amino acids general
DESCRIPTION
Amino Acids General. Amino Acids: Building blocks for peptides, proteins Some individually important (or converted to important molecules) Gly , Glu , Tyr neurotransmitters Tyr parent/precursor for epinephrine (adrenaline) - PowerPoint PPT PresentationTRANSCRIPT
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Amino AcidsGeneral
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Amino Acids:• Building blocks for peptides, proteins• Some individually important (or converted to important molecules)
• Gly, Glu, Tyr neurotransmitters• Tyr parent/precursor for epinephrine (adrenaline)• His stomach secretes HCl, symptoms for inflammation, colds.
• Essential (10)• needed for normal health• not synthesized by the body • must be supplied by diet
• Complete (animal) vs. Incomplete (vegetable) protein
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Amino AcidsStructure
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Amino Acid Structure:• Amide, CA, R-group (variable)• D/L Isomers
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Amino AcidsSide Chains
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AA – Side Chains:• Side chains determine the functionality of the AA b/c the –COOH and –NH2
groups react to form the backbone• 3 letter abbreviations (given on cheat sheet)
Classification Functional Group Property
Nonpolar -R (aliphatic or aromatic)
Hydrophobic
Polar -COOH, -NH2, -OH Hydrophilic
Acidic -COOH (extra) Lose H2 anion Salt Bridges
Basic -NH2 (extra) Gain H2 cation Salt Bridges
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Zwitterion
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Zwitterion: dipolar form of AA, found at biological pH’s (internal acid/base Rxn)
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Amphoteric
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Amphoteric: molecules with properties of both acid and base
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Formation ofPolypeptides
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Formation Reaction:• Dehydration reaction• CA + Amine Amide• Amide structure/Peptide bond/Peptide linkage
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Amide/PeptideBonds
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Polypeptides
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Polypeptides:• Small chains of AA (40-50 units)• Many ways to connect together (N!)• ~30 biologically relevant ones• Hormones or Nerve transmitters• Small changes structure HUGE changes in functionality
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ProteinStructure
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Proteins – General:• > 50 AA• Linus Pauling – 1954 Nobel Prize α-helix and β-pleated sheet• Fredrick Sanger – 1958 Primary structure of beef insulinClassification Description Examples
Primary #, kind, type and sequence of AA
Secondary Regular 3D structure, held together by H-bonds in backbone
α-helixβ-pleated sheet
triple helix
Tertiary Distinct 3D structure due to interactions between R-groups
H-bondsIonic bonds (Salt Bridges)
Disulfide bondsHydrophobicHydrophilic
Quaternary Complex proteinsMultiple units
Non-protein partsMetal ions
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Primary Structure
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Primary Structure:• #, kind, type, and sequence of AA• Fredrick Sanger (1958 Nobel Prize) Beef Insulin• Several years of work to sequence 51 AA• Hydrolyzed proteins into smaller fragments to analyze
• Edman Degradation – split AA at N-Terminal End
Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-LysGly-Phe-Phe-Tyr-Thr-Pro-Lys
Gly-Glu-Arg-Gly-Phe-Phe-Fragment 1:
Combined:Fragment 2:
Overlap
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Secondary Structure
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Secondary Structure:• Determined by H-bonds between AA-backbone
• α-helix AA 4 residues apart, R-groups towards outside
• β-pleated sheet AA far apart, R-groups face outwards
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Tertiary Structure
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Tertiary Structure:• Determined by interactions between R-groups• H-bonds: -COOH and –OH
• Ionic/Salt Bridges
• Disulfide Bonds
• Hydrophobic (form core of protein)
• Hydrophilic (face outwards to interact with water)
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Quaternary Structure
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Quaternary Structure:• Multiple protein units• Non-protein parts• Metal ions
• Ex: Hemoglobin• 4 subunits• Fe atoms
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Protein StructureSummary
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α-Helix
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α-helix Structure:• Secondary• Determined by H-bonds between AA-backbone• α-helix AA 4 residues apart, R-groups towards
outside
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β-Pleated Sheet
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β-pleated sheet structure:• Secondary• Determined by H-bonds between AA-
backbone• β-pleated sheet AA far apart, R-groups
face outwards
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H-bonds
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Secondary H-bonds:• Between the C=O and NH of backbone• Responsible for secondary structure
Tertiary H-bonds:• Between the C=O and -NH or -OH of R-groups• Responsible for tertiary structure
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Salt Bridges
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Ionic Bonds/Salt Bridges:• Tertiary Structure• Between –COO- and –NH3+ groups
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Disulfide Bonds
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Disulfide bonds:• Tertiary Structure• Between -SH and –SH groups• Mainly between Cys-Cys
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HydrophobicInteractions
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Hydrophobic Interactions:• Tertiary Structure• Between –R groups (Alkane and
Aromatic)• Interior of proteins to avoid water
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HydrophilicInteractions
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Hydrophilic Interactions:• Tertiary Structure• Exterior of proteins to interact with water• Polar groups (OH)• Acidic groups (COOH)• Basic groups (NH2)
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Identify 2°/3°Structure
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Protein Functions
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Protein Functions:• Structural Support – skin, connective tissue• Storage – Fe in Liver• Transport – O2 in Hemoglobin• Defense – antibodies, venom• Motion/Movement – muscles• Regulation – blood/glucose/insulin• Catalysis – Enzymes (Ch. 30!)
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Denaturation
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Denaturation: Loss of 3D conformation in a protein• Disruption of 2°/3°/4° interactions• Does NOT break 1° structure (hydrolysis)• Loss of biological activity• Causes of Denaturation
Cause Example1. Heat Cooking2. Acids/Base (pH) Lactic Acid3. Organic Molecules Ethanol/Isopropanol4. Heavy Metals Pb, Hg 5. Agitation Stirring6. UV Light7. Enzymes Digestion8. Salts Water purification
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XanthoproteicTest
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Xanthoproteic Test:• Detects Benzene rings• Yellow color• Phe, Try, Tyr
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Biuret Test
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Biuret Test:• Detects tri-peptides (must have at least 2 peptide bonds)• Cu2SO4
• Violet color
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NinhydrinTest
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Ninhydrin Test:• General test for AA• All AA blue• Pro, hydroxyproline yellow• Very sensitive 1 μg (10-6)
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Chromatography
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Chromatography: separation technique for AA• Difference in distribution between two
phases○ Solubility
○ Charge• TLC (thin-layer) – solid/liquid phase
○ Solvent Front (rate solvent moves)○ Differences in solubility cause AA to
travel at different rates in the solvent• Column chromatography (variation of above)
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Electrophoresis
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Electrophoresis: separation technique for AA• Charged particles separate in electric field (zwitterions)• Separation based on
○ Size – friction (sieve) ○ Charge – electric field
• Types○ SDS – masks charge/separate by mass/size
○ Isoelectric Focusing – AA separated by charge○ 2D – separate on both.
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Fredrick Sanger
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Fredrick Sanger:• Solved structure of beef insulin (1955)• Nobel prize 1958• 51 AA in two chains held together by disulfide bonds• DFNB + N-terminal end + hydrolysis to solve structure• “Paper shredder”