2: 2-(T2-first lecture) Protein Structure
- Page ID
- 64192
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Proteins are polymers of the bifunctional monomer, amino acids. The twenty common naturally-occurring amino acids each contain an α-carbon, an α-amino group, an α-carboxylic acid group, and an α-side chain or side group. These side chains (or R groups) may be either nonpolar, polar and uncharged, or charged, depending on the pH and pKa of the ionizable group. Two other amino acids occasionally appear in proteins. One is selenocysteine, which is found in Archaea, eubacteria, and animals and just recently found is pyrrolysine, found in Archaea. We will concentrate on only the 20 abundant, naturally-occurring amino acids.
- 2.1: Amino Acids
- 2.1.1: A1. Amino Acid Structure
- 2.1.1.1: Structure and Property of the Naturally-Occurring Amino Acids
- 2.1.2: A2. Amino Acid Stereochemistry
- 2.1.3: A3. Amino Acid Charges
- 2.1.4: A4. Introduction to Amino Acid Reactivity
- 2.1.5: A5. Reactions of Lysine
- 2.1.6: A6. Reactions of Cysteine
- 2.1.7: A7. Cysteine Chemistry
- 2.1.7.1: Review- Oxidation/Reduction (Redox) Reactions and Oxidation Numbers
- 2.1.8: A8. Reactions of Histidine
- 2.1.9: A9. In Vivo Post Translational Modification of Amino Acids
- 2.1.10: A10. General Links and References
- 2.4: Protein Folding - in Vivo and in Vitro
- 2.4.1: D1. Introduction
- 2.4.2: D2. Protein Folding In Vitro
- 2.4.3: D3. Folding of Single Protein Molecules
- 2.4.4: D4. The Denatured State
- 2.4.5: D5. Multiple Conformations from The Same Sequence
- 2.4.6: D6. Protein Folding In Vivo
- 2.4.6.1: Do you find biochemistry amazing?
- 2.4.7: D7. Redox Chemistry and Protein Folding
- 2.4.8: D8. Protein Transport Across Membranes
- 2.4.9: D9. Recent References
- 2.5: G. Predicting Protein Properties From Sequences
- 2.5.1: G1. Introduction to Bioinformatics, Computational Biology and Proteomics
- 2.5.2: G2. Prediction of Secondary Structure
- 2.5.3: G3. Prediction of Hydrophobicity
- 2.5.4: G4. Prediction of Membrane Protein Structure
- 2.5.5: G5. Prediction of Protein Tertiary Structure
- 2.5.6: G6. Proteomics Problem Set 1
- 2.5.7: G7. Proteomics Problem Set 2
- 2.5.8: G8. General Links and References