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Steph’s Book By: Stephanie A. Diaz Introduction Scientist is defined as “one learned in science; a scientific investigator; one devoted to scientific study; a savant.” In some aspects I fall under this category. I’ve never believed that something is correct just because someone told me. Everything has a reason, and I’ll go to great length to prove that there is reason behind every fact even those that people have a hard time believing, not everything is a “miracle”. My future goals in life are to graduate with honors, and continue my studies in medicine at the University of Miami in the infectious infection department. Then what ever occurs afterwards, I’ll let destiny choose my path. Education is what everyone needs to survive in today’s society. It doesn’t have to necessarily be book smarts, but have knowledge in some form. Some people are utter genius, however, there is no way they could ever drive a car, or ever have enough courage to ask for a raise or advancement. So they’re many different levels of education and knowledge. Not saying the words “I do” are the words that motivates me to challenge myself. I never want to say those words because I got pregnant, or there is no way I could support myself so I would have to say those 2 little words just to survive. “I don’t” Chapter 1 Briefly describe unifying themes that pervade the science of biology. N/A Diagram the hierarchy of structural levels in biology. http://occawlonline.pearsoned.com/bookbind/pubbooks/campbell_awl/cha pter1/medialib/0110.jpg Explain how the properties of life emerge from complex organization. It’s merely accents the importance of structure arrangement and applies to inanimate material as well as to life. Describe seven emergent properties associated with life. A. Order B. Reproduction C. Growth and development D. Energy Utilization E. Response to the environment F. Homeostasis G. Evolutionary Adaptation Explain how technological breakthroughs contributed to the formulation of the cell theory and our current knowledge of the cell. A Powerful instrument called the electron microscope has reveled the complex structure of cells. It showed that all cells are enclosed be a membrane that regulates the passage of materials between the cells and it’s surrounding. Distinguish between prokaryotic and eukaryotic cells. Prokaryotic- The DNA is not separated from the rest of the cell into a nucleus. They also lack the cytoplasmic organelles typical of eukaryotic cells. Almost all prokaryotic cells have tough external cell walls. Eukaryotic- By far are more complex, is subdivided by internal membranes into many different functional compartments, or organelles. The DNA is organized along with proteins into structures called chromosomes contained within a nucleus, the largest organelle of most cells. Explain, in their own words, what is meant by "form fits function." Depending what the object is possible of is what it can achieve. As in, a bird’s build makes flight possible. The correlation between structure and function can apply to the shape of an entire organism. List the five kingdoms of life and distinguish among them. Monera- The simpler structure of the prokaryotic cell distinguishes bacteria from the eukaryotic kingdoms Protista- Consists of unicellur eukaryotes and their relatively simple multi-cellular relatives. Plantae- Consists of muticellular eukaryotic that carry out photosynthesis. Fungi- Is defined, in part, by the nutritional mode of its members, organisms that absorb nutrients after decomposing organic refuse. Animalia- Consists of multicellular eukaryotes that ingest other organisms. Outline the scientific method. A. Question B. Hypothesis C. Experimental Design D. Collecting data E. Analyze data F. Interpretation G. Write it up Distinguish between inductive and deductive reasoning. N/A Explain how science and technology are interdependent. Technology, especially in the form of new instruments (electrons microscopes, for examples), extends our ability to observe and measure and enables scientist to work on questions that were previously unapproachable. Chapter 2 Define element and compound. Element- Any substance that cannot be broken down to any other substance. Compound- A chemical combination, in a fixed ratio, or two or more elements. State four elements essential to life that make up 96% of living matter. Carbon, Oxygen, Hydrogen, and Nitrogen Describe the structure of an atom Neutrons, Protons, and electrons. Neutrons and protons are packed together tightly to form a dense core, or nucleus, at the center of the atom. The electrons move about this nucleus at nearly the speed of light Define and distinguish among atomic number, mass number, atomic weight, and valence. Atomic Number- number of protons in the nuclei Mass Number- the