Assignment #1: Biological Molecules & the Chemistry of Life A. Important Inorganic Molecules Water 1. Explain why water is considered a polar molecule. The partial negative charge of the oxygen and the partial positive charge of the hydrogen create separation of charge. 2. What holds a water molecule together? A covalent bond What type of bond holds several water molecules together? Hydrogen bond Where will this bond form? Between the O of one water molecule and the H of another water molecule How would you describe this type of bond? a strong intermolecular force (between 2 molecules). Its not stronger than ionic or covalent but stronger than other intermolecular forces (London force or dipoledipole forces) 3. List 4 functions of water in the body. Give an example of each function. -acts as a solvent- helps to break down substances for transport in blood -lubricates- surrounds food when traveling down the esophagus -temperature buffer- hydrogen bonds absorb energy without affecting temperature -cohesive/ adhesive- when blood (55% water) travels it pulls the blood behind it because of the hydrogen bonding
Acids and Bases 4. Give the major characteristics of an acid and relate acids to the ph scale. Acids release a hydrogen ion (H+) when dissolved in water. ph of acids will be less than ph of 7 5. Give the major characteristic of a base and relate bases to the ph scale. Bases release a hydroxide ion (OH-) when dissolved in water. ph of acids will be greater than ph of 7 6. How many more H+ (in terms of concentration) would there be in a Buffers solution of ph3 than in a solution of ph8? ph is based on a logarithm (x10) scale. Every level of ph you go up you multiply it by 10 ex) 3 to 4 = x10, 3 to 5 = x100, 3 to 8 = x 100 000 Hemoglobin in red blood cells acts as a buffer by preventing a drop in ph of the blood. It is a tertiary protein that bonds to iron, which gives it its red hue when carrying oxygen. 7. a. Give another example of a buffer Bicarbonate (HCO 3 - ) can take a H + ion to create H 2 CO 3 to increase the ph b. What makes this buffer effective? The H 2 CO 3 can also release the H+ to lower the ph B. Some Important Organic Molecules Look at the dehydration and hydrolysis reactions in order to answer the following questions 8. Look carefully at the bonds formed during synthesis of a large molecule. Water is produced, where does it come from (be specific)? The OH - from one molecule and the H + from the other molecule come together to create water (lose water = dehydration) 9. When the reaction is reversed (hydrolysis) water is needed. What are the 2 roles water molecules play in this reaction? The water breaks apart the molecule into 2 molecules. The water also breaks apart and the OH - is added to one molecule while the H + is added to the other side.
Proteins 10. Although many proteins are enzymes, there are many other types of proteins in our bodies. Give 4 other types of proteins (HEATS: acronym to remember types) and their role in living things. Hormones- messengers in the body ex) Insulin sends a signal to the liver to store glucose Enzymes- speed up chemical reactions ex) lactase enzyme speeds up the break down of lactose sugar Antibodies- involved in the immune response. They target specific foreign bodies Transport- carry substances throughout the body ex) Hemoglobin carries oxygen to the cells Structural- help build the parts of the body ex) collagen in lips/ joints 11. Draw the structural formula of a typical amino acid. Circle the amino group, acid group and remainder (side chain). Label them. 12. Why are there twenty types of R groups? There are 20 different amino acids so there needs to be 20 different R groups 13. What is the difference between the amino acid cysteine and the amino acid alanine, be specific. Think R-Group (you will have to look this up). Cysteine s R-group is CH 2 -SH while Alanine is CH 3 14. Diagram the joining of 2 amino acids together through dehydration synthesis to form a dipeptide with a peptide bond. Highlight the peptide bond.
