Bio 211 Week 2 lecture notes
Bio 211 Week 2 lecture notes 10400
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This 8 page Class Notes was uploaded by Aleena Watson on Tuesday October 11, 2016. The Class Notes belongs to 10400 at Portland State University taught by Mandy Lee Hill Cook in Fall 2016. Since its upload, it has received 11 views. For similar materials see PRINCIPLES OF BIOLOGY I - BI 211 - 002 in Biology at Portland State University.
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Date Created: 10/11/16
Lecture notes 211 10/5 Housekeeping Midnight friday posting review questions for MT next wednesday These questions are previous exam questions Slightly different questions/materials Look at all previous exams No answer keys Use vocab no straight definitions Chapter 1-3 at least but probably thru chapt. 6 Spontaneous reactants have more order and potential energy - Favored in experiments (higher energy) Non-spontaneous reactions are the opposite More bonds you have you are adding potential energy Amino acid - always ionic (reacted with water) 5 things - Central carbon - R chain - Amino Use process of info to identifying amino acids: Acidic and basic - hydrophillic Polar side chain - (-) charge hydrophillic Non-polar side chain - no charge, no oxygen, hydrophobic New material: Isomers: - Structural isomer - Easiest to identify - Geometric isomer - Because of the double bond, the molecule is stuck in that specific position - Transbutine - mirrored, but upsidedown - cis - mirrored but molecules in different arrangement with relation to double bond in the center - Optical isomer - Mirrored images Polymer: protein with repeating unit - so an amino acid bound to an amino acid to an amino acid PEPTIDE BOND - how amino acids are linked to create proteins Condensation reaction/dehydration synthesis - Monomers that combine to make polymers - Then macromolecule polymers are created and make water Depolymerization (hydrolysis - hydro (water) lysis (break apart)) - Reverse previous process Proteins will not form spontaneously in a solution of amino acids and water because hydrolysis reactions are energetically favored. Dehydration sythesis: Peptide bond - has a lot of characteristics of a double bond. It gets stuck, linear because of the inflexibility of the bond. Requires energy Polypeptides bonds - Amino terminus (N-terminus) - Carboxyl terminus (C-terminus) - Synthesis (and numbering) proceeds N -> C 20 amino acids all have their own names and can be represented by a 3-letter acronymn Residue - amino acid chain (N-terminus to C-terminus, reading left to right) Peptide bonds - Backbone of protein, inflexible which stabilizes the growing polypeptide Protein structure - primary structure is a specific sequence of amino acids - So reading the residues left to right - If we change the primary structure of a protein it can have devastating impacts - Mutations are silenced in human bodies but is not always the case - Ie: sickled cell. Polypeptide should be: Pro-Glu-Glu but is Pro-Val-Glu Does not carry oxygen well Primary structure- amino acid sequence Secondary structure - motifs of amino acid sequence - (Alpha) helix - (Beta) pleated sheet Tertiary Structure - 99% of proteins final shape - Take 2ndary structure and fold it together hydrophobic on inside and hydrophilic outside - Domains of highly stable sections How proteins fold down is spontaneous reactions - and it’s not fast Chaperonins proteins - helps things go properly (folding) - They are taken in and refolded and if they do not refold for some reason they are DESTROYED Tertiary Protein structures: (final folded shape) - Hydrogen bond - Between polar side chains and peptide backbone or other R-groups - Hydrophobic - occurs within an aqueous solution with a hydrophilic polar side chain (this is intuitive, because aqueous solutions are water solutions and need to attract polar side chains which love water) - van der Waals - The further stabilized hydrophobic side chain electrical attraction phenomenon - Covalent - Disulfide (‘two sulfur“) bonds - Aka bridges - Strong links between polypeptides of the same type OR strong links between 2 completely separated polypeptides - Sulfhydrul groups - Ionic - Completely full and opposing charges so this would be between the acidic and basic groups Quaternary Structure - - When interactions and combinations happen between polypeptides Disulfide bonds/bridges Hair example: composed of amino acid residues - Disulfide bridges - Curly - bonds at different levels vs straight same levels Your hair is more fragile when wet! Hydrogen bonds break apart when hair is wet and that’s because instead of the H bonds connecting with the amino acids in your hair, it’s connecting with the water As it dries, they reform H-bonds with amino acids Folding is often regulated but is also spontaneous Disordered - inactive - takes less time to keep disordered, assembled and ready to go so our bodies keep proteins folded Ordered - active Unfolding of proteins Generated by a change in enviornment, such as: - Heat, salt concentration and pH imbalances Lecture notes 10/3 Housekeeping Extra credit (Katie announced it) - Link on d2l for survey do it within a week - Similar survey at the end of the course - Anonymous survey Lab this week (tina): - Plant pigments and pH - Shifts in cabbage color from purple to red/blue - Spectrophotometry - What they want us to walk away with from lab this week: knowing how to make a graph Oxygen most electron negative bond, then nitrogen, carbon Non polar covalent - long, weak bonds Polar covalent bonds - shorter, stronger bonds Biology takes place in water - Ionic bonds dissociate making them weaker in biology - Non polar covalent bonds strong in biology because they stay together in water Organic structure Ways to display molecules: 1. molecular formula (shortest way to display just with Letters and subscripts) 2. Structural