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BIOLOGY CHAPTER 2 - Element: substance w/unique defined properties that cannot be broken down through “normal” chemical means - Smallest representation is an atom - Each element is composed of one unique type of atom - Subatomic Particles - Proton: (+1 c...

BIOLOGY CHAPTER 2 - Element: substance w/unique defined properties that cannot be broken down through “normal” chemical means - Smallest representation is an atom - Each element is composed of one unique type of atom - Subatomic Particles - Proton: (+1 charge, in nucleus, mass of 1 dalton) - Neutron (No charge, in nucleus, mass of 1 Da) - Electron (-1 charge, surrounding nucleus, 0.00000001 mass) - Hadrons: associations of 3 quarks - Protons: 2 up quarks +1 down - Neutrons: 2 down quarks +1 up - Atomic number: number of protons an element has - (NOT TRUE) Classic Element Model: # protons = # neutrons = # e- (electrons) - Mass number = Total number of protons and neutrons - Isotopes: atoms of the same element that show variation in # of neutrons - Larger element gets the more variation there will be - Neutrons do not affect reactivity. All isotopes of element behave the same in a reaction - Some isotopes are STABLE, some unstable or radioactive - Electrons are the part of the atom that participates in chemical reactions - Chemical reactions are done to pair unpaired valence electrons - E- distributed in e- starved elements - Represents on a specific energy level - Outermost shell has most energy - Reactivity of atoms is determined by the distribution of electrons around the nucleus, especially in valence shell (outermost shell) BIOLOGY 8/26 - Types of bonds - Covalent Bonds - e- are shared between 2 elements/atoms (shown with lines, H-H, O=O, etc) - Depends on electronegativity (ability of an element to attract e-, depending on how many they have) - Two types, Polar and Nonpolar - Polar Covalent (example 1): the two elements differ somewhat in electronegativity. - The shared e- spend more time w/ the more electronegative element - This creates poles of partial charge - Nonpolar Covalent (example 2): the two elements are similar in electronegativity  - e- are shared equally between the two elements - No poles, no partial charge - Ionic Bonds - The two elements differ dramatically in electronegativity - The more electronegative element steals an e- from the lesser element - Results in the formation of ions - Cation = +1 charge - Anion = -1 charge - The bond is the attraction between opposite charges - Salt: any compound formed via ionic bond (not all normal salt) - Hydrogen Bonds - An attraction between partially charged regions on different (or same if big enough) polar molecules - Always shown with dotted line - The Properties of Water - H2O has several emergent properties that are caused because of Hydrogen bonding - Cohesion (and adhesion) - The ability for water molecules to stick to other water molecules - Creates surface tension - Adhesion: ability for water molecules to stick to other polar molecules - Regulating Earth’s temperature - Large bodies of water resist changes in temperature due to the hydrogen bonds - Temperature: avg. kinetic energy of a molecule - Each day a certain amount of solar energy must be absorbed to break hydrogen bonds before individual molecules can increase kinetic energy - No solar energy at night, energy absorbed during day is released into the atmosphere as heat. Hydrogen bonds reform and cycle restarts during the day, this leaves temp fairly constant day and night - Less Dense as a Solid (more regulation) - When water freezes the molecules lock into rigid lattice (XXX line) - Hydrogen Bonds uniformly separate adjacent water molecules - Ice floats, regulates/insulates body of water beneath preventing it from freezing solid - Water is the Solvent of Life - H2O breaks down/dissociates into: - OH- -> Hydroxide Ion - [OH-] = 0.0000001 M / 1x10^-7 M - H+ -> Hydrogen Ion  - [H+] = 0.0000001 M / 1x10^-7 M - These are considered the “neutral” state of water - Will never find pure water in nature - [H+] x [OH-] = 1x10^-14, pure number/constant - What is an Acid? - Anything that increases hydrogen ion [H+] concentration - An acid dissociates to release H+ - HCl -> H+ + Cl- - Strong acid shows complete