BMS 300 class notes
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This 13 page Class Notes was uploaded by Lyric Jamerson on Tuesday September 6, 2016. The Class Notes belongs to BMS 300 at Colorado State University taught by John P Walrond in Fall 2016. Since its upload, it has received 5 views.
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Date Created: 09/06/16
Day 1/ Water Monday, August 22, 2016 12:00 PM E-book is Required Objectives are the most important part Main discussion points Tutors for this class Get new material Tutorial class Videos Each lecture is recorded Learning tool Go to class Try rewriting notes Clear up things than the notes you took the first time Watch time for things not understood Go to that time on the video to relearn Recitation BMS 200 Organized around small group of students to discuss material Tutorials Sometimes need new ways of learning and take into small groups Small discussion White board, write out material Start next week Examinations Four unit exams 100 points 80 multiple choice Think about the question before you try to look for the answer The answer must match the story Try not to memorize the right answers 20 fill in the blanks Final Will cover everything Final is higher than unit score Final counts for the unit score Total is 500 points Make up exams WATER We need water in our lives In a range where water is liquid Simple molecule One atom of oxygen and two atoms of hydrogen Molecular weight is 18 Covalent bonds Compare and contrast nitrogen and oxygen Electrons equally shared In water hydrogen is slightly positively charged In water oxygen in slightly negatively charged Unequal sharing Gives water a dipole charge Gives water unusual characteristics Role of dipole moment Allows for solubility Ions that are hydrophilic Water loving Components of water 1 atom of Oxygen 2 atoms of hydrogen = one atome of H20-MW of 18 (MW= molecular weight) When a water molecule is put together There is an oxygen linked to the two hydrogens through a covalent bond Sharing individual electron Oxygen usually borrows electron from hydrogen Electrons tend to spend more time around the oxygen, giving it a negative charge Hydrogen has a partial positive charge At sea level water is liquid Why is water liquid at room temperature? Dipole moment Explain: O degrees and 100 degrees Compare to N2 MW of 28 -196 degrees Compare to O2 MW is 32 -193 degrees Compare to helium MW 4 -262 degrees Remember partial positive on hydrogen and partial negative on oxygen Hydrogen is going to interact with negative of oxygen Called hydrogen bond Two water molecules will interact for a small amount of time Allows water molecules to form a matrix of these bonds In fact be a liquid Boil Liquid to gas Freeze Liquid to solid Evaporate Go into gas at room temperature Miniscus Forms because of charge on the glass Dipoles will interact with the glass Interact with one another on outside Forms surface tension Day 2/ Water Wednesday, August 24, 2016 12:01 PM Change in ions Equilibrium where all ions are equally distributed through the water Sodium chloride ions Diffusion into water column Reaching equilibrium through water? Diffusion across a barrier Ions bounce across barrier Ion goes across barrier Ion selective channels Reaching equilibrium Water diffusion through aquaporin Osmosis Reaching equilibrium Hydrophilic and hydrophobic Lipids hydrophobic molecules Lacking charge Cant easily move through dipole moments Equally shared electrons Triglyceride structure Glycerol Three carbon alcohol? Fatty acid Phospholipid Fatty acid retains Hydrophobic Equally charged Hydrophilic Can live in both worlds Can live in water worlds Converting triglyceride into a phospholipid The basic structure of the phospholipid bilayer. Beaker of one liter of water Put in crystal of sodium chloride For each sodium ion , a corresponding chloride Forms a crystal. Sodium chloride is going to be 5.84 grams Into liter of water Is going to be a .1 mole of sodium chloride solution 100 mille-moler Imagine water molecules with partial positive and negative charges Allows them to bounce against sodium chloride Allows them to be liberated Negative end of water molecule will interact with positive charge on sodium Cl will act with positive on water molecule Allows them to interact with dipole moments Will distribute into equilibrium So that everywhere we look We have 100 mille-moles of sodium chloride 100 mille-moles of each 200 mille-osmolarity Example Perfume bottle corked Only closest people will smell it the first in a matter of seconds to minutes Other people in the room will notice as the fumes are evenly distributed throughout the room Two chambers with a barrier in the middle Say we have one liter on each