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BSCI 105 9/2/11Atomic Structure and Bonds• Thermonuclear fusion: E=mc2 (Hydrogen Atoms) Energy = Mass Lost * Speed of light squared.- What causes building of larger elements- Caused the creation of elements• Doppler Shift: the change in wavelengths as an object approaches and leaves• Sun burns hydrogen and makes helium• ATOMIC NUMBER: # of protons• ATOMIC MASS: # of protons + neutrons• Electron orbital shells are spherical.• 1s, first shell has least energy.• INERT: an element with only paired electrons• Lithium splits water, leaving a hydroxyl group and hydrogen gas.• ION: charged atom• OCTET RULE: 8 electrons in outermost shell• Covalent Bond- Sharing of electrons between atoms.- Equal sharing= NON-POLAR covalent bond (CH4)- Unequal sharing= POLAR covalent bond (H2O)• Polar dissolves in polar• CATIONS- Atoms that give up one or two electrons give them up to become positively charged- Monovalent cation- gave up one electrons- Divalent cation- gave up two electrons• ANIONS- Atoms that gain one or two electrons assume a negative charge- Monovalent anions- gains one electrons- Divalent anions- gains two electrons• Structure leads the function (structure of molecules)• Functional Groups- HYDROXYL group (OH)- always polar- METHYL (CH3)- non-polar- AMINO (NH2) -polar- CARBOXYL O= C - OH (COOH)– polar• A MOLE is a measure of concentration of solute in a solution• One MOLE= 6.02 x 1023• PRESSURE is the concentration of gas in a solution.• Atomic COMPOSITION gives a molecule a specific 3-dimensional shape, polarity, and chemical reactivity.9/7/11Water And Life• Water molecules have hydrogen bonds between an oxygen atom and another molecule’s Hydrogen atom. (When water is in its liquid form, Hydrogen bonds are very fragile, about 1/20th as strong as a covalent bond, and they break and reform very frequently- each lasting a few trillionths of a second)• Properties of Water• Four emergent properties of water: Cohesive behavior, Ability to Moderate Temperature, Expansion upon Freezing, and Versatility as a Solvent.- COHESION- Water molecules sticking together by polar hydrogen bonds.- ADHESION- Water molecules hang on to other surfaces.- Surface Tension- High boiling point (High specific heat)- Specific Heat- The amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1oC- Solvent- for other polar molecules- Evaporation- takes heat away (Sweating or Panting)- Forces non-polar molecules to adhere together in an organized structure- Only substance that freezes from top down (density decreases when frozen)- It ionizes or dissociates• At equilibrium, there is a ratio of products to reactants• Not all reactants become products• COLLOID- a stable suspension of fine particles in a liquid• MOLARITY- the number of moles of solute per liter of a solution• When water dissociates, it leaves a Hydrogen ion (H+) and a Hydroxide ion (OH-)• LAW OF MASS ACTION- restores equilibrium in a reaction. (Add reactants to one side of reaction, drives to other side)• Human pH: 7.4• ACID- donates a proton (H+)- The more Hydrogen H+ ions, the more Acidic• BASE- removes or accepts a proton (H+)- The more Hydroxide OH- ions, the more Basic• Life is based on macromolecules changing shape.• When you hyperventilate, your pH goes UP.- Lose protons- pH becomes very basic• pH of 1 molar is 0• pH of 10 molar is -19/9/11Proteins• All proteins have an amino group NH2 at one end, and a Carboxyl group COOH at the other end at pH 7.4, and R group in between.• Amino Acids:- Essential amino acids- must take into diet- Nonessential amino acids• If the pH of the protein is lowered, the protein’s charge becomes more positive- (By adding more protons- H+)• Blood can get more acidic with certain diseases (Diabetes)• Enzymatic Proteins regulate metabolism by acting as CATALYSTS- (Chemical agents that selectively speed up chemical reactions without being consumed by the reaction.• All proteins are unbranched polymers constructed from the same set of 20 amino acids.• Polypeptides- Polymers of amino acids• Peptide bond- Covalent bond between two amino acids• A protein’s function depends on its ability to recognize and bind to some other molecule.• Four levels of protein structure:1. Linear chain of amino acids2. Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone. (Coils and folds in polypeptide chains)a. Alpha Helixb. Beta Pleated Sheet3. Three-dimensional shape stabilized by interactions between side chainsa. The protein’s functional shapeb. Prosthetic group- not an amino acid, artificial group that helps function.c. Hemoglobini. HbF- Hemoglobin fetal- binds oxygen very tightlyii. HbA- Hemoglobin adult- binds oxygen less tightlyd. Hydrophobic interactions occur during formation of tertiary structure, where the hydrophobic side chains cluster in the center of the protein.e. Difulside Bridges- covalent bonds that further reinforce the shape of a protein.4. Association of multiple polypeptides, forming a functional protein• Denaturation- protein unravels and loses its native shape, causing it to become inactive- Due to alteration of pH, Salt Concentration, Temperature, etc…- Often Occurs when transferred from an aqueous solution to a nonpolar solvent, or overheat.• Chaperone Proteins- aids the correct folding of proteins• Protein Functions- Enzymes- Transport Sites (For polar molecules through membranes)- Membrane Channels- Intracellular structural elements- Extracellular matrix- Receptors for signal molecules• ORGANIC MOLECULES have at least carbon, hydrogen, and oxygen.• With any source of energy, it is very simple to make organic molecules starting with any variety of inorganic molecules.• ABIOGENIC- synthesis of organic molecules without life9/9/11Living• Growth• Response to Environment• Reproduction• Contains Cells• Respiration/ Metabolism• Different Levels of Organization• Homeostasis9/12/11Carbohydrates• Polymers- form by dehydration synthesis- Take out HO and H- Dehydration reaction- Two molecules bonded together with the loss of a water molecule• Hydrolysis- In order to break down a polymer, add water- Add H2O between polymer and unlinked monomer• Carbohydrates- Triose sugars- Pentose sugars- Hexose sugars• (Include Glucose and Galactose)- Monosaccharide- single sugar- Disaccharide- two sugar units- Tri- and


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UMD BSCI 105 - Atomic Structure and Bonds

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