BMS 300 1st Edition Lecture 4 Outline of Last Lecture I. Phospholipid orientation in water -micelle -liposome -planar bilayer II. Lipid mosaic model of biological membrane -transmembrane proteinsIII. Proteins as amino acid polymers -amino acid structure 1. amine 2. carboxylic acid 3. R-group -peptide bond formation IV. Protein primary structure -amino acid sequence V. Protein secondary structure -alpha helix-beta sheet VI. Protein tertiary structure These 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.-role of R-groups 1. non-polar/uncharged 2. polar 3. charged VII. Protein folding into geometric shapes Outline of Current Lecture I. Protein structure -role of R-groups in tertiary structure of a protein 1. folding of hydrophobic and hydrophilic R-groups 2. role of geometric shape (3D) in proteins function > liquid/substitute -role of R-groups in transmembrane protein 1. orientation of hydrophobic R-groups in lipid bilayer2. single pass across the membrane3. multiple pass as R channelsII. Structure of eukaryotic cells -prokaryotes1. bacteria 2. archaea -eukaryotes 1. specialization of function through membrane and compartments -chromosomes in the nucleus1. DNA molecules -histones as organizing and regulating DNA binding proteins -histones as species -ribosomes and endoplasmic reticulum Current LectureRole of R-groups in determining the 3D (geometric) shape of proteins-we can divide amino acids into 3 different categories: >non-polar, uncharged, hydrophobic -there is an equal sharing of electrons>polar, hydrophilic >charged-imagine this string of ribbons with things attached to it dunked underwater and it will form a 3D shape based primarily on the R-groups -the R-groups that hide or go towards the middle are hydrophobic and they “turn away” from the water-the hydrophilic R-groups will be facing towards the water -the amino acid sequence determines where we find the hydrophilic R-groups vs. the hydrophobic R-group-this will force the amino acids to have a certain shape -it isn’t simply the thermodynamics that determine the protein shape-if the molecule is all folded up there are regions of the molecule with a “binding pocket” -in these binding pockets there is substrate for enzymes—liquid -you need to have the perfect charge and structure for these “binding pockets” to form -if the amino acid doesn’t have the same exact shape it can’t get into the binding pocket to lower the energy of activation and create an enzymeThe structure of transmembrane proteins -take the phospholipid bilayer and imagine how we can thread a protein across it while still following the rules we made-when protein enters the lipid bilayer its constrained -the region of the protein that crosses the lipid bilayer is configured as a helix -if the thickness of the membrane is large which means it is going to need like 40 amino acids to reach all the way across -you are going to have to have hydrophobic amino acids that weave through the membrane -which means we have a single alpha helix across the membrane Generating a hydrophilic pathway (channel) from multiple alpha helix-for each time the protein passes the membrane it is going to pass across the membraneas an alpha helix-for this we will link together 4 to create a channel across -some of these R-groups will be pointed outward towards the other head groups -the R-groups as we work our way down will be pointed inward as they go down the staircase -hydrophobic R-groups to form a hydrophilic pathway*3D shape *low order state *hydrophilic pathway ***see imageProkaryotes-2 big groups>bacteria>archaea-lack intracellular membrane bound compartments -however they still obey the rules for DNA to RNA to protein (Central dogma) -there are no separate compartments for any of the pieces of the cell Eukaryote-nucleus in the middle of the cell -the membrane bound nucleus: all the Eukaryotic DNA is confined to the nucleus -eukaryotic DNA is organized into chromosomes >each chromosome is a molecule of DNA >46 chromosomes (23 mothers, 23 fathers)>1.8 meters long total (each one is several centimeters long)-the DNA binding protein called a histone-the histones form a “spool” around which the DNA wraps -the histones organize into sets of 8 called
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