side 100 mille-molar of sodium chloride on the left side Equals 100 mille-molar of sodium and 100 mille-molar of chloride Across barrier, put a handful of channels A sodium selective channel Chloride selective channel Think of ions as ping-pong balls A lucky chance will result in the ping pong ball going right through the sodium channel or chloride channel and go into the right side The probability at the start is that the ions would flow from left to right Later, equilibrium will be reached where 50 mille- moles of each ion will be on both sides The probabilities will be equal see it go from higher concentration to lower concentration Beaker with barrier NaCl on left side with 100mm H20 on other side Openings in barrier Called aquaporin Water channels Na Cl is occupying some space on the left side while there is more water molecules on the right side than left side Water molecules moving is greater from right to left This process is called osmosis Never reach pure water concentration The water molves right to left so water on right goes down while water volume on left goes up Hyperstatic pressure Pushing down on poles Reach a new kind of equilibrium Water is a polar molecule Oxygen tends to steal electrons from hydrogens Hydrogen bonds make water liquid at STP Normally in room temperature Water molecules generally doesn’t spend much time in a hydrogen bond with another water molecule NaCl in water Cubic structure of sodium chloride Each chloride is interacting with one sodium Put into water Also the ions to interact with water molecules Positive ions go to negative on water Negative ions go to positive on water Will distribute themselves evenly on each side over time Keep them equally spaced (equilibrium) Diffusion channels Reach ion concentration where ions are diffused evenly Water channels Water goes from one side to the other and because ions take up space, water will be higher on one side more than another Ions are hydrophilic Hydrophilic: water loving Lack of charge Hydrophobic: water fearing Lack of charge Layer of olive oil (new beaker) Triglycerfide Water on top Don’t move, will stay like it is Shake the beaker Disperse olive oil with tiny bubbles floating in the water for about 10 minutes They will later collect and form an oil slick on top of the water Olive oil is insoluable in water Triglyceride Three carbons with OH on each one Alcohol Fatty acid Carbocylic acids Long chain of carbons Always covalently linked to hydrogens Each carbon has two hydrogens Sometimes unsaturated Take hydroxide and combine with OH And generate HOH End up with carbon oxygen carbon bond Get ester bonds to the fatty acid All electrons are equally shared No charge and no dipole moments can get around All will stay together in the solution Day 4/ Water Friday, August 26, 2016 11:56 AM Protein structure o Primary structure amino acid sequence o Secondary hydrogen bonding Carbonyl oxygen to alpha helix or Beta sheets All based on hydrogen bonding Use negative and positive charge to generate secondary structure o Tertiary r-group interactions with water Either toward or away from water Determines three demensional shape Role of R-groups o Charged or polar Hydrophilic o Uncharged Hydrophobic Generating 3-d structure o Alpha helix and beta sheets o Arrangement of R- groups Enzymes/ binding Pockets and 3-d shape Threading alphahelasses o Lipid bilayer ? Role of hydrophobic region R-groups Forming a channel ? Primary protein structure - as amino acid sequence o Each bead is an amino acid o Important to know where they are and their function in a protein Secondary Protein structure o Derives from hydrogen bonding between amine hydrogens and carbonyl oxygen to create: Have slight positive and negative charges Alpha helix Beta sheet Hydrogen bonding between adjacent strands/ primary structure o Peptide bond Equal sharing of electrons Hydrogen bonding in an alpha helix o Looks like cork screw (blue) o Circles are amino acids (orange) Each amino acid is a "step" on a spiral staircase o Each amino acid goes around the circle by 100 degrees Have a name Maleic Single amino acid names Most likely to form an alpha helix o Hydrogens of amine and carbonyl hydrogen Pleated sheet o Big kink Glycine or proline o Start amino terminus o End is carboxyl terminus o Have interaction between two strands of amino acids with hydrogen bonding o Called antiparallel pleated sheet Both pleated sheet and alpha helix o Parallel organization Nitrogen toward carboxylic end Forms hydrogen bonding between the strands Secondary structure o Alpha helix Happens with every fourth on the alpha helix In the back bone of protein set Have hydrogen bonding o Antiparallel beta sheet Somewhere off screen is U-turn Will have interactions Electromagnetic