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Department
Biology
Course
BIOLOGY 1A03
Professor
Lovaye Kajiura
Semester
Winter

Description
CHAPTER 3: PROTEIN STRUCTURE AND FUNCTION & RELATED LECTURES a) Describe Stanley Miller’s spark-discharge experiment. Stanley Miller Experiment was an attempt to recreate the conditions of an arcahaic earth and to see how those conditions gave rise to more complex organic compounds. Procedure: There are two flasks both connected with glass tubing. One flask contains the main gases present in archaic earth which were ammonia, methane and hydrogen gas. There were two electrodes placed in the flask which were continously producing a spark discharge. The second flask contained 200 ml of water which was boiled constantly. The water vapour from this boiled water would travel through the glass tubing and enter the flask that contained the gases and would condense back into the flask with the water. Observations: Miller noticed that the flask that contained the water was undergoing a colour change. When a sample of the water was analysed it was found to contain many complex organic compounds. b) Discuss the reasons why Miller’s results are significant to the understanding of chemical evolution. Millers results were crucial in our understanding of chemical evolution. He attempted to recreate the conditions of life on archaic earth (electrodes --> lightning..etc) and was thus able to anylize how life on earth came to be through the formation of complex organic comounds. 2. What are some of the alternative hypotheses regarding chemical evolution? The example that Dr.Kajiura mentioned in class was that of the Murchison Meteorite. This Meteorite was named after the location in which it was found (Murchison AU). When the meteorite was analyzed it was found to contain many organic complex compounds. This gave rise to the hypothesis that complex organic compounds were formed on earth through extraterrestrial means (unlike Millers experiment which proposes that complex organic compounds were formed through the conditions found on archaic earth). 3. What did the analysis of the Murchison meteorite suggest with regards to chemical evolution? When the meteorite was analyzed, it was found to contain many organic complex compounds This gave rise to the hypothesis that complex organic compounds were formed on earth through extraterrestrial means. Although, some controversy states that the meteorite may have been contaminated as soon as it came to Earth and those finding are merely caused by contamination. 4. Define the terms “monomer” and “polymer”. Monomer: A small molecule that can covalently bind to other similar molecules to form a larger macromolecule. Polymer: Any large molecule composed of small repeating units (monomers) bonded together. The main biological polymers are proteins, nucleic acids, and polysaccharides. 5. a) Draw a diagram displaying the general condensation (dehydration) reaction between two amino acids. b) What type of the bond links between the two amino acids? Show how the bond is formed and the products. 6. In lectures, we reviewed that there are 20 major amino acids in living organisms. List the three main categories of amino acids. 1. Polar Side-Chains: Partial changes can form hydrogen bonds; soluble in water. 2. Non-Polar Side-Chains: No charges or electronegative atoms to form hydrogen bonds; not soluble in water. 3. Electrically charged side-chains: charged side chains form hydrogen bonds; highly soluble in water. 7. Differentiate between three types of isomers and provide an example of each. (a) Structural Isomers: Differ in the order in which their atoms are attached. i.e. Ethanol(C 2 O6 and Dimethyl ether (C H O2 6 (b) Geometric Isomers: differ in the arrangement of atoms around a double bond.i.e. Trans-2- butene (C H4) 8nd Cis-2-butene(C H ) 4 8 (c) Optical Isomers (Stereoisomers): mirror images of one another – they cannot be exactly superimposed. i.e. Alanine 8. In lectures, we discussed that molecular structure (shape or the arrangement of side groups) is a key factor influencing function. Discuss this concept with regards to the examples of the different types of DOPA (Dihydroxy Phenyl-Alanine) as related to the treatment of Parkinson’s disease. Molecular structure (shape or the arrangement of side groups) is a key factor influencing function because in regards to the different types of DOPA (Dihydroxy Phenyl- Alanine). DOPA has an optical isomer (meaning it has a mirrored twin of itself) and the difference between the two is enormous; one helps to treat Parkinson’s disease and one is biologically inactive. Therefore, the cause of the difference in function is due to the structure; since L- DOPA looks like the mirror image of R- DOPA but only L-DOPA helps treat Parkinson’s disease. 9. An amino acid has atoms or functional groups, linked to a central carbon atom. List the groups or atoms of an amino acid. Show the groups attached to the alpha carbon of phenylalanine. The groups or atoms that make up all amino acids are: an amino group, a carboxyl group, a side group and a hydrogen atom. The groups attached to the alpha carbon phenylalanine are as follows below: an alpha carbon atom with an alpha hydrogen atom attached, a carboxyl group, an alpha amino group and a side chain. 