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U-M BIOLCHEM 415 - Amino Acids and Protein Structure
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BIOLCHEM 415 1st Edition Lecture 2Outline of Last Lecture I. Four Major Classes of BiomoleculesA. Proteins, Lipids, Carbohydrates, Nucleic Acid II. Central Dogma describes transfer of information in the bodyOutline of Current Lecture III. LipidsIV. Eukaryotic v. Prokaryotic CellsV. Organelles in Eukaryotic CellsVI. Thermal Motions power biological interactionsVII. Weak Interactions are importantVIII.pH is important to maintainCurrent LectureLipid- composed of hydrophilic head and hydrophobic tails- amphipathic- functions include:- membrane formation- fuel source- signaling- bilayer membrane- two rows of lipids create membrane- hydrophilic face out- hydrophobic tails inside- most biomolecules can’t pass throughThese 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.- must be transported through membranes by proteins- trans membrane proteins- facilitate molecule transportationProkaryotic Cell membranes- no intracellular membranes- inner plasma membrane -> cell wall -> outer membrane Eukaryotic Cell membranes- membrane enclosed organelles- single out plasma membrane- cells are less rigid than prokaryotic cellsCytoplasm- inside of the cell membrane and outside organelles- shape maintained by cytoskeleton- transfers occur along cytoskeleton- it interacts with the organellesOrganelles in Eukaryotic Cells- nucleus: contains the genetic information (DNA)- mitochondria: cell powerhouse; produces ATP- chloroplasts: photosynthesis in plant cells- endoplasmic reticulum (ER)- Rough ER: has ribosomes and processes new proteins- Smooth ER: lacks ribosomes; variety of biochemical roles- golgi apparatus: sorts proteins- lysosome: digests material brought into cell and damaged organelles- Tay-Sachs disease: defect in lysosome functionCellular Export- Exocytosis- proteins transported outside cell- rough ER -> golgi complex -> secretory vesicle- examples of exported materials:- insulin, antibodies, digestive enzymes, neurotransmittersCellular Import- Endocytosis- bring biomolecules into cell- cell membrane encapsulates material then buds of (invagination)- Familial Hypercholesterolemia- defective endocytosis of insulin- high levels of blood cholesterol - can lead to heart attacks- Phagocytosis- large amounts of material brought into cell- example- immune cell (Macrophage) ingesting a bacteriaThermal Motions- weak bonds permit dynamic interactions- Brownian motion- random movement of molecules - caused by random fluctuations in environmental energy- initiates biochemical interactions- diffusion of molecules throughout cells, organisms, environmentStabilizing Forces- listed strongest to weakest1) Chemical (covalent) bonds2) Electrostatic bonds3) Hydrogen bonds4) Van der Waals 5) Hydrophobic- strength in the number of bondsAssume Biochemistry occurs in aqueous solutions- water molecules are asymmetric and polar Weak interactions are important- Electrostatic- Coulomb’s lawE = kq1q2/DrE – energy of the reactionq – charge of the ionsD – dielectric constantr – distance between the ions in Angstroms (Å)k – portionality constant- D =1 in a vacuum and 80 in H2O- water weakens theses reactions- due to polarity and the dipole created- partial charges on the molecule cancel out the ion charges- ion screening- this is why D in water is so large- Hydrogen bonds- electronegative atom and hydrogen- hydrogen is polarized- partial electrostatic interaction- optimal angle is 180- constantly breaking and reforming (Brownian motion)- these bonds are responsible for water’s cohesion- waters competes for H-bonds with biological molecules- reason for solubility- Van der Waals- nonpolar charged molecules- fluctuating asymmetry causes temporary dipoles- typical energies: 0.5 – 1 kcal/mole- the optimal contact distance: ~ 4 Å- multiple weak bonds account for biological stability- H-bonds and Van der Waals create DNA double helix- easily broken by enzymesHydrophobic Effect- spontaneous clustering of hydrophobic molecules- powered by increased entropy- water molecules form cages around nonpolar molecules- nonpolar molecules cluster together- results in less cage molecules- greater entropy in the water- examples- oil and water- formation of membranes- amphipathic phospholipidspH- -log10([H+])- important to control pH- for example: pH of bloodAcids have differing ionization tendancies- Ka = acid dissociation constant- Ka = [H+][A-]/[HA]- larger the Ka, the stronger the acid- Henderson-Hasselbalch equationpH = pKa + log10([A-]/[HA])Functional groups have specific chemical properties- affect the properties of the different


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U-M BIOLCHEM 415 - Amino Acids and Protein Structure

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