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Bio Foundations, Chapters 2 and 3 Notes

by: Hannah Kennedy

Bio Foundations, Chapters 2 and 3 Notes 10120

Marketplace > Kent State University > Biological Sciences > 10120 > Bio Foundations Chapters 2 and 3 Notes
Hannah Kennedy
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These notes include all information covered in chapters 2 and 3 in the lectures, key points indicated by Professor Grampa, and all key terms needed for the exam (indicated by a bold keyword)
Biological Foundations Honors
Professor Grampa
Class Notes
Biology, Biological Foundations, atoms, carbon, Macromolecules




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This 9 page Class Notes was uploaded by Hannah Kennedy on Friday January 29, 2016. The Class Notes belongs to 10120 at Kent State University taught by Professor Grampa in Spring 2016. Since its upload, it has received 155 views. For similar materials see Biological Foundations Honors in Biological Sciences at Kent State University.


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Date Created: 01/29/16
Copyright: © Hannah Kennedy, Kent State University 1 Chapter 2 1. Atoms a. Matter = all substances that have mass and occupy space b. Atoms = the composition of matter; too small to be seen with the naked eye i. all atoms have… 1. protons = positively charged component; located within the  central nucleus of the atom 2. neutrons = neutral charged component; located within the  nucleus 3. electrons = negatively charged component; circles the nucleus a. circle the nucleus in orbitals (layers) i. the innermost orbital is stable with 2 electrons  and all other orbitals are stable with 8 electrons  therefore most elements want to gain or lose  electrons to fulfill an 8 electron count ii. the overall charge of an atom is 0 because the number of protons and  electrons is typically the same 1. atom is neutral when the electrons = protons 2. atom is positive when the atom loses an electron a. more protons after an electron is lost 3. atom is negative when the atom gains an electron a. more electrons than protons after an atom gains an  electron c. atomic number = the number of protons d. atomic mass = protons + neutrons 2. Chemical bonds a. Molecule = a groups of atoms of the same element held together by chemical bonds i. Ex = O 2 H 2 b. Compound = a molecule containing atoms of different elements i. Ex = CO 2  c. 3 main types of  bonds i. Ionic bonds (intermediate in strength) = occur when atoms with  opposite charges are attracted to each other 1. Ex = NaCl 2. Atoms can form crystals, but often dissociate in water 3. Electrons are donated from one atom to the other and as a  result the atoms are not neutral + Na (lost electron)            Na Cl (gains electron)          Cl ii. Covalent bonds (strongest) = bonds that form when electrons are  shared between all atoms involved so that every single atom has 8  electrons Copyright: © Hannah Kennedy, Kent State University 2 1. Ex = oxygen has 6 electrons in outer orbital and it wants 2  more to get 8 electrons 2. Ex = hydrogen has 1 electron in outer orbital and it wants 1  more to get to 2 3. Ex = oxygen is stabilized by two hydrogens to get 8 electrons 4. Single bonds = when 1 pair of electrons is shared and shown  with 1 line connecting the atoms (weakest) 5. Double bonds = when 2 pairs of electrons are shared, shown  with 2 lines connecting atoms (intermediate) 6. Triple bonds = when 3 pairs of electrons are shared, shown  with 3 lines connecting atoms (strongest) 7. Nonpolar molecules = molecules in which electrons are  equally shared 8. Polar molecules = molecules in which electrons are unequally shared so that 1 area is slightly more positive and 1 area is  slightly more negative (due to electronegativity differences) iii. Hydrogen bonds (weakest in strength) d. 2 additional types of interactions i. Hydrophic interactions ii. Van der Waals interactions 3. Chemical reactions and bonds a. During a chemical reaction bonds are created and broken b. Reactants = the initial molecules that take place in the rxn c. Products = the molecules formed as a result of the chemical reactions taking place d. Rxn rate = the speed of a rxn; influenced by 3 things i. Temperature 1. The