dissociation (gives up all its hydrogen) - Irreversible - Weak acid shows incomplete dissociation - Reversible (sometimes) - Base - Anything that decreases [H+] - Directly removes H+ - Can also release a OH-, which binds and removes H+ - Reversible, same rules as strong and weak acid BIOLOGY 8/28 - pH = -log[H+]  - =log(1x10^4) - =4 - When [H+] (hydrogen) ions increase, pH decreases and vice versa - Each pH number represents a multiplication or division of 10 - Example: pH 6 has 10 times more H+ than pH 7 - pH 1 = 1,000,000 - pH 2 = 100,000 - pH 3 = 10,000 - pH 4 = 1,000 - pH 5 = 100 - pH 6 = 10 - pH 7 = 1 - pH 8 = 1/10 - pH 9 = 1/100 - pH 10 = 1/1000, etc - pH comes from the exponent of the H+ ion ([H+] = 1x10^-6, pH= 6) - [H+] x [OH-] always equals 1 x 10^-14 —--------FIRST QUIZ MATERIAL END—-------------------- - Chapter 3: The Molecules of Cells - Hydrocarbons form the basis of life - All organic molecules have a hydrocarbon backbone: - Properties of pure hydrocarbon: - Non-polar (not water soluble, does not like water) - Gasses - In life, an organic molecule has to have other elements attached to it, to convey polarity (then can interact with water) and to convey other properties associated with those elements - These are called functional groups - Hydroxyl (OH) - Alcohol (all have an f ending) - Conveys polarity - Carbonyl (=O) - Aldehyde terminal carbonyl (all have an -al ending) - Ketone: non-terminal carbonyl (all have a -one ending) - Carbonyls allow sugar to form rings in aqueous solution (our bodies) - Carboxyl (left image) - Double bonded oxygen and a hydroxyl on the same carbonyl - Functions as an acid  - Amino (NH_2) - Nitrogen atom bonded by two hydrogen - Functions as a base (amino acids, etc) - Phosphates (PO_4) - Complex - Phosphorus and Oxygen and hydroxyls - Functions as an acid - Sulfhydryls (SH) - Affects 3D structure of a protein (amino acids) - Cast off hydrogen on proteins and bond to each other - Disulfide bridge - Methyl (CH_3) - Non-polar - Very prevalent in biological molecules - Too many functions to list - Each gene has promoter that is methylated - Each gene has optimal methylation pattern - Optimal transcription (better bonding with enzymes, the right amount to not overproduce) - Your methylation pattern can change over time - Poor diet/exercise affect it as well - Worse it is the greater the change - Patterns are heritable from parent to child - Before having child spend 1 year dieting and exercising to reinforce good pattern BIOLOGY 9/4 - Carbohydrates - Simple sugars - Rapidly expelled from stomach - Absorbed via intestines (stomach empties faster, you then eat more often) - Causes blood sugar spike and insulin spike - Monosaccharides: - One unit long (⬡) - Glucose, fructose, etc - Disaccharides: - Two units long (⬡-⬡) - Sucrose (glucose + fructose) - Lactose (glucose + galactose) - Polysaccharides - 100-1000 units long - Complex Carbs (both made of Glucose alpha) - Slowly expelled from stomach/absorbed in intestines, stay full longer  - No blood sugar/insulin spike - Plant Starches, short/long-term energy storage - Glycogen/Animal Starches, short term energy only - Stored in liver/muscle - Non-Starches (fibers) - Made of glucose-beta, body can’t break that down - Soluble Fiber - Can be digested by gut bacteria, releases beneficial byproducts (vitamins) - Insoluble Fiber - Unable to digest at all, turns into poop - Food, mainly plant products, contain all these elements - Simple sugars, complex carbs, and fibers BIOLOGY 9/9 - Lipids - Fats (triglycerides), phospholipids, steroids - Glycerol w/ 1, 2, 3 or fatty acids -> (hydrocarbon + carboxyl) - Glycerol + 1 FAT = monoglyceride - Glycerol + 2 FAT= diglyceride - Glycerol + 3 FAT = triglyceride - Saturated Fat: no double bonds between Cs in the Fatty Acid Tail - Packed together tightly (solid at room temperature) - Unhealthy fat, hard for body to break down - Animal Products- Beef, Pork, Poultry - Long-Term energy storage in animals - Unsaturated Fat: one or more double bonds between Cs in the Fatty Acid Tail - Monounsaturated = 1 double bond - Polyunsaturated = > 1 double bonds - There’s a bend in the FAT at each double bond - Prevents tight packing (liquid at room temp, oils) - Healthy fat, easy for body to break down - Naturally occurring unsaturated