Bio Exam Review PDF - Principles of Life, Chemical Bonds, and Chemical Transformations

Here's a markdown conversion of the text in the images you sent: # ☆Bio Exam Review # ☆Chapter 1: Principles of Life # Chapter 2: Life's Chem & $H_2O$ Importance * All matter is made of atoms * Element - Substance with only 1 kind of atom * Atomic mass is measured in Daltons * $...

Here's a markdown conversion of the text in the images you sent: # ☆Bio Exam Review # ☆Chapter 1: Principles of Life # Chapter 2: Life's Chem & $H_2O$ Importance * All matter is made of atoms * Element - Substance with only 1 kind of atom * Atomic mass is measured in Daltons * $0.7x10^{-24}$ grams * Usually ignore electron weight * Atomic Number - Number of protons. Identifies element * Mass Number - Total # of protons & Neutrons ## Electron Shells: * Each shell has 1 spherical s orbital * Second & subsequent shells also have 3 *p* orbitals | Shell | Maximum Electrons | |--------------|--------------------| | First shell | 2 | | Second shell | 8 | | Third shell | 8 | The image is a diagram of electron shells for Hydrogen, Carbon, Nitrogen, Oxygen, Phosphorus and Sulfur. * Lower shells have more energy * *s*-orbitals have less energy than *p*-orbitals * If outer shell empty: More reactive * **Octet Rule**: atoms with at least 2 electron shells become stable with 8 electrons ## Electronegativity * Atom's tendency to attract electrons from another atom * Depends on: * \# of electrons in outer shell * $\uparrow$ electrons =$\uparrow$ electronegativity * How close electrons are to nucleus * $\uparrow$ closeness to nucleus = $\uparrow$ electronegativity ## Chemical Bonds * Attractive force that links atoms toegther to form molecules ## Types of Chemical Bonds * ☆ Ionic Bond - Highly electronegative atom pulls one or more electrons from atom with low electronegativity * Cations - Positive charge & attracted * Anion - Negative charge * Resulting molecules & salts * ☆ Covalent Bonds - Forms when 2 atoms share one or more pairs of electrons to attain stable electron configuration. * Each atom contributes on member of the electron pair * Double bond: atoms share 2 electron pairs * In order to happen: electronegativities must be similar # ☆Covalent Bonds, their characteristics & behavior * Orientation: Length, angle & direction of bonds are always the same * Strength & Stability: covalent bonds are very strong * Unequal sharing & occurs usually when 2 atoms are different * Nonpolar Bonds: Electrons shared equally * Polar Bonds: electrons pulled closer to the nucleus of the more electronegative atom * More electronegative atom: slightly - * Less electronegative alom: slightly + * Dipole - separation of opposite electric charges (AKA in polar covalent bond) * dipole-dipole interactions: slightly charged atoms can interact with other atoms o/weak ## Hydrogen bond * Attraction between slightly + charged covalently bonded hydrogen & slightly - charged covalently bonded nitrogen or oxygen ## Van der Waals interactions * Movement of electrons results in small temporary dipoles * These attractions are van der Waals * Very weak - but many tiny interactions lead to a significant force # ☆Chemical Transformations & Energy * Energy - capacity to produce change * Kinetic Energy - energy of movement *Includes thermal, sound and electromagnetic. * Potential Energy - stored energy *Includes - gravitational, elastic, chemical and nuclear. * Laws of Thermodynamics - govern changes in energy * 1st law: energy cannot be created or destroyed * 2nd law: when energy transforms, entropy increases * After energy transformation - some energy becomes unavailable to work. * Entropy can only decrease if energy is added to the system. * Chemical reaction - when atoms combine or change their bonding partners * Gibbs free energy (G) - total energy change calculated from difference between bond energy * Change in entropy * If G negative - the reaction is exergonic * Releases energy * If G positive - reaction is endergonic * Requires energy * Activation energy ($E_a$) - energy required to initiate the reaction * Required in Both Ender and Exer # ☆Chemical Bonds & Energy's relationships * Takes energy to break chemical bonds * When chemical bonds are made, energy released * Stronger bonds take more energy to break * More energy is released when strong bonds made # ☆Functional Groups: * Organic molecules: * Carbon-containing * Their chemistry is largely detemrined by functional gourps * Functional Groups: * Small groups of atoms with specific chemical properties * When they attach to larger molecule --> give those properties to it * 1 Biological molecule can have many functional groups * ☆ Methyl Functional Grouop: $CH_3$ * Class of Compounds: Alkyl * Nonpolar * Important modification of proteins & cytosine nucleotide * ☆ Hydroxyl Functional Group: OH * Class of Compounds: Alcohols * Polar * Involved in hydrogen bonding * Often in condensation reactions * Required in sidechain for phosphorylation of proteins * ☆ Sulfhydryl Functional Group: SH * Class of Compounds: Thiols * Polar * Can foram disulfide bridges to stabilize protein structure * ☆ Aldehyde functional group: COH * Class of compounds: Aldehydes * Polar * Very Reactive * Important in energy releasing functions * ☆ Keto functional