BioMedical Chemistry 3

Periodic Table Atomic calculations Protons neutrons = mass #- atomic # atomic # = electrons= atomic#-charge n = sublevel Orbitals · ↳ · (Sphere shaped orbital ↳ S (dumbell Orbitals P contain can shaped) electrons 2 for of total 8 number orbitals of n subshells inside I S S 1 X2 = 2 2 S, P P 3 x2 = 6 3 S, P 4 5 , < F electrons 2 contain S[P < D , sublevels A d pd , f gX2 7 f * each orbital = xz can = 10 14 hold 2 left to electrons electron configuration 2 * Ca : Is Is" 2p 35 3p5 (chlorine The M In size > - Atoms ↓ of an element electrons decreases from smaller increase bigger number of value in size going down a group right Significant Figures Display ↳ precise how Rules For 1 Determining digits Non-zero . 316 . 2 3 = Zeros 4 = . Leading 0 . = 35 000 decimal = 2 , . of Sig Figs significant other digits are significant not sig significant figs zeros 4 0 are are 2 - leading . Trailing Number Sig figs zeros 00035 is figs Sig between in 6 003 3 . measurement 035000 = 5 Zeros sig figs Sig figs are significant Ionic, Covalent, and Lewis Dot Structure Symbol : represent ↳ Lewis valence and to · draw electrons just : numurumu ↳ bond : ionic dots as with atom an attractive symbol element the due force valence electrons it's of all transfer to of one or eme electrons more bond : attractive covalent ↳ draw using atoms structures dot hydrogen · H2S of ing the to form only - Lewis due force bond I never a is central HCN atom BF3 a H S - - : F H-CEN : H electrons ⑧ = 02 o B-F ·F : SO2 · electronegativity more than 1 8 subtracting electronegativities by . miner gain electron ionic 1 2 . 3 4 Sodium . . . and Lithium and Oxygen barium and = molar Nat > - Li - Oxygen fluorine mass lose - bromine aluminum and Molarity ↓ compounds > - - 02 > - Na2 electron 0 "Br" -Li' Br' Alt Bate : 0 7 2 > - " > - Also Ba < F is ionic Writing names of ionic compounds * positive anion ion suffix cations will retains to bind e9 NaC nitrite 2 The the num one oxygen the element ; change Chloride Sodium the > - to Anions with of name : -ide . ~ yatomic anions a nitrate the form with atoms Suffix-ate . neutral or a bears compounds Chapter 4, Calculations and the Chemical Equation (multiply mol-atoms ↳ Avogadro's and converts between moles 1 mole go · 6 022 = back 2 the take molar & fu , eg : 5 Scientific notation mul = 2 4 1024 x . 30 x 102 3 + . 0x1024 # converts between moles atoms molar mass 1 mass . 81x1024 > - mol atoms - (divide mol of s cancels out #x02am seems divide by and mass 9 - mol (divide > - = H Ch mass the mol 24x182 = grams find . atom atoms , molecules calculating ↳ molar mass 1. 1023 moles to and x . from neg molc o oam s Number = 0 3005 . x 10 = 3 . 005 er ↑ g (multiply ↳ 3 . 01 mols & common bases subtract molar mass ↓ calculate eg : formula ↓ Mg(NOs)2 6 Hz0 · Mg N2 , 01z Hiz 256 40374 . = Te = 256 round to . gNHg -mol 14 N 3 ↑ molar 404 nearest thousandths 34 mass mass 3(1) + = 2 3 Ne mol Ne mol Ne = = = 179/mol 2 moN mass Net 1 mol = zog Ne 40 gNe 60 g Ne 60gve Chemical Formula terms vocabulary of grams Molar mass-mass in Chemical equation Shorthand eg : Nz(g) Chemical + - eg : [Na(s) + cle(g) of two 2AgO(s) Single - - 2Hg(k Replacement Compound A BC + - + two or + 02(g) : 1 atom B + Double-Replacement : ABICD-AD or 2NaCI > - Decomposition : Produce : all = of same atoms number of elements Ac Two more elements or compounds products more replaces eg : (h(s) compounds + from another 1AgNO > (aq) undergo in > - a a single the 2 Ag(s) CB Reduced + Acid: bases 2- 2c- Produce : accept reduced hydrogen ions hydrogen ions - AB bic it gained two electrons reactant AB-A compound + "change - Cle AtB (s) Oxidation