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35 Cards in this Set
- Front
- Back
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H2O, O, H (mass, number) |
molecular mass= 18 O - atomic # 8, atomic mass 16, 8 e- 1s2,2s2,2p4 (6 valence e-) H- atomic # 1, atomic mass 1, 1 e- 1s1 (1 valence e-) |
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H2O orbital, geometry, polarity |
2 bonds to H+, 2 lone pairs = 4sp3 orbitals Tetrahedral -- bent shape Water is electrically neutral b/c dipolar structure |
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Electronegativity O, H, C, S |
O= 3.4 (strong) H= 2.2 C= 2.55 S= 2.58 H C S very similar; e- attracted to O |
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H bonds |
weaker than covalent bonds but strange in conglomeration |
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Acid / Base |
Acid- proton donor, increases conc of H Base- proton acceptor, increases conc of OH Presence of acid/base changes pH of aqueous solution b/c it changes conc of H+ / OH- |
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Henderson Hasselbach Equation usage |
1. pH (if you know pKa & A/HA) 2. pKa (if you know pH & A/HA) 3. * ratio A/HA (if you know pH & pKa) |
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Ca geometry |
Tetrahedral (4 diff groups= stereoisomers L & D) In aqueous solution (pH7) AA exist as dipolar ions (zwitterions) |
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Proteins |
biological polypeptides, typically 50-200 AA |
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Primary structure |
linear sequence of AA residues that make up protein |
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Peptide bond geometry |
prevents free rotation among C-N bond Partial double bond character O, C, N have sp2 (trigonal planar) No free rotation, unfavorable would disrupt delocalization and p orbital overlap |
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Rotational bond angles definitions |
Phi O = angle of rotation around Ca-N bond Psi Y= angle of rotation around Ca-C bond O & Y are defined as O degrees when main chain atoms are on same side of Ca-N and Ca-C bond Rotation: clockwise +; counterclockwise - not all possible combinations of O and Y are allowed due to steric hindrance |
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Secondary structure |
structural organization of specific segments of a poly peptide chain |
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a helix |
simplest stable arrangement for a poly peptide w/ planar peptide bonds 3.6 AA per repeat coiled like C=O forms H bond w/ NH that is four residues down chain O= -60, Y= -40 |
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a helix handedness |
all a helix in naturally occurring proteins are R handed b/c proteins are L isomer L handed side chains will project inward (unfavorable) Peptide bonds are fixed planar/trans |
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B sheet |
regular repeating secondary structure in proteins extended conformation Antiparallel Parallel can have mixed sheet, antiparallel more stable than parallel b/c Hbonds are collinear interaction |
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Ramachandran Plot |
calculated sterically allow O & Y based on known atomic radii & bond lengths Found 75% combinations of O & Y values were not allowed |
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Turns & Loops |
segments of a helices and B-sheets in protein are connected by various types of turns and loops |
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Tertiary structure |
3D folded structure of polypeptide/protein determined by primary sequences of polypeptide chain. |
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Myoglobin |
single polypeptide chain w/ 8 a-helices connected by turns/loops (no B strands) contains heme group functions as oxygen storage protein |
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Ribbon diagram |
shows path of main chain of protein, secondary structures are visible |
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Space filling model |
shows all atoms of protein. better representation of what protein looks like |
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Myoglobin interior, surface |
Interior: consist almost entirely of non polar hydrophobic AA residues (V, L, M, F) Surface: consist almost entirely of polar charged hydrophilic AA (D, E, K, R) |
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Folding of polypeptide into a compact globular structure is drive by: |
1. nonpolar AA to cluster in interior of protein (minimize exposure to water) 2. polar & charged AA to be on surface of protein (exposure to water) 3. peptide CO & NH groups to form H bonds w/ other CO & NH groups through a-helices & B-sheets |
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Anfinsen Experiment General Principle |
all info needed to direct folding of a protein into a specific 3D native structure is contained in AA sequence (primary structure) |
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Anfinsen Experiment steps |
-start w/ pure ribonuclease (active) treat w/ B-mer to break ds bonds reducing cystine to cystenine (2 free sulfhydryl groups and B-mer joined) -add urea causing protein to unfold. disrupt H bond in water exposure of interior non polar residues to water more favorable -forming H bonds w/ NH & CO of peptide bonds disrupts H bond holding a-helix & B-sheets |
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Anfinsen Experiment reverse |
if remove urea & B-mer form denatured protein (biologically inactive), protein will spontaneously refold back into native state (biologically active). All disulfide bonds will reform in correct combinations |
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Monomeric/Multimeric |
single polypeptide chain multiple polypeptide chain (dimeric, trimeric) held together by H bond, hydrophobic interactions, electrostatic interactions |
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Quaternary structure |
spatial arrangement of subunits in a multimeric protein |
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Hemoglobin |
consist of four poly peptides 2 a-chains 2 B-chains two aB dimers associate to from a tetramer (dimer of dimers) |
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Globin fold |
a & B chains consist of a-helical segments in similar 3D arrangment |
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Heme Group |
complex organic ring (porphrin) w/ Fe2+ ion bound in center each a B subunits of hemoglobin (& myoglobin) contains a tightly bound heme group |
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T state |
tense, highly constrained by dimer-dimer interactions lower O2 binding affinity |
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R state |
relaxed, less constrained by dimer-dimer interactions, higher O2 binding affinity |
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Diff between concerted and sequential model |
Concerted: all 4 subunits of hemoglobin tetramer must be in same state (T or R) Sequential: all 4 subunits of a hemoglobin tetramer may be in diff states (T or R) |
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Oxygen delivery |
cooperative binding (& dissociation) of O2 allows hemoglobin to: -become more fully oxygenated at higher oxygen pressure (lungs) -release oxygen more efficiently at lower oxygen pressure (tissues) |
