Exam 1 study guide BIO 201 PDF

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Study Guide Exam 1 - BIO 201

EXAM 1 BIO 201 STUDY GUIDE - LECTURES 1 - 6 HOW TO STUDY FOR THE EXAM 1. The exam will be based on my PowerPoint lectures. You should study them and the notes that you took. 2. Study those sections in the book that I covered in class. If there are sections in the book that I did not cover, I will not use that information in the exam. On the other hand, you will need to know the information that I cover in lecture, even if it is not covered in the book. 3. I used certain figures from the book in my lectures. Know these figures. You might look at the books explanations of these figures and the figure legends in the book. - Sometimes I used figures from later chapters in the book. - Sometimes I used figures from sources other than the book. - You are responsible for all figures that I use. 4. Know the experiments that I talked about in class. Know the questions that were being asked and the hypotheses that were being tested. Know the experimental design, the results, and the conclusions. 5. Graphs and tables: If I went over a graph or table, be able to explain it. For a graph, what was being measured on each axis, and what was the trend that was seen. 6. There is a lot of information and details. If you just memorize details without organizing them into topics, then it is much more difficult to learn the material. The phrase, “can’t see the forest through the trees,” means that if you can’t organize the details into their logical groupings, you will miss the big picture. - Organize the information into large groupings - break the large groups into smaller groups - add the details to the smaller groups One way to do this is to create an outline of the lectures. 7. Try to identify concepts or rules that are applied throughout the set of lectures. For example: “Hydrophobic molecules do not dissolve in water.” If you can determine if a molecule is hydrophobic or hydrophilic, then you can determine if it will dissolve in water. Of course, another concept that is necessary for this analysis is the fact that water is a polar molecule. 8. I have posted a past Exam 1 in Blackboard. Initially, I do not want you to study the questions and the answers. What I want you to do, as we cover the material is the following: Read each question and write down what you need to know to correctly answer the question. There will probably be a number of things that you need to know. How do you use the things that you know to answer the question? This exercise is meant to help you understand how you are studying and learning, and what you should change in your studying techniques to improve your learning. You should be able to see what you need to know to do well on the exam. If you are not already doing so, you

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Study Guide Exam 1 - BIO 201

should modify your approaches to learning so that you incorporate these ideas into your studying. PROPERTIES OF LIFE; WHAT IT MEANS TO BE ALIVE. 1. What are the fundamental characteristics of life or of living organism? - Know these characteristics and be able to explain each one in detail - Be able to apply them to any organism or substance? - Which of the following are alive and why? - fly - fire - salt crystal - virus 2. The invention of the microscope helped give rise to the cell theory of life. - State and be able to explain this theory. 3. Since bacteria were too small to be easily detected, and since the idea of infection was not widely known or accepted, bacterial growths seemed to spontaneously arise in broth. This of course led to the theory of spontaneous generation. - State the theory of spontaneous generation. - Why was this contrary to the cell theory? - Describe Pasteur’s experiments to disprove spontaneous generation. - His experiments relied on the fabrication of a unique piece of glassware. Explain this piece of glassware and why it was so useful. EVOLUTION 1. Evolution is the change in the characteristics of a population or species over time. - Species are related by common ancestry. That means that they are genetically related. - Characteristics of species change over time - descent with modification. - The genes of the species change over time. 2. Natural selection is one of the mechanism by which the characteristics of a species and the genes of a species change over time. - Selection for the fittest or the survival of the fittest. - What is meant by fittest or fitness? - Fitness is a measure of the number of offspring that an individual produces. - The individuals that produce the most offspring are the fittest. - The fittest individuals will provide more genes to the next generation. - Those genetic changes which increase the fitness of an individual will be selected for and thus the genes or gene pool of the species will change. - Natural selection changes the characteristics of the population. 3. Natural selection involves adaptation. - Individuals that are best adapted to the current environment will tend to be fitter, that is, produce more offspring. 4. Artificial selection mimics natural selection - humans playing Mother Nature. - Corn, dogs, and broccoli were all used in class to demonstrate artificial selection. - Artificial selection mimics natural selection.

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Study Guide Exam 1 - BIO 201

5. Tree of life. Since species are related by common ancestry, and thus they are all genetically related, we can compare their genes to determine how closely related they are. These comparisons allow us to draw cladograms or phylogenetic trees that show the relatedness of species. - Primate evolution: lecture 2. If shown this slide, be able to discuss the relatedness of the different groups that are shown. Be able to identify the location of the common ancestors and most recent common ancestor of any two groups. - In general if given any phylogenetic tree, be able to discuss the relatedness of the different groups that are shown and be able to identify the location of the common ancestors of any two groups. - The three major domains of life - archaea - bacteria - eukarya 6. Scientific Nomenclature - What are the major units of length, mass, volume, and temperature used in science? - What do the abbreviations stand for? - Be able to express a unit in exponential form, e.g., 6 μm = 6 x 10-6 m = (6/1,000,000) m - Be able convert a measurement from one unit to another unit such as mg to ng. 7. Scientific method - hypothesis testing - This is one way, but not the only way that science is done. Intuition, accidents, serendipity, and wild guesses are also important in science. - Basic procedure - observe - propose questions - propose hypothesis to be tested - experiments or observations to test hypothesis - analyze data - accept or reject hypothesis - repeat the process with modified hypothesis - Example in lecture (Pasteur’s experiments) - What were the hypotheses? - How were they tested? - What were the results and conclusions? Why was one hypothesis rejected? THE CHEMISTRY OF LIFE 1. Biological evolution is an extension of chemical evolution. 2. Basic chemistry - Covalent bonds - strong bonds between atoms - provide stability to structures - Electron sharing - responsible for covalent bond formation between atoms - valence: number of unshared electrons available for bond formation - valence 1: H, Cl, Na - valence 2: O, S, Mg 3

