservation c. Production of vaccines d. Production of antibiotics e. All of the above C. Bioremediation - The use of microorganims to clean up waste (e.g. degrade oil spills, detoxify compounds that are harmful to the environment). D. Genetic Engineering = Introduction of genes from one organism into another to give it new features or abilities. E. Medical Microbiology = The study of disease-causing microorganisms (called pathogens). 1. In 1906, the three leading causes of death were infectious diseases (cdc.gov) Now, many infectious diseases have been eradicated. 2. Despite the eradication of many infectious diseases we must fight newly emerging diseases, the resurgence of old diseases and microorganisms that are becoming resistant to current treatment techniques. We are also just beginning to understand that many conditions, such as peptic ulcers, are caused by bacteria and cancers, such as cervical cancer, are caused by viruses. Practice: Which of the following is a reason for the resurgence of old diseases? a. A decline in the vaccination of children b. An increase in international travel c. both a and b d. none of the above F. **Despite the disease-causing potential of some microorganisms, most microorganisms are not pathogenic. In fact, those covering our body play a protective role by competing with pathogenic microbes.** G. Bacteria are good model organisms for study. Why? III. Macromolecules (proteins, carbohydrates, nucleic acids and lipids) *Be sure to review and understand the game questions for this section. A. Proteins Practice: Which one of the following is NOT a protein function? a. Transporting molecules from one location to another. b. Coordinating motion. c. Providing the genetic code for all of a cell’s properties. d. Providing mechanical support in eukaryotic cells. 1. Proteins are composed of 20 standard amino acids. Be familiar with the general structure of an amino acid (central carbon, amino group, carboxyl group, hydrogen atom and an R-group.) *Be able to recognize the names and abbreviations (both 3- and 1-letter) of these amino acids. I will provide the table with amino acid structures but I will not provide 1-letter abbreviations or information regarding the nature of the R group. Thus, be familiar with how amino acids are categorized according to the nature of their R group. 2. The amino acids are linked together by peptide bonds to form polypeptide chains. Each amino acid in a polypeptide chain is called a residue. Practice: What molecule is lost in the formation of a peptide bond? 3. Proteins have three or four levels of structure. The genetically determined sequence of their amino acids (e.g. Ile-Gly-Met-Phe...) is their primary structure. The regularly repeating structures (e.g. alpha-helix, beta-sheet and beta-turn) into which the polypeptide chain folds is called the secondary structure. The regularly repeating structures fold upon themselves to give a protein an overall 3- d structure called the tertiary structure. If a protein has more than one polypeptide chain, the way in which these chains arrange themselves with respect to one another is called the quaternary structure. Practice: The helices and sheets of amino acids form a protein’s a. primary structure b. secondary structure c. tertiary structure d. quaternary structure What does it mean if a molecule/structure is amphipathic? ANSWER: Amphipathic molecules have a dual nature. B. Carbohydrates Carbohydrates function as a source of carbon and energy (both immediate and reserve). They are components of cell walls (glycoproteins and glycolipids) and some external cell structures (capsule/slime layer). 1. Monosaccharides = simple sugars (glucose, fructose and galactose - 6 carbon monosaccharides, ribose - 5 carbon monosaccharide) *Be familiar with the structure of glucose and the reaction by which it forms a ring structure. Be familiar with how the carbon atoms are numbered in glucose. Practice: Are monosaccharides likely water soluble? 2. Disaccharide (two sugars) - maltose, lactose, sucrose. Monosaccharide subunits are joined by a glycosidic linkage. Practice: What molecule is lost in the formation of a glycosidic linkage? 3. Oligosaccharides (short chains (2 to 10) of sugars) 4. Polysaccharides (long chains of sugars that often have branches (e.g. glycogen)) *Glycosidic linkages in straight chain polysaccharides are 1,4 (between the 1st and the 4th carbon). Branched polysaccharides also have 1,6 glycosidic linkages. Practice: Which is/are TRUE of carbohydrates? a. They may serve as a source of food. b. They are hydrophilic. c. They may be bonded to proteins to form glycoproteins. d. They are a component of some bacterial capsules. e. all of the above. Practice: What is the basic difference between cellulose and glycogen? C. Nucleic Acids 1. DNA and RNA - composed of nucleotides which are composed of a 5 carbon sugar, a nitrogenous base and a phosphate group. Practice numbering the carbon atoms on the 5-carbon sugar. Why are these numbers so important to understanding the structure of not only nucleotides but the nucleic acids which they form? Practice: DNA contains a. sugars b. 3’-5’ phosphodiester bonds c. triacylglycerols d. peptide bonds e. c and d 2. Bases Purines - adenine and guanine (double-ring structure) Pyrimidines - cytosine, thymine and uracil (single ring) Practice: Which of the following is found in RNA but not in DNA? a. adenine b. cytosine c. thymine d. uracil 3. In nucleic acids, the nucleotide subunits are bound covalently (the 5’ phosphate binds to the 3’ hydroxyl). This linkage is termed a 3’-5’ phosphodiester linkage. 4. Covalent bonding of many nucleotides forms a single strand of nucleotides which, in DNA, then binds to a complementary strand via hydrogen bonds. The complementary strand runs in the opposite direction (antiparallel) to the first strand. Together they form a double-stranded helix. a. A single strand of nucleotides joined by 3’-5’ phosphodiester bonds always has polarity/directionality. It always has a 3’ end and a 5’ end. b. When the H-bonds that hold the two strands of DNA together are broken, this is called denaturation or melting. c. **If given a DNA sequence, be sure that you understand how to determine its correct complimentary sequence!! D. Lipids Practice: Which is/are TRUE about lipids? a. They are a major structural component of all cell membranes. b. They can serve as energy stores. c. They function in cell signaling and recognition. d. All of the above. 1. Triacylglycerols, steroids, sterols, waxes and phospholipids *Know the basic structure of a triacylglycerol **Be able to recognize the structure of a phospholipid. 2. ALL CELL MEMBRANES ARE SEMIPERMEABLE PHOSPHOLIPID BILAYERS. Know how phospholipids come together to form a PL bilayer. Be able to draw and label the hydrophilic and hydrophobic portions of a phospholipid bilayer. Practice: Why are fats (triacylglycerols) packed with power? IV. Classification and Nomenclature A. Domains Practice: Which of the following is/are not domains into which all living organisms can by classified? a. Helminths b. Bacteria c. Archaea d. Eucarya 1. Members of the domain Bacteria and Archaea are prokaryotes, they vary in size but are often 0.3 to 2 micrometers; they are single-celled and have no membrane-bound nucleus or organelles.