Amino Acids General Amino Acids: Building blocks for

Amino Acids General Amino Acids:  Building blocks for

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) 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

Amino Acids Structure Amino Acid Structure: Amide, CA, R-group (variable) D/L Isomers

Amino Acids Side Chains AA Side Chains: Side chains determine the functionality of the AA b/c the COOH and NH 2 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 Zwitterion

Zwitterion: dipolar form of AA, found at biological pHs (internal acid/base Rxn) Amphoteric Amphoteric: molecules with properties of both acid and base

Formation of Polypeptides Formation Reaction: Dehydration reaction CA + Amine Amide Amide structure/Peptide bond/Peptide linkage

Amide/Peptide Bonds Polypeptides 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 Protein

Structure Proteins General: > 50 AA Linus Pauling 1954 Nobel Prize -helix and -pleated sheet Fredrick Sanger 1958 Primary structure of beef insulin Classification

Primary Description #, kind, type and sequence of AA Examples

Secondary Regular 3D structure, held together by H-bonds in backbone -helix -pleated sheet

triple helix Tertiary Distinct 3D structure due to interactions between R-groups

H-bonds Ionic bonds (Salt Bridges) Disulfide bonds Hydrophobic Hydrophilic Quaternary

Complex proteins Multiple units Non-protein parts Metal ions

Primary Structure 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

Fragment 1: Gly-Glu-Arg-Gly-Phe-PheGly-Phe-Phe-Tyr-Thr-Pro-Lys Fragment 2: Combined: Gly-Glu-Arg-Gly-Phe-Phe-Tyr-Thr-Pro-Lys Overlap Edman Degradation split AA at N-Terminal End

Secondary Structure Secondary Structure: Determined by H-bonds between AA-backbone -helix AA 4 residues apart, R-groups towards outside -pleated sheet AA far apart, R-groups face outwards

Tertiary Structure 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) Quaternary Structure

Quaternary Structure: Multiple protein units Non-protein parts Metal ions Ex: Hemoglobin 4 subunits

Fe atoms Protein Structure Summary -Helix

-helix Structure:helix Structure: Secondary Determined by H-bonds between AA-backbone -helix AA 4 residues apart, R-groups towards outside -Pleated Sheet

-helix Structure:pleated sheet structure: Secondary Determined by H-bonds between AAbackbone -pleated sheet AA far apart, R-groups face outwards

H-bonds Secondary H-helix Structure:bonds: Between the C=O and NH of backbone Responsible for secondary structure Tertiary H-helix Structure:bonds:

Between the C=O and -NH or -OH of R-groups Responsible for tertiary structure Salt Bridges Ionic Bonds/Salt Bridges: Tertiary Structure

Between COO- and NH3+ groups Disulfide Bonds Disulfide bonds: Tertiary Structure Between -SH and SH groups

Mainly between Cys-Cys Hydrophobic Interactions Hydrophobic Interactions: Tertiary Structure

Between R groups (Alkane and Aromatic) Interior of proteins to avoid water Hydrophilic Interactions

Hydrophilic Interactions: Tertiary Structure Exterior of proteins to interact with water Polar groups (OH) Acidic groups (COOH) Basic groups (NH2)

Identify 2/3 Structure Protein Functions 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!)

Denaturation 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 Example 1. Heat

Cooking 2. Acids/Base (pH)

Lactic Acid 3. Organic Molecules Ethanol/Isopropanol

4. Heavy Metals Pb, Hg

5. Agitation Stirring 6.

UV Light 7. Enzymes

Digestion 8. Salts Water purification

Xanthoproteic Test Xanthoproteic Test: Detects Benzene rings Yellow color

Phe, Try, Tyr Biuret Test Biuret Test: Detects tri-peptides (must have at least 2 peptide bonds)

Cu2SO4 Violet color Ninhydrin Test Ninhydrin Test:

General test for AA All AA blue Pro, hydroxyproline yellow Very sensitive 1 g (10g (10-6) Chromatography

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) Electrophoresis 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. Fredrick Sanger 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

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