Biochem Ch4
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butterfly121278 on September 30, 2010
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31 terms
Terms | Definitions |
|---|---|
 primary structure | -sequence of amino acids linked by peptide bonds -includes disulfide bond -within same chain(ribonuclease) -between 2 chains(insulin) |
| conformation | -spatial arrangement of atoms -change occurs by free rotation of single bonds |
| One of a few stable ("native") conformations | -approx 300kJ/mol required to break single covalent bonds -approx 20kJ/mol required to break weak, non-covalent interactions |
| which bonds along backbone rotate freely? | ALL of them |
| C-N peptide bond | distance is shorter than expected for a single bond |
| Peptide bond | resonance structures - peptide unit is rigid & planar, almost always trans (torsion angle = 180 degrees) |
| Ramachandran plot for L-alanine residues | -glycine (R=H) - larger range of allowed angles -branched R groups - fewer allowed angles |
| significance of peptide resonance? | -rigidity enables proteins to have well defined forms -rotations between peptide units allow for folding variations |
| secondary structure | -local spatial arrangement of the proteins backbone into regular folding protein -AA seq-dependent...depends on steric interactions & H-bonding potential -stabilized by hydrogen bonds |
| Alpha Helix | -tightly coiled backbone w/ side chains extending outward (always right handed) -propensity of AA to take up an α-helical conformation-depends on properties of R group & context of AA neighbors |
| Beta-Pleated Sheets | -fully extended backbone -small R groups (Ala & gly) -anitparallel -parallel |
| Beta Turn | -tight loop -polypeptide chain reverses direction |
| Tertiary Structure | -overall 3D arrangement of all atoms in a protein |
| Tertiary structure stabilized | -hydrophobic interactions (London dispersion) -electrostatic ionic salt bridges -hydrogen bonds -covalent disulfide bonds |
| Quaternary Structure | arrangement of 2+ polypeptide chains (subunits) in 3D complexes -not found in all proteins |
| Hemoglobin | 2α chains, 2β chains, ea. w/ heme group |
| Fibrous Proteins | -polypeptide chains arranged in long strands or sheets -single type of secondary structure -simple tertiary structure -insoluble in H₂O (hydrophobic AA residues) -provide support, shape, & external protection |
| Globular Proteins | -water soluble -polypeptide chains folded into compact spherical shape -several types of 2ndary structure -function as enzymes, transport proteins |
| myogloblin (serum albumin) | function- oxygen binding protein of muscle cells stores O₂ & facilitates O₂ diffusion in rapidly contracting muscle tissue structure- single polypeptide chain 153 AA residues 1 Fe containing heme group Heme group binds to HIS 93 |
| Rules for folding globular proteins | 1. bury hydrophobic residues in protein interior, away from H₂O 2. maximize the # of hydrogen bonds & ionic interactions (avoid unpaired groups) |
| Motifs | -recognizable folding patterns involving 2+ elements of 2ndary structure & connection between them ex. coiled-coiled β-α-β loop β barrel α-β barrel |
| Domain | part of polypeptide chain that is independently stable & could undergo movement as single entity -different domains often have distinct function -extreme ex. vertebrate fatty acid synthase (7 enzymatic functions in 7 separate domains) then dimerizes |
| Denaturation & Folding | -synthesized by ribosomes -folding occurs during & following synthesis (native conformation) |
| Denaturation | loss of 3D structure sufficient to cause loss of function (not necessary to break covalent bonds) |
| Causes of Denaturation | -heat disrupts weak interactions -pH changes alter net charge - electrostatic repulsion -organic solvents (alcohol acetone), solutes (urea), & detergents (SDS) disrupt hydrophobic interactions - high salt conc. interferes w/ electrostatic interactions -reducing agents (β-mercaptoethanol) break disulfide bonds -mechanical stress disrupts weak interactions |
| loss of structure | abrupt loss of structure suggests that unfolding is a cooperative process |
| AA seq determines 3D structure | -denature/renature experiments w/ ribonuclease (destroy RNA enzyme) -folds properly even though the 8 CYS residues could cross link in 105 different ways |
| Molecular Chaperones | proteins that interact w/ partially folded polypeptides, facilitating correct folding pathways |
| Protein Disulfide Isomerase | shuffles disulfide bonds until correct ones are formed |
| Peptide Prolyl CIS-TRANS Isomerase | most end up trans |
| Protein misfolding can cause | -human genetic disorders -defects in 1° structure -defects in chaperones -inappropriate presence or influence of other proteins |
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