Exam 2 Study Guide - Amino Acids(13 Qs and Proteins(10 Qs...

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Amino Acids (13 Qs) and Proteins (10 Qs) Amino acid : organic acid with an α carbon COOH, NH 2 , H, R Nonpolar- R group is nonpolar and uncharged Polar- R group is polar and uncharged Basic- one or more NH 2 groups that can accept H + from R group + Acidic- ionizing COOH group on the R group (i.e., donates H) - NH 3 + | R----- C ---- COO - | H D- amino acid: on the right enantiomers can’t L- amino acid: on the left… ALL OF LIFE USES L-AMINO ACIDS be superimposed on Which is more stable? COOH or COO - ? NH 3 + or NH 2 ? … that which is stable tends to accumulate … HA is COOH and NH 3 + … COOH has the higher pK a b/c it is the weaker acid … A - is COO - and NH 2 Zwitterion : ion w/ opposite charges on different parts of it Henderson-Hasselbalch Equation : pH = pK a + log([A - ]/ [HA]) Glycine : Isoelectric Point : the pH at which an amino acid has no net charge… important in separating mixtures of amino acids and proteins… pK a = pH… 50% protonated Amino acids can act as acids or bases b/c the R group can accept or donate H +
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Peptide Bond : forms when the OH of a carboxyl group and the H of an NH 2 group are eliminated by dehydration synthesis .: bond between C=O and NH Protein : polymer of 100+ amino acids joined by peptide bonds (if <100 it is just a polypeptide rather than a protein) Peptide Backbone: N-C-C-N-C-C-N-C-C… R groups that extend out are “side chains” Primary Structure : sequence of amino acids in a protein (remember Kosinski’s belt) Secondary Structure : coiling of amino acid chain into a spiral ( α - helix or ß-pleated sheet) Tertiary Structure : folding of helix into complicated shapes due to attractions between side chains (Kosinski wrapped belt around arm and bent his arm)… Protein is at this level Quaternary Structure : way in which 2+ separate polypeptide chains fit together (slinky) Denaturation : ∆ tertiary/ quaternary structure of proteins caused by an environmental change that disrupts the attractions between different parts of the molecule… permanent or temporary Motif : common combinations in the secondary structures in a section of a protein Domain : compact region of the tertiary structure of a protein… coded by one exon and has one function Molecular Chaperone : protein that helps new proteins fold properly (folding is determined by the primary structure) by preventing them from sticking together Enzyme : protein that catalyze chemical reactions by bringing reactants close together on an “active site” Ribosome : RNA molecule that accelerate reactions, making in a non-protein enzyme Purine : nitrogenous base w/ 2 RINGS… ADENINE and GUANINE… “pure ag” Pyrimidine : nitrogenous base w/ 1 RING… CYTOSINE, URACIL, and THYMINE Nucleoside : pentose w/ a purine or pyrimidine attached to its C1 carbon Nucleotide : nucleoside w/ 1-3 Phosphate groups attached to its C5 carbon atom of the pentose Nucleotide Triphosphate (NTP) : nucleoside w/ 3 phosphate groups attached to the C5 carbon atom of the sugar… ex: ATP Nucleic Acid (9 Qs): polymer of nucleotides… P group joins the 5’ carbon of one sugar w/ the
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