reduction : transfer of negative charge ↳ electrons oxidized bic it lost two Mg-Mg + ze ↳ reaction a Chemical Reactions combination : joining eg notation [NHs(g) 3H(g) of mole 1 producing (n(NOs) (a) of partners" + B new Chapter 5, States of Matter: Gases, Liquids, and Solids of units common pressure atmosphere (atm) · tour · Converting Units temperature : k =c + 273 Pascal (Pa) · is atm 1 760 · 101 · equal Gas: mostly for kPa 3 . · 14 70 lbs/in · to : mmHg 760 · 2 . or psi made · As Gas P V, up constant , resulting Law : volume random atoms/molecules , and linear motion increases temperature Pressure from space small (kinetic energy) also laws Boyle's empty of , particle speed increases Change (vice versa) P2 Va = , Charle's Law : Comparing Volume + temperature = gas Law : Combination Combined of Boyle's Law + Charle's Law = Avogadro's first volume of moles Law : measured =* first second amount of of and volumes equal under the same of any conditions ideal of when amount · gas Law : Combination = at m L # moles same number volumea gas PV nRTkkewin the temp+ pressure · ideal contain gas R = of 0 0820 . all gas law · T p = = asked 213 1 molar . at sip 15K atm volume of any gas = 22 . 41 PT2 Chapter 5, States of Matter: Gases, Liquids, and Solids Boiling equal The ↳ polar Point : which at the pressure vapor of the liquid becomes atmospheric pressure to boiling point molecules Viscosity : of dependent is higher measure function · temperature of b P . a on than forces intermolecular nonpolar liquid's both attractive forces polar molecules tend molecules resistance between to flow molecules and molecular geometry complex · or to have higher Viscosity mmmmmm or · nonpolar decreases molecules as temperature increases than simpler Chapter 6 Solutions that solvent : Substance solution : it making solute : substance One dissolves the dissolved is eg : water solute into another throughout uniform , homogenous that substance Electrolytes NaCIss gets from formed are EnNa"(ng) Electrolytes: substance a dissolved eg : Salt that solutes soluble are compounds ionic Cl (a) + that produces ions solution in dissolved when in Water will · conduct electricity Concentration : how much solution in substance is dissolved in solvent given a mmm Physical properties-melting Chemical Properties - + solution boiling points reactivity Mi mass/volume percent formula V = solute ope &solute = 10 Vz = = M 2 dilution dilution after volume V amount of solute = mass of amount of solution : of # = A moles of liter p after molarity = dilution dilution before volume = M ,V 1 Molarity M (ppm) , before molarity = Me o (ppt) formula Dilution = solute in 9 volume of in m solute per of solute solution M-molarity n- # v - of moles volume of solution in liters Chapter 7 energy, rate, equilibrium Thermodynamics 1 energy . system: Specific of set reactants concepts molecules random · Molecular Kinetic of atoms + in substances , area around reaction a are : surroundings get Exothermic : freezing collide Free constant, in with eg heat melting : Bonds , boiling . Bonds surrounding need to need temperature be to to be made Fin + D = : involves k[A]" ((s) > - [Hz][C] Reaction only the A : products CH4(g) broken rise Combustion exothermic writing rate laws = i - C + EntrophyChange surroundings decomposition Reach progress 2Hz(g) energyatemperature - change(change a other its causing , condensation . formula : rate H-TS change each from heat colder releases , = It absorbs an k 6 Theory - & Endothermic : one reaction the disorder ( atoms + Enthalpy eg reacting motion molecules eg : the involved in reaction Basic · from converted only , products and of