formula (more information than structural) 3. Ball-and-stick models (3D shows bond angles, color matters) 4. Space-filling models (most accurate, relative sizes, color matters) That’s the basic chemistry we are going to do in this course. Carbon is the basis for all living things Organic means carbon Carbon can form 4 different bonds or 2 double bonds “Functional groups” REVIEW TABLE 2.3 - NEED TO KNOW MAJOR FUNCTIONAL GROUPS AS THEY APPLY TO BIO - Amino NH2 group - Carboxyl - C double bond OOH - Hydroxyl - Make molecules dissolve in water - Phosphate - Important for ATP - Sulfhydryl - Interact with each other, making a stable structural bonds Need its name, recognize formulas 6 functional groups, ID how it should act in a biological system Molecular weight - quantity of molecules using a unit of mole. Mass equal to weight expressed in grams Molarity - concentration, often times we are talking about something that is in liquid form Water is essential, critical for life to exist. When exploring other planets, we look for water to indicate life. Water is wacky: Oxygen is most electronegative, and that puts it above hydrogen. It kind of looks like Micky Mouse’s head upsidedown. Highly polar. They very reaidly form a 3rd type of bond: hydrogen bond. Partial charge from polar covalent bond which is exceptionally weak but in bulk they are strong - Hydrogen bond ex: belly flopping Likes H-bonds Water molecules exclude non polar molecules - Oil & water Hydrophobic- means “water-fearing” molecules non polar molecules shrink when conacting with water Hydrophilic - means “water-loving” molecules polar molecules which want to mix with water and bond with it Water and oil do not make solutions because they don’t mix. Water - “universal solvent” Solution vocab: - Solvent & solute Ionic (and polar) compounds dissolve in water Hydrogen bonding - Cohesion - attracted to water - Adhesion - attracted to unlike compounds Ice lightest form (least dense) of water. Ice floats because of hydrogen bonds Ice insulates water below it so life can form slowly below it Any other liquid would freeze from the bottom up! High specific heat because it takes a lot of energy to heat up and a long time to cool down Regulates life on earth High heat of vaporization (liquid to gas water) Evaporation cools you off and consumes heat REVIEW table 2.2!! Water ionizes (pH) Ionization - dynamic equilibrium pH Scale (log base 10 scale): Acid - below 7 Basic - above 7 Examples of basic/acidic substances and where they fall on the scale: Basic - Lye, household bleach Middle ground/ on basic side - baking soda, seawater, human blood Neutral - water Slightly acidic - milk, urine, black coffee tomatoes, wine Acidic - lemon juice, stomach acid Buffer - acts as a reservoir for hydrogen atoms Carbonic acid - major player in blood Bicarbonate - your body uses this if your blood is too acidic Chapter 3 Stanley Miller’s “Ocean Edge” experiment - explaining origins of the building blocks (see below...amino acids) Amino Acids - Building block molecules - Have 4 components: (central carbon bonded to:) 1. H atom 2. Amino functional group (as mentioned in chapter 2 notes) 3. Carboxyl functional group 4. R-Group (ionized forms of original molecule) - Combo of amino and carboxy functional group show us how molecules behave - Functional group charges are important a) They help the amino acid stay intact in a solution and therefore be able to come into contact with other solutes creating more bonds (what valence shells on hydrogen atoms always want) b) Chemical reactivity is affected by either a (+) or (-) charge - R-group aka “side chain” - unique aspect of the amino acid - In other words, all amino acids have those core components and this is how you can tell them apart from one another! YOU WILL WANT TO MEMORIZE THESE FOR THE EXAM - Review figure 3.2 p. 80!! - Different types of r-groups/side chains: - (charged) Acidic (2) - C bearing / (charged) Basic (3) - NH bearing - hydrophilic - (uncharged) Polar (5) - Oxygen bearing - hydrophilic - Nonpolar (10) - (the rest!) Hydrogen bearing - hydrophobic Other tips on remembering the groups: (YOU DO NOT NEED TO MEMORIZE ALL 20 INDIVIDUALLY) - Negative charge = narrows down to Acidic or Basic. If it has a (-) charge, it’s Acidic. Loses a proton (Vice versa for Positive charge…steps again) - Positive charge = narrows down to Acidic or Basic. We know now that Acidic has a (-) charge, so it has to be Basic. Gains a proton - Uncharged = O present? Then it’s going to be electronegative which is a polar covalent… giving us polar side chain - Not charged, no O? Last resort is nonpolar. Boom. Molecule vocab: Macromolecules - large molecules made up of tons of smaller molecules Monomer (“one part”)- smaller molecules within a macromolecule Polymer (“many parts”) - tons of monomers coming together to make a macromolecule Polymerization - process of monomers coming together as a polymer. Leads to creation of proteins Condensation reactions/ dehydration reactions - new bonds that in turn make the polymer loose a water molecule Hydrolysis - breaks the polymer apart and adds a water molecule Protein functions: Catalysis - catalyze (speed up chemical reactions). When a protein is acting as a catalysis, it is called an enzyme! Most important protein function Defense - you have heard the term antibody before. This is a protein that attack and kill viruses when you are sick and/or have a disease Movement - when a cell needs to move, it uses motor and contractile proteins to move. This is true when we use our muscles, even. Signaling - Carrying and receiving messages between cells in our bodies are a protein’s responsibility. Structure - Literally what it means. What we see, like hair and skin, these proteins keep red blood cells flexible and in the correct disk-like shape Transport - getting molecules into and out of the cell. Regulation - how genes are expressed