Lecture Notes Miderm1.docx

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University of California - Santa Barbara
Molecular, Cellular & Develop. Biology

Lecture 9-30-13 1. Review of cells a. Outside= lipid plasma membrane (olive oil) b. Nucleus contains genetic material (DNA, RNA) c. Pores facilitate entrance into cell d. Mitochondria (ENERGY) from food i. ATP e. Ribosomes = sites of protein synthesis i. Ribosomes decide what stays/ what leaves cell 1. Free ribosomes in cytoplasm 2. Bound in endoplasmic reticulum f. Cytoskeleton (like bones for cell) i. Fibers constantly changing shape 2. Plant cells a. Very strong cell wall “armor” b. Protects inside from water c. Chloroplasts (where plans do photosynthesis) 3. Biochemical point of view a. Chemical systems contain info & capability to grow & reproduce 4. Chemical structure a. “structure determines function” b. Building blocks of life i. What’s special about H, O, N, C? 1. Smallest atoms that form most stable covalent bonds 2. O, N, C readily form double bonds=strength & versatility 3. Carbon is especially remarkable a. Can stably single, double, or triple bond to itself b. Aliphatic chain = hydrocarbon chain 5. What else in cell? a. Phosphorus & sulfur b. Carriers of energy c. Protein structure d. Sulfur engaged in re-dox rxns 6. Molecules react a. Functional groups aka reactive groups= space of interaction (rxn) 7. Chemical bonds & forces a. Covalent bonds = strong (share e- pairs) i. In order to break covalent bonds (strong) 1. Need a catalyst (enzyme) – usually protein 2. Don’t need enzymes to break weak forces b. Ionic bonds: opposite charges c. Hydrogen bonds (polar aka asymmetry charge) i. Strong bc of small bond length d. Hydrophobic interactions (polar & nonpolar) e. Van der Waals: between nonpolar molecules 8. Macromolecules i. Proteins aka polypeptides 1. Monomer: amino acid ii. Carbohydrates aka polysaccharides 1. Monomer: monosaccharide (sugar) iii. Nucleic acid 1. Monomer: nucleotide iv. Lipids 1. Monomer: fatty acids b. Macromolecules built by condensation/ dehydration rxns i. Require ENERGY input (ATP) ii. Hydrolysis reactions= opposite of condensation rxns 1. Don’t need ENERGY input Lecture 10-1-13 1. H, O, N, C most common elements because they’re small a. Readily form double bonds b. Strength & versatility c. Carbon i. 4 valences ii. can bond to itself iii. aliphatic chain = hydrocarbon chain 2. Functional groups (intermolecular interaction) a. Hydroxyl –OH b. Carboxyl-COOH c. Amino-NH 2 d. Phosphate- PO 43- e. Sulfhydryl –SH 3. Condensation/ dehydration rxn requires ATP (ENERGY) a. ATP i. Adenine (aromatic bases) ii. Ribose (5-carbon sugar) iii. 3 phosphate groups 1. AMP (1 phosphate) 2. ADP (2 phosphates) 3. ATP (3 phosphates) a. ATP ADP +P i 4. LIPIDS i. Small macromolecules ii. Basis of cell membranes (outside of cell) iii. Important Energy storage material b. Fatty acids differ i. Length (usually 14, 16, 18 Carbons) ii. Saturation 1. Saturated: free-rotation 2. Unsaturated: rigid, less flexible, has kink in structure a. Less easy to stack together c. Glycerol = 3 carbon sugar d. Triglyceride= glycerol + 3 fatty acids + 3 ATP i. Used for stored energy (can be broken down form ATP) ii. Almost no charge asymmetry (insoluble) “oil drops” 5. Membranes i. Phospholipid: glycerol& 2 fatty acids ii. Polar head & nonpolar tail 1. Amphipathic = both hydrophilic & hydrophobic b. Phospholipid bilayer = membrane i. Function 1. Delineate cell limits (good in, bad out) 2. FLUID MOSAIC MODEL i. Basic structure of bio membranes ii. Lipid bilayer like “oil” iii. Need pores as channels (VIP entrances) b. Transmembrane proteins get things across i. All steroids have same