sum of protons plus neutrons in the nucleus of an atom Atomic Weight- The total atomic mass, or mass number Valence- Bonding capcity Given the atomic number and mass number of an atom, determine the number of neutrons. Subtracting the atomic number and mass number Explain the octet rule and predict how many bonds an atom might form. N/A Define electronegativity and explain how it influences the formation of chemical bonds. The attraction of an atom for the electrons of a covalent bond. The more electronrgative an atom, the more strongly it pulls shared electrons itself Distinguish among nonpolar covalent, polar covalent and ionic bonds. Nonpolar covalent- electrons are shared equally Polar covalent- If one atom is more electronegative than the other, electrons are share equally Ionic bonds-attraction between cations and anions Describe the formation of a hydrogen bond and explain how it differs from a covalent or ionic bond. It occurs when a hydrogen atom covalently bounded to one electronegative atom also attracted to another electronegative atom. Examples 1. Science as a process- Scientific method; Question, Hypothesis, experimental design, collecting data, analyze data, interpretation, write it up. 2. Evolution- How men transformed from apes to humans 3. Relationship of Structure to Function- Birds can fly, on account of, the shape of their wings, and body. 4. Interdependence in Nature- Everything in nature is dependant on each other, as in, soil feeds flower, flower feeds animal, animal’s wastes feeds soil, so on , and so on. 5. Science, Technology, and Society- Biology, Microscope, Educated Chapter 3 Describe how water contributes to the fitness of the environment to support life. All organisms familiar to us are made mostly of water and life in a world where water dominates climate and, many other features of the environment. Most cells are surrendered by water, and cells contain from 70% to 95% water. Describe the structure and geometry of a water molecule, and explain what properties emerges as a result of this structure. Water is an excellent solvent (The dissolving agent of a solution. Water is most solvent known). Water has a high heat capacity (The degree to which substance changes temperature in response to a gain or loss of heat). Water has a strong cohesion (The attraction between like substances), and high surface tension (A measure of how difficult it is to stretch or break the surface of a liquid). Water adheres (The attraction of unlike substance) to other molecules. Explain the relationship between the polar nature of water and its ability to form hydrogen bonds. Hydrogen bonds are weak bonds between molecules. They form when a positively charged hydrogen atom in one covalently bonded molecules is attracted to a negatively charged area of another covalently bonded molecule. In water, the positive pole around a hydrogen atom forms a hydrogen bond to the negative pole around the oxygen atom of another water molecule. List five characteristics of water that are emergent properties resulting from hydrogen bonding. 1.Solvent 2.Heat capacity 3.Cohesion 4.Surface tension 5.Adhesion Describe the biological significance of the cohesiveness of water. Cohesion due to hydrogen bonding contributes to the transport of water against gravity in plants. Explain how water's high specific heat, high heat of vaporization and expansion upon freezing affect both aquatic and terrestrial ecosystems. N/A Explain how the polarity of the water molecule makes it a versatile solvent. N/A Write the equation for the dissociation of water, and explain what is actually transferred from one molecule to another. H2O = H+ + OH- Explain the basis for the pH scale. The pH scale compresses the range of H+ an OH- concentrations by employing a common mathematical device: logarithms Examples 1. Science as a process- The dissociation of water 2. Evolution- Waters hydrogen bonding 3. Relationship of Structure to Function- Surface tension allowing “walking on water” 4. Interdependence in Nature- Humans are made up of 70% to 95% of water 5. Science, Technology, and Society- Chemistry, pH scale, Acid Chapter 4 Explain how carbon’s electron configuration determines the kinds and number of bonds carbon will form. Carbon has a total of six electrons, with two in the first electron shell and four in the second shell. Having four valence electrons in a shell that holds eight, carbon has little tendency to gain or lose electrons and form ionic bonds; it would have to donate or accept four electrons to do so. Instead, a carbon atom completes its valence shell by sharing electrons with other atoms in four covalent bonds. Each carbon atom thus acts as an intersection point from which a molecule can branch off in up to four directions. This to travel is one factor of carbon’s versatility that makes large, complex molecules possible. Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules. The skeleton vary in length and may be straight, branched, or arrange in closed rings. Some carbon skeletons have double bonds, which vary in number and location. Such variation in carbon skeletons is one important source of the molecular complexity and diversity that characterize living matter. In addition, atoms of other elements can be bonded to the skeletons at available sites. Recognize the major functional groups, and describe the chemical properties of organic molecules in which they occur. 1.Hydroxly Group (-OH) 2.Carbonyly Group (=CO) 3.Carboxyl Group (-COOH) 4.Amino Group (-NH2) 5.Sulfhydryl Group (-SH) 6.Phosphate Group (H3PO4) Examples 1. Science as a process- The balance of chemicals 2. Evolution- How things are not destroyed, but just rearranged 3. Relationship of Structure to Function- Carbons is very versatile 4. Interdependence in Nature- Nothing can be destroyed or made up 5. Science, Technology, Society- Organic Chemistry, Atom, People Chapter 5 List the four major classes of biomolecules. 1.Carbohydrates 2.Lipids 3.Proteins 4.Nucleic Acid Describe how covalent linkages are formed and broken in organic polymers. When a bond forms between two monomers, each monomer contributes part of the water molecule that is lost; one molecule prvides a hydroxyl, while the other provides hydrogen. To make a polymer, this condensation reaction is repeated over and over as each monomer is added to the chain. The cell must expand energy to carry out these condensation reactions, and the process occur only with the help of enzymes, specialized proteins that speed up chemical reactions in cells. Polymers are dissembled to monomers by hydrolysis, a process that essentially the reverse of Condensation. Describe the distinguishing characteristics of carbohydrates, and explain how they are classified. Carbohydrates include sugars and their polymers. Monosaccharides- They generally have molecular formulars that are some multiple of CH2O Disaccharide- Double sugars, consists of two monosaccharides joined by a glycosidic linkage, a covalent bond formed between two monosaccharides. Polysaccharides- They are polymers in which a few hundreds to a few thousands monosacchharides are linked together. Identify a glycosidic linkage and describe how it is formed. A covalent bond formed between two monosaccharides. For example, maltose is a disaccharide formed by linking two molecules of glucose. Describe the important biological functions of polysaccharides. Some polysaccharides are strong material, hydrolyzed as needed to provide sugar for cells. Other polysaccharides serve as building material for structures protecting the cell or the whole organism Explain what distinguishes lipids from other major classes of macromolecules. They have little or no affinity for water. The hydrophobic behavior of lipids is based on their molecular structure. Although they may have some polar bonds associated with oxygen, lipids consist mostly of hydrocarbon. Three important families of lipids are fats, phospholipids, and steroids. Describe the unique properties, building block molecules and biological importance of the three important groups of lipids: fats, phospholipids and steroids. Fats- Are large molecules, but they are not polymers. A fat is constructed from 2 kinds of smaller molecules; glycerol and fatty acids. Phospholipds- Are structurally related to fats, but they have only 2 fatty acids rather than three. Steriods- Are lipids characterized by a carbon skeleton consisting of four interconnected rings. Describe the characteristics that distinguish proteins from the other major classes of macromolecules, and explain the biologically important functions of this group. Proteins account for more than 50% of the dry weight of most cells, and they are used for structural support, storage, transport of other substances, signaling from one part of the organism against foreign substance. List and recognize four major components of an amino acid. 1.Hydrogen Atom 2.Carboxly Group 3.Amino Group 4.Asymmetric Carbon Explain what determines protein conformation. The complex architecture of a protein, we can recognize three superimposed levels of structure, known as primary, secondary, and tertiary structure. A fourth level, quaternary structure, occurs when a protein consists of two or more polypeptide chains. Define primary structure Is it’s unique sequence of amino acids. Describe the two types of secondary protein structure N/A Explain how weak interactions and disulfide bridges contribute to tertiary protein structure. N/A Describe quaternary protein structure. Is the overall protein structure that results from the aggregation of these polypeptide subunits. Define denaturation and explain how proteins may be denatured. A process in which a protein unravels and loses its native conformation, there by becoming biologically inactive. