Unit 1 Study Guide Chapters 2-5

Unit 1 Study Guide Chapters 2-5 Biochemistry

All questions within each section of the Unit Study Guide will be due on the day of the unit exam. Each section should be clearly labeled by section number and number of question for complete points.

 1-1: Read pages 32-39 ~ Atomic Review (On your own!!) Ch 2

 Skim: The Energy Levels of Electrons

 Skip: Electron Orbitals

 Study Table 2.1: Identify which of these elements are structural and which appear as ion. Structural elements are linked covalently to form molecules having particular functions. Ions can be used in their free dissolved state to convey signals or may be attached to larger molecules to give them special properties.

- The six key structural elements that build the majority of cells = CHNOPS!

 The importance of energy levels and the octet rule is to understand how many bonds the six key structural elements make. So, the key piece of information to be derived from Fig 2.8 is: How many more electrons are need to complete the atom’s outer shell? How does it get them? ... (By sharing in a covalent bond, for example.) How many bonds does an atom make? ... (One for each electron needed.) Simple as tinker toys.

Questions:

1. Distinguish between an element and a compound.

2. Identify the four elements that make up 96% of living matter. What elements account for most of the remaining 4%? So which of these are the 6 key structural elements? Make a table for these 6 key structural elements that includes: symbol, atomic number, how many valence electrons, how many bonds they can form. (You will need to know these!!)

3. Define the term trace element and give an example.

4. See Fig 2.3 a & b. What do the pictures of the corn and the goiter have to do with naturally occurring elements?

5. A common isotope of oxygen atom has 9 neutrons.

a. What are the atomic number and the mass number of this isotope?

b. Write a chemical symbol with a subscript and superscript.

c. Explain how two isotopes of an element are similar. Explain how they are different.

1 6. Describe two biological applications that use radioactive isotopes.

7. Define the terms energy and potential energy. Explain why electrons in the first electron shell have less potential energy than electrons in higher electron shells.

 1-2: Read pages 39-45 ~ Chemical Bonding (On your own!!) Ch 2

 Notice in Fig. 2.10 how the concepts of energy levels, valence and octet have finally been reduced to lines representing bonds (usually covalent) and how many of these bonds will be made by a particular element. You can, of course, memorize these numbers or, by remembering the concepts just reviewed, rapidly drive them from the element’s position in the period table. Knowing how many bonds are made by the principal elements will help you write and understand structures for compounds.

 Ionic bonds are important in biological system because they help give many large molecules, especially proteins, their three dimensional shape. They are also important in helping molecules recognize and interact with other molecules such as between certain enzymes and substrates.

 Hydrogen bonding is an extremely important concept in biology and you should understand them very well as well as be able to give examples, throughout the year, where they occur in molecular biological systems. Besides making water “sticky”, giving it important properties for life, H-bonds also act in all the rolls described above for ionic bonds. H-bonding is responsible for faithful DNA replication, protein synthesis, proper protein shape and function, forming cell membranes, strengthening cell walls, communication between hormones and their targets, etc., etc., etc….

 Van der Waals interactions are weak bonds that, in their cumulative effect, reinforce 3-D shape of larger molecules.

 The idea of function being related to form (shape) is one of the central themes of biology. We will see it at the molecular, cellular, tissue, organ, organismal and ecological levels again and again this year. This is another “biggie” and you should be able to give examples at all levels by the end of the year. You will have an ongoing assignment regarding this concept, so be ready!

Questions 1-2:

1. See Fig 2.10 & 2.11: Discuss covalent bonding.

2. See Fig 2.12: Discuss a polar covalent bond.

3. See Fig 2.13: Discuss ionic bonding.

4. Explain why strong covalent bonds and weak bonds are both essential to living organisms.

5. See Fig 2.17 a & b: Explain how the structure of a molecule relates to its function.

2 6. How are Hydrogen bonds formed? What is meant by the term electronegative atom? (You are going to need to dig this one up from the archives of chemistry).

7. Go to page 42 and look at the picture of the gecko. Explain how Van der Waals interactions allow the gecko to walk on walls.

8. Explain how a reversible chemical reaction reaches chemical equilibrium.

a. What is one factor affecting the rate of a reaction? Explain.

b. Does the reaction stop once it reaches chemical equilibrium? Why? (Any laws involved?)

 1-3: Read pages 47-56 ~ Water & pH (On your own!!) Ch 3

 Yes-sir-re, water! Don’t leave your body without it! It’s no accident that when scientists search for possibilities of extraterrestrial life they look for planets at the proper distance from a star to harbor liquid water.

 Think of it this way… Life is molecules interacting with one another in various ways. To do this, they have to move around. To move, they need to be in solution. What’s the number one special property of water?... (It is an excellent solvent in nature)

 Be able to list the special properties of water. As you read through these properties, notice how all of them are a consequence of H-bonding and how all are, in some way, important to life.

 Notice, in the section on pH, the dissociation reaction of carbonic acid is written twice. Remember your talk in chemistry about the importance of this reaction?

