BIO 101 Test 2 Study Guide
BIO 101 Test 2 Study Guide BIO 101
Virginia Western Community College
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This 23 page Study Guide was uploaded by jin1233 on Monday September 12, 2016. The Study Guide belongs to BIO 101 at Virginia Western Community College taught by Dr. Biscardi in Fall 2015. Since its upload, it has received 6 views. For similar materials see General Biology in Biology at Virginia Western Community College.
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Date Created: 09/12/16
Test 2 Study Guide (Chapters 2, 3, 5,6) Chapter 2: ALL MATTER IS COMPOSED OF ATOMS. MATTER HAS MASS AND OCCUPIES SPACE Atomic Structure Protons Neutrons Electrons POSITIVELY charged NEUTRAL particles NEGATIVELY charged particles Protons + Neutrons = particles Atomic number = number of atomic mass # of protons = # electrons Isotopes of an element Found in the “electron protons Every atom of a particular are created by having cloud” which are the orbitals element has the same different amount of surrounding the nucleus neutrons (still have Ions are charged particles – number of protons same amount of which are unbalanced protons) o Cation – MORE PROTONS than Located in the Nucleus electrons = net Each proton and neutron has a mass of POSSITIVE charge approximately 1 Dalton o Anion – LESS PROTONS than electrons = net NEGATIVE charge Terms to understand: Element – Any substance that cannot be broken down to any other substances by ordinary chemical means Atomic Mass – refers to amount of substance o Atomic mass = # Protons + # Neutrons Atomic Weight – refers to force of the gravity that exerts on the substance Radioactive isotopes – unstable and emit radiation as the nucleus breaks up Halflife – time it takes for ½ of the atoms in a sample to decay o Carbon dating uses this concept to figure out how old a fossil for instance it is. Carbon 12 well known for carbon dating Electron arrangement o Electrons have potential energy related to their position Electrons farther from the nucleus have more energy o First shell holds 2 electrons o Second, third, etc. shells each holds 8 electrons and must fulfil the “octet rule” Valence electrons – number of electrons in outermost energy level Test 2 study guide Octet rule – atoms tend to establish completely full outer energy levels Iner (nonreactive) elements have all eight electrons – aka Noble Gases Chemical bonds – what atoms are held together in molecules or compounds by o Molecules are group of atoms held together in a stable association Electronegativity – Atom’s affinity for electrons… Basically it means how greedy an atom is for electrons. Fluorine is the most electronegative of all elements Electron Shell Diagrams (Know how to draw those… look at PowerPoint if you don’t) Test 2 study guide Redox – During chemical reactions, electrons can be transferred from one atom to another O xidationIs L oss of o Still retain the energy of their position in the electronR eductionI s atom Only 12 elements are found in all living organisms (in substantial amounts) G ain of electron o C – Carbon o H – Hydrogen 4 elements make up 96.3% of human body o O – Oxygen weight o N – Nitrogen Remember CHON: o Na – Sodium o Cl – Chlorine o Ca – Calcium o P – Phosphorus C arbon H ydrogen O xygen o K Potassium o S Sulfur o Fe Iron N itrogen o Mg Magnesium Types of bonds Bonds Basis of Interactions Example Covalent Sharing of electrons Water (H O) 2 bonds Triple 3 pairs of shared electrons covalent N2 N N bond Double 2 pairs of shared electrons covalent O2 O O bond Single 1 pair of shared electron covalent H2 H H bond Ionic bond Formed by OPPOSITELY CHARGED IONS + ! Gain or loss of electrons forms ions Na Cl Na Cl Table salt, NaCl: Na gives up an electron (oxidation) and the Cl gains the electron (reduction) Test 2 study guide Hydrogen Sharing of Hydrogen atom δ" S bonds Water T O Hydrogen-Bond R δ+ δ+ δ" H H O N O G δ+ δ+ H H E S Hydrophobic Forcing of hydrophobic portions of molecules together Interaction in presence of polar substances T This allows water to form as many Hbonds as possible T and minimizes poor interactions with the nonpolar O molecule Like the phospholipid bilayer W van der Waals Weak attractions between atoms due to oppositely E polarized electron clouds. Water A striders K E S T Test 2 study guide The properties of water Property What it does Why it is important and an example Hydrogen bonds hold water molecules Able to move water in an Cohesion together upward direction. Ex: Leaves pull water upward from