outside Surroundings : everything the destroyed or created disorder/randomness increasing . be cannot another to 2 Laws reactants using progress brackets endothermic - positive Chapter ↓ AS ↳ favorable : As negative Exam * 40 on definitions * bring * he which a need A taking more in molecules more entrophy - disordered from becomes is decreasing Monday questions * 0 7 system the - calculators will provide formulas to review know gas is he laws providing ?? Centi , Kilo , mili polyatomic ions , how to name them , disorder is R -P decreasing 1 Chapter matter - that anything takes up space Scientific law : repeatedfcientific observations identisive properties color · density o volume Celcius freezing is point boiling point is 1000 Farenheight freezing point boiling O property dependent enthalpy-heat in entrophy-disorder - mass · meting point · Extensive · independent - Kelvin point boiling is 32 212F is transfer 0 °c at c > - point is + 273 15 . 373 15 . substance 6 Chapter # solution : : solute solvent : Combination Substance being substance doing Solubility : dissolve in Factors how dissolving the of in solute a . 3 . Pressure . Temperature 2 · I mass volume formula / volume ass= solute V S volume both * Collegative Properties mass/volume formula ofsolute = - oa Of formula ess/mass % et solute depend ppM point freezing · · point osmotic and PPM T = solute/g of got solute/g of got solute/gof PPM = g of solute/g Clarity solute m solution x103 ppt solution X10 Solution of solution 6 PPM transporting - K " = x 103 ppt xOGPPM ions and the across dialysis:remova,a across membrane 3 Nat membrane transport Formula M depression pressure cell ppT elevation transport #five g of = concentration Particles solute poiling · XO = on vapor Pressure lowering · PPT formula %_g soluteTo o . can temperature given a eg: water affect that 1 Polarity mass solute dissolved much solvent a + solvent of =moto a 7 Chapter Endothermic the so : being heat environment Exothermic heat : absorbed becomes being cold / released from it's melting the so surroundings ice is surroundings colder enthalpy entropy free DH : : SH As change change in heat? in disorder/randomness energy. AS D G # change heat in change in disorder free energy · When change the energy reactant side is in it is positive Sp on taneaus t spontaneous non temperaturee # dependent dependent a ·donemen Exothermic riting Rate Lawse just reactant Chapter 8 acids, bases and oxidation and reduction strong Dic Lowry Theory Bronstead they acids Hp Hi > non-reversible are dissociate A- + conjugate strong completely A cid base ↑ Acid : Base : It : donates a proton accepts a proton Stable , easy HATH" Proton conjugate acid base : What conjugate PH formula PH -log [It30 ] of O has acid the = pH find find 10g (3 - ② PH POH + PH 14 = - = 2 What · is alternate the POH 33 . 46 = . 50 x 10-3 M . What is it's PH ? 11 54 . conjugate - = 0 solution form : "[HsO + ] = CH30"] g = 6 00 ? . 10-PH 10 = [Hg0 ] = 1 0 . -6 x . 00 10-0 M increase acia H26O 3 ↓ PH with a of 1 +1 [OH-] pH ? from CHsO] find to - [IzOt] CO 3 soning charge by I bic hydrogen + is H ↑ NHz conjugated =decrease thea 2 NH, NHz- base When you take the hydrogen , you Eg : identify the Acid NH3 ↑ base + , base H20NH4" ↑ Acid has . + base = solution hydroxide sodium [H0-] concentration 14 mathematical conjugate -log [H0] = 2 46 = ⑤ 303- A -log [H0] = 10 x given · It form formula hydroxide same calculate to ↑ - 50 , concentration POH . base ↑ unstable laid POH pOH when the Acid become solution a A + Conjugate weak become + hydronium To has base the what : form to ↑ conjugate a cid , + conjugate acid + conjugate Eg : HO↑ conjugate b ase HF Acid & + base . coningate H20HgOt base & conjugate acid + base Fconjugate base - away create Chapter 8 acids, bases and oxidation and reduction hydronium Is0" · in : [Hg0 ] = · [OH-] = ↳ Kea = 1 (Hs0t] Formula : [Hg0t] answer : in equilibrium expressions 10 M x for [Hg0t] 1 = . 