Question | Answer |
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 |