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Transcript
Modified from Carley Karsten Lecture 8-10 Study Guide I have organized some terms and topic that I think are important. This does not mean that other topics mentioned during lecture or in the book will not be tested. This guide is meant to clarify and emphasize certain points, NOT to list everything you need to know. I will focus on tying things together across lectures, and giving real-life examples of the biological principles that we are learning. Details that I include that I think will be helpful, but that you don’t need to know, I will write in green. Questions to think about I will write in blue. Lecture 8: Carbohydrates and lipids Chemistry review: 1. Valence electrons = electrons in the outer ring of an atom that participate in bonding. These are the atoms that are SHARED in covalent bonds, and EXCHANGED in ionic bonds. a. atoms generally “want” to have eight electrons in their outer ring: bonds form so that as many atoms as possible can fill their outer rings. b. for the purposes of this class, remember that these common atoms have the listed number of valence electrons: Hydrogen – H – 1 *Hydrogen is unique because it only needs 2 valence electrons (rather than 8, like other atoms) in order to be stable. Carbon – C – 4 Nitrogen – N – 5 Oxygen – O – 6 c. Consider water: H—O – H Each H has one valence electron to share, and needs one more electron to feel stable (remember, hydrogen only wants 2). The O has six valence electrons to share, and needs two more to feel stable (it wants 8). When we put them all together, each H shares its single valence electron with O, giving O 8 total electrons, and O shares one extra valence electron back with each H, giving each H 2 total electrons. Draw a diagram like this one, pushing electrons around, to show how an ionic bond forms between Na (one valence electron) and Cl (7 valence electrons). Where do the charges on the atoms come from? 2. Drawing carbon-based molecules: in organic chemistry every point is a carbon and CH bonds are not shown. Look at the following examples: Name All atoms shown Structurally Accurate Short Hand Modified from Carley Karsten Propane C3H8 Isopropanol C3H80 I will be using this drawing style throughout this guide and my discussion. Please let me know if you have questions. Functional groups 1. Hydroxyl 2. Carbonyl 3. Carboxyl 4. Amino 5. Sulfhydryl 6. Phosphate 7. Methyl -OH -C=O -COOH -NH2 -SH -PO4 -CH3 polar polar polar / acidic polar / basic polar ionic nonpolar important for hydrogen bonding can give up an H to make –COOcan accept an H to make –NH3+ covalent bonds can form between –SH groups makes molecules unstable. source of energy. binds to nucleotides to change gene expression Carbon-based macromolecules = carbohydrates + proteins + lipids + nucleic acids 1. all are polymers in the sense that they are strings of smaller units connected by covalent bonds, BUT lipids are technically NOT polymers because their subunits are not all the same. a. polymerization = addition of monomers = lengthening of polymer = dehydration / condensation reaction Why is this called “dehydration”? (think about the role that water plays in the reaction) b. depolymerization = removal of monomers = shrinking polymer = hydrolysis 2. Carbohydrates a. polar molecules b. monomers = monosaccharides. Glycosidic bonds form between subunits. c. often contain hydroxyl, carbonyl, and methyl groups d. used for energy storage and cell structure 3. Lipids a. hydrophobic molecules b. ester linkage = bond between subunits c. rich in nonpolar functional groups made of lots of C—H bonds d. three types of lipids i. fats = glycerol + 3 fatty acids. What is the difference between saturated Modified from Carley Karsten and unsaturated fats? Why are saturated fats generally worse for health than unsaturated fats? ii. phospholipids = glycerol + 2 fatty acids + phosphate group + choline. Don’t worry about choline. What’s important here is that phospholipids are amphipathic- they have both hydrophobic and hydrophilic domains. This is very important for the plasma membrane, as you may remember. iii. steroids = based on carbon rings, therefore nonpolar. example: cholesterol. Lecture 9: Proteins Proteins do all the exciting things in cells: transmit signals, catalyze reactions, transport molecules and organelles, and more! Enzymes and receptors are both specialized types of proteins. Protein structure 1. Proteins are polymers. monomers = amino acids; polypeptide = string of amino acids. protein = polypeptide with 3D structure (folding, coiling, etc.) a. amino acids = amino group + α carbon + side chain + carboxyl group. The backbone of any polypeptide will follow this same pattern: The amino acid “backbone” is shown in blue. This is the repeating pattern (NC-C) that you should look for to identify a polypeptide. Note that the center carbon is the “α carbon”, or the carbon with a side chain (“R group”). Question: when a dehydration reaction takes place, which Hs and O leave as water? b. the side chain (or R group) is what determines how an amino acid behaves. If you are asked to identify whether an amino acid is