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5.1 Identity and Roles of Amino Acids Contain an amine group – Primary amine group Contain carboxyl group – Referred to as the alpha carbon R group –

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Presentation on theme: "5.1 Identity and Roles of Amino Acids Contain an amine group – Primary amine group Contain carboxyl group – Referred to as the alpha carbon R group –"— Presentation transcript:

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2 5.1 Identity and Roles of Amino Acids Contain an amine group – Primary amine group Contain carboxyl group – Referred to as the alpha carbon R group – Variable group – 20 different groups

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4 5.1 Identity and Roles of Amino Acids Stereochemistry – All amino acids but one are chiral – Stereochemistry is L

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6 5.2 Amino Acid Individuality: The R Groups Polarity differs – Polar Amino Acids Neutral Acidic Basic – Nonpolar Alkyl Branched Aromatics Unique

7 5.2 Amino Acid Individualities Functional Groups – Acid Groups Aspartate, Glutamate, Cysteine, Histidine, Tryosine – Basic Groups Lysine, Arginine, Histidine – Hydroxyl Groups Serine, Threonine, Tyrosine – Sulfur Groups Cysteine, Methionine

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9 5.3 Acid – Base Properties and Charge Titration and Net Charge – Henderson – Hasselbach equation illustrates the relationship between acid – base dissociation and charge – Amino acids have more than one dissociable group

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12 5.3 Acid – Base Properties and Charge Zwitterions – Two charged groups, but overall charge is zero – Most amino acids are in this form Zwitterions lead to altered pK values

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14 5.3 Acid – Base Properties and Charge Isoelectric point – pH at which zwitterion is exactly zero – Referred to as pI R groups can have dissociable groups – Acid, basic and sulfhydro groups

15 5.4 The Peptide Bond Covalent bond between amino group and alpha carboxyl group Dehydration reaction Referred to as amide or peptide bond

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17 5.4 The Peptide Bond Resonance properties – O, C and N bonds are delocalized – Creates partial double bond

18 5.4 The Peptide bond Amine and carboxyl groups are no longer acids or bases N- terminal end is only amino group not in peptide bond C- terminal end is only carboxyl group not in peptide bond

19 5.5 Peptides and Proteins Peptide – short chain or less than 25 amino acids – Can have biological properties Protein – more than 25 amino acids Referred to as macromolecules – Are polymers

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21 5.6 Levels of protein structure 4 levels of hierarchy – Primary – Secondary – Tertiary – Quaternary

22 5.6 Levels of Protein Structure Primary – Sequence of amino acids – Complete description for peptides – Determines its complete spatial arrangement

23 5.6 Levels of Protein Structure Secondary – Regular repeating structures – Three main types Alpha helix – spiral chain – Hydrogen bonds satisified intramolecular – R groups determine water solubility – Certain amino acids favor – Certain amino acids are helix breakers

24 5.6 Levels of Protein Structure – Three main types cont. Beta sheets – Resembles corrugate plate – Hydrogen bonds between backbone peptide bonds – Anti parallel and parallel forms Loops and Random Coils – Indeterminate in structure – Serve to link other secondary structures

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26 5.6 Levels of Protein Structure Tertiary – Three dimensional arrangement Quaternary – Three dimensional arrangement of multi subunit proteins – Individual protein chains

27 5.6 Levels of Protein Structure Domains – Combination of secondary structural elements – Also referred to as motifs or super secondary structure

28 5.6 Levels of Protein Structure Domain examples – TIM domain – SH2 domain – PTB domain – NAD binding domain – EF hand domain

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31 5.7 – Protein folding Two studies helped increase our understanding RNase experiment – Enzyme was inactivated with heat and then cooled – On cooling activity resumed – Suggest we can denature and refold a protein GroEL experiment – Helps protein fold correctly – Increases rate – Often referred to as a chaperone protein

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33 5.8 Oxygen binding in myoglobin and hemeglobin Myoglobin (Mb) and Hemeglobin (Hb) are oxygen binding proteins in mammals Similar protein structures – Mb – single chain Tightly bound to heme – Hb – four chains 2 Alpha and 2 Beta chains 4 heme molecules bind

34 5.8 Oxygen binding in myoglobin and hemeglobin Heme – Prosthetic group that binds oxygen – Four linked pyrrole rings – Each Nitrogen is chelated to central Iron

35 5.8 Oxygen binding in myoglobin and hemeglobin Binding of oxygen occurs differently – Fractional saturation of oxygen – Y = [MbO 2 ]/([Mb] + [MbO 2 ]) – Mb stores oxygen in muscle cells Releases when levels become depleted

36 5.8 Oxygen binding in myoglobin and hemeglobin – Hb binds oxygen with positive cooperatively When one oxygen binds, it helps the other oxygen bind S shaped curve Saturated with oxygen in the lungs and releases in tissue capillaries

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38 5.8 Oxygen binding in myoglobin and hemeglobin Bohr effect – Diminished binding of oxygen when increased pH – Adaptation at high altitudes 2,3 Bisphophoglycerate – Lowers binding of O2 to hemeglobin – Provides more oxygen to tissues

39 5.9 Protein purification and Analysis Purification – Extraction comes first Properties must be intact – Must have way to measure protein – Must minimize denaturation

40 5.9 Protein purification and Analysis – Physical methods are often used – Fractionation depends on differences between proteins Solubility Size Charge

41 5.9 Protein purification and Analysis Types of chromatography that may be used – Ion exchange column chromatography – Size Exclusion chromatography – High Pressure Liquid Chromatography – Gas Liquid Chromatography – Affinity Chromatography

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43 5.9 Protein purification and Analysis Analysis – UV light Tryptophan and tyrosine absorb Can estimate amount of protein – NMR Great for small molecule

44 5.9 Protein purification and Analysis Analysis cont. – X-Ray Produce pattern of diffraction Mathematical manipulation – Mass Spectrometry – Electrophoresis Can identify various proteins present Can be a test of purity


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