group: OH * Class of compound: Ketones * Polar * Important in carbs & Energy Reactions * ☆ Carboxyl functional group: Ate=0 * Class of compounds & carboxylic acids * Charged * Acidic * ionizes in living tissues to foram -Coo- ($H^+$) * Reacts with amino group to foram peptide bond * ☆ Amino Functional Group: H-N-H * Class of Compounds Amine * Charged * Basic * Accepts $H^+$ in living tissues to foram -$NH_3$ * Reacts with carbocyl group to foram peptide bond * ☆ Phosphate functional group: P in middle * Class of Compounds: Organic phosphates * Charged * Acidic * ionizes in living tissues to foram-O-P-$O_3^{2-}$ * Enters into condensation reations, usually with inorganic phosphate * When bonded to another phosphate, hydrolysis is strongly ergonic # ☆Chapter 3: Macromolecules * Macromolecules - large molecules foamed by cavalent linkages of smaller molecules * Proteins * Carbohydrates * Nucleic acids * lipids * All but lipids are polymes * Polymer = many units * Created by covalent linkage of smaller molecules (called monomers) * foamed and broken apart in reations involving $H_2O$ * Condensation - removal of water creates a covalent bond between monomers * Hydrolysis - the addition of water breaks covalent bond between monomers *☆Lipids!* * Hydrocarbons (C & H atoms) * Insoluble in $H_2O$ due to nonpolar covalent bonds * When close together - Weak additive Van der Waals interactions hold them together * Store energy in C-C & C-H bonds * Play structural role in cell membranes * Fat in bodies = thermal insulation * Triglycerides (Simple lipids) * Fats - Solid at room temperature * Oils - Liquid at room temperature * Very little polarity & are extremely hydrophobic * Structure * 3 Fatty Acids: Non-polar hydrocarbon chain attached to a polar carboxyl group (COOH). * One glycerol, an alcohol with hydroxyl (-OH) groups * Synthesis involves 3 condensation reations The image is a diagram of the synthesis of triglycerides. * ☆ Fatty acids: * Chains can vary in length and structure * Amphipathic - They have a hydrophobic and a hydrophilic tail * Saturated Fatty Acids * All bonds between carbon atoms are single & saturated with hydrogens * Unsaturated Fatty Acids * Hydrocarbon chains have one or more double bonds causing kinks in preventing molecules *Two fatty acids & a phosphate compound bound to glycerol:* * phosphate group has a nagative charge making that part of the molecule hydrophobic * Bilayer in aqueous environments * Hydrophobic tails pack together * Hydrophilic heads face outward * Good for Bio membranes # ☆Carbohydrates: ### Roles: * Source of stored energy * Transport stored energy within complex organisms * Structural Molecules - give many organisms their shapes * Recognition of signaling molecules that can trigger specific bio responses * Large group of molecules that have similar composition, but differ in several important prooperties. * Composition: $C_n(H_2O)_n$ or $C_n(H_2O)_n$ *Types:* * Simple Sugars -Small carbs * Some larger polymers of the simple sugars * Simple Surgues - carbis with 12 or few cahons * Monosaccharides - 5 -6 carbons, usually in a ring (pentoses and hexoses) * Disaccharides - 2 monosaccharides linked by glycosidic bond * Oligosaccharides - 3 - 10 monosacchardies joined by glycosidic bonds * Often bonded to protiens and liptides on cell sulaces * Recoginiton signals* * Polysaccharides - large polymers are Man sacharides, chans cam be bearching Starches- famly of polysacchandites of glucose Glycogen highly beared. ☆ ☆Main eragy storage molecule* Examples of Polysaccahridies contud. ☆ Cellulose * Most abundent carden conting Very stabled a gaal stractural *☆Nuecle Acid's* nueclic acids * polymers specialited for Storage tarnision use of depetic info * DAN * deory ibonu eleic acid. ARN ☆ Ribondeic Ald. ☆Monames of nuecleic aceds and nue cleotides Nue cleotied ☆ pentose (sCardon) Suger & m-Con tain Baset phesphate group Nuiclaside pantes ingar ☆m-containng Bese. Bases aF nuecleic aud ☆Primidmes ☆ single nig Qpuimes ☆ dawble Ring Swgus of nueclee aceds. ☆ deeny Vibone ☆ in Dana. &Ribo Se☆ In ARN Nucleotids Famation ☆Acans in Condensateon ceaclions to fam phosphadester Lin Sages #s Cardon of ave vibose 3 Cardon of next vibe se farms chain of alternating Sugar & plosplute Malecules ☆ CAKA plosphate Bactbane + ☆ Grow in as a to 3 divection. *oligomeledeotides ☆2monomecs Nenelectides. 20m 20Mamels & include Small ARN ☆ impor tan for DAN ceplucations gene xpression patel nueleatides long est poly mers in living Werld RAN ace. ☆DAN deubel Sirands. + ☆heled togeshery by complomentiry Bese pacin using H-band t bases de Analo & Addene utth thy me * cytosine urd Quanme (G☆G) 3 faun ☆ (AT) 3 fam ☆ farn hydragan ARN ( A dewine url Uradil (44). Q ☆ Band sin ARN & AND ☆ strang bunt mat stronger then cavalat Bese pars seperate utth Sinell ☆ Amaund of amargy. DNA Sirand Charactenstecs ☆Ani pallel * can in opposite Divechens is ends opposite. ☆Ledder tusts inter daubel helix. sugar phospha t gruups☆ fieds of Ledder ☆hydrogen banded bares Rungs RAN Structuce. single Istanded. ☆ offen fatds in a self to fam Short dawble standeed. ☆ ✩Acans By compliemontry Bese paring Siruchce desermined by arden af Bares. ☆ a cant gels 3D Shape Thanks to dawble Sirand ☆affets hauw ☆ in teact, with others Malecales