Cell Molecular Biology- Chapter 1 and Chapter 2 Course Objectives
Cell Molecular Biology- Chapter 1 and Chapter 2 Course Objectives Bio 214
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This 4 page Study Guide was uploaded by Lauren Maddox on Saturday March 12, 2016. The Study Guide belongs to Bio 214 at James Madison University taught by Dr. Doyle in Fall 2015. Since its upload, it has received 33 views. For similar materials see Molecular and Cell Biology in Biology at James Madison University.
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Date Created: 03/12/16
BIO214 - Chapter 1 and 2 Objectives After completing chapters 1 and 2, you should be able to answer the following questions. 1. What are the three tenets of Cell Theory? (Chapter 1) 1. All organisms are composed of one or more cells. 2. The cell is the structural unit of life. 3. Cells can only arise by division from a pre-existing cell. 2. How are prokaryotic cells similar to eukaryotic cells? How do prokaryotes differ from eukaryotes? (Chapter 1) Eukaryotic has nucleus. Prokaryotes are tiny, have tough protective cell wall. Pro’s reproduce by dividing into two. Pro’s can live in an inorganic substances. Eu’s are bigger and more complex, can live in single celled organisms or multicellular assemblies. Membrane-enclosed organelles. They have the nuclear envelope. They have a mitochondria, and an ER. 3. What do ‘the Unity of Life’ and how does that tie into the Central Dogma mean? (Chapter 1) they are building blocks, they have genetic instructions- DNA. Flow of information- dna to rna to protein- central dogma. Everything is made from cells. In every cell DNA is made from the same set of four monomers, called nucleotides, strung together in different sequences. In every cell, the information encoded in the DNA is read out, or transcribed into a chemically related set of polymers called RNA. A subset of these RNA molecules is in turn translated into yet another type of polymer called a protein. 4. How can many different types of cells be produced in an organism, when all cells have the same DNA? (Chapter 1) 5. When is an atom most stable? As a consequence of this, how many bonds does a carbon atom form? Most stable when the electron shells are filled. Carbon can only form four bonds 6. What are the following organic chemical groups? alcohol or hydroxyl group, carboxyl group, carbonyl group, phosphate group, amino, methyl, and sulfhydryl groups. Be familiar with which of these can act as acids and bases in the cell (see Panel 2-1, also your lecture notes for the structures of the functional groups). –OH is the hydroxyl group. C=O is the carbonyl group. –COOH is the carboxyl group, in water it loses an H+ ion to become –COO-. Methyl- CH3-. Phosphate is O=p-O-O. Amino group- H2N. R-S-H is sulfhydryl 7. What is electronegativity, and how can this affect the properties of a chemical bond? Varies in number of protons, how far the outer electrons are from the nucleus. Electronegative atoms exert a greater attractive force on shared electrons. They will generate a partial positive or partial negative charge. They form polar covalent bonds 8. Covalent bonds and polar covalent bonds – how do these differ? Polar covalent bonds can lead to s+ and s- charges on the surface of a molecule. If the charges match, molecules can interact. Weak ionic interactions-strength in numbers. If hydrogen is involved- hydrogen bonds. Polar covalent bonds give water unique properties-h20 forms hydrogen bonds-thermal properties. Molecules that can also form hydrogen bonds-very soluble in water. Covalent bonds- sharing of electrons, balance of forces. Covalent bonds formed when two atoms share a pair of electrons. Covalent bonds in which the electrons are shared unequally are known as polar covalent bonds. 9. Please describe each of the following non-covalent interactions, including: ionic attractions, hydrogen bonds, van der Waal's Forces, and Hydrophobic Forces. Which are the strongest and which are the weakest? Hydrogen bond- weak attraction between electronegative atom and a hydrogen bonded to an electronegative atom. Important in the folding of a polypeptide chain and in holding together the strands of a double stranded DNA molecule. Hydrophilic- loves water. Hydrophobic- hates water, uncharged, with few or no hydrogen bonds. Holds together phospholipid portions of dissolved molecules in order to minimize their disruptive affect on the hydrogen bonded network of water molecules. It makes proteins to function as enzymes possible. Van der Waals attraction- non-covalent, a form of electrical attraction caused by fluctuating electric charges that arise whenever two atoms come within a very short distance of each other. Play role in the attraction between macromolecules with complementary shapes. Ionic bonds are formed when electrons are donated by one atom to another. Ionic is much weaker than covalent in water. Hydrophobic is stronger than hydrogen and van der Waals. Hydrogen is stronger than van der Waals. 10.What are the four classes of ‘macromolecules’ and what is the monomer, or building block, for each class? What are the basic functions of these main categories of molecules? Sugars-polysaccharides, glycogen, and starch (in plants). Sugars are carbohydrate monomers. Sugars can form interchangeable stereoisomers- alpha and beta. Sugars are linked by condensation reactions. Once they are linked, sugars are locked in the alpha or beta configuration. Monosaccharaides can be linked by covalent bonds-glycoside bonds- to form larger carbohydrates. Glucose is broken down, releasing energy that the cell can harness to do useful work. Cells use simple polysaccharides composed only of glucose units-principally glycogen in animals and starch in plants, as long term stores of glucose, held in reserve for energy production. They also make mechanical supports-cellulose forms plant walls. Smaller oligosaccharides can covalently linked to proteins to form glycoproteins or to lipids to form glycolipids. The sugar side chains of these two in the plasma