CLS Review 10-11

CLS Review 10-11 - WebQuest for AP Biology CLS Review The...

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Unformatted text preview: WebQuest for AP Biology CLS Review The Beginning of THE Quest: The Dilemma of the AP Bio student We welcome you to a long journey: the journey of the Bio student. It is long. It is grueling. It is horrendous... well not really. It's just a lot of work. But don't worry, Your task: Read through this powerpoint and learn what we're attempting to teach you. Answer the questions given underneath each section. Compile your answers into one word document and email your answers to Learn this stuff now. You'll be glad you did the night before the AP exam. What you're getting yourself into: List of the Major Review Topics We have divided your CLS Review Assignment into 8 different topics. Included in each section are links, definitions, and any necessary labs that you will need to know for the exam. We have not provided the answers to everything, therefore, you SHOULD use your AP Bio book from school so that you can do some learning on your own. Don't groan, its good for you. The following topics will be covered as a part of your CLS Review . Let's take a look at what they are: WATER CARBON MACROMOLECULES REACTIONS DNA PROTEIN SYNTHESIS GENE EXPRESSION & ONCOGENES DNA TECHNOLOGY STEM CELLS & HOMEOTIC GENES WATER (Summary) Water (H2O) is vital to all living organisms. A water molecule is asymmetrical and has polar bonds (unequal distribution of charge). Water exists in all three physical states of matter (solid, liquid, and gas). Hydrogen bonding (where the H atom of one molecule is attracted to an electronegative atom of another molecule) contributes to water's organized structure. Water has some specific properties, including: cohesion, adhesion, and surface tension, and is a versatile solvent because of its polarity. Hydrophilic substances are "water-loving" and soluble (hydro = water, philo = loving), whereas hydrophobic substances are "water-fearing", and are not water-soluble. BUFFERS AND ACID PRECIPITATION (Summary) In various cellular functions and processes, the bicarbonate buffering system (where, in the blood, carbon dioxide is changed into bicarbonate ions, which helps keep a pH level of 7.4) plays an important role. Buffers are substances that attempt to minimize large and sudden shifts in pH. Acid precipitation is mainly caused by the combustion of fossil fuels by cars, industries, and other sources which utilize fossil fuels. Acid precipitation can harm the environment severely, since it alters soil pH levels and can damage ecosystems. WATER, BUFFERS, ACID PRECIPITATION (Questions) Review questions: 1. Describe the structure and geometry of the water molecule, and explain what properties emerge as a result of this structure 2. Describe how water contributes to the fitness of the environment to support life 3. Distinguish between hydrophilic and hydrophobic substances 4. Explain how the polarity of water molecule makes it a versatile solvent. 5. List 4 characteristics of water that are emergent properties resulting from hydrogen bonding 6. Write the equation of the dissociation and reformation of water 7. Using the bicarbonate buffer system as an example, explain how buffers work 8. Describe the causes of acid precipitation and explain how it harms the environment CARBON & MACROMOLECULES (Summary) Carbon has 4 valence electrons and thus is able to form single, double, and triple bonds with itself and also with hydrogen, oxygen, and nitrogen. Because of its versatility, carbon is known as the building block of life. The small organic molecules created by carbon, hydrogen, oxygen, and nitrogen are called monomers. Several monomers bound together form a polymer. Macromolecules are large organic polymers that are divided into four classes: carbohydrates, amino acids, nucleic acids, and lipids. Carbohydrates are sugars, either simple sugars (monosaccharides) which consist of only one unit, or multiple sugars (disaccharides and polysaccharides) which consist several monosaccharides put together. CARBON & MACROMOLECULES (Summary) Amino acids are the building blocks of proteins. There are 20 different types of amino acids, each with a different side group. All amino acids have a carboxyl group and an amino group in common. Chains of amino acids form a polypeptide, which connects with other polypeptides to form a protein. Nucleic acids are the building blocks of DNA and RNA, or the hereditary material. A nucleic acid itself is a polymer of several nucleotides, which consist of a 5-carbon sugar, a phosphate group, and a nitrogenous base. Lipids are the fats in the body that store large amounts of energy. Fats are insoluble in water. CARBON & MACROMOLECULES (Summary) Some questions to ponder upon....(and write down the answers to) 9. Explain how carbon's electron configuration determines the kinds and number of bonds that carbon will form. 10. Label the four major components of an amino acid. 11. Explain how monomers are used to build polymers. 