Unit I Study Guide - Professor: Elizabeth Feeser PDF

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Professor: Elizabeth Feeser...

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Biology 141 Study Guide – Unit I Instructions: Write out answers to each question immediately after the class meeting in which we cover each topic. Chapter 1 & BioSkills 1. How do an observation, a hypothesis, and a prediction differ? What makes a hypothesis useful for scientific investigations that try to explain the natural world? Give examples of hypotheses that are and are not scientifically useful. State the null hypothesis that corresponds to each of your examples. Observation- what you can see & directly measure Hypothesis- proposed explanation for limited observations Useful b/c they introduce original ideas to test, they specify specific relationships you will expect to see between variables, and they allow you to identify controls and variables to test Ex. Good: Squirrels’ diets consist exclusively of acorns. Null: Squirrels’ diets consist of a variety of different foods. Bad: Squirrels find acorns to be tasty. Null: Squirrels do not like the taste of acorns. Prediction- guesses about future outcomes based on hypothesis 2. What are the key steps in hypothesis testing? What are the essential characteristics of a scientific experiment? Design an experiment to test the hypothesis that squirrels prefer nuts over chicken wings. Specify which conditions should be held constant across all experiments and describe one or more controls you would include. Key steps: Create a precise/specific hypothesis & make predictions Design observational or experimental study to test predictions Essential characteristics: Control (noun)- checks for factors, other than one being tested, that might influence outcome Constant- keep experimental conditions same Replicates (more data points)- makes data & conclusions more reliable Ex. Hypothesis: squirrels prefer nuts over chicken wings Null: squirrels prefer chicken wings over nuts Control: squirrels given choice of eating just wings (100 squirrels); squirrels given choice of eating just nuts (100 squirrels) Constant: same squirrels, same time of nuts, same type of chicken wings, same type of squirrels Replicates: use the same group of 300 squirrels Experimental group: squirrels given choice of eating either wings or nuts (100 squirrels)

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3. What is the difference between a hypothesis and a scientific theory? Hypothesis is a more specific, proposed explanation, whereas scientific theory is a welltested, more broad/general explanation for various scientific phenomena. 4. What is the hypothesis of Spontaneous Generation and how does Cell Theory challenge that hypothesis? Explain the Pasteur experiment, including the purpose of the swan-necked flasks. Why did Pasteur boil the broth in both types of flasks? For each type of flasks, what is the outcome predicted by Spontaneous Generation? By Cell Theory? Spontaneous generation- living organisms arise spontaneously from nonliving matter Cell theory challenges b/c one component of theory is that all cells must come from preexisting cells Pasteur experiment- involved the use of a swan-necked flask & bacteria growth; no bacteria growth in swan-necked flask opposed to bacterial growth in regular flask disproved spontaneous generation theory Purpose of swan-necked flask is to trap bacteria in air, preventing them from getting into nutrient broth Purpose for boiling was to kill all preexisting bacteria Predictions: Spontaneous Generation: there would be bacterial growth in BOTH types of flasks Cell Theory: there would be bacterial growth in the regular flask and NO bacterial growth in the swan-necked flask 5. What observed patterns support the theory of evolution by natural selection? Be sure to define the terms evolution and population in your answer. What are the two conditions required for natural selection to occur? Overtime, the traits belonging to individuals in a population (a group of organisms that live together/exist together in the same environment) change as the overall population evolves (the gradual development/change in traits of populations of organisms over time). Traits that are more advantageous to the organisms’ overall finesses are more abundant in the population because those with disadvantageous traits are unable to reproduce as well. 2 conditions for natural selection: Differential reproduction- organisms are able to produce offspring with variable traits Heritable variation- traits much be heritable, meaning that they can be passed on from one generation to the next 6. How does artificial selection differ from natural selection? How would you artificially select for a particular characteristic? In artificial selection, humans purposefully select and breed individuals with certain traits that they find desirable. Whereas in natural selection, traits are selected naturally & randomly; in other words, randomly distributed traits that are more advantageous to certain individuals in certain environments give them a better chance of survival, therefore a better chance of reproducing and passing on their traits.