Study Guide Exam 1 - BIO 201

- valence 3: N, P - valence 4: C - C is the most versatile atom since it can form 4 covalent bonds - Electronegativity: the ability to hold electrons - atoms with high electronegativity hold electrons tighter - O>N>C=H - If one atom hold electrons stronger than a polar bond is formed. - Bonds between C and H, and C and C are nonpolar - equal sharing of electrons. - Electron sharing continuum: Lect. 3: 23 - Ways of displaying a chemical structure: Lect. 3: 18 3. Properties of water support life - water is polar because of two characteristics - two polar H-O bonds - the two bonds are at an angle less than 180o - water can form hydrogen bonds - hydrogen bonds with other water molecules: cohesive - hydrogen bonds with polar molecules (hydrophilic molecules): adhesive - does not hydrogen bond with nonpolar molecules (hydrophobic molecules) CHEMISTRY OF LIFE 1. Importance of Carbon in life - chemically versatile - can form 4 bonds - can form linear and cyclic molecules - can form polar and nonpolar, uncharged and charged molecules. - common groups that can bond with carbon: Table 2-3 2. Macromolecules of life - carbohydrates (polysaccharides) - lipids (not covered on Exam 1) - proteins - nucleic acids 3. For each of the macromolecules, -know the structures - subunits used to make each macromolecule - functions CARBOHYDRATES 1. Common carbohydrates - sugars: mono and disaccharides, e.g., glucose, fructose, sucrose, lactose - large polysaccharides: e.g., cellulose, glycogen, chitin, starch, peptidoglycan 2. Major functions - energy storage - structure - cell identity 3. polysaccharides are polymers of monosaccharides

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Study Guide Exam 1 - BIO 201

- condensation reaction to add a monosaccharide - basic structure of a monosaccharide - formula: (CH2O)n - nomenclature: prefix + ose; e.g., triose, pentose, hexose - OH (hydroxyl) and CHO (carbonyl) groups make sugars polar and hydrophilic. - common pentoses and hexoses exist as ring structures 4. Energy storing carbohydrates - carbohydrates as a source of energy - polymers of glucose - Starch (plants), glycogen (animals) - α-glycosidic linkages: easy to break; necessary for quick glucose production - When are these carbohydrates hydrolyzed to produce glucose for energy? - Plants: fruit ripening; - fruit becomes sweet and soft (starch also adds stiffness to the fruit) - amylase hydrolyzes starch - Animals: any time of high-energy needs - phosphorylase hydrolyzes glycogen 5. Structural polysaccharides - major roles in adding strength and stability - cell walls of plants, bacteria, and fungi - exoskeletons of arthropods (insects and crustaceans) - β-glycosidic linkages: difficult to break; important for strength and stability - long linear strands of polysaccharides held together by chemical bonds - hydrogen bonds: cellulose and chitin - covalent bonds: peptidoglycan 6. Cell-identity polysaccharides – Fig. 5.6 - part of glycoproteins - oligosaccharides (short polysaccharides) attached to proteins - protein portion spans the cell membrane - oligosaccharide portion sticks out on the surface of the cell - cell-surface antigens - displayed on the surface of cells - diversity of polysaccharides give cell types unique identities - an example: ABO blood system -type A: A glycoprotein - type B: B glycoprotein - type AB: A and B glycoproteins - type O: neither glycoproteins - Use this information to determine which blood types each blood type can safely get transfusions from. - Remembering that we normally do not make antibodies to our own antigens, what antibodies (anti-A, anti-B) will persons of each blood type make? - What antigens will the universal donor have on its red blood cells? - What antibodies will the universal recipient produce?

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Study Guide Exam 1 - BIO 201

LIPIDS 1.What are lipids? - Large carbon-based molecules that share the property of being highly insoluble in water. - Not as large as the other macromolecules. - Not polymers of repeating subunits like other macromolecules. - Three major groups: fats, steroids, phospholipids 2. Fats - Energy storage: gram per gram higher than carbohydrates - Structure: triglyceride - glycerol + 3 fatty acids - fatty acid structure - carbonyl group: acid - long hydrocarbon chain: fatty - ester linkage between glycerol and fatty acids - long hydrocarbon chains give the fat its properties - non-polar, hydrophobic - the longer the chain, the higher the hydrophobic interactions and the more stable (solid) the fat - degree of saturation with H - saturated: maximum C-H bonds - high hydrophobic interactions; increase stability - usually solid at room temperature - unsaturated: less than maximum C-H bonds - more C=C double bonds; normally in the cis configuration - lower hydrophobic interactions; decreased stability - polyunsaturated fats are usually fluid at room temperature – oils - trans-unsaturated fats - man made in food industry - behave like saturated fats: high hydrophobic interactions, high melting temp - Use beeswax, butter, and safflower oil to discuss the properties that determine the differences in solidity of these fats. 3. Steroids - Basic structure