12. Explain how organic polymers contribute to biological diversity. 13. Distinguish between a saturated and unsaturated fat and list some unique emergent properties that are a consequence of these structural differences. 14. Distinguish between monosaccharides and disaccharides. REACTIONS (Summary) Energy is what runs living things. The substance of life is the transfer of energy from one living thing to the other. These energy transfers are accommodated by chemical reactions. The sum of all these chemical reactions that take place in a cell is known as the phenomena of metabolism. There are several categories that a reaction can fall into. An exergonic reaction is one that releases energy. An endergonic reaction is one that absorbs energy. Usually both are necessary for the cell to function (e.g. the energy released from an exergonic reaction is absorbed by an endergonic reaction). REACTIONS (Summary) Another classification of reactions is whether or not they are catabolic or anabolic. Catabolic reactions or pathways break down molecules and anabolic reactions or pathways build molecules. Again, both are necessary for metabolism. A redox reaction is another way to categorize a reaction. This type of reaction includes an oxidation and a reduction. An oxidation occurs when a reactant loses an electron and a reduction occurs when a reactant gains an electron. Usually, the electron lost by one molecule is accepted by the molecule that it is reacting with. Many reactions occur within a single living organism. The biological catalyst that helps these chemical reactions to occur is called an enzyme. These globular shaped proteins decrease the activation energy of a reaction, or in other words, the energy required for a certain reaction to take place. Enzymes are substrate specific, meaning that each enzyme will only bind to one type of molecule. (To learn more about enzymes, refer to the link on the next slide). REACTIONS (Summary) Enzyme Lab Click here for a thorough look at AP Biology Lab 2: Enzyme Catalysis LINK: Some questions to ponder upon....(and write down the answers to) 15. Give an example in nature for the following: endergonic reaction, oxidation, catabolic pathway, enzymes. 16. What are biological catalysts called? 17. What is the importance of ATP in a cell? 18. List the three components of ATP and identify the major class of macromolecules to which ATP belongs. 19. Explain how substrate concentration affects the rate of an enzyme-controlled reaction. 20. Describe how oxidations and reductions are involved in energy exchanges. 21. Explain why organic molecules that have an abundance of hydrogen are excellent cellular fuels. REACTIONS (Links) Click here if you kinda get it, but kinda don't and want something to solidify your knowledge. Hyperlink: Click here if you REALLY don't understand what the heck is going on. Hyperlink: The coolness of enzymes Hyperlink: DNA (Summary) Structure of DNA made up of three parts: deoxyribose, phosphate group, nitrogencontaining base four nitrogen containing bases: adenine (A), guanine (G), cytosine (C), and thymine (T) purines: two ringed bases (Pure Apples are Good) pyrimidines: one ringed bases (Pyrimidines Take Cash) Complementary base pairing adenine-thymine (Apples are Tasty); cytosine-guanine (Carrots are Gross) *Personas importantes: James Watson and Francis Crick (1953) Picture: DNA (Summary) DNA as the hereditary material In 1928, Frederick Griffith conducted an experiment with rats and two strains of the bacteria Streptococcus pneumoniae. When the virulent S-strain was injected into rats, the rats got pneumonia and died. The rats did not die when injected with the non-virulent R-strain. When Griffith injected heatkilled S-strain bacteria and live R-strain bacteria into rats, the rats still died. From the dead rats, Griffith was able to isolate live S-strain bacteria, showing that something had transformed the live R-strain bacteria into the virulent S-strain bacteria. In 1952, Alfred Hershey and Martha Chase's experiment established DNA as the hereditary material rather than protein. In their experiment, Hershey and Chase labeled the outer protein coat (the capsid) with radioactive sulfur and labeled the viral DNA with radioactive phosphorus. When the viruses infected bacteria, the phosphorus was found inside the bacteria, and sulfur was found in the solution surrounding it. This showed that DNA was the genetic material, not protein. DNA (Summary) DNA Replication DNA reproduces through a process called replication. The enzyme helicase unzips the two strands of DNA, creating a replication fork. DNA only replicates in the 5'-to-3' direction. The strand that can be copied continuously is the leading strand. The other is the lagging strand. The lagging strand is formed in small pieces called Okazaki fragments. Later, the enzyme DNA ligase connects the Okazaki fragments to produce a continuous strand. DNA (Questions) QUESTIONS: 22. Draw a 2-D diagram of DNA including all four bases and the structure of the backbone. 