Chemistry review for Bio 260 answer key

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1 Chemistry review for Bio 260 answer key Atomic structure Q1. What are the atomic numbers for Nitrogen and Oxygen? A. Nitrogen is atomic number 7. Oxygen is atomic number 8. Q2. If an atom has 11 protons, what element does it belong to? Which element has the atomic number 17? What is the atomic number of Sulfur? A. Atoms with 11 protons are Sodium atoms. Chlorine is atomic number 17. The atomic number of Sulfur is 16. Q3. What is the atomic weight of an atom with 15 protons and 15 neutrons? A. 30. Q4. Atom A has 7 protons and 7 neutrons. Atom B has 7 protons and 8 neutrons How are Atom A and B related to each other? A. A and B are isotopes of the element Nitrogen. Q5. An atom has 8 protons, 7 neutrons and 7 electrons. Does it have the same atomic weight as Atom A or B? Is it same element as Atom A or B? Explain. A. This atom has the same atomic weight as Atom B but it is not the same element because A and B have 7 protons and this atom has 8 protons. Q6. Atom X has 11 protons, 11 neutrons and 10 electrons. Atom Y has 11 protons, 11 neutrons and 11 electrons. Do these belong to the same element? Do these have the same atomic weight? Do they have the same atomic charge? How do you define the relationship of these atoms to each other? A. Atom X and Y are the same element because they have the same numer of protons. They have the same atomic weight because the number of protons and neutrons is the same. However Atom X has a charge of +1 because it has one more proton than electron. This means X is a positively charged ion. Atom Y is the non- ionized, or neutral, form of this element. Q7. A chloride ion has 17 protons and 18 electrons. What is its atomic charge? A sodium ion has a charge of +1. How many electrons does it have? A. The charge of a chloride ion is - 1. All sodium atoms have 23 protons and so a +1 positively charged sodium ion must have only 22 electrons.

2 Q8. What is the atomic charge of a Hydrogen ion that has lost its electron? The H+ ion s charge is +1. Q9. What is the chemical formula for water? What atoms are in C6H12O6 and how many of each? H2O. 6 Carbon, 12 Hydrogen and 6 Oxygen atoms. Q10. Which element has 16 protons? Diagram the nucleus and electron shells of a neutral atom of this element. Include all the electron shells and show how many electrons are in each one. DRAW! Q11. Is neutral Nitrogen a stable atom? How many bonds can Nitrogen make? What about each of these atoms: H, O, S and P? Neutral Nitrogen has 7 protons and 7 electrons. There are 2 electrons in the inner shell and 5 in the next outer shell, which can hold 8, leaving 3 spaces. So Nitrogen is unstable, and can make 3 bonds with other atoms. H needs only 1 electron to fill its outer shell so can make 1 bond. Oxygen needs 2 electrons so it can make 2 bonds. Sulfur also can make 2 (it has 6 electrons in an outer shell that can hold 8). Using this logic you would predict that Phosphorus can make 3 which is true but when bonding to some atoms, like Oxygen, it can make 5! The reasons are more complex than we have time or need to go into in this course. See this site as a beginning of an explanation if you are interested: in- the- phosphate- ion Q12. Diagram the atomic structure of neutral atoms of Fl and Ne be sure to note the number of electrons in each electron shell. Use these diagrams to explain the difference in reactivity. DRAW! Fluorine needs one electron to fill its outer shell whereas Neon is already stable with a full outer shell. Q13. Draw a neutral Oxygen atom, noting the number of electrons in its outermost shell. Now draw two Hydrogen atoms and join them to the Oxygen atom. Why is water H2O, rather than HO? DRAW! Oxygen needs to fill its outer shell with two electrons to become stable. So it needs two Hydrogens to each share an electron.

3 Q14. How many pairs of electrons are in a triple bond? Diagram N2 gas in two ways first by making an atomic diagram of two N atoms and showing how they share electrons when covalently bonded, and then with a line diagram. One covalent is bond whenever an atom shares one of its electrons with another and vice versa so the atoms share a pair of electrons. In a triple bond, each atom shares 3 electrons, for a total of 3 pairs. DRAW! Q15. O2 gas molecules are joined by a double covalent bond. Do you think the two Oxygen atoms share these four electrons equally or unequally? The Oxygen atoms have the exact same electronegativity so they will pull on the two pairs of electrons equally forming a nonpolar double covalent bond. Q16. Compare the electronegativity of H to O or N is it lower or higher? H has an electronegativity of 2.1. O (3.5) and N (3.0) are both more electronegative than H. Q17. In ammonia (NH3), Nitrogen is bonded to 3 Hydrogen atoms. Are the N- H bonds polar or non- polar? Do ammonia molecules have a charge? Explain. Since N is more electronegative (attracts electrons better) than H, the electrons shared between N and H in the N- H bond are pulled closer to N, leaving the H partially positively charged and N slightly negatively charged. The NH bonds by definition are polar covalent bonds. Q18. Lithium has 3 protons and 3 electrons in its neutral form. Why are neutral Li atoms unstable? Describe how Li ions of +1 charge are formed. Lithium has a full inner shell but its outer shell has only a single electron. It is easiest to become stable by losing the electron in its outermost shell. Now there are only 2 electrons but 3 protons giving an overall charge of +1. Q19. Table salt is made of Sodium and Chlorine ions. Draw diagrams of neutral Chlorine and Sodium atoms. Next to the neutral form, draw each atom in its ionized form. Label your ion drawings with the atomic charge. Use this to explain how Sodium and Chlorine atoms are connected in table salt. When salt is dissolved in water, explain why the ions come apart. The positively charged sodium atoms attracts negatively charged chlorine atoms, forming a solid regularly stacked crystal. In water the slight negative

