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BioMG 3350 Quiz 1

BioMG 3350 Amino Acid Classifications - Quiz 1

Glycine (Gly) Nonpolar alipathic Provides least amount of steric hindrance in proteins Not particularly hydrophobic
Alanine (Ala) Nonpolar alipathic Saturated hydrocarbon R group Important in hydrophobic interactions
Proline (Pro) Nonpolar alipathic The only amino acid with a substituted alpha-amino group Influences protein folding by forcing a bend in the chain
Valine (Val) Nonpolar alipathic Saturated hydrocarbon R group Important in hydrophobic interactions
Leucine (Leu) Nonpolar alipathic Saturated hydrocarbon R group Important in hydrophobic interactions
Isoleucine (Ile) Nonpolar alipathic Saturated hydrocarbon R group Important in hydrophobic interactions
Methionine (Met) Nonpolar alipathic
Phenylalanine (Phe) Aromatic Hydrophobic and neutral at any pH
Tyrosine (Tyr) Aromatic Has -OH group that contributes polarity and H-bond capability Polar group makes it both hydrophobic and hydrophilic Can be phosphorylated
Tryptophan (Trp) Aromatic Hydrophobic and neutral at any pH
Serine (Ser) Polar uncharged
Threonine (Thr) Polar uncharged Has -OH group that contributes polarity and H-bond capability
Cysteine (Cys) Polar uncharged Can form disulfides in the right oxidizing conditions
Asparagine (Asn) Polar uncharged
Glutamine (Gln) Polar uncharged
Lysine (Lys) Positively charged
Histidine (His) Positively charged The only amino acid having an R group with a pKa near 7 Important in the active site of some proteins
Arginine (Arg) Positively charged
Aspartate (Asp) Negatively charged
Glutamate (Glu) Negatively charged
Peptide bond It is substituted amide linkage It is formed in a condensation reaction
Affinity chromatography Taking advantage of unique structural or functional properties of a protein, this technique specifically removes the protein of interest from solution.
Electrophoresis Proteins are separated on the basis of their ability to migrate in an electric field, an indicator of relative size.
Phosphorylation The most common form of post-translational modification
Isometric point Where the net charge on the amino acid is zero
pKa the pH at which there is a 50:50 ratio of protonated/deprotonated species for a specific ionizable group
Chromatography separate based on properties of protein charge, size, hydrophobicity
SDS Gel Hydrophobic parts of the protein bind to the hydrophilic, negative parts of SDS, causing the protein to unfold. Then, a reducing agent is added to break the covalent disulfide bonds. Voltage is applied and they are ran through a gel.
Consensus sequences Short stretches of highly conserved sequences
X-ray crystallography Measure how the crystal diffracts x-rays main limitation: crystals can be very hard to grow
Nuclear magnetic resonance (NMR) Produce the protein using heavy-isotope labeled amino acids and then measure chemical shifts of protein in solution in an NMR machine. main limitation: Currently limited to small-medium proteins <300 amino acids
Cryo-EM (electron microscopy) Protein sits in different orientations in ice and is show with electron beam from above. A detector collects the shadows(electron density). Need large proteins >200kDa
Surface tertiary structure Shows the solvent-accessible surface of the protein
Space-filling Shows every (non-hydrogen) atom as a sphere with appropriate radius
Ribbon/cartoon Traces the polypeptide backbone, highlights secondary structure
Hydrophobic effect most important weak force for determining protein structure
two main movement constraints in peptides planar peptide bond and steric hindrance
trans 180 degrees
cis 0 degrees
Ramachandran Plot Shows permissible psi, phi angles
coil structured but no pattern
loops unstructured because of multiple configurations becomes structured when bound to other proteins



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