carbon ring structure Lecture 10-2-13 1. Lipids = small macromolecules a. Cell membranes i. Plasma membrane on outside of cell ii. Organelles iii. Nucleus, mitochondira, ER, golgi, lysosomes b. Fatty acids & glycerol i. Fatty acids= long amphipathic chain + carboxyl group 1. Saturated: single bonds, flexible 2. Unsaturated: double bonds, rigid 3. Used for lipid bilayer (cell membrane) 2. Polysaccharides = polymers of sugars a. General formula : (CH 2) n b. How sugars differ i. Number of carbons (3-7) ii. Orientation of H/OH @ each carbon iii. Ex: cellulose 1. Plant cell wall “armor” 2. Beta-1,4 glycosidic linkages c. Starch & glycogen  energy storage i. Fuel can drive ATP synthesis d. Cellulose- linear e. Starch- branched f. Glycogen – highly branched i. Glycogen is “glucose in the bank” 1. Can break glucose molecule for ENERGY ii. Human glycogen storage diseases 1. Von Gierke Disease a. Patients build glycogen stores butcant access it 2. Cori’s disease a. Make glycogen incorrectly b. Can’t access it with regular mechanisms 3. Proteins a. Most abundant molecules & most versatile in cell Enzymes Speed up biochemical rxns Structural proteins Provide physical stability & movement Defensive proteins Regulate & respond to nonself (i.e. antibodies) Signaling proteins Control physiological processes (i.e. antibodies) Receptor proteins Receive & respond to chemical signals Membrane transporters Regulate passage across cell membrane Storage proteins Store amino acids Transport protein Bind & carry things around organism b. How can proteins do so much? i. 20 different amino acids ii. proteins can be chains of thousands of aa’s long 1. vast # of possibilities of aa’s c. Generic amino acid structure has 1 amino group & 1 carboxyl group Lecture 10-4-13 1. Polysaccharides a. Glucose (α & β) i. Alpha: we can digest (helix) ii. Beta : cellulose sheets (ribbons) “we don’t eat wood) 2. Proteins do so much (versatile) a. But not genetic material b. Amino acids i. Have amino group ii. Have carboxyl group iii. 20 diff kinds 1. 5 aa’s have +1/-1 charge (polar) 2. 5 aa’s have charge asymmetry (polar) 3. 7 aa’s are nonpolar 4. 3 special a. proline has kink b. glycine most simple (has nothing but 1H) c. cysteine i. has sulfhydryl group ii. can form covalent disulfide bond c. How do we build proteins? i. Covalently attach aa’s  long chains ii. Fold them into 3-D shapes 1. Use condensation/dehydration rxn (ATP) 2. Form peptide bond between aa’s iii. Why do we fold proteins 1. Max “weak forces” a. Hydrogen, ionic, van der waals, hydrophobic 2. Minimize “bad stuff” d. 4 levels of protein structure i. Primary : amino acid monomers w/ peptide linkage ii. Secondary: α-helix or β-pleated sheet 1. Alpha helix (pauling) a. H-bonds 4 amino acids away w/ the coil b. We form αhelix if R groups allow it 2. Beta sheet a. aa’s can be any distance apart b. needs to be antiparallel to form c. must alternate for structure to form properly iii. Tertiary structure 1. Intramolecular folding a. Most commonly w/ weak forces b. Exception w strong bonds i. Covalent bonds can form under oxidizing conditions (outside cell) between 2 cystines disulfide bridge ii. Covalent bonds don’t form under reducing conditions (inside cell) iv. Quaternary structure 1. Intermolecular folding interactions a. Multiple independent polypeptide chains b. Form non-covalently c. 2+ subunits held together by many weak forces (stable) d. ex: hemoglobin (2 αHb & 2 βHb snuggle together) e. ex: antibodies: chains held together w/ covalent disulfide bonds 2. *some proteins have no 4° structure (i.e. lysosome) e. Protein denaturization i. Disrupts the 3° & 2° structure of a protein & destroys protein’s bio functions 