0 x 10-14 solution a 10-PH = [Hg0t] final included temperature room [Hg0"]20H] Calculate not 10- M x 1 are ion at water + · , hydronium pure liquids ion - = 10 = 1 0 . 3 . 99 x 10 - 3 99 . M of nitric acid for which pH = 3 . 99 . Chapter 9 the nucleus, radio activity, and nuclear medicine key · · · knowledge natural radioactivity Writing balanced natural and Radioactivity Nuclear man Symbols : Nuclide : Specific radiation ↑ or atoms describe type the of nucleus to atomic nucleus write equation (negative charged (positively alpha particle (2 energy (atomic midterm: know nuclear particle lose by radiation emitting released rays how position of Measurement radioactivity releasing nuclide Beta of applications radioisotopes made unstable : Particles ↳ equation . nuclear Medical Terms vocabulary Radiation : · charged charge) symbol mass defined by its , mass protons + number ( neutrons Chapter 10 Organic compounds covalent - Gas - a temperature room and in soluble - inorganic - Alkenes - contain atleast 1 double bond Alky hes - at least Alkan - only bond triple es single bonds Aromatic - 3 db unsaturated 3 sb cy loalkanes -unsaturated structure eons -keletal physical properties of hydrocarbons nonpolar · not · · o water Low less soluble melting dense + boiling point pressure Chapter 10 saturated hydrocarbons * forms stable carbon Organise covalent bonds with other carbon atoms inorganic compounds and organic , - structure melting covalent : : molecules solubility : , non Point : lower boiling + bonds nonpolar , water (election sharing electrolytes melting point , intermolecular forces broken easily insoluble -Inorganic · · ionic Three water · · water bonds (electron transfer dimensional soluble , structure dissociating into ions-electrolytes soluble higher boiling his isomer : trans isomer : points same side Opposite side P = To condense the structure Draw the (line) Skeletal - 1-bromo-3- of structure Chlorocyclohexane Br * For a reaction as combustion product CO2 Ocoxygen ( You and reactant would the be H2O . and I Ch [UPAC 1 . . 2 identify the longest carbon number the · substituents 3 . Write . When 4 for names · · · atoms the to lowest possible = Carbon Continuous substituent each a Alkanes in first chain (parent chain) Substituent (branch or number alphabetical branch/substituent order occurs before more the than stem once di + ri Tetra Aromatic hydrocarbons : alternating eg : CH3 CHz-CH ↑ ↑ CHs-CH-CH-CHCH-CHC I CHz 5- ethyl-2 , alkyl group 3-dimethylheptane double bonds in a ring name (longest chain Chapter 11 unsaturated hydrocarbons Alkenes Alkane : Alkynes and Saturated : unsaturated Alkane : Carbon-carbon Single Alkene : Carbon-carbon : triple carbon-carbon IUPAC the name 2 number = carbon of atoms benzene ring of following the 2 I ↓ CHz-CH n + bond CH3 = CnH2n bond double bond , Aromatic hydrocarbons : contain Give single bonds terms vocabulary Alkyne hydrocarbons only have compounds structure number of substitute carbons located CH-CH-CHz-CH-CHz ↑ ↑ location name Benzenes 112 phenol - -COOH 0 I ! anisole aniline . benzene cyclo - I Nitrobenzene · ethylbenzene benzene name the will rings Disubstituted · bonds CH2CHz NO2 always have mm Benzene groups in acid Benzoic alphabetical order 6 C has doesn't of double CH3 OH ↓ 6-Chloro-4-methyl hept-2-ene substitute - bond number ↓ toluene double have bonds double bond Chapter 12 alcohols, phenols, thiols, and ethers As molar Diols · triols and hydroxyl single Nomenclature 1 . . 