BMB 251 1st Edition Lecture 5 Outline of Last Lecture I. Nonspontaneous reactionsII. Free Energy (∆ G)III. Electron carrier moleculesIV. GlycolysisV. Citric acid cycleVI. Electron transport chain/Oxidative phosphorylation Outline of Current Lecture VII. Proteinsa. Side chains:i. Acidicii. Basiciii. Uncharged, polariv. NonpolarVIII. Polypeptide foldinga. Noncovalent bondsIX. Configuration X. ComplexesXI. Four levels of organizationXII. Restrictions of 3D movementsCurrent Lecture- Clicker: How can a nonspontaneous reaction proceed in a cell?o By coupling it to a spontaneous reactiono **Cannot heat up a cell to make a reaction proceed; lowering concentrations create less collisions, which also does not help a reaction proceed- Proteins: long polymer chains composed of monomeric amino acidso Can be positively charged, negatively charged, polar or nonpolaro Amino acids polymerize to make proteins via condensation synthesis between their N-group (amino group) and C-group (carboxyl group)o Side chains in amino acid give them uniqueness; otherwise, all amino acids are very similar Acidic Side chains:- Aspartic acidThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- Glutamic acid Basic side chains- Lysine - Arginine - Histidine Uncharged, polar side chains- Asparagine- Glutamine- Serine- Threonine- Tyrosine- **Although the amide (N) is uncharged at a neutral pH, it is polar. The OH- groups in the last three side chains are polar as well- Serine and threonine are phosphorylated by the same enzyme Nonpolar side chains - Alanine- Valine- Methionine- Tryptophan Charged side chains interact strongly with water, polar side chains still somewhatinteract with water and nonpolar do not interact at all with water-they interact with each other instead- Polypeptide chains can fold onto itself, making 3D conformationso Protein folds as it’s being synthesizedo Depends on the noncovalent interactions Ionic bonds Hydrogen-bonding Van der Waals attractionso These noncovalent forces often create both a hydrophilic layer and a hydrophobic core Protein wraps itself in a way that the hydrophobic amino acids are on the inside of the structure while the hydrophilic ones remain on the outside to associate with watero ***Scientists have discovered that all that is needed for a protein to fold is the intracellular interactions of the amino acid side chains Used a process of adding in urea solvent to denature the proteins, adding in a higher concentration of glucose and ATP, and waiting to see if it would create phosphorylated ATP (definition of a functional protein). It worked, showing that all that was needed were the amino acids.- Configuration: chemical formula; in order to change the configuration, bonds would have to be brokeno One configuration can have multiple conformations because atoms can rotate around the bond axis and be in many different positions- Complexes: multiple subunits that functional proteins very often assemble into- Four levels of organization in the structure of a protein:o Primary structure: simply the amino acid sequenceo Secondary structure: fairly short range of local integrations between parts of the backbone with nearby other parts of the backbone Alpha helices (spirals that look like DNA helices) Beta sheets (arrows)- Can either be going in the same orientation direction or can fold back and forth on itself, making H-bonds between each of the sheetso Tertiary structure: all of the secondary structures fold into final globular conformationo Quaternary structure: subunits (different polypeptides) come together to create a larger,functional unit- Collisions and noncovalent bonds restrict 3D movement of the polypeptide chaino Peptide bonds do not really rotateo Side chains can always be rotated around their single bondso Phi and psi angles are created within each amino acid (technically, but are not always present), which rotate around each
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