PROTONS are positive and are part of the nucleus of the atom; NEUTRONS are neutral and also compose part of the nucleus of the atom; ELECTRONS are negative and circle around the nucleus in various orbitals.
2.What is the symbol for each of the following elements? (You should know these&emdash;they will be useful throughout the course.)
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Element |
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Element |
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Element |
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Carbon |
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Sulfur |
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Phosphorus |
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Hydrogen |
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Chlorine |
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Calcium |
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Oxygen |
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Potassium |
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Iron |
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Nitrogen |
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Sodium |
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Magnesium |
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3. Distinguish among the following sets of terms. Illustrate each term with an example.
atom, ion, isotope, molecule, and compound - an atom is the smallest component of matter that has the properties of an element (e.g., carbon); an ion is a charged atom--one that has lost or gained an electron (e.g., Na+); an isotope is an atom that has lost or gained a neutron in its nucleus (e.g., 14C); a molecule is one or more atoms of the same or different elements joined by covalent bonds (pure carbon, carbon dioxide, or protein); a compound is a substance composed of at least two kinds of elements (e.g., salt, water).
polar and nonpolar bonds - a polar bond is formed by covalently joining two atoms of different electronegativities. This creates a stronger pull on electrons from one atom than the other so the shared electrons spend more time around one of the atoms than the other. This unequal sharing creates a partial negative charge on the more electronegtive atom and a partial positive charge on the less electronegative atom (e.g., C - O, H - O). Nonpolar bonds are formed when the two atoms being joined have very similar electronegativities and the electrons are shared essentially equally (e.g., C - C, C - H).
ionic, covalent and hydrogen bonds - ionic bonds are electrical attractions between positive and negative ions. Ionic bonds are weak in aqueous systems such as cells because water dissolves these bonds (Na+Cl- ). Covalent bonds are strong, essentially permanent bonds that hold most organic molecules together in aqueous solutions. They can be polar or nonpolar, but they are created because the two atoms share one or more pairs of electrons (O=O, O-H-O). Hydrogen bonds are formed by the attraction between partial positive and partial negative charges created by polar covalent bonds.
organic and inorganic compounds - an organic compound is one that contains carbon (CO2, CH4, C6H12O6...); an inorganic compound does not contain carbon (H2O, NO2, NaCl...).
hydrophilic and hydrophobic - a hydrophilic substance dissolves in water because it has charged or polar atoms in its structure (H2O, Na+, -COO-). A hydrophobic substance does not dissolve in water because its atoms are all (or mostly) uncharged (e.g., CH4, oil).
4. What determines the electrical charge of an atom or molecule?
The electrical charge of an atom is determined by the relative numbers of protons and electrons it contains. If there are more protons, the atom is positively charged; if there are more electrons, the atom is negatively charged. In a molecule, the overall charge can be the sum of the component charges, but especially if the molecule is large, different parts of the molecule can have different charges.
5. What kind of bond can be polar? What makes a bond polar? What are some examples of polar bonds? What are some examples of non-polar bonds?
Only covalent bonds can be polar. A covalent bond is polar when the electron pair is shared unequally between two atoms that differ in electronegativity. The electrons spend more time around the more electronegative atom, giving it a partial negative charge. The electrons spend less time around the less electronegative atom, giving it a partial positive charge. Some of the common polar bonds in living systems are C-O, C-N, H-O, and P-O. Some of the common nonpolar bonds in living systems are C-C, H-H, C-H, and C-S.
6. Water is the most abundant molecule in your body. What properties of water are important for many life-sustaining processes and for the structural integrity of your cells? How is hydrogen bonding important for these properties?
Water is polar and as such, it has several properties that make life as we know it possible (or more accurately, life as we know it evolved because water is polar!). Hydrogen bonding within and among molecules depends on an aqueous (water) environment. Cohesion of water molecules (because of hydrogen bonds) creates surface tension and allows water to be pulled to the tops of tall trees. Because of cohesion, water has a high specific heat, which moderates temperatures on the earth, and a high heat of vaporization, which allows water to be used to cool the body. Water dissolves the vast majority of inorganic compounds found in nature and is a universal solvent. Finally, and not necessarily related to its polarity, solid water (ice) floats. If ice sank, then water bodies would freeze solid in cold area winters, killing all the life forms within them.
7. Which of the following statements about a covalent bond is FALSE?
a. It is stronger than a hydrogen bond. TRUEb. A covalent bond can form between two atoms of the same element. TRUE
c. Only a single covalent bond can form between two atoms. FALSE
d. A covalent bond results from the sharing of at least two electrons by two atoms. TRUE
e. A covalent bond can form between atoms of different elements. TRUE
f. All of these are true about a covalent bond.
8. What defines a substance as an acid? A base? What is pH? What is a buffer?
An ACID is a substance that increases the hydrogen ion concentration of a solution. Most commonly, this happens because the substance releases a hydrogen ion when it goes into solution (e.g., -COOH becomes -COO- + H+ in water).
A BASE is a substance that reduces the hydrogen ion concentration of a solution. This most commonly happens because the substance picks up a hydrogen ion when it goes into solution (e.g., -NH2 becomes -NH3+ in water).
PH is the scale by which we measure the concentration of hydrogen ions in a solution. Specifically, pH = -log[H+]. As acidity rises, pH goes down. In a neutral solution, pH = 7.