more heated the reactants are the faster the reaction will  happen due to increased collision of atoms ii. Concentration of reactants and products 1. The more reactants are present (high concentration) the faster  the rxn 2. The more products are present (high concentration) the slower  the rxn will be  a. Could even drive the rxn back towards the products and reverse the rxn iii. Catalysts 1. Speed up the rxn 2. Reduce the activation energy of the rx by allowing less energy  to be put in and used to run the rxn 3. Ex = enzymes 4. Water a. Makes up 2/3 of our bodies  b. Common solven Copyright: © Hannah Kennedy, Kent State University 3 c. 2 H atoms bound to an oxygen via single covalent bonds d. Stable and neutral e. Forms weak hydrogen bonds i. Considered to be more of an attraction rather than an actual bond 1. The attractions happens btwn net negative regions of 1  molecule and net positive regions of another ii. No electrons are shared, donated, or received iii. Stabilize the 2 strands of DNA by becoming strong in numbers. 1. Makes it easy to separate and create new DNA (replication) 2. Makes it easy to break and re­create during temporary RNA  creation (transcription) f. Cohesion = a characteristic that describes the intense attraction water  molecules have for  one another; allows water to be liquid at room  temperature g. Surface tension = characteristic that explains the bonds between water  molecules are strong enough to withstand some force i. Ex = a water bug in a pond sitting on the surface h. Adhesion = characteristic that states that water tends to form hydrogen  bonds with anything that is polar i. Nonpolar molecules, in contrast, don’t form hydrogen bonds (lipids) i. Specific heat = the amount of energy required to break hydrogen bonds i. High for water j. Heat of vaporization = the energy needed to change a liquid into a gas i. High in water which requires a lot of energy to break its bonds; this  energy is in the form of heat and is released from the body when sweat evaporates, thus cooling the organism k. Solubility = the ability of a molecule to separate when dissolved in water i. Solute = component being dissolved ii. Solvent = component doing the dissolving iii. The negative end of oxygen orients itself toward the positive ions iv. The positive hydrogens orient themselves toward any negative ions l. Hydrophilic molecules = molecules that have net negative and net positive regions so they can form hydrogen bonds with water i. Ex = proteins, carbohydrates, nucleic acids m. Hydrophobic molecules = molecules that don’t form hydrogen bonds with  water and are more attracted to each other than to water i. Ex = lipids 5. pH scale a. pH scale = a logarithmic scale that ranges from 1 to 14 i. 1­6 is acidic 1. Ex = HCl acid, stomach acid, lemon juice, pop, black coffee,  urine, tomatoes, vinegar, beer 2. More hydrogen ions ii. 7 is neutral Copyright: © Hannah Kennedy, Kent State University 4 1. Ex = pure water, blood iii. 8­14 is basic/alkaline 1. Ex = seawater, baking soda, household ammonia, household  bleach, sodium hydroxide 2. Less hydrogen ions b. water can dissociate into ions and the free hydrogen ions influence the pH of  a solution H 2 OH ­­  H + Water hydroxide       hydrogen c. buffers = pH stabilizers; resist change by binding to or releasing hydrogen  ions i. most common biological buffer system is in the blood ii. when a solution is too acidic a buffer will bind to the excess hydrogen  ions, sequester them and increase the pH iii. when a solution is too basic a buffer will release additional hydrogen  ions and lower the pH iv. the common human body buffer system: ­­ + H 2   +     CO 2 H 2O 3 HCO  3   +     H Water       carbon carbonic bicarbonate   Hydro                  dioxide acid acid                gen 1. the law of mass action = states that the buffer equation will  shift from wherever there is more of something to wherever  there is less of something 2. ex = if blood becomes acidic, the body recognizes that there are  too many hydrogens and therefore the bicarbonate ion  (negative charge) is used and binds to the free hydrogen ions  (positive charge) to form carbonic acid (intermediate) which  then separates into water and carbon dioxide 3. ex = if the blood becomes