10. List and elaborate upon the four levels of protein structure: primary, secondary, tertiary, and quaternary. The four levels of protein structure are: primary, secondary, tertiary and quaternary. First of all the primary structure is comprised of the series of unique amino acids that complete the sequence of every protein. Note that the R- group present on each amino acid affect its solubility and chemical reactivity. Some examples of primary structures are the amino acid sequences that form hemoglobin (if one amino acid in the structure is changed the structure of the protein is deformed and denatured). Second of all the secondary structure is comprised of a sequence of amino acids of a protein that are linked together in different forms through hydrogen bonding. Secondary structures are distinctively shaped sections of proteins that are stabilized largely by hydrogen bonding that occurs between the carboxyl oxygen of one amino acid residue and the hydrogen on the amino group of another. Two examples of a secondary structure are: alpha helices and beta pleated sheets (proteins can take on these structural shapes). Examples of alpha helices are finger nails and hair; an example of beta pleated sheets is silk. Third of all the tertiary structure results from interactions between R- groups or between R- groups and the peptide backbone. Each contact between R- groups causes the peptide- bonded backbone to bend and fold, each contributes to the distinctive three-dimensional shape of a polypeptide. There are four types of interactions: between hydrogen atoms and carboxyl groups, hydrophilic and hydrophobic interactions, covalent bonds that form between sulfur atoms (disulfide bonds) and ionic bonds that form between groups that have full and opposing charges. Finally, the quaternary structure is the combination of polypeptide subunits that form proteins. The individual polypeptides may be held together by bonds or other interactions among R- groups or sections of their peptide backbone. Some examples of quaternary structures are: hemoglobin, insulin and collagen. 11. What is the difference between the normal condition and the sickle cell condition with regards to the primary level of protein structure? The difference between the normal condition and the sickle cell condition with regards to the primary level protein structure is one amino acid change in the sequence that forms the protein of hemoglobin. One single change in the amino acid sequence causes red blood cells to change from their normal disc shape to a sickled shape that cannot carry oxygen throughout the body sufficiently 12. State an example of a 4 structure protein. An example of a quaternary structure is hemoglobin. 13. What is the function of chaperone proteins (or chaperonins)? The function of the chaperone proteins are is to take in unfolded proteins that have been denatured, and to refold them properly so that they function normally again. 14. What are prions and why are they significant? Prions are certain proteins that can act as infectious, disease-causing agents; they are involved in mad cow disease, mis-folded prions cause the brain of humans and other mammals to disintegrate. 15. Discuss the significance of optical isomers with regards to the thalidomide tragedy. The significance of optical isomers with regards to the thalidomide tragedy is that the difference between using the one they did in that medication versus the optical isomer of it could have prevented the tragedy from happening. Since the one used caused the blood vessels meant to go to the limbs didn’t develop properly, however the optical isomer of it would have had no effect on the blood vessels needed for the development of the babies’ limbs. CHAPTER 4: NUCLEIC ACIDS AND THE RNA WORLD & RELATED LECTURES 1. Draw a diagram of the general structure a nucleotide, and clearly label each of the components. 2. How can the structural formulas of pyrimidine’s and purines be distinguished from one another? The purines are adenine and guanine. The pyrimidines are cytosine, uracil and thymine. They can be structurally distinguished, by the number of rings in their structure. Purines have a double ringed structure, while pyrimidines have a single ringed structure. 3. Draw a clearly labeled diagram of the formation of a phosphodiester linkage. Display how the two monomers are linked and the products. 4. Describe the structure of the double helix. The structure of DNA is extremely stable which allows it to replicate itself. The DNA contains many hydrogen bonds, which allow for the structural integrity of the molecule. However, hydrogen bonds are relatively weak singularly. Due to the major grooves and minor grooves in the structure, certain enzymes such as DNA helicase are able to enter the structure and unwind the complementary base pairs. As such the DNA structure has been separated. Using the empirical rules discovered by Erwin Chargaff, it could be concluded that each DNA strand serves as a template which can now be used to form a new strand. In this case, enzymes and different types of RNA enter the structure and add the complementary base pairing by attaching free nucleotides to the structure. Soon after the helical structure is reformed and now 2 copies of that DNA exist as a result of its semiconservative manner of replicating. 5. Explain and elaborate upon how the double helix structure facilitates the copying of DNA. If the hydrogen bonds between the base pairs are broken, the DNA helix can separate. Each strand of DNA can serve as a template for the formation for a new strand. Free nucleotides attach according to complementary base pairing. When the new strands polymerize to form a sugar-phosphate backbone, secondary structure is restored. 