 Acid precipitation (rain) is just the first of our examples of the complex interrelationship between science, technology and society.

Questions:

1. What are the four emergent properties of water (and their sub-categories) resulting from H- bonding.

2. Explain why is water the perfect biological solvent? Explain the importance of hydrogen bonding. Use the term hydration shell in your answer.

3. Explain the saying, “It’s not the heat, it’s the humidity”.

Questions 1-3 cont…

4. How can the freezing of water crack a boulder?

5. What is the relevance to water’s high specific heat to living organisms? Discuss

a. the importance of water to an organism living in its environment.

b. water’s importance to an organism’s physiology.

3 6. Is “normal rain” also acid rain? Explain.

7. Define pH, acid, and base.

8. Explain how buffers work.

 1-4: Read pages 58-66 ~ Carbon (Isomers on your own; I will cover the rest) Ch 4

 Carbon, Carbon, Carbon,…all living things are carbon based creatures! What about the structure of carbon?... It allows carbon molecules to possess so many functions!

 Functional groups give character to organic molecules. Carbon and hydrogen have similar electronegativities and so make boring, non-polar molecules (“do not play well with others”). But when you replace the hydrogen atoms, on the carbon backbone, with groups of atoms containing oxygen, nitrogen, phosphorus, and sulfur, interesting things happen. These atoms hog electrons and result in polar bonds. This give the molecule a certain magnetic-like quality that makes it respond to, and be influenced by, its neighbors.

 See Fig 4.10: You should be able to identify and provide examples of general functional properties of the important functional groups of organic chemistry.

 Pay particular attention to subtleties. The carboxyl group looks like it should behave like a combination of a carbonyl and alcohol (hydroxyl). Wrong! It’s a completely different beast and behaves like an acid in aqueous solution. A biological molecule in a cell containing a carboxyl group will have generally lost its hydrogen atom and have a negative charge. This will give it special properties such as attraction to positive charges on other molecules.

Questions:

1. What types of isomers are represented in the following molecules?

Questions 1-4 cont…

2. Describe how carbon skeletons may vary, and explain how this variation contributes to the diversity and complexity of organic molecules.

3. See Fig 4.9: and explain how different functional groups attached to the same base molecule can influence the functional properties of that molecule.

4. What is the chemical similarity between gasoline and fat?

5. Create a table and include the functional groups Hydroxyl, Carboxyl, Amino, Phosphate, and Sulfhydryl of organic molecules, the structural formula for each, and give examples of a type of molecule/substance where you would find these functional groups.

 During the rest of the unit, you should gain a profound understanding that the use of the molecules of carbohydrates, lipids, protein, and nucleic acids (created from combining the atoms CHNOPS) is important for obtaining cellular energy (ATP), storage, enzymes, membrane structure, genetic information, overall structure of cell. etc... These molecules and their building blocks are obtained by the exchange between an organism and its environment. All living things must eat somehow!

 1-5: Read pages 68-69 ~ Intro to Macromolecules Ch 5

 The classes of large biological molecules can be simplified by recognizing that they are fabricated from smaller subunits linked in a particular manner. These subunits (monomers) react by condensation synthesis (also called dehydration synthesis; I use this term) to form macromolecules (polymers). These macromolecules can subsequently be broken back down into their subunits by hydrolysis (as during digestion).

Questions:

1. List the 4 macromolecules and their corresponding monomers.

2. What is the role of water in a reaction that involves dehydration synthesis (condensation reactions)?

3. What is the role of water in a reaction that involves hydrolysis?

4. After you eat cheese (protein), what types reactions must occur for the amino acid monomers in the protein of the cheese to be liberated from the cheese protein structure? What type of reactions must occur for these amino acids to be converted into proteins your body?

5  1-6: Read Pages 69-77 ~ Carbohydrates & Lipids Ch 5

 Learn the ring structure glucose, Fig 5.4b. Notice that some of the OH groups point up and some point down? Why is this? What if some of the directions were reversed?

 In Fig 5.5, come away with an overview of how a condensation (dehydration) synthesis links monosaccharides into longer chains (polysaccharides).

 In Fig 5.7, notice all the difference a little change in shape makes. Starch is gooey and digestible, cellulose is rigid (keeps plants upright) and is only digestible by particular microorganisms with the right enzymes.

 Lipids are the odd group of the macromolecules. Fats are still formed by dehydration synthesis but only three fatty acid monomers are needed to make a complete molecule. The other classes of macromolecule can be hundreds to millions (in the case of DNA) of subunits long.

 Notice the scarcity of oxygen and lack of nitrogen in lipids. Since they are mostly composed of carbon and hydrogen with similar electronegativities, there is almost no polarity in the bonds of lipids. This means they don’t mix well with water and other polar molecules within the cell. They are hydrophobic.

 Fig 5.12 is important. It shows how one end of a fat can be made hydrophilic by the attachment of a charged phosphate group (usually connected to additional charged or polar functional groups). These phospholipids are the basis of cellular membranes.