the roots Hydrogen bonds absorb heat when Water stabilizes the High specific heat they break and release heat when they temperature of organisms and form, minimizing temperature changes the environment. High heat of Many hydrogen bonds must be broken Evaporation of water cools vaporization for water to evaporate body surfaces Ex: sweating cools organisms Lower density in Water molecules in ice are crystalized, Because ice is less dense than solid form they are spaced far apart because of water, it floats. hydrogen bonding Ex: Lakes do not freeze solid, allowing other life in lakes to survive the winter Solubility Polar water molecules are attracted to Many kinds of molecules can ions and polar compounds, making move freely in cells, these compounds soluble. permitting a diverse array of chemical reactions. “Like dissolves like” Ex: Salt dissolving in water Water is the universal solvent Chemical Chemical reactions are influenced by: reactions Involves the Heating reactants increases the rate formation or breaking of Temperature of reaction because the reactants chemical bonds Reactants = collide with one another ore often original molecules, Concentration Reactions proceed more quickly on the left of reactants when more reactants are available, side of the chemical equations Products = and products allowing more frequent collisions molecule resulting Increases the rate of a reaction, from Catalysts shortens the time needed to reach reaction, on the right side of the equation 6H 2 + 6CO 2 C H 6 12equilibrium Reactants Products Test 2 study guide Ex: Test 2 study guide Acids and Bases: + Water can form ions: H O OH + H 2 Hydroxide Hydrogen ion ion pH reflects the Pure water: concentration of + + [H ] of 107 mol/L = pH of 7 hydrogen ion [H ] considered to be neutral in a solution NEITHER acidic nor basic Properties of Acids and Bases Acids Bases [H ] donor [H ] acceptor + Any substance that dissociates in water to Substance that COMBINES with H increase the [H ] (and lowers the pH) dissolved in water, this lowers the [H ] (and raises the pH) The stronger an acid is, the more H it produces and the lower its pH Buffers – Substance that resists changes in pH RELEASING hydrogen ions when a BASE IS ADDED ABSORBING hydrogen ions when ACID IS ADDED Example: blood pH stabilized by an acid base pair: carbonic acid (acid) and bicarbonate ion (base) – + + + Water Carbon Carbonic Bicarbonate Hydrogen (H2O) + dioxide acid ion + ion (CO2) (H2CO3) (HCO3) (H ) Test 2 study guide Chapter 3 Macromolecules: • Polymer – built by linking monomers • Monomer – small, similar chemical subunit Macromolecules Polymer Monomer Function Example s Starch, glycogen Energy storage Potatoes t r Structural support in y Cellulose Glucose Strings of celery o (Modified Glucose for Chitin)lant cell walls r a Chitin Insects and fungi use this fCrab shells C Structural support s Nucleotides i DNA sugar + phosphate + Encodes genes Chromosomes A nitrogenous base i o (A, C, G, T/U) l o DNA T Needed for gene u RNA o RNA U Messenger RNA N Sugar is deoxyribose in DNA expression or ribose in RNA s Functional Amino Acids Catalysis; transport Hemoglobin e Central carbon atom o Amino group P Structural Single hydrogen Support Hair; silk Variable R group And three Butter; corn oil; Fats fatty acids Energy storage soap And two Glycerol fatty acids, Phosphatidylcholin Phospholipids phosphate, Cell membranes e and polar R i group i L Prostaglandins* 5Carbon rings with Chemical messengers Protaglandin E nonpolar tails (PGE) Membranes; Cholesterol; Steroids * 4 fused carbon rings hormones estrogen Pigments; structural Terpenes * Long carbon chains support Carotene; rubber * - probably not on the test (textbook example) Test 2 study guide More Macromolecules examples! (textbook example lol…) Cellular Structure Polymer Monomer t CH 2H a d O y H H h H b OH H r HO OH a C Starch grains in a chloroplast P H OH P P Nitrogenous,base G T T P AP G i C A P P c P P C A P O P G Phosphate i P T A C group 5carbon,sugar l P P u PP P OH N Nucleotide Chromosome DNA strand Ala Ala Val n Val Ser CH 3 e H t N C C OH r H P Intermediate filament H O Polypeptide Amino Acid O H H HH H H H H HH H HO C C C C C C C C C C C C H H H H H H H H H HH H d i i L Fatty acid Adipose cell with fat droplets Triglyceride Test 2 study guide DNA vs. RNA Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) ? Blueprint of a cell, encodes information for RNA uses information in DNA to specify T amino acid sequence of proteins sequence of amino acids in proteins I A H W Double