23. How did Griffith and Avery's experiments show the transforming principle of DNA? 24. Explain the significance of using sulfur and phosphorus labels in the Hershey and Chase experiment. 25. Using the diagram of the DNA replication fork, please explain the roles of DNA ligase, primer, helicase, single strand binding protein, Okazaki fragments, and DNA polymerase in DNA replication. 26. Why is there a difference between the leading and lagging strand? How is the lagging strand synthesized? 27. Distinguish between a pyrmidine and a purine. What is the importance of these two structures in DNA? DNA (Links) Griffith & Avery animation @ Hershey & Chase animation @ PROTEIN SYNTHESIS (Summary) Transcription animation: Definition: process by which genetic information is copies from DNA to RNA Process: 1) RNA polymerase binds to the promoter of a specific gene (*promoter marks the beginning of the DNA chain that will be transcribed) 2) RNA polymerase separates DNA molecule in that region (*only one of the separated DNA chains, the template, is used) 3) RNA polymerase attaches to the first DNA molecule of the template chain 4) complementary RNA nucleotides will be added on (*adenine with uracil; guanine with cytosine) 5) stops with RNA polymerase reaches termination signal Picture: Products (aka transcripts): mRNA, tRNA, rRNA PROTEIN SYNTHESIS (Summary) Translation: process of assembling polypeptides from information encoded in mRNA Process: 1) ribosome attaches to start codon (AUG) on mRNA transcript 2) each mRNA codon is paired with its tRNA anticodon 3) form a polypeptide chain Picture: PROTEIN SYNTHESIS (Questions/Links) 28. Describe the structure of DNA. Explain the "base-pairing rule" and describe its significance. 29. Distinguish between the leading strand and lagging strand. 30. Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3' end. 31. Explain the roles of DNA ligase, primer, helicase, and the single strand binding protein. link to look at 12replication.html (lecture notes about DNA replication) GENE EXPRESSION & ONCOGENES (Vocabulary) Promoter Region: a base sequence which signals the starting place of gene transcription (its where RNA polymerase binds to begin transcription) Operator: short sequence near the promoter which helps in transcription by working with proteins that aid in transcription Operon: a promoter and operator (they're paired together, remember? If you don't, look at the definitions above) pair that works with multiple genes. The lac operon (lactose operon) is the best known example Repressor: Protein which keeps RNA polymerase from binding to the promoter site Enhancer: DNA part (aka regulator) which is very far away from the promoter. It helps transcription by working with the proteins involved in transcription Inducer: molecule that binds to and stops the repressor Differentiation: divergence in structure and function of different cells as they become specialized during development Oncogenes: cancer causing genes Proto-oncogenes: "normal" genes, the genes that code for regulatory proteins (non cancerous) GENE EXPRESSION & ONCOGENES (Summary) Gene expression is complicated, but FEAR NOT. You only need to know the basics, which is rather simple. The way most of us learn gene expression is through the example of the lac operon. The lactose operon is the group of genes involved in the process of lactose digestion (as you can probably tell by the name). It only functions if the inducer (which is lactose in this case) is present. This makes sense since the genes on the lac operon shouldn't be read if the organism doesn't need it, right? Therefore, when lactose is present, it attaches to a place near the repressor and allows for the transcription of the genes. If there is no lactose then, there is no gene transcription and thus no enzymes are made. In prokaryotes, operons are the main form of gene control and expression. In eukaryotes, there can be controls in the transcription and translation processes (just know they exist) Cancer can occur when something goes wrong and mutates a proto-oncogene into an oncogene. There are three types of mutations that can cause this: movement of DNA within the genome, a cell having too many copies of a certain oncogene, and point mutations GENE EXPRESSION & ONCOGENES (Questions/Links) Questions for you to answer: 32. Define differentiation and describe at what level gene expression is generally controlled. 