Amino Acids and Peptide Bonds PDF

AMINO ACIDS Proteins workhorses of the cell one or more polypeptides - polymers of amino acids stabilized by weak noncovalent forces Perform a great portion of cellular activities: ○ To tissues and organs: structure (keratin) support (actin filaments) ○ Con...

AMINO ACIDS Proteins workhorses of the cell one or more polypeptides - polymers of amino acids stabilized by weak noncovalent forces Perform a great portion of cellular activities: ○ To tissues and organs: structure (keratin) support (actin filaments) ○ Controls metabolism through: hormones (oxytocin) enzymes (catalase) ○ Immune system: protection (Immunoglobulin G) Type Function Example Enzymes Catalyze biochemical reactions Amylase (e.g. Digestion, blood clotting, - begins digestion replication, transcription, of carbohydrates translation) by hydrolysis Hormones Regulate body function Insulin - Carry messages to - facilitates the use receptors of glucose for Coordinate events within and energy generation between cells Storage proteins Make essential substances Myoglobin available when needed - stores oxygen in muscles Transport proteins Carry substances through body Serum albumin fluids - carries fatty acids (e.g. Carriers - respiration and in blood metabolism) Structural proteins Provide mechanical shape and Collagen support - Provides structure (e.g. in hair, skin, eyes, to tendons and muscle, silk) cartilage Protective proteins Defend the body against Immunoglobulin foreign matter - aids in the destruction of invading bacteria Contractile proteins Do mechanical work Myosin and actin - govern muscle movement Amino Acids linked by peptide bonds to form a polypeptide ○ α-amino acids make up proteins Attached to the carbon next to the -COOH group Made up of: ○ amino group (NH3+) = pKa ~ 10 ○ carboxylate group (COO-) = pKa ~ 4 ○ R-group side chain Under physiological pH: ○ Carboxyl group = unprotonated ○ Amino group = protonated ○ Isolated amino acid = both negative and positive 20 standard amino acids used when proteins are synthesized during translation differ based on their R groups (overall chemical characteristics) ○ Hydrophobic ○ Polar ○ Charged 9 essential amino acids ○ Cannot be synthesized by the organism ○ Must be supplied in the diet ○ These are: Valine Leucine Isoleucine Threonine Methionine Histidine Lysine Phenylalanine Tryptophan 19 of 20 are chiral ○ from the asymmetry of the alpha carbon Only Glycine is achiral ○ two hydrogen atoms attached to alpha carbon Chirality is classified using D-and L- notation ○ Almost all naturally occurring amino acids are L-amino acids Hydrophobic Amino Acids Almost always located in the interior of the molecule ○ among other hydrophobic groups ○ where they can avoid interactions with water Have nonpolar side chains ○ interact very weakly or not at all with water Lack of reactive functional groups ○ do not directly participate in mediating chemical reactions Most have aliphatic (hydrocarbon-like) side chains  ○ Alanine (Ala) ○ Valine (Val) ○ Leucine (Leu) ○ Isoleucine (Ile) ○ Phenylalanine (Phe) Contain H-bond capable atoms but the bulk of their side chains are nonpolar ○ Methionine (Met) with an S atom ○ Tryptophan (Trp) with an NH group Special case: Proline ○ Unique among amino acids ○ Aliphatic side chain is covalently linked to its amino group Polar Amino Acids Can be found on the water-exposed surface of proteins Can also occur in protein interior ○ If there is another H-bonding side chain nearby Contain H-bonding groups  ○ Can interact with water Has hydroxyl (OH) groups: ○ Serine (Ser) ○ Threonine (Thr) ○ Tyrosine (Tyr) Has thiol (SH) groups: ○ Cysteine (Cys) Has amide (NH2) groups: ○ Asparagine (Asn) ○ Glutamine (Gln) Has polar imidazole ring: ○ Histidine (His) Special Case: Glycine ○ Only H atom side chain = Cannot H-bond ○ Included because neither hydrophobic nor charged Some polar side chains can ionize at physiological pH values ○ Depending on the presence of nearby groups that increase their polarity ○ Histidine Can act as an acid and base neutral (basic) His protonated = imidazolium ion (an acid) ○ Cysteine SH group deprotonated = thiolate anion SH group oxidizes with another SH group = disulfide bond ○ Serine, Threonine, Tyrosine Very weakly acidic OH ionize = OH groups (strong bases in chemical reactions) Charged Amino Acids Located on the protein’s surface ○ charged groups can be: surrounded by water molecules interact with other polar or ionic substances. Always charged under physiological conditions Negatively charged (COO- group): ○ Aspartate (Asp) ○ Glutamate (Glu) Positively charged (NH group): ○ Aspartate (Asp) = NH3+ ○ Glutamate (Glu) = NH2+ Amino Acid Abbreviation 3-letter code = first three letters of amino acid’s name 1-letter code Unknown amino acid: X Initial letter not shared: C H I M S V ○ Cysteine (C) ○ Histidine (H) ○ Isoleucine (I) ○ Methionine (M) ○ Serine (S) ○ Valine (V)  More than one amino acid: A G L P T (assigned to the most frequently occurring or structurally most simple) Winner Loser Alanine (A) Asparagine (N) - analogous amides Aspartate (D) - charged, acidic amino acids Arginine (R) [Phonetic] Glycine (G) Glutamine (Q) - analogous amides Glutamate (E) - charged, acidic amino acids Leucine (L) Lysine (K) - K near L Proline (P) Phenylalanine (F) [Phonetic] Threonine (T) Tyrosine (Y) - Nearest to T, other letters taken Tryptophan (W) - bulky double ring = bulky W Amino Acid pK values (Ionizable groups) Group pK C-terminus 3.5 Asp 3.9 Glu 4.1 Cys 8.4 N-terminus 9.0 Tyr 10.5 Lys 10.5 Arg 12.5 Isoelectric point (pI) pH where molecules carry. no net electric charge (neutral) In a molecule with two ionizable groups, the pI lies between the pK values of those two groups: ○ pI = 1/2 (pK1 + pK2) ○ pK1 = carboxyl group ○ pK2 = a-amino group ○ pKR = side chain group Amino acids that do not have side chains that ionize ○ pI = average of pK1 and pK2 HOW do faulty protein structures lead to disorders such as Alzheimer’s disease? When some protein structures are disrupted, the molecules tend to aggregate, eventually impairing cellular functions and producing the symptoms of disorders such as Alzheimer’s disease. Post-translation (645 - p.611) Amino acid side chains can be covalently modified Almost all occur after the polypeptide chain has been synthesized