fields holding the two strands together o Parallel beta pleated sheet Off set some what 3-d/ tertiary structure o Interaction of r groups with water Hydrophobic R groups (green blocks) Hydrophillic I between hydrophobic r groups (blue) End up with a shape that the hydrophilic point out and hydrophobic are tucked inside, facing each other Creates a binding pocket that fits sucrose that produces glucose and fruitose Day 3 /Water Thursday, August 25, 2016 11:54 AM Triglyceride structure Three ester bonds to three fatty acids Phospholipids structure Two fatty acids (hydrophobic) One phosphate head group (hydrophilic) Feeling molecule Interact with both water and no water Association of phosphate head groups with H2O Surface Turn tails upward and heads face the water Micelle Very rare in biology Can form them Are unstable because of hydrophobic tails Liposome Stable structure Bilayer of phospholipids Plana A bilayer Lipidmosa: Model of the membrane Transmembrane protiens in phospholipid bilayer Going from outside to in and inside to outside after adding protein Protiens as amino acid polymers Only 20 amino acids Laid out from one to the next Amino acid structure Peptide bond Amine carboxylic acid R-group Make strings of amino acids 2 ovaliants Linked by peptide bond Primary structure Amino acid sequence Orientation of molecule Amino terminus Carboxylic terminus Secondary structure Hydrosenbonding for a helix beta sheet Continued from yesterday Glycerol Carboxcylic Acid Form a new bond called a ester bond Carbon on carbon to the fatty acid Can do three times for each fatty acid Now becomes a triglyceride Triglyceride Carbon linked to a ester bond linked to a fatty acid 3-carbon alcohol Highly uncharged molecule Gives it a hydrophobic water insoluble characteristic Going to then change into a phospholipid Will look like triglyceride Down on last carbon Can now be linked to another structure Oxygen (4) Phosphorous Has charge Group negatively charged Head group Can be a: Choline Serine Ethanolamine End toward phosphorous is charged Can change characteristics so second fatty acid group is hydrophobic And head with phosphorous is hydrophilic Amphipathic Both feeling Head with two legs Phosphate head group (head) Fatty acid side chains (legs) Phospholipid interaction with water Beaker Filled with water Surface tension with water molecules Take salt shaker Filled with phospholipids Sprinkle phospholipids onto the surface of the water How are they going to orient themselves Will orient with respect to the dipole moments Head will face water Tails face out of the beaker. Will form single uniform layer Doesn’t tell how we form a biological membrane. Try 1 Micelle Not thermodynamically very favorable. Add proteins and a bunch of things Micelle Unstable New beaker with water Individual head groups will turn around and face the water with the tails pointing inward Spherical structure However, micelle is unstable One water slides in and breaks the whole thing apart They do exist but are highly unstable Need to create a thermodynamically stable structure in water Try 2 Liposome Bilayer of phospholipids New beaker Circle of phospholipids with tails going in Orient phosphate with another layer inside with tails facing and heads are opposite each other. Will form a well where it will be a stable structure with water in the center and surrounding the outside Planar phospholipid bilayer Image of phospholipids stacked one to another Tails pointing inward Forms phospholipid bilayer Outside top Bottom inside Diameter of head is 1 nanometer A billionth of a meter 1000 nm/umeter Plane of bilayer that extends for long distances Remember tail is hydrophobic Ions need to move outside to inside or inside to outside Hard for charged particles to move through hydrophobic region Requires another character Oval structures Transmembrane protein Phospholipid mosaic model of the biological membrane Great long bilayer that is penetrated by protein Has a hydrophilic pathway from out to in and in to out Proteins as polymers of amino acids What is an amino acid? Simple molecule NH 2 With a c and c linked with oxygen and hydroxide This is a carboxylic acid This is an amino acid Can also have an r group Can have twenty possible r groups Lead to the twenty amino acids R groups can be Uncharged Hydrophobic Charged hydrophilic Polar Hydrophilic Dehydration Take h and oh to make h2o Form carbon and nitrogen bond Peptide bond Can form several peptide bonds between carbon and nitrogen Doesn’t matter if five or five hundred amino acids linked Right end is carboxy terminous Left end is amino terminus Generated q primary amino acid sequence and the primary structure of protein
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