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I would choose an individual with the desired characteristic and I would breed this individual with another one of its species possessing the same desired characteristic as well, in order to increase the chances of their offspring inheriting the desired trait. 7. Explain how genotype determines phenotype. Your answer should include a description and an illustration of the flow of genetic information in a cell. Flow of Genetic Information: DNA (genotype) -> mRNA -> proteins -> traits (phenotype) An organism’s DNA, their genotype, codes for specific messenger RNAs, that code for specific proteins, that manifest as/determine specific traits possessed by the organism (its phenotype). 8. What are the similarities and differences between organisms in the three domains of life? What do the nodes and branches of a phylogenetic tree indicate? Use genetic information to generate a phylogenetic tree, and interpret information given in a phylogenetic tree. A similarity is that most organisms possess ribosomal RNA. A similarity between the domains Bacteria and Archaea is that both contain prokaryotes. A difference is that all the organisms have different ribosomal RNA sequences. A difference between Eukaryotes and the other two domains, is that Eukaryotes possess nuclei and other membrane-bound organelle while the organisms in the other domains do not. Nodes as which the tree diverges, or forks represent where common ancestors split into new species Branches in the tree indicate individual species and/or populations over time Understanding phylogenetic trees: The more similar the sequence of ribosomal RNA in organisms, the more closely related they are. Distance on the tree does NOT accurately display relationships. Use the nodes to determine how closely related two species are. For instance, although two species may be adjacent on a tree, if they do not share a common ancestor than this is an indication that they are not closely related. Nodes can be rotated, which means that all species from the same common ancestor are equally related to another specific species from another ancestor. 9. How can the independent and dependent variables in an experiment be distinguished? Given data from an experiment, plot data on a graph. Be sure to label the graph and both axes. Independent variables are those that are purposefully manipulated. The X axis on a graph Dependent variables are those that measure the effect of the manipulation of the independent variable. In other words, they change as a result of changing the independent variable. The Y axis on a graph 10. Analyze and interpret data presented in tables, graphs, or sentences. Convert data from words to figures and figures to words. Look for patterns and trends between data points. Evidence of Causation? Positive (increasing) or Negative (decreasing)?

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Chapter 2 & BioSkills 1. Define all of the bold-print vocabulary words in Sections 2.1, 2.2, and 2.5. 2.1 Element- a substance that cannot be broken down into two or more substances Atomic number- the number of protons in a single atom of an element Mass number- the sum of protons and neutrons in an atom Dalton- the unit used when measuring the masses of subatomic particles (equal to the amu) Isotopes- forms of an element with the same number of protons but a different number of neutrons (therefore different mass numbers) Atomic weight- the average of all the masses of the isotopes of a given element, based on abundance Radioactive isotopes- unstable isotopes; occur because the nucleuses of these isotopes eventually decays & releases energy (radiation) Orbitals- electrons move around nuclei in these specific regions Electron shells- contains varying specific number of orbitals, which contain electrons Valence shells- the outer electron shell of an element Valence electrons- electrons found in the valence shell Valence- the number of unpaired electrons found in the valence shell Chemical bonds- attractions that bind atoms together Covalent bonds- strong attraction where 2 atoms share electrons Molecules- substances that are held together by covalent bonds Compounds- atoms of DIFFERENT elements bonded together Electronegativity- the pulling of electrons toward the nuclei of bonded elements Nonpolar covalent- covalent bonds that involve the equal sharing of electrons Polar covalent- covalent bonds that involve the unequal sharing of electrons; formed between atoms with highly different electronegativities; creates partial charges Ionic bonds- bond between two atoms in which electrons are transferred; creates full charge Ion- an atom or molecule that carries a full charge Cation- a positively charged ion; created by loss of an electron Anion- a negatively charged ion; created by gaining an electron 2.2 Solvent- an agent for dissolving substances Solution- a homogeneous mixture of two or more substances Solute- the substances that are being dissolved Hydrogen bond- attraction between an H atom with a partial positive charge and another highly electronegative atom with a negative charge Hydrophilic- substances that interact with water through the forming of hydrogen bonds; water loving Hydrophobic- substances that do not interact with water and do not readily dissolve; water hating Hydrophobic interactions- when nonpolar molecules clump together and interact with each other due to being surrounded by water Cohesion- attraction between like molecules Adhesion- attraction between unlike molecules