4 charge on the O of the polar OH group attracts the sodium ions, while the positive charge on the H of water attracts the chlorine ions, dissolving the crystal into its component ions. Q20. In the compound ammonia, NH3, Nitrogen is bonded to three Hydrogen atoms. Do you think ammonia molecules form Hydrogen bonds? Explain. Yes. The N- H groups are all polar, meaning that the electrons shared between N and H spend more time near the N, leaving the H partially positively charged and N slightly negatively charged. The negative charge on N would interact with the H end of OH groups in water. The positive charge on the H would interact with the O end of OH groups in water. Q21. Compare a Hydrogen bond between two water molecules to the polar covalent bond joining O to H in a water molecule what is the difference? The bond between O and H in a single H2O molecule is a polar covalent bond the unequal sharing of a pair of electrons between O and H. This is distinctly different from a H bond that forms between a polar side group on one amino acid and the polar side group on the other. The former is INTRA(within)molecular interaction; the latter is INTER(between)molecular interaction. Q22. When lakes and ponds freeze, the ice floats, leaving liquid water at the bottom. Why might this be important for the survival of marine life? There will be liquid water for much longer in some cases, year- round despite sub- freezing temperatures on land. Aquatic life forms especially ones that can t escape their pond or lake would not die from the cold. Q23. List consequences to life on earth if water did not exhibit capillary action. If plants couldn t suck water up due to capillary action from the roots, they would have to rely on haphazard absorption after rain landed on the leaves. Plants in dry areas would probably mostly die, along with anything that depended on plants to survive day to day. In short, it would be a disaster. Q24. Use the hydrophobic effect to explain why olive oil separates from vinegar and how when making chicken stock, you separate the fat from broth. Olive oil is hydrophobic and vinegar is acetic acid diluted with water. The oil molecules cluster together away from the water molecules. Similarly as you boil chicken meat and bones, the fat forms droplets that separate from the protein- and- water broth. The fat floats so you skim it off the top to remove it. Q25. Estrogen and testosterone are steroids. How do they get into cells?

5 Nonpolar steroids can pass right through the cell membrane. (So can gases like oxygen and carbon dioxide.) Q26. Red blood cells are put into a cup of pure water. Predict what happens. Is this a hypotonic, hypertonic or isotonic situation? This is a hypotonic situation (outside is more dilute than cell interior). Water will cross the plasma membrane by osmosis in an attempt to dissolve the more concentrated cell interior and eventually the blood cells will burst. Q27. Protozoans (single- celled animal- like eukaryotic organisms eg. amebas) are abundant in fresh water. Predict what happens when pond protozoans are transferred into sea water. This is a hypertonic situation (outside is more concentrated than cell interior). Water inside the protozoans will leave by osmosis to try to dilute the extra salt in the sea water. This will cause the cytoplasm to shrink and dryp up; protozoans could become dehydrated and may eventually die. Q28. Draw an atomic diagram of a water molecule. Now remove the proton of one of the H atoms what does this leave behind? Hint: it is a negative ion. Q29. What is the ph of pure water? The ph of pure water is 7. In pure water [H+]=10-7. Negative log of 10-7 is 7. Q30. The concentration of H+ ions in tomato juice is What is the ph of tomato juice? The ph of stomach acid is 2. Which has a higher concentration of H+ ions, tomato juice or stomach acid? How much more concentrated is it? ph of tomato juice = - log[10-4 ] = 4. Stomach acid at lower ph has higher H+ (proton) concentration. The difference is 2 log units and each unit is a 10- fold difference so stomach acid is 100x more concentrated than tomato juice. Q31. NaOH is composed of Na+ and OH- ions held together by ionic bonds. If you add NaOH to water, what happens to the ph and why? The ph rises because the NaOH dissociates into Na+ and OH- ions. The OH ions soak up excess protons (H+) in the water, reducing the proton concentration. ph is a measure of proton concentration. Q32. Is methane organic or inorganic? Explain. What about CO2?