Questions 1-6:

1. See Fig 5.7: Explain the difference between α-glucose and β-glucose.

2. What do the carbohydrates cellulose, glycogen, starch, and chitin have in common structurally?

3. What type of covalent bond is formed between the monomers of carboyhydrates?

4. Distinguish between the glycosidic linkages found in starch and cellulose. Explain why the differences are biologically important.

5. What type of covalent linkage is formed between a glycerol and fatty acid.

6. What is an example of a saturated fat and unsaturated fat? How do they differ in both structure and behavior at room temperature?

7. Compare and contrast a fat and a phospholipid.

8. Why are lipids hydrophobic?

9. Name the principle energy storage molecule in plants and animals.

 1-7: Read pages 77-85 ~ Proteins Ch 5

6  Proteins are probably the central most important concept in biology. Period. A study of biology looks at how they are formed, how their structures are related to their function and how they behave. Almost all questions you might ask of a biological nature would eventually lead to proteins for the complete answer.

 Fig. 5.17: You do not need to memorize these amino acid structures (some college professors would make you do this!). You do, however, need to be able to draw the structure for a generic amino acid using the letter R to represent the variable region (side group). Also recognize that amino acids can be grouped into four distinct categories according to the characteristics of their side groups. These side groups give the amino acids personality. This is important in determining how the protein folds into its three dimensional shape and how it interacts with other molecules (which is what proteins do).

 Study the four levels of protein structure. Especially important is your detailed understanding of how these four levels of structures are maintained. Fig 5.20 summarizes the four ways in which protein structure is maintained. Because of these bonds, proteins achieve a certain shape which gives them a certain function.

 Some proteins only achieve their final form when in association with other polypeptides or non-protein helper molecules such as the heme group in hemoglobin. This is what is meant by quaternary structure.

 Pages 84 and 85 should reinforce the importance between the structure of a protein and how it does its job.

Questions:

1. See Fig 5.21: Describe the difference between a normal RBC and a sickle cell RBC. What are the implications for someone with sickle-cell disease?

2. Name two scientific approaches that have contributed to determining protein structure.

3. Amino acids all have the same basic structure; they all have an amino acid group, a carboxyl group, and a hydrogen atom. Draw a the basic structure of an amino acid.

4. What properties of amino acids make them unique to each other?

5. Explain what determines protein structure and why it is important.

6. Explain how primary structure of a protein is determined.

Questions 1-7 continued:

7. Name two types of secondary protein structure. Explain the role of hydrogen bonds in maintaining secondary structure.

8. Explain how weak interactions and disulfide bridges contribute to tertiary structure.

9. Name four conditions under which protein may be denatured.

7 10. Can a denatured protein undergo renaturation? Explain.

 1-8: Read pages 86-89 ~ Nucleic Acids Ch 5

 Since proteins are made from patterns in DNA, nucleic acids are as essential to a discussion of life as the proteins themselves. Notice how understanding the structure of DNA is much simpler than that of a protein. There are only four choices of subunits and they are ordered in a sequence rather than being folded in complicated, unique ways. Different proteins have different shapes. Most DNA has the same overall shape; different sequences of bases do not change the overall shape whereas amino acid sequences affect a protein’s shape and, therefore, function.

Questions:

1. What are two differences between ribose and deoxyribose? (One of the answers is in their names!)

2. Why is one end of one side of the DNA molecule labeled 5’ and the other end of the same side labeled 3’?

3. What does it mean when DNA is described as having 2 sides of polynucleotides running antiparallel?

4. What type of bonds hold the nucleotides together creating the backbone (the support sides) of DNA? What type of bonds hold the two sides of polynucleotides together at the nitrogen bases?

5. Referring to your answer in #5, what is the importance of these types of bonds at these locations within a DNA molecule?

8 What chemistry are you responsible for entering AP Bio? You must study on your own; some or all of this content will show up on your first unit test.

 Atoms:

- Subatomic particles and their charges

- Atomic structure

 6 key structural elements (CHNOPS)

- Atomic #

- # of valence e- ; # of bonds each can form

 Difference between element, atom, compound, molecule

 Bonding - The octet rule

- Ionic bonds (know what an ion is!!)

- Covalent

- Van der Waals interactions

- Polar covalent

- Hydrogen bonding

 Have a general understanding of isomers

 Understand the properties of water that make it a great natural solvent.

 You can’t take the pH of anything without water. Why? Well, water needs to dissolve substances to release the ions to be measured in pH. Know what pH is measuring, the pH scale, what acids give off in water, what bases give off in water.

 How to calculate the moles of a substance! This was an AP test question last year! Molecular Weight = the sum of all the masses of the atoms in a molecule

9 Ex. 1 dozen = 12 units 1 mole (mol) of a substance = 6.022 X 1023 molecules Mole = MW in grams Molarity (M) = # of mole of solute/L of water

Most of these topics are covered in sections 1-1 through 1-3. You must do those sections on your own; they will not be given specific attention during class lecture. These are prerequisites to this course!

Also from the summer packet, a general understanding of cell organelle functions for the next unit