BIOL 200 Notes up to Midterm

BIOL 200 Notes up to Midterm - Lecture 1 Chemical...

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Lecture 1: Chemical Foundations - life occurs in a watery environment o biomolecules can be classified as hydrophilic (sugars), hydrophobic (fat), and amphipathic (phospholipids) - covalent bonds: strong bonds, small distance between atoms o carbon: most important atom, can form 4 covalent bonds o ie methane (tetrahedral), formaldehyde - noncovalent interactions: weaker, larger distance - common functional groups biomolecules: hydroxyl, acyl, carbony, carboxyl, sulfhydryl, amino, phosphate, pyrophosphate - common linkages: ester, ether, amide - polar bonds: O-H, C-O, N-H, P-O b/c of electric dipole moment - in water, covalent bonds >> noncovalent interactions; c-c bonds are especially strong - a single noncovalent interaction is unstable at biological temperatures; however, in a biomolecule, it is additive and very stable - the hydrolysis of ATP phosphoanhydride bond is -7.3 kcal, which is stronger than some covalent bonds but less than C-C bonds Lecture 2 - Noncovalent interactions: ionic interactions, hydrogen bonds, van dar walls interactions o Ionic interactions; NaCl has strong interaction, dissolve happily in water because it forms HYDRATION SHELL; for close contact protein-protein, water needs to be excluded o Ion-channel protein/Tetrameric channel: mediates transport of K+ from inside to outside of cell; transmembrane protein; hydration shell give selectivity of ion K+ channels because potassium ion is bigger than Na+ ion. There are amino acid residues that come in contact with the ion with polar oxygen atoms that are spaced like a hydration shell o Hydrogen bonds: in liquid water, dynamic network of hydrogen bonds; solubility in water depends on its ability to form hydrogen bonds, ie methanol, methylamine, peptide group, ester group o Van der waals interactions: weak, result from transient dipoles; occur in all types of molecules; form only when atoms are very close o Hydrophobic effect: aggregated state of hydrophobic molecules; hydrophobic surface area exposed to water is reduced; water population less ordered, higher entropy, energetically more favorable o Specificity of association between biological macromolecules is based on multiple noncovalent interactions precisely spatially organized Building Macromolecules - Monomers to polymers: amino acids polypeptide (peptide bond for protein); nucleotide nucleic acid (phosphodiester bond); monosaccharide polysaccharide (glycosidic bond); in each case, when addition of monomer, molecule of water is released; all covalent bonds - Large structures based on noncovalent bonds: cytoskeleton
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o Actin filament, microtubule: Non-covalent bonds are easy to form and undo, thus the polymers are very dynamic o Lipid membrane: hydrophobic environment in the leaf (inside), hydrogen bonds & ionic interactions at exterior of membrane - Building blocks: amino acids o Base + acid = amphoteric o Alpha carbon atom that makes 4 covalent bonds o Hydrogen bond o Carboxy group COO- and amino group NH3+, make up backbone of protein, peptide bond with each other o
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