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32 Cards in this Set
- Front
- Back
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General Info of Amino Acids
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*proteins
*most abundant & functionally diverse molecule -enzymes and polypeptide hormones: metabolism -contractile proteins in muscle: movement -in bloodstream, hemoglobin and albumin -immunoglobulins fight microbes *display an incredible diversity of functions *share a common structure: polymers of amino acids |
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Structures of Amino Acids
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* > 300 different amino acids in nature
* ~ 20 common in mammalian proteins -coded for by DNA -a carboxylic group, an amino group, and a side chain (ex. proline) *alpha-carbon atom *R-group dictates the role amino acid plays in protein *classification based on R-group *nonpolar or polar (acids and bases) *at pH 7.4: the carboxylic group is dissociated to carboxylate ion (-COO-), and amino group is protonated (-NH3+) |
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Names of Amino Acids with Nonpolar Side Chains
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*glycine
*alanine *valine *leucine *isoleucine *phenylalanine *tryptophan *methionine *proline |
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Properties of Amino Acids with Nonpolar Side Chains
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*does not bind or give off protons or participate in hydrogen or ionic bonds
*promotes hydrophobic interactions >How are nonpolar amino acids located in protein? 1) protein in aqueous solutions (polar environment) -R groups of nonpolar amino acids tend to cluster together in interior of the protein 2) in a hydrophobic environment (a membrane) -nonpolar R-groups are found on the outside surface of the protein, interacting with the lipid environment |
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Proline (nonpolar)
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*differs from other amino acids in that proline's side chain and alpha-amino N form a rigid five-membered ring structure
*has a secondary (rather than primary) amino group (aka an imino acid) *proline tends to be found in... -fibrous structures (ie collagen) -interrupts alpha-helices in globular proteins |
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Names of Amino Acids with Uncharged Polar Side Chains
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*serine
*threonine *tyrosine *asparagine *glutamine *cysteine |
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Properties of Amino Acids with Uncharged Polar Side Chains
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*zero net-charge at neutral pH
*serine, threonine and tyrosine: -can participate in H-bonding -attachment site for phosphate group -attachment site for oligosaccharides *asparagine and glutamine: -can participate in H-bonding -attachment site for oligosaccharides (amides) *disulfide bonds (many extracellular proteins; albumin) *-SH groups of two cysteines can become oxidized to form a dimer, cysteine, which contains a covalent cross-link called disulfide bond (-S-S-) *active site of many enzymes has cysteine (-SH) |
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Names of Amino Acids with Acidic Side Chain
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*aspartic acid
*glutamic acid |
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Names of Amino Acids with Basic Side Chains
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*histidine
*lysine *arginine |
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Properties of Amino Acids with Basic/Acidic Side Chains
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Acidic Side Chain:
*proton donors *at physiological pH, fully ionized, - charge Basic Side Chain: *accept protons *at pH 7.4, fully ionized, + charge Histidine: *weakly basic, its side chain can be either positively charged or neutral, depending on the ionic environment *role in hemoglobin |
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Abbreviations and Symbols for Commonly Occuring Amino Acids
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*each amino acid name has an associated three-letter abbreviation and a one letter symbol
*one letter symbol is used in protein sequencing |
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Optical Properties of Amino Acids
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*alpha-carbon of each amino is a chiral carbon
*optically active carbon atom *can exist in two forms, L and D *L and D are mirror images of one another *L and D are stereoisomers, optical isomers, or enantiomers *all amino acids in proteins are found in L-form *D-form amino acids are found in some antibiotics, plants and bacteria *the only amino acid that is achiral is glycine |
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What is sickle cell anemia?
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Sick cell anemia is caused by a point mutation in DNA that changes the sixth amino acid in the beta-globin chain of hemoglobin from polar glutamate to nonpolar valine
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What causes the pain symptoms?
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Red blood cells sickle more frequently, especially under conditions of low oxygen tension. The result is a vaso-occlusive crisis in which the sickled cells clog capillaries and prevent oxygen from reaching cell (ischemia), thereby causing pain
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What causes sickle cell anemia?
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The enhanced destruction of the sickled cells by the spleen results in anemia.
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What selective advantage to people with sickle cell anemia have?