6. Describe the technique of gel electrophoresis. Why is this technique useful for biologists? This process uses electricity to separate DNA fragments by size as they migrate through a agarose gel matrix. It is used to map the order of restriction fragments within chromosomes, to analyze DNA variation within a population by restriction fragment length polymorphisms (RFLPS) and to determine the nucleotide sequence of a piece of DNA. CHAPTER 5: AN INTRODUCTION TO CARBOHYDRATES & RELATED LECTURES 1. List some of the major functions of carbohydrates. - Energy Source: glucose is rapidly metabolized - Energy Storage: starch and glycogen - Structural support: cellulose, chitin, cartilage - Transport of energy source: sucrose (plants), lactose (milk) - Cell surface signals: cell communication and cell-cell recognition. 2. Show how ring formation occurs in glucose. Draw the ring structures and differentiate between the  and  forms. - Oxygen from the 5-carbon bonds to the 1-carbon, resulting in a ring structure - Alpha-glucose: OH group at C1 is below the plane of the ring - Beta-glucose: OH group at C1 is above the plane of the ring 3. Distinguish between the terms monosaccharide, disaccharide, and polysaccharides. Monosaccharide: a small carbohydrate, such as glucose, that has the molecular formula (CH 2) and cannot be hydrolyzed to form any smaller carbohydrates. Disaccharide: A carbohydrate consisting of two monosaccharides (sugar residues) linked together. Polysaccharide: A linear or branched polymer consisting of many monosaccharides joined by glycosydic linkages. 4. Draw a diagram of the glycosidic linkage in maltose. Clearly label the linkage and show the monomers that joined to form maltose. 5. Name the specific linkages joining the monomers in starch, glycogen, cellulose, chitin, and peptidoglycan. Starch: alpha-1, 4-glycosidic linkage Glycogen: alpha-1, 4-glycosidic linkage Cellulose: beta-1, 4-glycosidic linkage Chitin: beta-1, 4-glycosidic linkage Peptidoglycan: beta-1, 4-glycosidic linkage 6. Name examples of polymers in which the following sugars are present: ribose, deoxyribose, glucose, and galactose. - Ribose is found in RNA - Deoxyribose is found in DNA - Glucose is found in plants (used for energy), human cells; blood stream (used for energy) - Galactose is most commonly found in dairy products i.e. milk. It is broken down from lactose by the enzyme lactase to produce galactose and glucose. 7. Describe the structure of a branch point in glycogen and label the linkages. Glycogen is a chain of glucose subunits held together by alpha-1, 4 glycosidic bonds. Glycogen is a branched structure. At the branch points, subunits are joined by alpha-1, 6 glycosidic bonds. Branches occur every 8-10 residues. 8. Distinguish between the following conditions: lactose intolerance and galactosemia. Lactose Intolerance: - The inability to produce lactase (enzyme), which breaks down lactose into glucose and galactose. - Autosomal recessive trait -Diagnosis: Hydrogen breath test, stool sample **Growth hormone in cows related to acne Galactosemia: - Lacks enzyme that breaks down galactose into glucose **rare disease** - associated with renal failure, enlarged liver and cataracts in your eyes (visual acuity) and brain damage. - Can tell by chemicals and detoxification 9. Describe the symptoms of each of these conditions. Symptoms of Lactose Intolerance: -Symptoms begin anywhere from 30 minutes to 2 hours after consuming dairy - diarrhea, flatulence, gas, cramps, bloating, vomiting, etc. Symptoms of Galactosemia: - jaundice, vomiting, poor feeding, insufficient weight gain, lethargy (weak, lazy), irritability and convulsions. CHAPTER 6: LIPIDS, MEMBRANES, AND THE FIRST CELLS & RELATED LECTURES 1. State an important difference between the lipids and the other major groups of macromolecules in terms of the number of monomers and how they are linked, and their interaction with water. Lipids are largely non-polar and hydrophobic – meaning they do not dissolve readily in water (lipids do however, dissolve in non-polar organic compounds). This is because they have a significant hydrocarbon component. 2. List the main types of lipids and describe their functions. Fats: The main function of fats in the body is to provide energy. Fat also help in forming structural material of cells and tissues such as the cell membrane. They also carry the fats soluble vitamins A, D, E and K into the body and help in the absorption of these vitamins. Some fats supply essential fatty acids. Steroids: Most steroids are hormones (like glucocorticoids, testosterone, and estrogen). They are often sex hormones, or they act to regulate the immune response. The key steroid molecule, from which all other steroids are synthesized, is cholesterol. Phospholipids: 1.Act as building blocks of the biological cell membranes in virtually all organisms. 2.Participate in the transduction of biological signals across the membrane. 3.Act as efficient store of energy as with triglycerides. 4.Play an important role in the transport of fat between gut and liver in mammalian digestion. 5. An important source of acetylcholine, which is the most commonly occurring neurotransmitter substance occurring in mammals. 3. a) Draw a glycerol molecule. b) A fatty acid becomes covalently bonded to glycerol. Show the bond or linkage structure. Name the type of reaction involved in this process and state the specific linkage formed. Ester linkages join the glycerol and 3 fatty acids. This is a condensation reaction. 4. Indicate the carbon numbers of four common fatty acids. Specify which are saturated and unsaturated. Also describe how this may be indicated in their molecular formulas. FATTY ACIDS SATURATED OR UNSATURATED MOLECULAR FORMULAS Oleic Acid Unsaturated The cis double bond kinks the molecule. Stearic Acid Saturated Has a straight chain, with no double bonds Elaidic Acid Unsaturated The trans double bond does not kink the molecule Palmitic Saturated Has straight chain, with no double bond 5. List the
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