1. Heat 2. Change pH 3. Expose hydrophobic part  protein precipitates out of sol f. Renaturation: assembly into functional protein (sometimes possible) g. Chaperonins i. Protein needs help ii. Enters barrel & lid “milkshake” iii. Leaves w correct folding h. Mutations i. Errors in primary protein sequence ii. Alters protein structure & fxn Lecture 10-7-13 1. Mutations a. i.e. Color blindness b. change in protein structure & function c. β- Hemoglobin i. sickle cell ii. change in 1aa’s mutation iii. β Hemoglobin A (normal) #6 aa is glu – iv. β Hemoglobin S (sickle cell) #6 aa is val – 1. hydrophobic, nonpolar 2. How are proteins synthesized? a. Nucleic acids i. Monomers: nucleotides (3 components) 1. Aerobatic base (5) i.e. A, T,C, G, & U for RNA) 2. Ribose or deoxyribose 3. 1,2, or 3 phosphates 3. DNA vs. RNA a. Sugar: deoxyribose vs ribose b. Bases: DNA (A,C ,T ,G) but RNA (A,C, G, U) 4. Linking Nucleotides Together a. Condensation/dehydration rxn i. Energy different than protein/lipid/sugar synthesis b. In nucleotide, have: nucleotide triphosphate i. Break 2 phosphate group in ATP ii. Monomer in nucleic acid synthesis 5. What is chemical nature of genetic material? a. Griffith Experiment i. S bacteria (virulent) ii. R bacteria (nonvirulent) iii. S- cell debris (harmless) & R- cell (harmless) mixed together = harmful B.I.: What is transferred from S-cell debris to R-cells? Which sample can transform R-cells  S cells? * DNA = genetic material b/c tube #3 had no S-cells (need DNA) b. DNA facts i. Only found in nucleus ii. Amount of NDA – constant except for reproductive cells (half DNA) iii. DNA never degraded (under normal circumstances) Lecture 10-8-13 1. Nucleic acid (made of nucleotides) a. Base (5 types) i. Purines (2) bigger ii. Pyrmidines (3) smaller b. Sugar i. Ribose ii. Deoxyribose c. Add phosphate group 2. Linking nucleotides together a. Break phosphate groups w/ condensation rxn b. Form phosphodiester linkage + water 3. Hershey & Chase experiment (DNA, not protein is genetic material) a. Phage= viruses that infect bacteria i. Can hi-jack cell to duplicate phage into hundreds ii. Marked DNA & protein w/ radioactive materials iii. Looked in supernatant fluid (light enough to enter cells) & found DNA 4. Structure of DNA a. Double stranded helix b. 2 sugar phosphate backbones on outside c. bases on inside d. 10 base pairs / complete turn e. constant diameter i. 1 purine & 1 pyrimidine per base pair 1. A double bonds to T 2. C double bonds to G f. Anti-parallel 5. Functions of DNA a. Copies itself precisely to get exact copies as “blueprints” b. Direct cell’s activity so that it fxns properly 6. DNA replication is semiconservative a. Meselson- Stahl Experiment i. Used density labeling 1. Heavy isotope of Nitrogen: N used with N 14 2. Combined & centrifuged -> 2 bands 3. Model results a. Semiconservative: first generation showed intermediate density ( N – N)4 15 14 i. ( N – N) continued to appear in subsequent generations b. conservative replication: both high density ( N – 1N) & low density ( N – N) but no 15 14 intermediate ( N – N) c. dispersive replication would have been intermediate but DNA of this density would not continue to appear in subsequent generations Lecture 10-9-13 1. facts from x-ray data a. XNA is helical like spiral staircase b. More than one chain c. DNA has long & narrow structure w/ constant width 2. DNA replication i. “replication fork” 1. leading strand formed continuously 2. lagging strand formed in Okazaki fragments 3. primase= primer b/c DNA polymerase can’t start new chain 4. need RNA polymerase 5. single stranded DNA binding protein keeps template
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