basic, the body recognizes that there  is too much carbon dioxide and therefore carbon dioxide binds  to water to form carbonic acid which then splits into  bicarbonate acid and hydrogen ions Chapter 3 1. Carbon a. The predominant atom that makes up many biological molecules b. Organic molecules = molecules that contain carbon atoms c. Used a lot for its ability to form 4 covalent bonds, all of which can be used to  store energy d. The most popular use of carbon is in hydrocarbon chains i. Hydrocarbon = carbon + hydrogen Copyright: © Hannah Kennedy, Kent State University 5 1. There is an even distribution of charges 2. Nonpolar molecule e. Functional groups = other atoms within biological molecule that provide  polarity; capable of forming hydrogen bonds Functional Group Macromolecules Hydroxyl Carbs, proteins, nucleic acids, lipids Carbonyl Carbs, nucleic acids Carboxyl Proteins, lipids Amino Proteins, nucleic acids Sulfhydryl Proteins Phosphate Nucleic acids Methyl proteins 2. Macromolecules a. 4 main macromolecules (polymers) i. Carbohydrate ii. Nucleic acid iii. Protein iv. Lipid b. Polymers = large molecules; the end product c. Monomers = smaller subunits that make up polymers; the building blocks i. Carbohydrate 1. Monosaccharide = simple sugar = carbohydrate monomer 2. Carbon, hydrogen, and oxygen are in a 1:2:1 ratio a. (CH O2 n i. n = number of carbons ii. 6 carbon monosaccharide: C H 6 (12u6 se) 1. Ex = glucose, fructose, and galactose  (isomers) iii. 5 carbon monosaccharide: C H5O 10 5 1. Ex = ribose and deoxyribose (isomers) 3. Isomers = molecules that have the same chemical formula but  have different structures, 2 kinds a. Structural isomers = molecules that have the same  formula but have a different number of bonds OR  different types of bonds on each carbon b. Stereoisomers = molecules that have the same  formula but have a different number AND different  types of bonds on each carbon with a different  orientation in space 4. Disaccharides = joined monosaccharides that are formed  through dehydration synthesis; C H O12 22t11the 1 oxygen  and 2 hydrogens missing from the dehydration synthesis Copyright: © Hannah Kennedy, Kent State University 6 a. Maltose = glucose + glucose i. Very sugary, think “malt” milkshakes b. Lactose = glucose + galactose i. Lactose intolerant people don’t have the enzyme  needed to break lactose into glucose and  galactose c. Sucrose = glucose +fructose 5. Polysaccharides = monosaccharides and disaccharides  formed together a. Several different types i. Starch = polysaccharide that contains only  glucose ii. Glycogen = the stored form of glucose in  humans iii. Cellulose = the stored form of glucose in plants iv. Chitin = a polymer of N­acetylglucosamine  (monosaccharide) that makes up the exoskeleton  of insects and crustaceans  ii. Nucleic Acids 1. Nucleotide = nucleic acid monomer 2. 3 main types a. DNA = deoxyribonucleic acid = the nucleic acid that  contains the genetic information of the cell in the form  of genes (46 single chromosomes, 23 sets of  chromosomes) i. Deoxyribose contains only H ii. Double stranded and coiled into a helix 1. Double strands are joined together by  complementary base pairing between  nitrogenous bases and through H bonding between those bases iii. Contains 4 nitrogenous bases 1. Adenine (compliment: thymine OR uracil) a. Makes 2 H bonds 2. Guanine (compliment: cytosine) 3. Cytosine (compliment: guanine) a. Makes 3 H bonds 4. Thymine (compliment: adenine) b. RNA = ribonucleic acid = short­lived complimentary  copy of a gene that provides instruction on how to make  a protein; short lived i. Ribose contains OH ii. Single stranded Copyright: © Hannah Kennedy, Kent State University 7 iii. Contains 4 nitrogenous bases 1. Adenine (compliment: thymine OR uracil) a. Makes 2 H bonds 2. Guanine (compliment: cytosine) 3. Cytosine (compliment: guanine) a. Makes 3 H bonds 4. Uracil (compliment: adenine) c. ATP = adenosine triphosphate = the main source of  energy in cells 3. General structure: sugar­phosphate backbone + nitrogenous  bases a. Sugar phosphate backbone = “upright parts of the  ladder” = alternating phosphate groups + 5­carbon  sugar (ribose or deoxyribose) i. Each sugar has a covalently bound nitrogenous  base ii. Nitrogenous bases = “rungs of the ladder”;  classified by 2 things 1. Purines = double­ring molecules that  include adenine and guanine 2. Pyrimidines = single­ring molecules that include cytosine, thymine, and uracil iii. Proteins 1. Amino acid = protein monomer a. 20 amino acids  b. Amino acid = central carbon + amino group + carboxyl  group + “R” group i. The R group is the characteristic component of  each amino acid and is the determining factor on  what makes each one different 1. R group determines polarity c. Dipeptide = 2 amino acids joined together via  dehydration synthesis  d. Polypeptide = many amino acids linked together in a  primary structure; polarity of the amino acids affect the  way the protein folds i. Secondary structure = a more complex protein arrangement made from primary structures  made of 2 components 1. Alpha helix = spiral coil 2. Beta sheet = pleated sheet a. Both are stabilized by H bonds Copyright: © Hannah Kennedy, Kent State University 8 rd ii. Tertiary structure = 3  level of organization =  more compact molecules made of several alpha  helices and several beta sheets to form 2 types of  structures 1. Fibrous structure = long and thin 2. Globular structure = round iii. Quaternary structure = 4  level of  organization = several similar proteins come  together to form a larger molecule 1. Ex = hemoglobin; made of 4 globular  proteins e. Chaperone proteins = proteins that oversee protein  folding to make sure that the proteins are folding  properly and if proteins aren’t they will use ATP to  break bonds,  unfold the protein, and refold it the right  way i. Ex = heat shock proteins = chaperone proteins that help proteins to refold after being exposed to head ii. Ex of a disease that results from faults or  missing chaperon proteins = cystic fibrosis iii. Denaturation = the loss of conformation and of  function of the protein that occurs in response to  changes in temp, pH, presence of ions, and lack  of ions 2. Various functions of proteins a. Enzymes  i. catalysts to speed up chemical reactions b. Defense i. recognizes foreign molecules such as bacteria,  pathogens, and fungi c. Transport i. Movement of molecules within cells and  throughout the organism d. Support i. Strength and structure of body components e. Motion i. Muscle contraction and relaxation ii. Sperm motility f. Regulation i. Messengers that communicate between cells g. Storage i. Ions are stored until they are needed Copyright: © Hannah Kennedy, Kent State University 9 iv. Lipids 1. Fatty acid = lipid monomer 2. Composed of nonpolar hydrophobic molecules made of mainly  hydrocarbon chains 3. In a water­based environment they separate from water and  clump together 4. 4 classes a. Fatty acids = chain of carbon and hydrogen with a  carboxyl group on one end, 2 kinds i. Saturated fatty acids = a fatty acid in which  all carbon atoms are linked by single covalent  bonds causing it to be straight ii. Unsaturated fatty acids = a fatty acid in which 1+ double bonds are present between carbon  atoms that cause it to be bent 1. The energy stored in these covalent bonds can be broken down and stored in high­ energy phosphate bonds of ATP b. Triglycerides = formed of glycerol and 3 fatty acids  joined at the carboxyl end of each fatty acid; synthesized in the liver and stored in adipose tissue to be used for  energy when needed i. Triglyceride = glycerol backbone + 3 fatty acids 1. Formed by 3 water molecules being  removed via dehydration synthesis when  the 3 fatty acids are put onto the  backbone c.  Phospholipids = 2 fatty acids + glycerol backbone +  phosphate head i. Polar part: phosphate head ii. Nonpolar part: fatty acid tails 1. Together they form the lipid bilayer 2. Amphipathic = containing both  hydrophilic and hydrophobic regions d. Steroids = cholesterol based; 4 rings of carbon atoms in the general skeleton with characteristic side groups  placed around them to determine which steroid is which i. Ex = testosterone, estrogen, and cortisol d. Dehydration synthesis = a process in which monomers are joined together  (created bonds) by removing a water molecule e. Hydrolysis = a process in which polymers are broken down into monomers  (broken bonds) by adding a water molecule


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