15. a) When does a polypeptide become a protein? tertiary structure b) Where does this occur in a cell (think protein synthesis from bio 11)? in the cytoplasm 16. Describe the four structures proteins can assume in terms of what they are made of and the bonds holding them together. Make a sketch (very simple), for each, labeling relevant bonds. Primary- linear chain of amino acids joined by peptide bonds Secondary- Alpha helix or Beta Sheets created by hydrogen bonds Tertiary- Multiple Alpha and beta folded and joined by ionic, covalent or disulfide bonds Quaternary- multiple polypeptides joined together
17. What is meant by protein denaturation and what is its significance in living organisms (specifically enzymes). The bonds that allow the protein to fold break and the protein unravels. This protein loses its function Carbohydrates 18. By looking at a structural formula of a molecule, how would you know you were looking at a carbohydrate? CH 2 0 ratio 19. How is a monosaccharide converted to a disaccharide? Give examples. What is the molecular formula for glucose? dehydration reaction C 6 H 12 O 6 20. How are monosaccharides converted to polysaccharides? Dehydration reaction to create a disaccharide then another dehydration reaction to create 3, 4, 5 etc 21. Distinguish between starch and glycogen and sugars (e.g. sucrose). Why is glucose such an important molecule? Starch and glycogen are both polymers of glucose. Glycogen is highly branched. Glucose is used in cellular respiration which produces ATP 22. How would you distinguish a cellulose molecule from a starch molecule? Why is cellulose indigestible? cellulose uses alternate bonding while starch is on the same side. Humans do not have the cellulose enzyme
Lipids 23. Explain how a neutral fat (triglyceride) is synthesized (created). 3 dehydration reactions to join 3 fatty acids to the glycerol (3 water molecules created) 24. Explain how a neutral fat (triglyceride) is hydrolyzed (broken apart). Hydrolysis reaction 3 water molecules used 25. Define what saturated and unsaturated fats mean. A C H bond is considered energy rich. How much more energy do fats carry per gram than carbs? You will have to look this on up Saturated- single bonds only. Maximum number of hydrogens Unsaturated- double bonds as well. 26. Compare trans unsaturated fats to unsaturated fats and explain why one is more healthy than the other. The double bond of trans fat causes a linear molecule to be created unlike the unsaturated which kinks. These contribute to low-density lipoprotein levels which clog arteries and can lead to heart attack or stroke Phospholipids 27. Differentiate between a lipid and a phospholipid (phosphate group) 28. Where are phospholipids found in our body? The cell membrane, vesicles, lysosomes Steroids 29. a. What is the base molecule of steroids? 4 fused carbon rings How are steroids different from other lipids? function and structure b. Where are they made in the cell? SER In the body? Testes, ovaries, kidneys c. List 2 examples of steroids. Cholesterol, testosterone
Nucleic Acids DNA, RNA & nucleotides- we will be going into more detail with these polymers in the future but you must know their basic structure and function now 30. What molecules make up the DNA backbone? Phosphate and deoxyribose sugar Are they the same in RNA? no phosphate and ribose sugar 31. What are the 3 components of a nucleotide? phosphate, pentose sugar, nitrogen base 32. Which nitrogen bases are complimentary in DNA? A-T, G-C In RNA? A-U, G-C 33. Sketch a molecule of ATP and describe its structure. Adenine base, ribose sugar and 3 phosphate molecules 34. What process produces ATP? Cellular Respiration How many ATP molecules can be made from a single glucose molecule? 36-38 Gross 30-34 Net 35. Why is ATP the energy currency of the cell? All cells use ATP for energy 36. Copy out the ATP cycle. Since this is a cycle what does this tell you about this molecule? It is recycled not destroyed 37. How does our body use ATP? Breaks off a phosphate to release energy ENZYMES: BIOLOGICAL CATALYSTS 38. What is the general role of enzymes? To speed up chemical reactions How do they aid digestion? Allow molecules to be broken down so they can be absorbed 39. To what group of biological molecules do they belong? Proteins
40. What process in the cell synthesizes enzymes? Protein synthesis 41. What is the name for the reaction type that includes all digestive reactions? Hydrolytic 42. Explain thoroughly why the reaction is called hydrolysis, and as part of your answer make a diagram as given in Fig. 6.6, Pg. 107. Use a dipeptide as the substrate, Label the active site, substrate (and its name), the actual enzyme for dipeptide digestion, and its source in your diagram. Also label: enzyme/substrate complex, products induced fit, lock & key fit, H 2 O, H +, OH -, and hydrolysis. 43. Describe what an active site is and why it is significant (lock and key)? The area of the enzyme where the chemical reactions takes place. It has a specific shape that a specific substrate match (lock and key) 44. What is meant by the term optimal temperature? (don t simply use the word best, but rather explain why it is the best temperature) Temperatures that are too low cause the active site to shrink lock and key and induced fit will be affected. Temperatures that are too high can cause the active shape to expand and no longer fit the substrate 45. What is meant by the term optimal ph? (as above). The specific ph that the enzyme works the best. If ph fluctuates it affects the active site and may cause the enzyme to denature. no function 46. Will an enzyme catalyze a reaction if its active site is deformed? (i.e. if the enzyme is said to be denatured). Why? No, Lock and key fit and induced fit no longer available 47. Name 2 ways that an enzyme could become denatured. Just did see above 48. Once denatured, can an enzyme regain its 3D shape? Not likely. The folding process is very specific while a protein is being produced.
49. What do COFACTORS do? How do they work? They are vitamins or minerals. They bind to the allosteric site on enzymes and change the shape of the active site so it BETTER fits the substrate 50. What is the name of organic cofactors? vitamins 51. Contrast competitive and non-competitive inhibitors Competitive inhibitors bind to the active site and prevents the substrate from joining. No enzyme action. Non-competitive inhibitors bind to the allosteric site of the enzyme which changes the shape of the active site so it no longer fits the substrate. No enzyme function