Helix Single polynucleotide strand r u 2 polynucleotide strands connected by H c bonds u t S g AT Contains RIBOSE instead of Deoxyribose i CG Contains Uracil instead of Thymine i a AU s a CG B P P P P P phosphatese9 P C P T T P backbone A G Ribose.phosphate G backbone A P G U P A P A m P a C P g P C A Bases U P a P D P G Bases T A P P P P G Hydrogen1bonding P Occurs1between1base9pairs Biological molecules are Carbon based: Test 2 study guide Carbon can form up to 4 Functional Structural Found covalent bonds Group Formula Example In Framework of biological H H carboD hydrates, molecules consists primarily of carbon bonded to Hydroxyl OH H C C OH proteins, nucleic o Carbon H H acids, Ethanol lipids o Oxygen o Nitrogen H O o Sulfur O carboD Carbonyl H C C H hydrates, o Phosphorous C nucleic o Hydrogen H acids Hydrocarbons – molecule Acetaldehyde consisting only of carbon O H O and hydrogen Carboxyl C H C C proteins, o Nonpolar lipids OH H OH o Functional groups Acetiacid add chemical properties H O H H Amino N HO C C N proteins, nucleic H CH3 H acids Dehydration synthesis Alanine Formation of large COOH molecules by REMOVING Sulfhydryl S H H C CH 2 S H a water molecule proteins Monomers are JOINED NH2 TO FORM Polymers Cysteine H O 2 O– OH OH H O HO H HO H Phosphate O P O– H C C C O P O– nucleic acids O H H H O– HO H Glycerol>phosphate O H Hydrolysis H Methyl HO C C NH 2 Breakdown of large C H molecules by ADDING a H C H proteins H water molecule H Polymers are BROKEN Alanine DOWN to Monomers Test 2 study guide H2O HO H HO H HO H Extra Info!!! Carbohydrates – molecules with a 1:2:1 ratio of carbon, hydrogen, oxygen o C – H covalent bonds hold much energy; good energy storage molecules Monosaccharides o Other 6 carbon sugars = Fructose and Galactose Polysaccharides – long chains of monosaccharides linked through dehydration synthesis Protein functions include: o Enzyme catalysis o Defense o Transport o Support o Motion o Regulation o Storage Lipids Loosely defined group of molecules with one main chemical characteristic o INSOLUBLE in water because high proportion of NONPOLAR CH bonds – HYDROPHOBIC o Fats, oils, waxes, some vitamins and steroids Fats o Triglycerides Composed of 1 glycerol and 3 fatty acids o Fatty acids Saturated – NO double bonds between Saturate carbon atoms HIGH melting point ANIMAL origin Unsaturated – 1 or more double bonds LOW melting point PLANT origin Unsaturate Trans fats produced industrially Phospholipids o Composed of Glycerol, 2 fatty acids (nonpolar tail), phosphate group (polar head) o Form all biological membranes Test 2 study guide Phospholipid bilayer – more complicated Water structure where 2 layers form o Hydrophilic heads point outward o Hydrophobic tails point inward toward each other Water o Basic structure of a cell membrane Test 2 study guide Amino acids joined by dehydration synthesis Peptide bond Primary'StruThe shape of a protein determines its function Primary Sequence of amino acids structure R H H O R H H C C N C C N C C N C H O R H H O R The primary structure can fold into a pleated sheet, or turn into a helix Secondary Interaction of groups in the peptide structure backbone helix sheet α"helix β"pleated)sheet Tertiary Final folded shape of globular structure protein Stabilized by a number of forces Final level of structure for proteins consisting of only a single poly peptide chain Quaternary Arrangement of individual chains structure (subunits) in a protein with 2 or more polypeptide chains Test 2 study guide Chaperones (Chaperone proteins)– help protein fold correctly Deficiencies in chaperone proteins implicate in certain diseases o Cystic fibrosis (heredity disorder) – in some individuals, proteins appear to have correct amino acid sequence by fails to fold Denaturation – protein loses structure Properly(folded(protein and function Due to environmental conditions o pH o Temperature o Ionic concentration of solution Denaturation Denatured protein Chapter 5: Membrane Membrane Structure – Phospholipid arranged in a bilayer with globular proteins in the bilayer Fluid mosaic model – “mosaic” of proteins floats in or on the fluid lipid bilayer (boats on a pond) Extracellular matrix1proteinGlycoprotein Glycolipid Proteins Glycoprotein Cholesterol Actin1filaments of1cytoskeleton Peripheral) protein filamentsate of1cytoskeleton Test 2 study guide CELLULAR MEMBRANES HAVE 4 COMPONENTS Composed of… That are… Picture? Interior Protein Network Peripheral or Intracellular membrane proteins Cell surface markers Glycoproteins and glycolipids Phospholipids: Consists of Glycerol – 3 Carbon polyalcohol 2 fatty acids attached to the glycerol o NONPOLAR, HYDROPHOBIC Phosphate group attached to the glycerol o POLAR, HYDROPHILIC Spontaneously forms a bilayer o Fatty acids inside, phosphate groups on both Phospholipid Bilayer surfaces (outside) Flexible matrix, barrier Hydrogen bonding of water holds 2 layers to permeability together bilayers = fluid Individual phospholipids and unanchored proteins can move through the membrane Test 2 study guide Integral membrane proteins Span the lipid bilayer (transmembrane proteins) NONPOLAR regions are embedded in the interior of the bilayer POLAR regions are protruding from both sides of bilayer Membrane Proteins have various functions: Transporters Enzymes Cellsurface receptors Cellsurface identity markers Celltocell adhesion proteins Outside Inside cell cell Transporter Enzyme Cell)surface)receptor Transmembrane Proteins Integral membrane proteins called Integrins Cell)surface)identityCell6to6cell)adhesion Attachment)to)the)cytoskeleton Attachments to the cytoskeleton Transmembrane domain Spans the lipid bilayer Hydrophobic amino acids arranged in helixes Proteins need only a single transmembrane domain to be anchored in the membrane, but they often have more than one domain aMany(transmembrane(domaidomain(transmembrane( Test 2 study guide Movement of molecules across cell membranes (phospholipid bilayer) Diffusion: Osmosis: Will continue until the Net diffusion of WATER across a membrane from HIGHLOW SOLUTE concentration concentration is the same in all regions = equilibrium is reached “Water moves to where it is saltiest” MAJOR BARRIER to crossing a Aquaporin proteins facilitate osmosis Passive cell membrane is the HYDROPHOBIC INTERIOR Transport o Repels polar molecules but not nonpolar molecules Water Movement of Uremoleculelecules molecules o Limited permeability to small Semipermeable through the polar molecules membrane membrane o Very limited permeability to large polar molecules and NO ATP energy needed ions Molecules moves from Channel proteins: HYDROPHILIC ion channels when open, HIGHLOW concentration Facilitated diffusion: allow passage of ions Molecules that cannot cross Gated channels – can open or close in response membrane easily, may move to electrical or chemical stimulus through membrane proteins Carrier proteins: Membrane – SELECTIVELY BIND specifically to molecules they assist PERMEABLE Can help transport both ions and other solutes (some sugars and amino acids) Concentration difference across the membrane Selective Proteins Active transport PHAGOcytosis: Cell takes in particulate Requires energy – matter Endocytosis: ATP used Movement of PINOcytois: Cell takes in only FLUID directly or (pino like Pinot Grigio is a liquid) indirectly to fuel substances Receptormediated endocytosis: Bulk INTO the cell Moves substances Specific molecules are taken in after they bind to from Transport a receptor LOWHIGH Exocytosis: concentration Movement of substances OUT of a cell Requires use of Plants use to export cell wall material highly selective Animals use to secrete hormones, neurotransmitters, digestive carrier proteins enzymes Test 2 study guide Chapter 6: Energy and Metabolism Thermodynamics – branch of chemistry concerned with energy changes Energy – capacity to do work o 2 states o Many forms of energy Mechanical Heat Most convenient way of measuring energy 1 calorie = heat required to raise 1 gram of water 1C Sound Electric current Light Radioactivity o Energy comes from the SUN o Photosynthetic organisms capture this energy o Stored as potential energy in chemical bonds REDOX Reaction o Oxidation – Atom or molecule loses an election o Reduction – Atom or molecule gains an election Higher level of energy than oxidized form Laws of thermodynamics: o 1 Law: Energy cannot be created nor destroyed, it can change from one form to another. During each conversion, some energy is lost as heat. The total amount of energy in the universe remains constant. o 2 Law: Entropy (disorder) is continuously increasing. Energy transformations proceeds spontaneously to convert matter from a more ordered/less stable form to a less order/more stable form Test 2 study guide Endergonic vs. Exergonic Reactions Endergonic Exergonic Not spontaneous, requires input of energy Spontaneous Products have higher energy than reactants Products have less energy than reactants Energy is absorbed Energy is released Positive Gibbs Free Energy Negative Gibbs Free Energy Reaction rate depends on the activation energy