fats are cis-unsaturated (Hydrogen on same side of the double bond) - Plant/Fish Diet - Essential Nutrients: things that body can’t make, must be eaten - Hydrogenation: convert oil to solid at room temperature - Used to extend shelf life - Produces Trans-Unsaturated Fats (Trans fat) - Trans Fat - Act just like saturated fat, unhealthy - Phospholipids: the primary component of membranes - Only biological diglyceride - Steroids: four fused rings; functional groups determine function  - Non-polar - Steroids only differ in functional groups - Cholesterol —-> - Only one functional group, hydroxel (HO) - Essential component of cell membranes - Primarily non-polar, requires transport molecule to carry it through bloodstream - Two types of carrier molecules - LDL (Low Density Lipoprotein) - “Bad” carrier molecule, wants to stick to artery walls, forms plaque - Animal Diet - HDL (High Density Lipoprotein) - “Good” carrier molecule, no sticking to artery walls - Can remove LDL to reverse plaque/clot - Plant/Fish Diet (especially Fatty fish) - Sex Hormones : Birth Control - Prevents ovulation, making body think its pregnant - Prevents implantation of fertilized egg - Proteins - Made of amino acids - 20 different amino acids in life that we know it - Polypeptides: 100s or 100s of units long, peptide bond - R = Residue (variable group on molecules that have a common backbone) - Non-polar (-CH_3) - Polar (-OH, -SH) - Acidic (-carboxyl) - Basic (-NH_2) BIOLOGY 9/11 - Proteins - Proteins are functional units - Structure determines function - Primary: chain of amino acids, held by peptide bonds (covalent) - Secondary: generated by H bonds between function groups on the backbone, no R - Alpha helix - Beta pleated sheet - Tertiary: creates true 3-D structure - Generated by interactions between residues - Polar R: H bonds  - Acidic/basic R: Ionic bonds - Cysteines (sulfhydryl): disulfide bridge (covalent) - Non-polar R: hydrophobic interactions - Aggregate together to avoid water - Quaternary: - Only applies to proteins with > 1 polypeptide in the functional unit - Polypeptide: one chain of amino acids - The polypeptides are held together by the same interactions in tertiary - Essential Nutrients (EAA/Essential Amino Acids) - There are 8(9 when you’re born) nutrients your body can’t make - Complete Protein: includes all 8 EAA (Animal Diet0 - Incomplete Protein: doesn’t include all 8 (Plant Diet) - Vegetarians must make sure they combine plant products to get all 8 - Regulation of Blood Sugar - Pancreas releases insulin when blood sugar levels are high, insulin targets all body cells, tells them to remove sugar from blood - Pancreas releases glucagon when blood sugar levels are low, glucagon targets liver and tells it to break down glycogen & release glucose to blood - Diabetes: cells can’t remove sugar (glucose) - Type 1 (juvenile onset): insulin dependent, typically an autoimmune disorder. White blood cells destroy the beta cells that make insulin - Type 2 (adult onset): non-insulin dependent, down-regulation of insulin production (due to shifts in methylation pattern on the gene for insulin), remediated by changes in diet and exercise - Nucleic Acids - Two types - Deoxyribonucleic acid - Ribonucleic acid - Made of nucleotides - Adenine, Cytosine, Guanine, Thymine, Uracil - Difference between DNA and RNA - RNA: sugar is Ribose, 2’C has a hydroxyl - DNA: sugar is Deoxyribose 2’C doesn’t have a hydroxyl - Nitrogenous Bases - Purines: 2 rings structure (Adenine, Guanine) - Pyrimidine:1 ring structure (Cytosine, Thymine, Uracil) - Making a nucleic acid: a chain of nucleotides, can be hundreds or thousands long - Phosphodiester linkage holds them together (covalent) - Bond is between the phosphate on the 5’C & the OH on 3’C  - Special properties of DNA 1. Always double stranded 2. Always double helix 3. Complementary Base Pairing (A-T, G-C) Purine-pyrimidine: constant width 4. Antiparallel (running in opposite directions), orients nucleotides for optimal base pairing - Special properties of RNA 1. Always single stranded 2. Folds onto itself and base pairs with itself (every RNA molecule has a unique conformation/shape) 3. Act as enzymes 4. Complementary Base Pairing (A-U G-C) BIOLOGY 9/16 (CHAPTER 4) - Domains - Eukarya - Eukaryotic Cell type (internal