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Study Questions for Test 1.docx

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Lovaye Kajiura

Study Questions for Test #1 Chapter 3: Protein Structure and Function 1. A) Miller wanted to know if it was possible to recreate the steps in chemical evolution by simulating the Earth’s conditions. He did this by designing a microcosm of ancient Earth. A large flask (representing atmosphere) contained gases methane, ammonia and hydrogen (all have free energy) and it was attached to another flask (representing ocean) which contained 200 mL of water. As miller heated the water, vapour circulated continuously through the system. If the molecules in the simulated atmosphere reacted with one another, the rain would carry them to the ocean, creating a simulated version of the prebiotic soup. Miller then started sending electrical discharges across the electrodes and the experiment, driven by heat energy and the energy in the electrical discharges had recreated the start of chemical evolution. B) Miller proved that Chemical evolution readily occurs if simple molecules with high free energy are exposed to a source of kinetic energy. The sparks and heating had led to the synthesis of compounds that are fundamental to life: amino acids. 2. Alternative hypothesis regarding chemical evolution include Murchison meteorite (macromolecules came extraterrestrially) and hydrothermal vents (macromolecules came from water). 3. This suggested origin of life may have come extraterrestrially instead of by chemical evolution and macromolecules may have been found on the surface of a meteorite. 4. “Monomer” refers to a subunit or building black of a polymer where as a “polymer” refers to large molecules composed of several connected subunits, which are identical or similar. 5. A) B) Peptide bond between the carboxyl group of one and the amino group of the other. 6. The three main categories of amino acids are: Nonpolar, polar and electrically charged. 7. The three types of isomersare : 1. Structural isomers: have the same atoms but differ in the order in which covalently bonded atoms are attached. Ex: ethanol and Dimethyl ether 2. Geometric Isomers: have the same atoms but differ in the arrangement of atoms or groups on either side of a double bond or ring structure. Ex: trans-2-butene and cis-2-butene 3. Optical isomers: have the same atoms but differ in the arrangement of atoms or groups around a carbon atom ( are mirror images of each other and cannot be superimposed) Ex: all amino acids except Glycine have optical isomers/ L-Dopa and D-Dopa 8. There are two types of Dopa: L-Dopa; the beam of light reflected through it will go to the left and D-Dopa; the beam of light reflected through it will go to the right. They are optical isomers and thus, both have the same structural formula. However, only L-Dopa is effective against Parkinson’s disease. 9. All amino acids have a central carbon attached to an amino functional group, a carboxyl functional group, a hydrogen atom and a side chain, or R-group. In the case of phenylalanine, the R-group is a Ch2 molecule attached to a ring structure. 10. Primary: the unique sequence of amino acids in a protein that are stabilized by peptide bonds. Secondary: distinctively shaped sections of proteins that are stabilized largely by hydrogen bonding that occurs between the carboxyl oxygen of one amino acid and the hydrogen on the amino group of another. (Alpha helices and beta pleated sheets). Tertiary: This is a shape formed by side chain interactions which include: ionic bonds, hydrogen bonds, disulphide interactions, and van der walls interactions. Quaternary: Combination of polypeptide units or a complex protein that is attributed to the 3-D arrangement of its subunits. 11. In some individuals, haemoglobin has a Valine instead of a glutamate at the amino acid numbered 6. Valines side chain is very different from the R-group in glutamate. The change results in a protein that that tends to crystallize instead of staying in solution when oxygen concentrations in the blood are low and when haemoglobin crystallizes, the rbcs that carry the protein adopt a sickle shaped and can no longer efficiently transport oxygen. 12. Examples of a 4 structure protein are: Haemoglobin, Collagen, Insulin and any kind of enzymes. 13. Chaperone proteins facilitate folding for renaturation after proteins are denatured. 14. Certain infectious, disease causing proteins are called prions. They are misfolded proteins that can induce other proteins to take the altered form. Ex: mad cow disease. 