polar, nonpolar, or ionized, look at the side chain ONLY. The amino group and the carboxyl group in the amino acid backbone are part of EVERY amino acid, and thus don’t affect any single amino acid’s function. The side chain is what matters!! c. amino acids are connected by peptide bonds (which are covalent bonds) that are formed by dehydration reactions *Note: polypeptides, cytoskeletal filament polymers, polysaccharides, and nucleic acids ALL use dehydration reactions to form. They also all have polarized ends – for example, microtubules have plus and minus ends, polypeptides have amino and carboxy ends, and nucleic acids have 5’ and 3’ ends. d. polarized ends: i. amino end = “N terminus” because it’s based on –NH2 group ii. carboxy end = “C terminus” because it’s based on –COOH group 2. four levels of protein structure Modified from Carley Karsten a. primary: amino acid sequence. determined by covalent (peptide) bonds between amino acids. b. secondary: coils and folds. determined by hydrogen bonds between amino and carboxy groups in the backbone. c. tertiary: complex folding. determined by all kinds of bonding between any of the different R groups. strongest possible R group interactions are between two amino acids containing sulfur (disulfide bridge). d. quaternary: two or more polypeptides interacting. 3. environmental effects on protein structure a. pH / salt concentration / temperature: usually only affects higher levels of structure, but if you get REALLY extreme then you can mess up even primary structure. Why would this be? (think about the kinds of bonds involved in primary structure vs. secondary or tertiary structure) b. chaperone proteins help proteins to fold correctly, and to STAY folded correctly c. proteins that aren’t folded properly are degraded by proteasomes (remember: enzymes are usually named with “-ase” at the end… “proteasome” = “protease” = “protein” – “ase” = something that chops up proteins) Lecture 10: Nucleic acids and ATP Nucleic acid structure = string of nucleotides 1. nucleotide = nitrogenous ring + sugar + phosphate group(s) a. nitrogenous ring = rings made of carbon and nitrogen. Either pyrimidine (one ring) or purine (two rings). i. pyrimidines = C, T, U (T exists only in DNA, and U exists only in RNA) ii. purines = A, G b. sugar = 5-carbon ring. DNA uses deoxyribose, RNA uses ribose. Deoxyribose = ribose without a hydroxyl group (“de-oxy” means “without oxy”). c. phosphate group = -PO4. Important for linking together the sugars of adjacent nucleotides to make a polynucleotide. 2. DNA is double stranded: THIS IS IMPORTANT! a. the double helix structure is formed from hydrogen bonds between base pairs. We will talk more about this in a couple weeks when we get into transcription, etc. b. considering the sugar/phosphate backbone of DNA, there are two distinct ends: i. phosphate end – 5’ ii. hydroxyl end – 3’ these ends arrange “antiparallel” to each other. That is, the 5’ end of one strand of the DNA double helix will be next to the 3’ end of the other strand. Again, we will talk more about this in a couple weeks. For now, just remember the term “antiparallel” Energy 1. EXERGONIC reactions: HIGH low energy state. May also think about this as going from an unstable to a stable state (e.g. a molecule losing a phosphate group). Since the system is losing energy, these reactions can occur spontaneously. Modified from Carley Karsten 2. ENDERGONIC reactions: low HIGH energy state. Alternatively, going from a stable to an unstable state (e.g. adding a phosphate group to a molecule). These reactions require an input of energy to occur. Thus, they can’t occur spontaneously. 3. ATP is the most common source of cellular energy because it can donate phosphate groups. a. ATP = ribose + adenine + 3 phosphate groups. b. The three phosphate groups are what make ATP so energetic: all those negative charges crammed together “want” to get away from each other. When they do, ATP goes from a high energy state (3 phosphates, unstable) to a low energy state (2 phosphates, stable), thereby releasing energy (exergonic reaction). Question: look at the structure of ATP. Which other macromolecule does it most resemble? (carbohydrates, lipids, proteins or nucleic acids) 4. ATP is constantly regenerated a. cellular respiration (more details in the next lecture) uses fuels such as glucose to CREATE more ATP b. ATP hydrolysis occurs all the time and everywhere in order to power cellular activities such as transportation, signal transduction, and building macromolecules 5. Enzymes a. allow reactions to occur using LESS ENERGY by changing the shape or location of reagents b. allow reactions to happen FASTER because there is less energy needed c. allow reactions to be SPECIFIC because the shape of the active site is specific d. enzymes are usually named with “-ase” at the end, and whatever comes before the “-ase” usually gives some hint as to what the enzyme acts on (e.g. peptidase breaks down peptides; lipase breaks down lipids; cellulase breaks down cellulose; lactase breaks down lactose… people lacking the enzyme lactase are unable to digest lactose, a sugar found in milk, and become lactose intolerant)