Bio 240 Test 1 Study Guide
Bio 240 Test 1 Study Guide Bio 240
U of L
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Popular in Biology
This 17 page Study Guide was uploaded by tpnguy09 on Thursday June 30, 2016. The Study Guide belongs to Bio 240 at University of Louisville taught by Dr. Rabin in Winter 2016. Since its upload, it has received 23 views. For similar materials see Biology in Biology at University of Louisville.
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Date Created: 06/30/16
Chapter 2: Chemical context of life 1/7/16 Why Chemistry? ● Bombardier beetle defense against ants ● Redox reaction ● Multidisciplinary science Matter Sodium+chlorine→sodium chloride (solid + liquid→salt (solid compound)) ● Diverse form ● Elements (92 in nature), compounds ● 6 Essential elements (CHONPS) ( carbon, hydrogen, oxygen, nitrogen, prosperous, sulfur) ● Trace elements Atom ● Smallest unit with the properties of an element ● Nucleus ● Protons (+charges) ● Neutrons (no charge) ● Atomic number: protons, and determines what the element is, it doesn’t changes ● Mass number: protons + neutrons, can change, like isotopes Isotopes ● Same element with different # of neutrons ● Same atomic # ● Different mass # ● Can be used for o Carbon dating o Atomic bomb ▪ Iran and Uranium enrichment Energy levels of electrons ● First shell (2e-) ● Second shell (8 e-) ● Third shell (8e-) ● Moving outward from atomic nucleus: energy absorbed ● Moving inward from atomic nucleus : energy lost ● Electron configurations? ( SPDF) ● Chemical behavior of atom depends on o Valence shell o Valence electrons Periodic Table ● Atomic number, element symbol, atomic mass ● Ordered by shells Chemical bonds ● When atoms combine to form molecules and ionic compounds o Incomplete→complete valance shells o Will only combine with another element that completes each other shells o Full 8e- ● Atoms share or transfer valence electrons o Hydrogen bonds? Covalent bond ● Two atoms sharing a pair of valence electrons ● 2H can share bonds to become H 2 ● Pure element ● Compounds vs. molecule ● Single bond ● Double bond ● Note valence electrons ● Examples o Hygrogne H2 o Oxygen O2 ( double bond) o Water H2O o Methane CH4 Electronegativity ● Attraction of a particular atom for the electrons of a covalent bond ● Nonpolar covalent bond (equal pulling) ● Polar covalent bond ( unequal pulling) o Ex. Water ▪ 1H and 1 O are negative ▪ 1H is positive o Partial charges; negative and positive o Not pulling hard: positive o Pulling hard: negative ● Ionic bond o So unequal in valence shell attraction that electron stripped away o Bond is formed due to opposite charges ● NaCl→Na+Cl- o Sodium atom, chlorine atom→sodium chloride o Na=cation o Cl=anion ● Strong bonds, when you break them apart, they release more energy ● Weak chemical bonds o What’s the advantage? ▪ Easier to break, o Hydrogen bonds ▪ Weak bond individually, but when there are a lot of them they can become strong ▪ Ex. Water ( H2O) and Ammonia (NH3) ● H positive, N negative Water and Carbon 1/12/16 Importance of Water ● 70-80% composition of cell is water ● Polar covalent bonds→polar molecule ● Hydrogen bonds give water its properties (4) ● Usually in cytoplasm ● Hydrogen bond= H—H ● Polar covalent bonds =H-O-H (unequal sharing, slightly positive and also negative) ● Water can make up to four hydrogen bonds 1. Adhesion/cohesion o Cohesion of water molecules o Adhesion of water to cell walls (combine to other things) o Hydrogen bonds ▪ Allow transport against gravity in plants o Ex. Surface tension ▪ Overfull water glass (can be overfilled a little bit, because water molecules bond to one another and also to the glass) 2. Moderation of Temperature o Heat: kinetic energy transfer o Specific heat: heat gained/ lost for 1g to change by 1 degree o Water has high specific heat ▪ Water in iron pot on stove ▪ It is difficult for water to boil because of the hydrogen bonds; hydrogen bonds are stuck together and must be broken apart so that they can move more and