33. Distinguish between proto-oncogenes and oncogenes. Describe the genetic changes that can convert proto-oncogenes to oncogenes. Links (if you have further questions): Gene Expression: f_eukaryotes/eukaryotes.html tml Oncogenes and Proto-Oncogenes: DNA TECHNOLOGY (Vocabulary) Restriction Enzymes: enzymes which cut DNA at specific places "sticky-ends": single stranded ends of DNA that occur after being cut by restriction enzymes Recombinant DNA: DNA that is a combination of DNA from different sources created through cutting DNA with restriction enzymes and connecting the sticky ends) Vector: something that moves DNA from one source to another Gel Electrophoresis: technique used to separate DNA fragments for study based on the size of the DNA fragments Polymerase Chain Reaction: technique used to make large quantities of a particular part of DNA in a short period of time DNA TECHNOLOGY (Summary) Restriction enzymes are used to cut up DNA at specific places. Different restriction enzymes cut DNA at different places along the nucleotide sequence. An example of a restriction enzyme is ECO RI. DNA cut by restriction enzymes have sticky ends which we can connect to other pieces of DNA with the help of DNA ligase. This creates recombinant DNA. An example of a vector is a bacteria plasmid which can be used to carry specific portions of human DNA (such as the part that codes for the creation of insulin) and produce enzymes and proteins that the bacteria normally cannot. Gel electrophoresis (remember doing this in Bio Honors?) is coming back to haunt you for AP Bio. Well, not really. It's rather simple, so don't worry. All you need to know is that DNA is cut up with restriction enzymes and placed in wells at the negative end of the gel. An electric current is then run through the gel, and the DNA fragments migrate down the gel to the positive end. The smaller pieces travel faster than the larger pieces. It is commonly used in forensics for figuring out whodunit or "who's the real mummy or daddy". DNA TECHNOLOGY (Summary) Cloning is how we get large quantities of a piece of DNA we are interested in. Plasmids are often used for cloning portions of DNA. Plasmids and the desired DNA are cut by restriction enzymes. They are placed together in a solution and shocked hoping to form recombinant DNA through bacterial transformation. Not every bacteria housing plasmids may take up the foreign DNA so the bacteria are tested and the ones that have not taken up the foreign DNA are killed off. Polymerase Chain Reaction works by adding DNA polymerase, nucleotides, and primers specific to the sequence of DNA that you wish to replicate to create a mixture. The mixture is heated to separate the DNA strands and then cooled to let the primers latch on. DNA polymerase then replicates the DNA over and over until a huge amount of DNA is created. DNA TECHNOLOGY (Questions) 34. Explain how the creation of sticky ends by restriction enzymes is useful in producing a recombinant DNA molecule. 35. Outline the procedures for cloning a eukaryotic gene in a bacterial pasmid. 36. Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure. 37. Explain how gel electrophoresis is used to analyze nucleic acids and proteins and to distinguish between two alleles of a gene. 38. Describe how gene manipulation has practical applications for environmental and agricultural work. DNA TECHNOLOGY (Lab/Links) AP Bio Lab you should remember and review for the AP test: Links: Polymerase Chain Reaction (nice animation and interactive site) .html Cloning: oning.shtml Stem Cells & Homeotic Genes (Summary) Stem cells are the cells from the early stages of human development that can turn into other, more specialized cells later on (such as liver cells, nerve cells, and others). They are important to medicine because they can provide a promising cure for major human diseases (such as Parkinson's and cancer). Homeotic genes are "regulatory genes" that assist in identifying and developing an organism's various body segments. Stem Cells & Homeotic Genes (Questions) 39. Describe the two important properties of stem cells. Explain their significance to medicine 40. Describe how homeotic genes serve to identify parts of the developing organism Links: Stem Cells: Homeotic Genes: Lab Reviews The AP Exam also consists of essay questions and to answer those you will need to understand 12 different labs that you have done or will have done in CLS, Bio Honors, and AP Bio. The following link: lists all 12 labs you will need to know. Some you have done already. They are LABS 2 and 6. Review those and here's your last question: 41. A divorced couple are fighting over a baby. The woman claims that the baby is hers and that her husband is not the father. The husband disagrees. There are 2 other men in addition to the husband that could be the father. Design an experiment with gel electrophoresis that will determine who the father is. Make sure to describe your steps, draw a diagram of the gel, and how you will obtain your results. To make things easier, you may choose who the real father is in designing your experiment, just make sure you let us know who you decide on. Bibliography Books: Anestis, Mark. 5 Steps to 5: AP Biology. San Francisco: McGraw Hill, 2002. Campbell, Neil A. and Jane B. Reece. Biology Sixth Edition. San Francisco: Benjamin Cummings, 2002. Massengale, C. "AP Biology Chapter Objectives and Outlines." 2005 < pter_objectives%20&%20outlines.htm>. Websites: ...
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This note was uploaded on 03/28/2011 for the course BILD 1 taught by Professor Chen during the Winter '11 term at UC Riverside.

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