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AA & Protein Struct

Medical Biochemistry

Nonpolar, aliphatic amino acids (7) -Hydrophobic and GENERALLY found in interior of water soluble proteins -Gly, Ala,Val, Leu, Ile, Pro, Met
Aromatic amino acids (3) -Hydrophobic and often found in interior of water soluble proteins -Phe, Tyr, Trp
Polar, uncharged amino acids (5) -Found in both the interior and exterior of protein structure -Ser, Thr, Cys, Asn, Gln
Amino acids with ionizable side chains (5) -R group can donate or accept protons -Asp, Glu, Lys, Arg, His
Two special/ unique amino acids, why? Gly- only amino acid not having an asymmetric/ chiral alpha center Pro- secondary alpha amine generated by the R group,forming a ring
Sulfure containing amino acids Met and Cys
Amino acids with carboxylic side chains (2) and amino-like side chains (3) -negatively charged/ acidic at pH of 7 -Asp and Glu -Positively charged and basic -Lys, Arg, and His
Structure and deffinition of Peptide Bonds -connect amino acids to form polypeptide chains -dehydration between a-carboxyl of one amino acid and a-amino group of another -hybrid of 2 resonance states, imparting partial double bond characteristics preventing free rotation around bond -planar & f
Primary Structure -Amino Acid sequence -determines 3D structure and biological function of protein -Amino (N) terminus or free amino goup at one end -Carboxyl (C) terminus or free carboxyl group at one end
Written form of a polypeptide chain N-terminus to C-terminus
Secondary Structure -segment of polypeptide chain that has regular repeating structure -result from H-bonding interactions between C=O and H-N groups -a-helices and B-pleated sheets
a-helices vs. B-pleated sheats a-helices-rod shaped,tight spirals (r-handed) -each C=O h-bonds to H-N 4 amino acids down chain B-pleated sheets-2+ polypeptide chains align side by side -interchain H-bonding of C=O and N-H groups -R groups project up and down -Paralell or Antiparal
Sharp bend in primary structure -Pro residue disrupts H-bonding forming bend and further disrupting H-bonding down stream
Reverse turns in B-pleated sheets -typically forms at water-peptide interface of protein surface -H-bonding between C=O of 1st and H-N of 4th amino acid stabalize -salt bridges,metal ions,disulfide bonds add more stability -often in antiparalell sheets
Supersecondary Structures aka Structural Motifs -assist in protein folding -interactions between newly folded and previously formed structures
Tertiary Structures give 1 example... -3D structure -interaction of secondary structures and non-ordered regions of polypeptide chain -Myoglobin (Mb)
Prosthetic groups What is a protein that lacks the prosthetic group. -organic molecules permanently bound to protein -Apoproteins lack the prosthetic group
Final functioning protein structure... How are they stabalized? -Native structure -folded through favored pathways in cooperative manner -supersecondary structures, H-Bonding, salt bridges, hydrophobic forces and van der Waal's attractions -folding assisted by chaperones
What can cause proteins to become disrupted or denatured? Why? -increase in temperature -detergents -pH extremes -agents like urea and guanidinium hydrochloride -these factors disrupt non-covalent bonds that maintain the folded conformation
Quaternary Structure give an examples... -Proteins that contain 2+ subunits -Hemoglobin (Hb
Oxygen binding to a heme... -binds 4 O -doesn't bind with equal affinity -as O increases, heme binds O more efficiently -binding O to a-Hb transforms Hb from T form to R form (valine residue moved from B-Hb binding sights) -causes positive allosterism
Allosterism -binding of one molecule influences the ability of other molecules to bind at different sights -positive and negative -binding of O to Hb
2,3-BPG, CO2, and H influential behavior in Hb 2,3-BPG- stabilizes T form by binding in central cavity H- binds to histidine,+ charge residues form salt bridges w/ aspartate, stabilize T form CO2- facilitates deprotonization in lungs and R form, binds to N terminal forms carbamates and T form
HbF v. HbA1 Why do the differences matter? -HbF= predominant form in fetus (2nd and 3rd trimester) =increases O affinity by reducing affinity for 2,3BPG = Histidine replaced with serine -HbA1=tetramer of a2B2, most common in adults (90%)
Hemoglobinopathy - mutant hemoglobins giving rise to clinical problems - unstable structure increases or decreases O affinity or increases rate of oxidation of heme Fe2+ to Fe3+
Post translational modification -modifications that occur after protein has been synthesized -occur while growing polypeptide is still attached to ribosome
Protein Domains -lobes, caused by folding of large polypeptide chains -segregate structure and/or function -domains connected by flexible linker regions -different enzyme activities sequestered in distinct, folded domains
Collagen and the importance of amino acid comp and sequence, unusual amino acids and their function, importance of vitamin-C and iron in formation -most abundant protein (1/4 ttl proteins) -35% glycine + 11% alanine, w/ proline -4-hydroxyproline(V-C) + 5-hydroxylysine allow triple helix -glycine every 3rd sequence=structure and stability -peptide-proline,peptide-hydroxyproline=strength and rigid
Proteins in: Sickle Cell Anemia, Scurvy, and Prion disease Sickle Cell Anemia=valine instead of glutamate (sticky hydrophobic patch B subunits) Scurvy=insufficient Vit. C, crucial forming hydroxyproline and insufficient hydroxylysine (extracellular covalent cross links and glycosylation. Prion=misfolded protein
Created by: MastamikeOD
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