turn into water vapor o Due to …. o Allows life ▪ Coastal temps have less drastic temp changes: water absorbs heat until it reaches land ▪ Our bodies ● Water in our cells absorbs the heat on hot days and moderate the temperature so that we don’t overheat o Evaporative cooling ▪ Transformation from liquid to gas ▪ Evaporation→surface cooling ▪ Stabilizes our temperatures ▪ 8 mins at 212 degree F ▪ Effect of high humidity ▪ Heat is released during sweating and evaporates into the air so that we don’t overheat ▪ Water→ heat rises, more heat absorbed by water, less heat elsewhere ( high humidity) 3. Expansion upon freezing ● Hydrogen bonds in ice are more “ordered”→ice less dense→ floating ice ● If ice sank, water would eventually freeze solid, making life impossible ● Ice: hydrogen bonds are stable ● Liquid water: hydrogen bonds break and reform 4. Water as versatile solvent ● Solvent(the mixture, usually liquid) vs. solute(what you are mixing in) ● Ex. Solute: salt, solvent: water ● Aqueous solution ● Water is the solvent ● Versatile solvent (due to charges; positive and negative?) ● Hydration shell around ions ● Nonionic polar molecules (sugars) ● Large polar molecules with ionic/polar regions (proteins) ● Water does not want to form shells around nonpolar molecules, because they have no charge ● Ex. Oil and water don’t mix ● Hydrophilic: “love water” ● Have charge or partial charge ● Hydrophobic: “fear of water” ● Lipids ● Cell membranes ● No charge Acids and bases ● H+ is transferred to another water→ hydronium (H3O+) ● Leave hydroxide (OH-) behind ● H+ represents the hydronium ion ● H+ and OH- ● 2H2O→hydronium ion ( H3O+) +hydroxide ion (OH-) 2H2O←hydronium ion (H3O+) +hydroxide ion (OH-) ● Basic solution: more OH- than H+ ● Neutral: same amount of H+ and OH- ● Acidic solution: more H+ than OH- ● Strong acids and bases o Strong acid HCL dissociates completely in water: ▪ HCl→H+Cl_ High H+ o Strong base HaOH dissociates completely in water ▪ NaOH→ Na+ +OH- Low H+s ● Weak acids and bases o Reversible reactions o Ammonia, NH3, acts as a weak base: ▪ NH3 +H+→NH4+ NH3 +H+←NH4+ ● Carbonic acid, H2CO3, acts as a weak acid: ● H2CO3→HCO3- ● The pH scale o The product of H+ and OH- is constant ▪ [H+][OH]=10^-14 ▪ pH+ pOH=14, and look at exponent o What is pH of solution with [H+] of 10^-8? ▪ 8 ( from exponent) o What is pH of solution with [OH-] of 10^-8? ▪ 14-8=6 ● Below 7=acidic ● Above 7=basic ● pH of your stomach is b/t 3 and 4 ● blood and tears are slightly basic Buffers ● the internal pH of most living cells must remain close to pH 7 ● What is a buffer? Why is it needed? o Keeps the pH as close as possible to whatever that pH is supposed to be ● Carbonic acid in blood o Ex. Acid invades your blood stream, with a buffer, it helps to keep your pH constant Carbon Compounds and Life ● Aside from water, living organisms consist mostly of carbon-based compounds ● Inorganic compound ● Organic compound Molecules with Carbon ● Carbon can form four covalent bonds (why?) o Make large, complex molecules possible ● Most frequent partners: o Hydrogen ( valance=1), oxygen (valence=2), nitrogen, carbon Hydrocarbons ● Organic molecules consisting of only carbon and hydrogen ● Hydrocarbons can undergo reactions that release a large amount of energy (gasoline) 1/19/16 nd 2 half of monomer lecture ● Know: o Polymers and monomer o Dehydration and hydrolysis reactions o Carbohydrates o Lipids Proteins ● 50% of the dry mass of most cells ● Structural proteins ( provide support) o Nails, hair ● Storage proteins ( provide amino acids for growth) o Ex. Egg yolk in egg ● Contractile proteins ( helps moment) o Help move muscles ● Transport proteins ( helps transport substances) o Moves substances from one place to another place ● Enzymes ( help chemical reactions) o Significantly speed up reactions Amino acids Monomer is amino acid ● Organic molecule with carboxyl and amino groups ● R groups o Left: 2 H to N o Mid: R and H bond to C o Right: O and OH bond to C ● For every amino acid there is an …….