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature. Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules. A biological molecule that allows organisms to reproduce, polymers composed of monomers called nucleotides joined by covalent bonds between the phosphate of one nucleotide and the sugar of the next nucleotide. Summarize the functions of nucleic acids. N/A List the major components of a nucleotide. 1.Pyrimidine 2.Purines Distinguish between a pyrimidine and a purine. Pyrimidine- Is characterized by a six-membered ring made up of carbon and nitrogen atoms. Purines- Are larger, with the six-membered ring fused to a five-membered ring. List the functions of nucleotides. N/A Briefly describe the three-dimensional structure of DNA. The DNA molecule is usually double-stranded, with the sugar-phosphate backbone of the polynucleotides on the outside of the helix. In the interior are pairs of nitrogenous bases, holding the two strands together by hydrogen bonds. Example 1. Science as a process- The different types of structurs 2. Evolution- The DNA 3. Relationship of Structure to Function- The Double Helix 4. Interdependence in Nature- Biomolecules 5. Science, Technology, Society- Organic biology, RNA, DNA Chapter 6 Explain the role of catabolic and anabolic pathways in the energy exchanges of cellular metabolism. Catabolic pathways release energy by breaking down complex molecules to simpler compounds and anabolic pathways consume energy to build complicated molecules form simpler ones. Distinguish between kinetic and potential energy. Kinetic energy is the energy of motion, and potential energy is energy that matter possesses because of its location or structure. Explain, in your own words, the First and Second Laws of Thermodynamics. The First law of thermodynamics mainly is that energy cannot be created or destroyed it is just always there, and the Second law explains that the energy just changes form (change in entropy). Describe the function of ATP in the cell. ATP is the cell’s energy shuttle; it powers cellular work by coupling exergonic to endergonic reactions. List the three components of ATP and identify the major class of macromolecules of which it belongs. N/A Explain how ATP performs cellular work. ATP drives endergonic reactions by transfer of the phosphate group to specific reactants, making them more reactive. Therefore, cells can carry out work, such as movement and anabolism. Explain the relationship between enzyme structure and enzyme specificity. ….the specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substance. Explain the induced fit model of enzyme function and describe the catalytic cycle of an enzyme. Induced fit brings chemical groups of the active site into positions that enhance their ability to work on the substrate and catalyze the chemical reaction. The catalytic cycle of an enzyme starts by the substrate binding to the active site to form an enzyme –substrate complex. In most cases, the substrate is held in the active site by weak interactions, such as hydrogen bonds and ionic bonds. Side chains (R groups) of a few of the amino acids that make up the active site catalyze the conversion of substrate to a product, and the product departs from the active site. The enzyme is then free to take another substrate molecule into its active site. Explain how substrate concentration affects the rate of an enzyme-controlled reaction. The enzyme binds to its substrate. While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product of the reaction. Explain how enzyme activity can be regulated or controlled by environmental conditions, cofactors, enzyme inhibitors and allosteric regulators. Temperature is one environmental factor important in the activity of an enzyme. Up to a point, the velocity of an enzymatic reaction increases with increasing temperature. Cofactors are ions or molecules for some enzymes to function properly. Inhibitors reduce enzyme function and because allosteric regulators attach to an enzyme by weak bonds, the activity of the enzyme changes in response to fluctuating concentrations of the regulators. Distinguish between allosteric activation and cooperativity. Allosteric activation is the binding of an activator to an allosteric site which stabilizes the conformation that has a functional active site. Cooperativity is when an enzyme has two or more subunits and there is an interaction with a substrate molecule which triggers a favorable conformational change in all other subunits of the enzyme. Examples 1. Science as a process- Metabolism 2. Evolution- Energy 3. Relationship of Structure to Function- Fats 4. Interdependence in Nature- Lipids 5. Science, Technology, Society- Physics, Hydrolysis, Enzymes