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Surface tension- a cohesive force cause by the attraction between molecules at the surface of a liquid Specific heat- the amount of energy required to raise the temperature of one gram of substance by 1 degree Celsius Heat of vaporization- the amount of energy required to change 1 gram of water from a liquid to a gas Chemical reaction- the interaction of two substances that results in a new substance; the original substance cannot be restored Reactant- the initial molecules in a chemical reaction Product- the resulting molecules in a chemical reaction Chemical equilibrium- when forward and reverse reactions proceed at the same rate, the quantities of the reactants and products remains constant Mole- refers to the number 6.022e23 Molecular weight- the sum of all atomic weights of atoms in a molecule pH- the expression of the concentration of protons in a solution; pH = -log[H+] 2.5 Organic compounds- molecules that contain carbon Functional groups- critically important groups contained in organic compounds 2. How do covalent and ionic bonds differ? What type of bonds hold together biological molecules? In covalent bonds, valence electrons are shared either equally (nonpolar) or unequally (polar) between atoms; these covalent bonds hold together biological molecules (they are the strongest because biological molecules are in an aqueous environment). In ionic bonds, valence electrons are transferred between atoms. 3. What determines whether a covalent bond is polar or nonpolar? What types of atoms will form each type of bond? What impact does polarity have on biological properties? Polar covalent bonds involve the unequal sharing of electrons between atoms; atoms with extremely different electronegativities form these types of bonds. Nonpolar covalent bonds involve the equal sharing of electrons between atoms; atoms equal or relatively similar in electronegativities form these types of bonds. Polarity has a large impact on biological properties. For instance, it is involved in how certain molecules interact with one another. Elements with opposite charges tend to attract each other. This makes water a great solvent because it gives water molecules a positive end (the H atoms) and a negative end (the O atom).

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4. Interpret and draw representations of biomolecules (i.e., glucose) using molecular formulas, structural formulas, and models. What can you learn from a chemical structure? Molecular formula: C6H12O6 Structural formula: Ball & Stick Model:

Space-filling Model:

From a chemical structure, you can learn about what type of atoms are present in a molecule, how the atoms are bonded to each other, the shape of the overall molecule, and the charges or partial charges present in the molecule. 5. What type of bond is a hydrogen bond? What atoms participate in hydrogen bonds? Why are hydrogen bonds important in biology? A hydrogen bond is a noncovalent bond; partially positive hydrogen atoms and partially negative atoms (i.e. O or N) participate in hydrogen bonds. This type of bond is important in biology because it is extremely abundant, so despite the fact that it is a relatively weak bond, the sheer amount of these bonds allows them to do things such as stabilizing protein structures (secondary, tertiary, and quaternary structure) and giving water many of its life-giving properties (high specific heat and heat of vaporization, universal solvent, high surface tension, ice denser than water, etc.). 6. What types of molecules are soluble in water? What types of bonds are present in hydrophobic and hydrophilic molecules? Hydrophilic (or polar) molecules are soluble in water. In hydrophilic molecules, polar bonds are present. In hydrophobic molecules, nonpolar bonds are present.

7. Where on the pH scale do various biological compartments fall? Calculate the pH of a given solution. Acids fall on the left end of the pH scale (aka acids have a pH < 7); greater concentration of protons. Neutral solutions (like water) are in the center of the pH scale (aka neutrals have a pH = 7). Bases fall on the right end of the pH scale (aka bases have a pH > 7); lower concentration of protons.