(Look up) ● Basics=positive charge ● Acids=negative charge Polypeptides (or just Protein) ● C- terminus and N- terminus ● Look into polypeptide bonds ● Peptide bond ● Unique AA sequence Protein Structure and function ● A functional protein ha the o Correct sequence o Correct shape ▪ Ex. Antibody protein and protein from flu virus ● A protein’s sequence determines its structure and ● A protein’s structure determents function Four levels of Protein Structure ( sequence) ● See for levels of protein structure Collagen ● 40% of the protein in a human body ● Join cells together and gives them elasticity o Ex. Stretching cheeks ● Formed by 3 hekacies o Basically 3 strings wrapped around each other ● Means “ glue-producing” and comes from the Greek Hemoglobin ● Found in RBCs, carries oxygen What determines protein structure? ● Physical and chemical conditions o Changes in pH, salt concentration, temperature ● Denaturation ● Normal protein→denaturation→ denatured protein ● Denatured protein→renaturation→normal protein ● Denatured protein are useless Nucleic Acids ● Two types of nucleic acids ● Deoxyribonucleic acid (DNA) ● Ribonucleic acid (RNA) ● DNA→mRNA→protein Nucleotides ● Monomers called nucleotides ● Sugar, phosphate, base ● ● ● ● 5’C is end with phosphate in the beginning ● 3’C with carbon sugar in the end DNA ● The outer helix is the phosphate backbone ● Inner bases o A→T o C→G ● Held together with hydrogen bonds b/t bases ● Antiparallel orientation of the two DNA helixes DNA in Evolution ● DNA is passed from parents to offspring ● DNA differences b/t people ● Relatedness seen in DNA similarity 1/21/16 The World of Cells ● Robert Hooke (1665) o Corks o Saw series of rectangles o Named cells cause they look like monk’s living quarter ● Cell theory (1830s) o All living things are composed of cells o All cells come from other cells Light Microscope ● Light passes through the specimen ● Lenses magnify the image ● Magnification ● Contrast ● Resolution ● Place diagram of microscope here (search for one) ● Light travels through the specimen through the objective lens, bounces through a mirror and hen through the ocular lens, then to your eye ● Sometimes the specimen is still hard to see, so you need to apply contrast by dying it Resolution ● Ability to distinguish two adjacent objects or points from one another ● Increased magnification doesn’t always increase the resolution ● Resolution: distinguish more points, more shape in an object Electron Microscopy (EM) ● Higher resolution and can make out more details ● Transmission electron microscopy (TEM) o Shoot electron through a specimen and bounces off of them o More detail o 2D ● Scanning electron microscopy (SEM) o Electron bounces off of the surface of a specimen and doesn’t go though it o Good for 3D picture Prokaryotes ● Domains bacteria and archaea ● First seen 3.5 billion years ago ● Characterized by having o Nucleoid o No nucleus ● Components: o Ribosomes o Cell wall o Cell membrane o Flagellum o Chromosome o Plasma membrane ● Usually need TEM to see Eukaryotes ● Protest, fungi, animals, and plants ● First seen 2 billion years ago ● Characterized by having: o DNA in a nucleus o Membrane-bound organelles ● Generally much larger ● Component: o Ribosomes o Flagellums o Cell membrane o Mitochondria o Nucleus o Usually not a cell wall ● Easier to see? ● Difference b/t plant and animal cells o Plants have Chloroplast : convert light into energy and makes oxygen o Plants have cell walls o Plants have vacuole: big storage place; can hold various things like water and poison ● Eukaryotes and Prokaryotes o Basic features of all cells ▪ Plasma membrane ▪ Cytoplasm(cytosol) ▪ Chromosomes ▪ Ribosomes ● Plasma membrane ▪ Should have polar head (likes water), phospholipid, and nonpolar tails, and hydrophobic environment (tails) ▪ Half likes water, half hates water o Selectively permeable: proteins are selectively and only have 1 job, only allow certain things through o Glycoproteins o channels o enzymes o search and insert