membrane are thought to help protect the cell surface. Fatty acids- fats and membrane lipids. They serve as a concentrated food reserve in cells- broken into energy. They are stored in the cytoplasm, in the form of fat droplets composed of triacylglycerol molecules. When a cell needs energy, the fatty acid chains can be released from triacylglycerol’s and broken down into 2 carbon units. Amino acids-proteins. A peptide chain holds amino acids together. All amino acids exist as optical isomers in p-forms and L-forms, L-forms are found in proteins. Nucleotides- nucleic acids. Pyrimidine’s- C, T, AND U. Purines- G and A. Nucleotides can be short term carriers of chemical protein. ATP participates in the transfer of energy in hundred of metabolic reactions. Nucleotides have role in the storage and retrieval of biological information. RNA contains A, G, C, and U. DNA contains A, G, C, and T. DNA is more stable, with hydrogen bonded helices, and is a long term repository for hereditary information. RNA is a more transient carrier of molecular instructions. 11.Describe each of the following classes of molecules – what kinds of atoms are present in each? carbohydrate, nucleic acid, amino acid, or fatty acid. You will have to be able to identify what class a molecule belongs to on exams. Sugars- CH2OH, H, C, HO. Fatty Acid- O=C, HO on one side, H on the other, lots of H-C- H bonds. Amino acids- H2N, H, C, CH3, COOH-à H3N, C, H, COO. H2N is an amino group, COOH is a carboxyl group, and CH3 is side chain. Nucleotide- O- P=O-O, CH2-C-H, H-OH, H-C=N-C, NH2-C=N-C-H 12.How are fatty acids used to build up fats and phospholipids using a glycerol molecule? Fatty acids are stored in the cytoplasm of many cells in the form of fat droplets composed of triacylglycerol molecules- compounds made of 3 fatty acid chains covalently joined to a glycerol molecule. When a cell needs energy, the fatty chains can be released from triacylglycerol’s and broken down into 2 carbon units. In phospholipids, the glycerol is joined to two fatty acid chains. The remaining –OH group on the glycerol is linked to a hydrophilic phosphate group, which is then attached to a small hydrophilic compound. 13.How do phospholipids and other amphipathic molecules arrange chemically in an aqueous solution? Phospholipids have 2 fatty acids and a phosphate group attached to the glycerol. They aggregate to form cell membranes. They spread out over the surface of water to form a monolayer, with their hydrophobic tails facing the air and their hydrophilic heads in contact with the water. 14.What do the terms saturated and unsaturated mean? Saturated-has no double bonds between its carbon atoms and it contains the maximum number of hydrogen’s. Unsaturated- one or more double bonds along their length. These double bonds create kinks in the hydrocarbon tails, interfering with their ability to pack together, and it is the absence or presence of these double bonds that account for the difference between hard(saturated) and soft (unsaturated) fats. 15.What are steroids? What class of compounds do they best fit in with? Fatty acids- 16.What is the general structure of an amino acid? Be able to circle the R group, if given a drawing of an amino acid on the exam! If given the structure of an R group, or side chain, be able to tell what category that amino acid belongs to. Amino acids- all possess a carboxylic acid group and an amino group, both linked to their alpha carbon atom. MEMORIZE THE STRUCTURES 17.What are the four categories of amino acids, and what are two members of each category? Basic amino acids-positive charge at neutral pH- lysine, arginine, and histidine. Acidic amino acids- negative charge at neutral pH- aspartic acid, glutamic acid. Uncharged polar amino acids- serine, threonine, tyrosine. Nonpolar amino acids- lucine, proline 18.What is a peptide bond? Be able to circle one on an exam. The covalent bond between two adjacent amino acids in a protein chain. They are formed by condensation reactions that link one amino acid to the next. 19.What are the differences between RNA and DNA in terms of their chemical structure? RNA- contains the bases A, G, C, and U. DNA- contains A, G, C, and T. 20.How nucleotides are put together into nucleotide chains? What are the 5' and 3' ends – how do they differ? One chain of a DNA molecule- nucleotides are connected on sugar-phosphate backbone, phosphodiester linkages, nitrogenous bases form ladder rungs. 5’ is phosphate group and 3’ end is sugar group. The long polymers are where nucleotide subunits are linked by the formation of covalent phosphodiester bonds between the phosphate group attached to the sugar of one nucleotide and a hydroxyl group on the sugar of the next nucleotide. Nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by a condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation. 21.In general terms, how are macromolecules made? Adding subunits assembles macromolecules. Different type of subunits results in different type of macromolecule. They have different proteins. Subunits are added by condensation reactions, covalent bonds are formed between each subunit, with the loss of water. An enzyme is needed to break the subunits a part. Non- covalent bonds are what is holding the shape together. Ionic bonds between dna and protein. Hydrogen bonds between strands of dna. Macromolecules are made from a set of monomers that are slightly different from one another. The polymer chain is not assembled at random from these subunits; they are added in a particular order- a sequence. The single covalent bonds allow rotation of the atoms they join-polymer has great flexibility. This allows the single-chain macromolecule to have unlimited number of shapes. The weaker interactions however make the polymer adopt a shape, which is determined by the linear sequence of monomers in the chain. These conformations determine the chemistry and activity of these macromolecules and dictate their interactions with other biological molecules.
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