2 3. . 4 . 5 IUPAC Oh of become than insoluble with those water in only containing alkane OH the OH Br is Carbon oh replaced With -01 . before inserted the -ol Suffix . C-1 . * OH - numbering is at is 2 name lower the of R-OH : Chain alcohols : Cyclic soluble more Alcohols : the position alcohols , group given is The are longest : The-e - increases mass hydroxyl takes group Priority 4 1 3 3 4- bromo pentanol Nomenclature : Ethers 1 alkane 2 . 3 . of name Chain Shorter longest is named longest . . 2 number . 3 add 4 name . - O - R chain alkoxy attached to the oxygen substituent - ane--oxy Nomenclature : Thiols : 1 R : parent parent chain chain Suffix-thiol substituents Phenols R - SH CH , CH Eg : , -SH ethane-1-thiol HS - CHzCHz-SH ethane-1 , 2-dithiol a Chapter 13 aldehydes and ketones Ketone oxidized be not can Carbonyl group - carbonyl group : end of chain carbonyl group Aldehydes R - O It I - 2 to carbons in Ketones O C attached R H R'R C - - R ↑ Carbonyl involving Reactions ↳ oxidation of primary - following alcohols Oxidize alcohols and Ketones alcohols dehydes to removes - are Oxidation > - Aldehyde - reaction hydrogens two Carboxylic > alcohol Alkane oxidation This Ketones Oxidize to Do not oxidize alcohols Tertiary - Aldehydes the secondary - group acid secondary > - Ketone > - (no oxidation further alcohol Alkane territory alcohol > - (no further with C oxidation reduction - Nomenclature Ketones 1 2 3 Parent . replace- . C . = 0 has with 3 . . replace number - > carbonyl Hemiacetal product of reacting with number possible Aldehydes with and - = 0 one Parent chain : longest . 1 - lowest Nomenclature 1 chain longest chain : : chain t acetal group carbonyl group Aldehyde alcohol . or 1 . is insert Carbonyl al group , the Ketone before at the - one end suffix Hemiceral Acetal and Formation OR OH ↓ I R - C - OR R - C - OR I R R = hydrocarbon OH Ht I CHsCHz-C-OCH + product of reacting with Acetal acetal Aldehyde alcohol . I it Hemiacetal and OCHz CHOHCHCHz-C-OCHst H Hemiacetal R is the or Ketone He Chapter 14, carboxylic acids and carboxylic derivatives Functional Group Formulas O O It It Ar-c-OH R C OH - acid Aliphatic carboxylic Carboxylic Aromatic - acid G Il Nomenclature Carboxylic 1 Carboxyl . 2 3 ending replace -e . If . carboxyl I Benzoic carbon is carbon Acid 1 with groups R-C-OH : acid -oic are present -dioic use Derivatives Acid thalic acid cool O benzoic OH acid acid - - O O Il c - OH - - - OH CH3 acid -Todobenzoic carboxyl · i CH - CH group - of 12 Phenyl - acid - oft Pheno · Tolnic terms know ↓ CHz " / I/ · COOH group = (benzene) - when the benzene ring is a substituent on CH2 ↑ 12 · · hydroxyl group alkoxy group R - R-O OH derived commonly from alcohol found in by removing ethers hydroxyl group a chain Carboxylic of Oxidation acids : > - Ethanol boiling Points ↳ carboxylic the Acetaldehyde carboxylic of form acids boiling point Acetic acid intermolecular hydrogen than alkanes (ethers links acid creates reaction to the amino of group dipeptide water released It H / H -u H - HH O i- - + H - j c " - - o H I H Glycine V E 0 = H - amino acid ? Alanine H Her--i ↓ - amino acid? I He It H O is - % I CHs peptide bond Camide bond) O o Chapter 17: lipids Glycerides H O ↓ ↑ It H - o -2- oH H H O - - -- - ↓ R + = c - of H -b H fatty acid ol C - c - o - R + o - - C - H water Ot it H monoglyceride Glycerol (alcohol) sphingolipids sphingosine NHzt sm OH OH Esterification : fatty acid O ↓ R - C - OH + fatty HO-R 2 + alcohol + water O H theat > - ester -- R - alcohol C - orz + H - olt water ester acid hydrogenation : unsaturated fatty acids acids Chalha)Chchich 2Hz = ch(Chal , Cooh can , be converted saturated Ni -- CHglChalig 200H fatty Chapter 21: carbohydrate metabolism Hydrolysis reactions carbohydrate CH2OH CH2Ol ↑ ↑ O > - T o HO ↑ I H O CH2Ol l to monosaccharide Olt of ↑ glycosidase o Oh Out ; CH2Ol ↑ oh O to of + monosaccharide disaccharide glycolysis · requires · products pyruvate of energy in 1 . 