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Study Guide Exam 1 - BIO 201

- 4 ring structure - side groups added to the ring distinguish different steroids - Functions - cholesterol: part of animal cell membranes - hormones: control cell and organ functions and development 4. Phospholipids - Structure - glycerol + 2 fatty acids + phosphate - compare to structure of fats - has both a hydrophilic head and a hydrophobic tail - Amphipathic - The dual nature of the structure of phospholipids determines how they interact with water and the structures that they form in water. - hydrophilic head hydrogen bonds with water - hydrophobic tails interact with themselves and are sequestered from water. - micelles and lipid bilayers are formed - Lipid bilayers - The basic structure of a cell membrane - Lipid bilayers can rearrange into liposomes. - minicells Proteins 1. Proteins are polymers of amino acids. - condensation or dehydration reaction to add a monomer to a growing polymer - amino acid structure - know the basic structure; be able to draw it - R groups; side group; determine properties of the amino acid - Be able to apply electronegativity rule to determine polarity and solubility of amino acid R group in water - do not need to memorize the structure of the R groups, but you should be able to determine if it is polar or nonpolar, charged or uncharged, acidic or basic, hydrophilic or hydrophobic. 2. Primary structure of a protein - sequence of amino acids from N terminus to C terminus - Be able to identify N and C termini if given a structure - Peptide bond formation: be able to draw the formation of a peptide bond; Fig. 3.5 3. Secondary structure of a protein - hydrogen bonding between amino acids - Two different types of secondary structures: Fig. 3.10 - α-helix: forms a cylinder - β-sheet: forms a flat sheet 4. Tertiary structure of a protein - flexibility of the bonds in the primary structure allows proteins to fold into many shapes - additional hydrogen bonding, hydrophobic interactions, and sometimes disulfide bonds and ionic bonds stabilize the tertiary structure: Fig. 3.11a - this is the active structure of most proteins.

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Study Guide Exam 1 - BIO 201

5. Quaternary structure - some proteins bind to other proteins to form a quaternary structure 6. Changes in the structure of a protein can drastically alter its activity - e.g., sickle cell anemia - single amino acid change in the primary structure: glutamic acid to valine - Tertiary and quaternary structures change as a result, and the final shape of hemoglobin and the function of hemoglobin changes - Long hemoglobin quaternary structures cause the cell the sickle NUCLEIC ACIDS (The extent of the material will depend on how far I get in Lecture 6.) 1. There are two major types of nucleic acids - DNA: deoxyribonucleic acid - RNA: ribonucleic acid - Deoxyribo and ribo refer to the type of sugar found in DNA and RNA, respectively. Nucleic refers to the fact that nucleic acids were first isolated from cell nuclei. Acid refers to the acid nature of nucleic acids, caused by the phosphate groups. 2. Nucleic acids are polymers of nucleotides - know the structure of a nucleotide. - deoxyribose or ribose: Be able to draw the structure of the sugar showing the location of the carbons - phosphate group: Be able to draw the structure of a phosphate. Which carbon of the sugar is the phosphate attached to? - nitrogenous base - purines: adenine and guanine - pyrimidines: cytosine, thymine (DNA), uracil (RNA) - Do not need to know the exact structure of the bases. - know the differences between the structure of a ribonucleotide and a deoxyribonucleotide. - know the differences between the structure of RNA and DNA. 3. Primary structure of a nucleic acid - linear sequence of nucleotides connected by phosphodiester bonds - The phosphodiester bond. Know this structure. - Nucleotides in nucleic acids are linked by phosphodiester bonds - Bond is between the 5' C of one sugar and the 3' C of the adjacent sugar - condensation reaction - Sugar-phosphate backbone with nitrogenous bases sticking out - Directionality or orientation of the nucleic acid primary structure - 5'end: free phosphate attached to a 5' C - 3' end: free hydroxyl (OH) attached to a 3' C 4. Secondary structure of a nucleic acid - hydrogen bonding between bases - A hydrogen bonds with T (DNA) or U (RNA) - C hydrogen bonds with G - DNA: intermolecular hydrogen bonding; two strands of DNA - RNA: intramolecular hydrogen bonding: one strand of RNA 5. Secondary structure of DNA 6. RNA secondary structure

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Study Guide Exam 1 - BIO 201

- intramolecular hydrogen bonding - hairpin, stem-loop structures 7. RNA has a tertiary structure caused by folding of the molecule; DNA does not 8. RNA molecules can form quaternary structure by hydrogen bonding between different RNA molecules. 9. RNA is structurally and functionally more diverse than DNA. 10. RNA and DNA compare and contrast 11. Both RNA and DNA can be self-replicating molecules

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