15. Thalidomide is a combination of two optical isomers; one was used to reduce morning sickness (sedative) while the other interfered with blood vessel development and resulted in babies being born with missing limbs. This drug may be used for cancer as it can cut off blood supply to cancerous tumours, slowing growth. Chapter 4: Nucleic Acids and the RNA World 1. Nitogenous base is attached to carbon #1 of the sugar while the phosphate group is attached to carbon #5. 2. Purines are double ringed and include: Guanine and Adenine. Pyrimidines are single and include : Cytosine, Uracil, Thymine (CUT) 3. The polymerization reaction involves the formation of a bond between the phosphate group of one nucleotide and the hydroxyl group of the sugar component of another nucleotide. The result of this condensation reaction is called a phospodiester linkage or bond. 4. Two antiparallel strands twist into a double helix, with the sugar phosphate backbone on the outside and the nitrogenous bases on the inside. The molecule is stabilized by hydrophobic interactions between the bases in its interior and by hydrogen bonding between the complementary base pairs A-T and C-G. Rosalind Franklin discovered, through her work in X-ray crystallography, key measurements that were continuously repeated throughout the structure. These numbers are 3.4 nm (the length of one turn of the helix which is also 10 rungs), 0.34 nm (the distance between two bases) and 2.0 ( the width of the helix). Furthermore, the strands on the DNA run antiparallel which supports the finding that the structure of the DNA is a double helix. 5. 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 if 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 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 can 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. 6. Gel electrophoresis is a technique used to separate DNA, RNA, or protein molecules using an electrical field applied to a gel matrix.In order to separate the different fragments, the DNA is added to a gel-like matrix. Later, an electrical current is passes through the matrix and separates the different sized molecules on the basis of their molecular weight. The smaller the molar mass of the molecule the farther down it will travel across the gel matrix It is useful to biologists for: * diagnosing genetic diseases * genetic engineering (recombinant DNA) * evolutionary relationship between plants and animals Chapter 5: An Introduction to Carbohydrates 1. The major functions of polysaccharides include: energy source, energy storage, transport of energy source, structural support and cell surface signals. 2. In aqueous solutions, carbohydrates tend to form ring structures. In glucose, the carbon that is numbered 1 in the linear chain forms a bond with an oxygen atom and with a hydroxyl group that can be oriented in two ways. The differences between the two forms lies in whether the hydroxyl group on carbon number 1 is above (Beta-Glucose) or below (alphs-glucose) the plane of the ring. The beta form is more common because it is more stable than the alpha form. 3. Monosaccharaides: simple/single sugars such as Ribose, Deoxyribose, Glucose and Galactose Disaccharides: double sugars that consist of two monosaccharaides, which are joined by a condensation (dehydration) reaction. Ex: Maltose, Sucrose, Lactose Polysaccharides: are sugars that form when many sugar monomers combine. Ex: Starch, Glycogen, Cellulose, Chitin and Peptidoglycan 4. The hydroxyl groups from the 1-Carbon of the first alpha glucose and 4-Carbon of the second alpha glucose react to produce an alpha 1,4-glycosidic linkage and water. Two alpha glucose react to form Maltose. 5. Polymers Linkages Starch –Amylose -Alpha 1-4 glycosidic linkages ( unbranched) -Amylopectin -Alpha 1-6 and alpha 1-4 glycosidic linkages (branched) Glycogen Alpha 1-6 and alpha 1-4 glycosidic linkages(branched) Cellulose Beta-1,4-glycosidic linkages Chitin Beta-1,4-glycosidic linkages Peptidyglycan Beta-1,4-glycosidic linkages 6. Ribose- RNA Deoxyribose- DNA Glucose- starch, glycogen Glycogen- lactose 7. Glycogen is a polymer of alpha glucose monomers and has alpha-1,6-glycosidic linakges occurring in every 10 glucose subunits which is why it is highly branched. It also has alpha-1, 4-glycosidic linkages. 8. In Lactose Intolerance, adults do not produce the enzyme, lactase, which splits lactose into glucose and galactose. At the exposure of lactose, individuals may show symptoms such as bloating,
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