Biology Molecules and Cells, week 1/25 notes
Biology Molecules and Cells, week 1/25 notes 200001
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This 6 page Class Notes was uploaded by Audrey Notetaker on Friday January 29, 2016. The Class Notes belongs to 200001 at Boston College taught by Danielle Taghian in Spring 2016. Since its upload, it has received 20 views. For similar materials see Molecules and Cells in Biology at Boston College.
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Date Created: 01/29/16
Chapter 2: Covalent Bonds and Weak Chemical Interactions 1/25/16 Elements in organisms: 99% C, N, O, H 0.9% P, S Cl, Na, Mg, K, Ca Four major small organic compounds in cells (macromolecules) Sugars (carbohydrates) o Quick energy o Structural support o Form polysaccharide Fatty acids (lipids) o Long hydrocarbon chains o Cell membranes o Bigger long term energy Amino acids (proteins) o Polymers form protein o Form protein Nucleotides o Building blocks of RNA and DNA Macromolecule Monomer unit Covalent bond Nucleic acids (DNA, RNA) NUCLEOTIDE Phosphodiester Proteins Amino acids Peptide Carbohydrate Monosaccharides Glycosidic bond Lipids (phospholipids and Fatty acid and Ester bond triglycerides) glycerol Covalent: sharing of electrons equally electronegative; stable; strongest bond Single bond = free rotation Double bond = no rotation Polar: slight electronegative difference, electron more towards O in H2O Unequal sharing of electrons results in dipole (partial charges) Non polar: electrons equally shared, little electronegativity difference (lipids) Ionic: big electronegative difference (NaCl), transfer of electron(s); ions are formed Non covalent bonds: rely on attractive and intermolecular forces Salt bridges: ionic interaction between salts: strongest Hydrogen: HO. HN, HF / electronegative atom attracted to another electronegative atom o Two strands of DNA interact this way Van der Waals: occasional dipole moments in non polar molecules; weakest Hydrophilic interactions molecules interact with water via hydrogen bonds (polar) Hydrophobic no interaction with water (non polar) Insoluble in water; shields itself from water Lipid bilayer Electronegativity: measure of the tendency of an atom to attract a bonding pair of electrons Chapter 23: Water and Carbon, Protein Structure and Function 1/27/16 Capillary Action: the ability of liquid to flow up a narrow tube against gravity Adhesive – molecules stick to the wall Cohesive – molecules stick to each other if the adhesive force is greater than the cohesive, then the liquid will creep up the side (i.e. water) if the cohesive force is greater than the adhesive, then the liquid will bulge (i.e. mercury) *water has a high surface tension * Liquid water is more dense than solid ice Ice: Hydrogen bonds are arranged in an open crystal pattern water: fewer hydrogen bonds so liquid can pack more closely together Functional Groups Name & Structure Examples Properties Methyl lipids Nonpolar. Hydroxyl Alcohols and sugars Polar. Hydrogen bonds with water to help dissolve molecules. Enables linkage to other molecules by condensation. Carbonyl Sugars Polar. Contribute to making molecules water- soluble. Can be very reactive. Important in carbohydrates and energy releasing reactions. Carboxyl In fatty acids and Acidic. Ionizes in living tissues to form COO- + amino acids and H . Enters into condensation reaction by giving up -OH. Some carboxylic acids important in energy-releasing reactions. Amine Basic. Accepts H in living tissues to form + -NH 3 Enters+into condenstation reactions by giving up H . Phosphate Negatively charged. Enters into condensation reactions by giving up -OH. When bonded to another phosphate, hydrolysis releases much energy. Sulfyhydryl By giving up H, two -SH groups can react to form a disulfide bridge (S-S), thus stabilizing protein structure because it's a covalent bond. Amino acid The “R” group determines the function of the amino acid side chain Alpha Carbon: amino group, H, R, and carboxyl group is attached; central carbon atom Amino group ionizes to NH3+ and carboxyl group to COO which makes them more reactive *know how to draw a hydrophobic, charged, and polar amino acid Chapter 3: Proteins 1/29/16 (Amine Bond) Peptide bond: condensation reactions bond the carboxyl group of one amino acid to the amino group of another amino acid Produces the bond + water Electrons shared between carbonyl group and peptide bond allow for some double bonds *only alpha amino acids can form secondary structures (main/central carbon) Protein: Pieced with domains Polypeptide: flexible and has directionality Four levels of structure o Primary unique sequence of amino acids; just the code; determines 3D structure, function Has an amino end, and a carboxyl end, in the middle are amino acids connected with peptide bonds Changing one of the amino acids in the sequence can completely change the structure and function of the protein. Does not always cause a change, but change can be drastic (cancerous, sickle cell, etc.) o Secondary local confirmation of polypeptide chain; formed and stabilized by hydrogen bonds Each 360 turn = 3.6 aa at 1.5 A(angstroms) rise/aa; the peptide bond of every 4th aa interacts via hydrogen bonds which are parallel o the axis of the alpha helix while the aa side chains are perpendicular Alpha helix CO group forms hydrogen bond with NH every 4; mostly found on outside of proteins Met, ala, leu, glu, lys Beta sheets often denoted by arrows Consists of beta strands joined by hydrogen bonds formed between carbonyl and imine groups of neighboring backbones Pleat is caused by the position of the alpha carbons above and below the plane of the sheet Tyr, phe, trp and thr, val, Ile and pro Beta turn: allows peptide chain to reverse direction Proline and glycine are more prevalent in beta turns Random coils: no defined helix or beta sheet o Tertiary interactions/intermolecular forces form to maintain overall structure of protein Get hydrophobic amino acids to the inside of the protein and get hydrophilic amino acids to the outside so the protein can interact with water Results from o Quaternary form follows function; two or more proteins interact with one another Two proteins = dimer Four proteins = tetramer (hemoglobin) Similar looking proteins may not have the exact same amino acid sequence (primary structure)
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