required – larger activation energy proceeds more slowly Activation energy: The extra d energy required to destabilize existing i p uncatalyzed bonds and start the chemical reaction p catalyzed u ) ' Activation 2 ways the rate can be increased: ( y ' r energy 1. Increasing energy of reacting g e e E Activation molecules (heating it up) n ' ' e 0 energy 2. Lowing activation energy e s r e Reactant (catalysts does this) F e R Catalysts: substances that influence y g Product Energy'released chemical bonds which lowers the e n E activation energy Course'of'Reaction CANNOT violate laws of thermodynamics Enzymes = biological catalysts Most are proteins, some are RNA NOT CONSUMED OR CHANGED in reactions Test 2 study guide Shape: stabilizes a temporary association between substrates – specific “lockandkey” between enzyme and substrate Substrate – The molecule acted upon by the enzyme 1.Thesubstratesucrose, 3.The#bindinofthesubstratand# consistofglucoseand enzyme#placesstreson#theglucose– fructosbonded#together. fructosbond,and#thebond#breaks. 2.The#substratbindstotheactivsite Glucose Bond oftheenzyme,forminganenzyme– substratcomplex. Fructose H2O 4.Productsare releasedand theenzyme#is freto#bindother substrates. Activesite Enzyme sucrase Active site: Where the substrate binds to the enzyme, forms enzymesubstrate complex Precise fit of substrate into active site Induced fit: Applies stress to distort particular bond to lower activation energy Rate of enzyme – catalyzed reaction o Optimum% temperature Optimum% temperature%for%enzyme t forhuman% enzyme from%hotsprings%prokaryote a depends on concentrations of substrate and e % enzyme. o e t Any chemical or physical R 30 40 50 60 70 80 conditions that affects the enzyme’s Temperature% of%Reaction%(˚C) 3D shape can change rate a. o Optimum temperature and Optimum pH o t Optimum% pH%forpepsin Optimum% pH%for%trypsin a e % o e t R 1 2 3 4 5 6 7 8 9 pH%of%Reaction Test 2 study guide Inhibitors – OPPOSITE OF SUBSTRATES, they decrease enzyme activity when they are bind Competitive vs. Noncompetitive inhibitor Competitive Noncompetitive Competes with substrate for active site Binds to enzyme at a spot other than the Looks like the substrate, fits into the activeactive site site, doesn’t do any thing Causes shape to change that makes enzyme unable to bind to substrate Substrate Substrate Active Inhibitor Active Inhibitor site site Enzyme Enzyme Allosteric"site Competitive"inhibitor"interferes Allosteric"inhibitor"changes with"active"site"of"enzyme"so shape"of"enzyme"so"it"cannot substrate"cannot"bind bind"to"substrate a."Competitive"inhibition b."Noncompetitive"inhibition Allosteric Enzymes – Acts like a thermostat, can turn chemical reactions on and off. They exist in active and inactive forms Allosteric Inhibitor – binds to allosteric site and REDUCE enzyme activity Allosteric Activator – binds to allosteric site and INCREASE enzyme activity, turns off when it has enough ATP Adenosine triphosphate: ALL CELLS USE (some form of) ATP Composed of RIBOSE (5 carbon sugar), ADENINE, CHAIN OF 3 PHOSPHATES ADP – 2 Phosphates AMP – 1 Phosphate (lowest form of energy Test 2 study guide ATP H 2 Energy)from Energy)for exergonic endergonic cellular cellular reactions processes P ADP i ATP Cycle (shown above) ATP Hydrolysis drives endergonic reactions Endergonic – TAKES IN o ATP Hydrolysis is exergonic energy, like a cold pack ATP not suitable for longterm energy storage, great for (+G) instant energy Exergonic – RELEASES o Fats and carbohydrates are better at longterm energy, like fire (-G) storage Metabolism: total of all chemical reactions carried out by an organism Anabolic reactions (anabolism) Catabolic reactions (catabolism) Uses energy that are added in to build up “Harvest” energy by breaking down large molecules. molecules to smaller molecules. Like anabolic steroids, they make small This releases energy people bigger Initial'substrate Biochemical pathways (shown on the– ight) Enzyme1 Product of one reaction is the substrate for the next. Intermediate substrate'A Feedback inhibition (shown bel– ) Enzyme2 Intermediate Endproduct of pathway binds to an allosteric site on enzyme substrate'B that catalyzes first reaction in pathway Enzyme3 Shuts down pathway so raw materials and energy are not substrate'Ce wasted Enzyme4 Initial Initial substrate substrate End'product Enzyme'1 Intermediate Enzyme'1 substrate''A Enzyme'2 Intermediate Enzyme'2 substrate'B Enzyme'3 End'product Enzyme'3 End'product a. b.
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