A BUFFER is a substance that can either pick up hydrogen ions from the solution when they are abundant or release them to the solution when they are scarce. In this way, buffers minimize changes in the pH of a solution despite environmental factors pushing the hydrogen ion concentration to vary (e.g., H2CO3 will lose a hydrogen ion to solution if pH goes up, but the resulting HCO3- will pick up a hydrogen ion from solution if the pH goes down.)
9. List the functional groups covered in lecture. What are their structures? What are their properties?
hydroxyl (-OH) polar
carboxyl (-COOH --> -COO-) acid
amino (-NH2 --> -NH3) base
sulfhydryl (-SH) forms disulfide bonds
phosphate (-PO4-2) acid, buffer
10. What characteristic unites the lipids? What are the three main groups of lipids? What are the functions of each group?
Lipids are united by being hydrophobic molecules; they are large biological molecules, but they are not polymers. The three main groups are fats, sterols and phospholipids. Fats store energy, provide insulation, and cushion some organs like the kidneys. Sterols function as hormones and cholesterol is an important component of membranes. Phospholipids are the main component of membranes.
11. What is a fatty acid? How do saturated and unsaturated fatty acids differ?
A fatty acid is a long carbon backbone with only hydrogens attached except at one end where there is a carboxylic acid. Three fatty acids are attached to a single glycerol molecule to form a fat. Saturated fatty acids contain only single bonds between adjacent carbons and therefore have as many hydrogens as could possibly attach to the carbon backbone...two at each internal carbon and three at the end carbon. Saturated fatty acids have a zigzag structure, but are linear overall, which allows them to pack tightly together and become solid at room temperature. Unsaturated fatty acids have at least one double bond between adjacent carbons, and therefore have fewer than the maximum possible number of hydrogens. The double bond causes a "kink" in the otherwise linear overall structure of the fatty acid. These kinks make unsaturated fatty acids unable to pack densely, and so they remain liquid at room temperature.
12. Describe the general structure, monomer, and function of each of the three classes of macromolecules. Give several examples of each class.
Carbohydrates are sugars and their polymers, which can be linear or branched. They have roles in energy storage (glucose, glycogen, starch) and structural support (cellulose, chitin).
Proteins are amino acids and their polymers, which are always linear. They have roles as enzymes, membrane components (transport proteins, surface recognition proteins, signal receptors), structural components (hair, nails, chromosome scaffolding), DNA regulatory molecules, defense molecules (antibodies), hormones (insulin), and contractile proteins (actin and myosin).
Nucleic acids are nucleotides and their polymers, which are always linear. Nucleic acids have roles in information storage (DNA), information transfer within a cell (RNA), and energy transfer (ATP).
13. Glucose is the only monomer for several different polymers. In what way do these polymers differ?
Starch, glycogen, and cellulose all consist of only glucose monomers, but differ in the way the glucose units are put together. Starch is produced by plants, has "alpha" linkages, and can be linear or sparsely branched. Glycogen is produced by animals, has "alpha" linkages, and is extensively branched. Cellulose is produced by plants, has "beta" linkages, and is always linear. Animals produce the enzyme to break the alpha linkages in starch and glycogen, but only prokaryotes have the enzyme necessary to break the beta linkages in cellulose. Therefore, cellulose produced by the plants we consume passes through our digestive tracts undigested as "fiber."
14. What comprises the primary, secondary, and tertiary structures of a protein? What bonds are responsible for each of these levels of protein structure? Between what portions of the protein do these bonds form? Be as specific as possible.
The primary structure of a protein is the sequence of amino acids connected by the peptide bonds. The secondary structure of a protein is either an alpha-helix or a beta-pleated sheet, formed by regular hydrogen bonding between the repeating backbone structure of the amino acids. The tertiary structure of a protein is the 3-dimensional shape the protein takes on based on interactions between the R-groups. These interactions include disulfide bonds, hydrophilic/hydrophobic interactions, ionic attractions and hydrogen bonds among the R-groups.
15. Quaternary structure of a protein ...
a. is when there is more than one subunit in a protein. TRUEb. is usually unrelated to the function of the protein. FALSE
c. is present in only some proteins. TRUE
d. is held together primarily by covalent bonds. FALSE
e. is best described by its order of amino acids. FALSE
16. Draw a diagram (cartoon) of a nucleotide and label the sugar, the phosphate, and the nitrogenous base.
17. How do DNA and RNA differ structurally? What is the major role of each one in the cell?
DNA is double-stranded, it contains the nitrogenous base thymine as well as adenine, cytosine, and guanine, and it contains deoxyribose as its sugar. RNA is usually single-stranded, it contains uracil rather than thymine in addition to adenine, cytosine, and guanine, and it contains ribose as its sugar. DNA stores information long-term and passes that information on from generation to generation. RNA transfers information from the nucleus to the cytosol within a cell (although occasionally transmits information to progeny!). RNA also plays roles in protein synthesis as a component of ribosomes and as tRNA, which correctly matches up an amino acid with the nucleotides that code for it.
18. What nucleotide is commonly used by cells in energy transformations? What are its forms? How do their energy levels compare?
ATP (adenosine tri-phosphate) is the nucleotide that is most commonly used by cells for energy transformations (GTP is also used occasionally). ATP has the highest energy, ADP (adenosine di-phosphate) has less energy, and AMP (adenosine mono-phosphate) has the lowest energy level of the three.