6 Methane is organic and Carbon dioxide is not. Organic molecules have C- H bonds. If they don t, then they aren t considered to be organic. Q33. Which of the listed functional groups contains double bonds? Look at the leftmost atom in all these diagrams are all their bond requirements being met? Why is there a line leading to the left what is attached there? Which of the listed functional groups can make H bonds and why? Double bonds: The line leading to the left is the unfilled bond that will be attached to some molecule. H bonding groups: hydroxyl, carboxyl, amino, sulfhydryl so, yeah, all of them. This is because in OH, COOH and NH2, there is a polar covalent bond involving Hydrogen. The same is true of SH groups but the H bonding is much weaker because S and H have more similar electronegativity than either O- H or N- H. Q34. Sugars, fats, protein and DNA all contain C- H bonds. Are they organic or inorganic? Organic. By definition an organic compound is one containing C- H bonds. Q35. Draw a fatty acid with 3 Carbons in the backbone all joined by single bonds. (Don t forget to add H atoms as needed and attach a carboxyl group at the end. Note: the C in COOH is not counted as part of the backbone). Now draw a fatty acid with the same number of Carbons but with two double bonds in the backbone. Using the terms in the paragraph above, compare these molecules. Q36. MAKE A FAT!! Draw glycerol and 3 fatty acids (choose the length of the C backbone and if they are saturated or unsaturated). Circle the atoms that will be used to make water. Now draw the triglyceride made from these components. Why is triglyceride synthesis also referred to as a dehydration reaction? Q37. MAKE A PHOSPHOLIPID! Use the fatty acids in the previous question as your raw materials. Don t forget use only two fatty acids and put a phosphate on instead. Don t worry about adding the identifying group to phosphate those details aren t needed in this course. Q38. Are steroids polar or nonpolar? Hydrophilic or hydrophobic?

7 Nonpolar their rings of C- H bonds are rigid and nonpolar. The occasional OH group is not enough to make this class of molecule hydrophilic. Q39. Are carbohydrates polar or nonpolar? Hydrophilic or hydrophobic? Polar because of the frequent OH (hydroxyl) groups on the molecule and hydrophilic because hydroxyl groups easily interact with water molecules. Q40. Which human organs make and store glycogen? Hint: there are two! Read your text or search the web to find the answer! Muscle and liver. Q41. What enzyme do we use in order to synthesize glycogen? What enzyme in our saliva allows us to break starch down into glucose subunits? We use glycogen synthase enzyme to make glycogen from glucose. Amylase in our saliva breakds the polysaccharide starch down into glucose subunits. Q42. Can any animals digest the cellulose in plants to get glucose? Hint: this relies on a symbiotic relationship between animals and microbes. Cows and other quadrupeds live in symbiosis with microbes in their stomachs that can digest the cellulose and release the glucose for use by the host animal. Q43. Explain why it s so hard to clean clogged plumbing or remove tartar. Bacteria in these biofilms have a glycocalyx sugar coating which helps them stick to the plumbing or to tooth enamel, and protects them from cleaning chemicals and abrasion. Q44. Which amino acid R side chains contain the following: a hydroxyl group; a carboxyl group; Nitrogen; Sulfur; a sulfhydryl group; indole group; ability to form Hydrogen bonds. (Hint: search online to find an indole group.) Hydroxyl: Serine, Threonine and Tyrosine Carboxyl: Aspartate and Glutamate Nitrogen: Tryptophan, Asparagine, Glutamine, Lysine, Arginine, and Histidine Sulfur: Methionine and Cysteine Sulfhydryl: Cysteine Indole: Tryptophan Can form H bonds: All the polar amino acids ie. Serine, Threonine, Cysteine, Tyrosine, Asparagine and Glutamine. Also Tryptophan and Histidine.

8 Q45. What molecule is released as waste when peptide bonds form? H2O Q46. Diagram the reaction breaking a dipeptide down into its amino acids subunits. Hint: it s precisely the reverse of dehydration synthesis! Q47. There are 8 different monosaccharides in human glycoproteins. The sugars in the chain can be linked in different orders, and have different branch structures and lengths. Glycoproteins act as ID badges and allow cells to identify and interact with each other. How does the variety of chain structures make this feasible? You can link together 8 different sugars in chains of various lengths and with different branches that produces a lot of different combinations; it is easy to build a unique chain that identifies a specific cell as distinct from many others. Q48. What is the other common name for this type of synthesis? What other macromolecules are built using this type of reaction? What type of reaction do you think breaks DNA or RNA down into nucleotides? Dehydration synthesis! Triglycerides, phospholipids and di- and poly- saccharides are all made using dehydration/condensation reactions. In the next section on ATP we ll also see that ATP is made by dehydration synthesis using a molecule of ADP plus inorganic phosphate. Hydrolysis is used to break down most macromolecules including DNA and RNA. Q49. Pure iron (Fe) exposed to Oxygen becomes Fe 3+. Compare Fe to Fe 3+ ; which is the oxidized and which the reduced form of iron in this example? Pure iron (Fe) is the reduced form. The Fe 3+ ion has been oxidized (electrons were removed).

9 Q50. ATP stores energy short term. What molecules store energy long term? Triglycerides are the lipid form of energy storage and polysaccharides like glycogen and starch store energy as well for longer than ATP.