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Equation for finding pH of a solution: pH = -log [H+] [ ] represents “concentration of …” H+ represents + charged hydrogen atoms Chapter 3 1. What role do condensation/dehydration and hydrolysis reactions play in biological processes? Condensation/dehydration reactions are involved in the bonding of monomers, like amino acids. In the polymerization of amino acids, this reaction causes the C (from the carboxyl group of one amino acid) and N (from the amino group of another amino acid) to bond covalently, resulting in the loss of a water (H2O) molecule. The type of bond formed is a peptide bond. Hydrolysis reactions are the opposite of dehydration reactions. They break apart polymers by adding H2O. 2. What determines the properties of a particular amino acid? Properties of amino acids are determined by their R group compositions (side chains). These make amino acids unique by giving them unique properties and charges (charged, polar/partially charged, and noncharged/nonpolar). How they do this, is that the molecules and atoms in the R groups interact with each other and water in different ways, causing such charges, or the lack thereof, to form. 3. Draw the chemical structure of the polypeptide Ile-Gln-Tyr-Lys. Label the side chains and peptide bonds. Explain the terms N- and C-termini and indicate each on your drawing. [NO need to memorize side chains]

N- terminus is the free amino group at the beginning of the residue chain. C- terminus is the free carboxyl group at the end of the residue chain. (charges exist in the termini because molecules are in an aqueous environment and they interact with water; amino group acts as base & gains a proton to acquire positive charge, carboxyl group acts as acid and gives away a proton to acquire negative charge)

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4. Give three examples of proteins and state the function of each. How can proteins serve such diverse functions? Antibodies: fight off/defend body from disease-causing antigens Lactase: breaks down sugar lactose so body can use for energy & nutrients Insulin: regulates glucose metabolism by controlling blood-sugar content Proteins can serve such diverse functions because of their diverse R groups, R group properties, and the subsequent folding of the proteins into unique shapes (shape determines function). 5. Explain how secondary, tertiary, and quaternary levels of structure depend on primary structure. Give an example of a how a change in amino acid sequence can alter protein structure and function. The properties of the molecules in the primary structure result in unique interactions in secondary structure (aka hydrogen bonds form between molecules in the primary structure’s backbone, resulting in either an alpha helix structure or a beta pleated sheet structure). Further folding occurs in the tertiary structure, which is dictated by the properties of the R groups in the primary structure (noncovalent bonds like hydrogen bonds, van der waals, ionic bonds, and hydrophobic reactions occur between the molecules in the R chains, causing the unique folding to occur). In the quaternary structure, multiple polypeptide chains bond together (same bonds that are present in the tertiary structure), which is again determined by the properties of the molecules in the R groups of the primary structure. Changes in amino acid sequences can alter protein structure and function. For example, in individuals with sickle cell anemia, the amino acid Glutamate, in the primary structure of the protein hemoglobin (Hb), is replaced by valine. Since these two amino acids have extremely different properties, this causes the hemoglobin protein to change shape due to differences in molecule interactions (at the secondary and tertiary levels; Hb changed from hydrophilic to hydrophobic) and therefore differences in protein folding. 6. Is protein shape fixed? Explain, citing at least one example. No, protein shape is NOT fixed. Some proteins do not even fold and/or function until certain bodily environmental conditions are met. Others change shape when specific environmental conditions are met and/or when certain substances are present in the environment. For instance, in extremely hot or acidic environments, the bonds and other molecular interactions holding the protein’s shape may be broken, therefore causing the protein to unfold (denature) and chance shape. Proteins can also naturally change shape to carry out their functions (conformation change). For instance, certain proteins remain unfolded until they need to actively perform a function. Enzymes are an example: some enzymes change shape after binding to specific substrates at their active sites or even to bind to their substrates in the first place (induced-fit: enzyme’s active site changes shape to better fit with substrate). Adenylate kinase is a good example of an “induced-fit” enzyme. 7. What is an enzyme? What is an active site? An enzyme is a special catalytic protein that helps to speed up/catalyze certain reactions An active site is the site on an enzyme in which substrates bind and react to. Chapter 5

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1. What features distinguish one monosaccharide from another? How can small changes in monosaccharide structure affect function? The placement/position and orientation of either the carbonyl group (C=O) or the hydroxyl group (O-H) are the features that help to distinguish between monosaccharides. The number of carbons present and the types of glycosidic linkages formed (either alpha or beta linkages & between which carbons) can also be a differentiating factor between monosaccharides. Small changes in...