diagram here (hydrophilic region, hydrophobic region, hydrophilic region, phospholipid, proteins, and carbohydrate side chains ) o Surface Constraints ▪ 1 ▪ Total surface area: 6 ▪ Total volume: 1 ▪ Surface to volume ratio: 6 o Ex. ▪ 5 ▪ 150 ▪ 125 ▪ 1.2 o The inside is getting bigger but the surface is not increasing at the same rate o Ex. ▪ 1 ▪ 750 ▪ 125 ▪ 6 ● Nucleus o Contains most of the cell’s DNA/genes o Most conspicuous organelle o Nuclear envelope (look this up) ● Chromosomes o Each chromosome is one long DNA molecule associated with histone proteins ▪ DNA+ proteins=chromatin o Chromatin condenses to form chromosomes as a cell prepares to divide ● Ribosomes o Protein synthesis o rRNA (60%) + protein (40%) 1/26/16 Chapter 6( Continue) The Endoplasmic Reticulum ● Functions ○ produces variety of molecules ○ is connected to the nuclear envelope ● smooth and rough ER ● Rough ER ○ has bound ribosomes ○ has bumps all over it ○ is a membrane factory for the cell ○ where secreted, organelle proteins are made ○ ● Smooth ER ○ synthesize lipids ○ doesn’t have ribosomes ○ is not involved in protein synthesizes ○ synthesizes lipids ○ stores calcium ○ detoxifies drugs and poisons ● ● Golgi Apparatus ○ transport vesicle from the rough ER move to the Golgi ○ new vesicle is formed and then transport it away from the Golgi ○ “pita” ○ moving protein and lipids ○ “UPS”:Vesicles ○ ● Lysosomes ○ sac of hydrolytic enzymes ○ acidic environment ○ polymers→ monomers (degraded) ○ enzymes→ pH of 4? ● Phagocytosis ○ bringing in food ○ plasma membrane-- >lysosome-- >disgestive→ digestion ○ food vacuole-->digestion ○ cellular respiration afterwards ○ ● A u t o p h a g y ○ “ e a t i n g oneself” ○ lysosome-->digestion ○ per oxi so me (vesicle)-->digestion ○ ● Phagocytosis in immune cells ○ similar to phagocytosis for food, but is for a immune cells looking for micros of bad cells and taking care of them ● Vacuoles ○ central vacuole in plants ○ up to 90% volume of plant ■ organic molecules ■ water ■ gas (algae float because they have gas in them) ■ poisons (marijuana, cyanide) ■ parts of plants ● cytosol ● central vacuole: takes up a large amount of the cell because plants don’t move ● nucleus ● cell wall ● chloroplast ● ● Endomembrane System ○ interconnects the: ■ nuclear envelope ■ ER ■ golgi ■ lysosomes ■ vacuoles ■ plasma membrane ● Chloroplasts and Mitochondria ○ cells require a continuous energy supply to perform the work of life ○ two cellular power stations ■ 1.) chloroplast--light energy to food energy ■ 2.) mitochondria-- food energy to chemical energy ○ thylakoid: inner and outer membranes, space b/t membranes ○ granum: stroma (fluid in chloroplast ○ find pic of thylakoid, granum, and stroma ○ find pic of mitochondria ■ outer membrane ■ inner membrane ■ cristae ■ matrix ■ space b/tmembranes ■ shape is so that it has more surface area and it helps create more ATP (energy) ● Evolutionary Origins ○ enveloped by a double membrane ○ contain bacterial size ribosomes and circular DNA molecules ○ grow and reproduce somewhat independently in cells ○ know difference b/t shape of prokaryotic and eukaryotic cells ● The Cytoskeleton ○ network of fibers ■ roles ● support, maintenance of shape ● motility vía motor proteins ■ microtubules (train tracks) ■ microfilaments ■ intermediate filaments ○ pretty important for animals because they do not have a cell wall like plants ● Cell Junction in Animal cells ○ neighboring cells communicate ■ tight junctions (watertight) ■ desmosomes (fastener) ■ gap junctions (communication) ● Cell walls of plants ○ extracellular structure found in plants, prokaryotes, fungi ○ protection, support, prevents excessive water uptake ○ cellulose polysaccharides, proteins ● antibiotics ○ antibiotics were first isolated from mold in 1928 ○ used with civilians after WWII ○ drastically decreased death from bacterial infections ○ many target bacterial cell wall→ if used on humans and animals, most likely won’t kill us
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