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The frequency of sickle cell anemia in parts of equatorial Africa in which malaria was endemic in the past is 1 in 25 births
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Acidic and Basic Properties of Amino Acids
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*amino acids in aqueous solutions contain weakly acidic alpha-carboxyl groups & weakly basic alpha-amino groups
*each of the acidic and basic amino acids contains an ionizable group in its side chain *free amino acids and peptides can act as buffers HA <--> H+ + A- BH+ <--> B + H+ *what are acids? proton donors *what are the acidic aa? Asp, Glu *what are the basic aa? Lys, Arg, His |
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Titration of an Amino Acid
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*isoelectric point (pI) is the pH at which an amino acid is electrically neutral (+ = -)
*Ala has only two dissociable hydrogens *alpha-carboxyl and alpha-amino group *pI = ave pKa1 & pKa2 |
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pKa and pI values
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pKa1: alpha-carboxylic group
pKa2: alpha-ammonium ion pKa3: side chain group pI = 1/2 (pKa1+pKa2) aspartic and glutamic acid: pI = 1/2 (pKa1+pKa3) Lysine, Arginine and Histidine: pI = 1/2 (pKa2+pKa3) |
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Other Applications of Henderson-Hasselbalch Equation:
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pH=pKa+log(A-/HA)
1)bicarbonate as a buffer: *an increase in HCO3- causes the pH to rise *pulmonary obstruction causes an increase in CO2 and causes pH to fall 2) drug absorption: *at the pH of the stomach (1.5) a drug like asprin (weak acid, pH=3.5) will be largely protonated and, thus, uncharged *uncharged drugs generally cross membranes more rapidly than charged molecules *eq can predict ionic form of drug |
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Structure of Proteins
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*proteins: amino acids joined together by peptide bonds
*linear sequence of amino acids contains necessary information to create 3-D shape *four organizational levels: primary, secondary, tertiary, and quaternary *there are general "rules" regarding the ways in which proteins fold, certain structural elements are repeated in a wide variety of proteins -simple combination of alpha-helices and beta-sheets -complex folding of polypeptide domain |
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Primary Structure of Proteins
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*linear sequence of amino acids
*joined covalently by peptide bonds *amide linkage between alpha-carboxyl group of one amino acid and the alpha-amino group of another -partial double-bond character, rigid -generally a trans bond *all amino acid sequences are read from the N to the C-terminal end of the peptide *abnormal amino acid synthesis can cause improper folding and impairment of normal function *polypeptide, "residue" *peptide bonds of proteins can be broken with prolonged exposure to a strong acid or base at elevated temperatures is the only way to hydrolyze peptide bonds nonenzymatically |
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Secondary Structure of Proteins
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* composed of alpha-helices, beta-sheets and beta-bends
Alpha-Helix: *most common helix *spiral structure, 3.6 aa/turn *tightly packed, coiled backbone core *side chains outside -keratins, fibrous proteins, mostly alpha-helices: rigid -myoglobin, highly alpha-helical but flexible *keratin are in hair and skin *proline tends to disrupt alpha-helices charged amino acids: glu, asp, his, lys, arg amino acids with bulky side chain: trp |
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Beta-Sheets in Proteins
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*all of the peptide bond components are involved in H-bonding
*unlike alpha-helices, beta-sheets are composed of 2 or more peptide chains (beta-strands) *the surface of beta-sheets appears pleated, often called (beta-pleated sheets) *parallel and antiparallel (with the N-terminal and C-terminal ends of beta-strands alternating) sheets |
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Beta-Bends (Reverse Turns, Beta-Turns)
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*reverse the direction of a polypeptide chain helping it form a compact, globular shape
*often found on the surface of protein molecules and often include charged residues *four amino acids: one of which may be proline -glycine, smalled R-group, is commonly found |
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Nonrepetitive Secondary Structure
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* ~50% of an average globular protein is organized into repetitive structures, alpha-helix and/or beta-sheets
*the remainders have a loop or coil conformation *these nonrepetitive secondary structures are not "random", but simply less regular structure *the term "random coil" refers to the disordered structure obtained when proteins denature |
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Supersecondary Structures (motifs)
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*alpha-helices, beta-sheets, nonrepetitive sequences, beta-bends
*motifs are usually produced by packing side chains form adjacent secondary structural elements close to each other *example: proteins that bind to DNA contain one or more of a limited number of motifs |
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Tertiary Structure of Globular Protein
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*tertiary structure is determined by the primary structure of a polypeptide chain
*amino acids are arranged with hydrophobic side chains in interior and hydrophilic groups generally on the surface of the molecule *Domains are functional and 3-D structural units of polypeptides (the basic units of structure and function) * >200 amino acids in length generally consist of two or more domains |
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Interactions Stabilizing Tertiary Structure
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1) disulfide bonds:
a covalent linkage, (-SH) of each of two cysteine residues to produce a cysteine residue 2) hydrophobic interactions: * nonpolar side chains tend to be located in the interior of the polypeptide molecule * polar or charged side chains tend to be located on the surface of the molecule in contact with the polar solvent 3) hydrogen bonds: serine and threonine (-OH) 4) Ionic Interactions: (-COO-) aspartate or glutamate interact with (-NH3+) of lysine |
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Protein Folding
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*controlled by interactions between the side chains of amino acids
*occurs within seconds to minutes *employs a shortcut via all folding possibilities *H-bonds, ionic bonds, hydrophobic interactions, and disulfide bonds *results in a low-energy state *chaperones interact with the polypeptide at various stages during the folding process |
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Protein Misfolding
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*misfolded proteins are usually tagged and degraded within the cell
*If fails, intracellular or extracellular aggregates of misfolded proteins can accumulate with age *Deposits of these misfolded proteins are associated with a number of diseases |
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Quaternary Structure of Proteins
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*monomeric proteins consist of a single polypeptide chain (many)
*others may consist of two of more polypeptide chains that may be structurally identical or totally unrelated (subunits) *the arrangement of these polypeptide subunits is called the quaternary structure of the protein *subunits are held together by noncovalent interactions, H-bonds, ionic bonds, and hydrophobic interactions |