3 - 4 ATP (output 2 Aip and animals . glucose noncarbohydrate from glucose makes from glycogen starting materials Lactate . 2 : gives pentose (synthesizes Glyconeogenesis phosphorylation NADH and from Products catabolism substrate-level : source Major cytoplasm anaerobic = oxygen no , the Carbohydrate for pathway · in occurs : . Glycerol Most occurs Insulin : acids amino in The Glycogenolysis liver hormone : insulin Glycogen is released degradation is by pancreas controlled in by response to Glucagon hyperglycemia 2 Chapter 19: enzymes of classes 1 . Oxidoreductases are · · . 2 · · · · between transferred : Catalyzes Oxidation-reduction Credox) reactions , electrons molecules dehydrogenase oxidases Transferases Catalyze : the transfer of functional groups (methyl , amino , phosphate eg-hexokinase methyl transferases Kinases 3 . Hydrolases · enzymes : eg-Amylase proteases , Catalyze , Lipase esterases hydrolysis of chemical bonds, Using H20 to break down substrates Chapter 22: aerobic respiration Citric pyruvate · · pyruvate pyruvate cycle / Acid from is is used in glycolysis is added to cycle Kerbs the into transported Coenzyme reaction glycolysis A to the form for mitochondrial Acetyl COA further oxidation matrix which is further oxidized to Chapter 21: carbohydrate metabolism Chapter 22: aerobic respiration cycle Citric acid pyruvate 1 . 2 converted then . further For . 3 glycolysis from Allosterically binding of acetyl the acetyl regulated group is reactions : site allosteric the acetyl carbon 2 reactions the when occurs to , < group to of activity enhance thiol group enzyme inhibit or activated be the an matrix CC must group bonded can the mitochondrial into transported is is enzyme's > - activation Coenzyme A controlled by activity. Glycolysis (cytoplasm) glucose · (CH , 06) energy . 2 · Pyruvate · - - · converted is into acetyl-cot (acetyl COA) , Producing cycle acetyl-cot the enters 3 NAPIt citric glucose one 1 FADH 6 NADI 1 ATP 2 FADI 2CO2 electron · pyruvate of molecules decarboxylation acid each - 2 NADH I , into pyruvate Citric - ATP 2 pyruvate each per . 3 output : down broken is NADH NADH each energy transfer conversion Alanine 4 CO2 molecule electrons oxidized is ATP cycle chain transport carries is 2 acid used of to , NADT which electrons to lose some transportIt acids amino Transaminase returns - produces - produces membrane . inner molecules pyruvate for and mmm Aspartate transaminase cycle . acid energy . across into citric the to oxaloacetate num citric cycle glutamate I NADH Chapter 23: fatty acid metabolism Bile salts and digestion · by liver produced fluid digestive fats of absorption and stored in duodenum in gallbladder (1st small Emulsification by · 1 hydrolyzes . 2 leaves . lipase pancreatic fatty 1st middle acid and 3rd fatty acid fatty acids from triglycerides degradation Step 1 : B-oxidation product Step 2 : 3 : Ketone · · · activated : hydride ions are of C-C formation - Step ATP requires - - B- hydration of the acyl group used to bond double double reduce bonds bodies hydroxybutyrate Ace tune Aceto acetate Lipid resting working Heart regulation muscle muscle muscle uses fatty acids uses glycolysis prefers Ketone for bodies energy FAD producing FADH2 . intestine) .