nucleus/internal membrane system) - Includes both single/multi cell organisms - Bacteria - Prokaryotic Cell type (no nucleus/internal membrane system) - Single celled only - “Germs” - pathogenic bacteria - Archaea - Prokaryotic Cell type - Extremophiles - have many adaptations for extreme environment - Single celled only - Genetically more similar to Eukarya than Bacteria - Parts of the Bacterial Cell (prokaryotic) - Glycocalyx - Sugar coat outside cell wall - Two types - Capsule - Rigidly organized polysaccharide, capsules makes bacteria more pathogenic (“hides” bacteria from immune system) - Staph aureus - Slime layer - Loosely organized polysaccharide, helps bacteria stick to surfaces and initiate infection - Strep mutans - Cell Wall - Primary component is peptidoglycan (a polysaccharide cross-linked with short protein segments.)  - Good target for antibiotics - Two types - Gram positive CW - Thick layer of peptidoglycan bound to cell membrane by teichoic acids - Gram negative CW - Thin layer of peptidoglycan w’ a second outer membrane - External Structures - Flagella - External to CW - Made of protein called flagellin (good target for antibiotics) - Whirls in circle for motility/movement - Fimbriae - Same structure but shorter, used to stick to surfaces and initiate infection - Sex Pilus - Hollow tube connecting builder and receiver - Not every bacteria can make it, must have special gene (builder) - Any bacteria can receive pilus (not same species) - Builder replicates DNA and sends it through pilus to receiver - Receiver may “eat”/metabolize DNA or integrate it into its own chromosome - Bacteria can easily share antibiotic resistance this way BIOLOGY 9/18 - Bacteria DNA - One main chromosome, not linear but circular - Carries all the genes for survival under “normal” conditions - It’s attached to the plasma membrane at one spot: nucleoid region - Plasmids: small circular DNA fragments - Carry genes that may convey an advantage (ex. Antibiotic resistance, gene for sex pilus) - Ribosomes - “Reads” nRNA, builds a protein - Two subunits: (size, density and structure) - Large: 505 - Small: 305 - Assembled: 705 - Good target for antibiotics - Formation of the Endospore - A desiccated (dried up) cell wrapped in protein coat - Response to adverse environmental conditions - Can exist in nature indefinitely - When good conditions return, cell rehydrates and comes back to life - Bacillus anthracis (anthrax) - Parts of a Eukaryotic Cell - Cell Wall - Plants: cellulose - Fungi: chitin - Animals: no CW, instead extracellular matrix (holds tissues together) - Flagella - Inside plasma membrane/cell wall, not outside - Complex structure - 9 x 2: 9 pairs of microtubules (protein tubulin) + 2 central microtubules - dilated/undilated back and forth for motility - Cilia: same structure but shorter - For motility in one direction (sweep) - Nucleus - Contains genomic DNA - Nucleolus: contains genes for RNA enzymes - Nuclear envelope: double membrane, the outer membrane is continuous with the rough ER - Nuclear pores: regulate what enters and leaves nucleus - Nuclear lamina: a network of intermediate filaments that supports the shape of the nucleus - Endoplasmic Reticulum - Network of tubules surrounding nucleus - Rough: has a “granulated” appearance due to the presence of ribosomes - Processes proteins w/ a special destination - Builds new - Smooth Endoplasmic Reticulum - Doesn’t have a granular appearance - Makes fats/ steroids - Builds new cell membrane, phospholipids - Detoxification of non-polar drugs - Adds an OH, then the drug can be filtered out by kidneys - Ribosomes - Reads nRNA, builds proteins - Large: 605 - Small: 405 - Assembled: 805 - Both subunits have a protein part and an RNA part - RNA part is made by nucleolus  - Protein part made by ribosomes in the cytoplasm - Enters nucleus & is assembled w/ RNA part at the nucleolus - Completed subunit leaves the nucleus - The 2 subunits exist independently of each other - When there’s a mRNA, whatever subunits are closest will bind - If the mRNA codes for PSD, then the ribosome goes to rough ER - Ribosome binds to a pore in the rough ER - The ribosome releases the protein to the lumen of the rough ER - When finished, the subunits of the ribosome dissociate from each other, the mRNA and from rough ER