Chem/Phys (5)

Structural formulas for H:

# of valence e- = 1 Usual # of bonds = 1 1) hydrocarbon (alkane, alkene, alkyne) 2) hydride, H- 3) hydroxide, OH- 4) proton, H+ 5) hydronium, H3O+ https://www.varsitytutors.com/mcat_physical-help/defining-classifying-acids-and-bases (stereochemistry of covalently bonded molecules)

Structural formulas for C:

# of valence e- = 4 Usual # of bonds = 4 1)alkane 2)alkene 3)alkyne 4)aromatic rings *LAH= lithium aluminum hydride, LiAlH₄. It's used as a reducing agent in organic synthesis, especially for the reduction of esters, carboxylic acids, and amides. The solid is very reactive toward water, releasing gaseous hydrogen (H₂) (stereochemistry of covalently bonded molecules)

Structural formulas for Si:

# of valence e- = 4 Usual # of bonds = 4 1)silane 2)silicon dioxide (stereochemistry of covalently bonded molecules)

Structural formulas for N:

# of valence e- = 5 Usual # of bonds = 3 *when N makes 3 bonds, it has a lone pair 1)amine 2)amide 3)imine 4)hydrazone 5)oxime 6)nitro compound 7)diazo compound 8)nitrile/cyanide 9)azide (stereochemistry of covalently bonded molecules)

Structural formulas for P:

# of valence e- = 5 Usual # of bonds = 3 or 5 1)phosphorus compound 2)phosphite 3)phosphate (stereochemistry of covalently bonded molecules)

Structural formulas for O:

# of valence e- = 6 Usual # of bonds = 2 1)alcohol 2)ether 3)aldehyde 4)ketone 5)carboxylic acid 6)acyl halide 7)anhydride 8)amide 9)ester 10)ozone (stereochemistry of covalently bonded molecules)

Structural formulas for S:

# of valence e- = 6 Usual # of bonds = 2 or 6 1)thiol 2)sulfide, S^2- 3)sulfite 4)sulfate *way to remember: sulfATE (hungry, attached to 4 oxygens, wants to eat them all); sulFITE (it wants to fight. Attached to 3 oxygens with a lone pair on S. Like horns) (stereochemistry of covalently bonded molecules)

Structural formulas for Cl:

# of valence e- = 7 Usual # of bonds = 1 1)chloride 2)hypochlorite 3)chlorite 4)chlorate 5)perchlorate (stereochemistry of covalently bonded molecules)

Structural formulas for F:

# of valence e- = 7 Usual # of bonds = 1 1)fluoride (stereochemistry of covalently bonded molecules)

Calculate the pI of a neutral amino acid that has pKa values of 2.15 and 9.63.

(2.15+9.63)/2 = 5.9

In order to determine how much base to add to an acidic solution (or how much acid to add to a basic solution) in order to cause neutralization, use the following formula:

(a)[A](Va) = (b)[B](Vb), where a is the number of acidic hydrogens per formula, A is the molarity of the acid, Va if the volume of acid, b is the number of H+ ions the base can accept, B is the molarity of the base, Vb is the volume of base. (acid/base equilibria)

How does a cis vs trans (or a Z vs E) structure affect mp and bp?

*A cis conformation (or a Z conformation) means substituent groups are on the same side. This causes rigidity of the double bond, sometimes even causing a long chain to bend. The more double bonds the chain has in the cis configuration, the less flexibility it has. When a chain has many cis bonds, it becomes quite curved. Bc of this, the molecules cannot stack together tightly. This results in a lower mp and bp. *A trans conformation (or an E confirmation) means substituent groups are on opposite sides. As a result, they do not cause the chain to bend much, and their shape is similar to straight saturated fatty acids. Bc of this, the molecules can stack together well, so they have higher mp and bp. Note: most fatty acids in the trans configuration (trans fats) are not found in nature and are the result of human processing (hydrogenation) (separations and purifications)

Common functional groups, amide:

*Amides are usually regarded as derivatives of carboxylic acids in which the hydroxyl group has been replaced by an amine (NR2). (stereochemistry of covalently bonded molecules)

Common functional groups, acid halide or acyl halide:

*An acid halide (also known as an acyl halide) is an organic compound derived from carboxylic acids by replacing a hydroxyl group with a halide group. way to remember: aCyl halide (derived from a Carboxylic acid); vs aLKyl halide (derived from an aLKane) (stereochemistry of covalently bonded molecules)

The common-ion effect and its use in laboratory separations:

*The common-ion effect is simply Le Chatelier's principle applied to Ksp reactions. AgCl (s) ↔ Ag+ (aq) + Cl- (aq) *The common-ion effect says that if you add Cl- to the solution above, then less AgCl would dissolve. *For example, if you add NaCl to a saturated solution of AgCl, then some AgCl will crash out of solution. *Another example: more AgCl can dissolve in pure water than in water containing Cl- ions. *In laboratory separations, you can use the common ion effect to selectively crashing out one component in a mixture. *For example, if you want to separate AgCl from a mixture of AgCl and Ag₂SO₄, then you can do so by adding NaCl. This will selectively crash out AgCl by the common ion effect (Cl- being the common ion). (solubility)

Common functional groups, hemiacetal:

*a compound that results from the addition of an alcohol to an aldehyde or ketone (stereochemistry of covalently bonded molecules)

Common functional groups, cyanohydrin:

*a functional group in which a cyano/nitrile and a hydroxy group are attached to the same carbon atom. The carbon is also attached to two R groups. *note: a cyano group or nitrile/cyanide consists of a carbon atom triple-bonded to a nitrogen atom (stereochemistry of covalently bonded molecules)

A lewis base ______. And a lewis acid _______.

*a lewis base/nucleophile/ligand donates a pair of nonbonding e-. It has lone pairs on their central atom. Ex= NH₃ *a lewis acid/electrophile accepts a pair of e-'s. They don't have lone pairs on their central atom. Ex= BF₃ (bonding)

Absolute vs relative configurations:

*absolute= R vs S; cis vs trans; D vs L *relative= (+),d vs (-),l Relative configuration is always defined in relationship to another chiral center. The direction a molecule rotates plane-polarized light is a prime example of relative confguration (stereochemistry of covalently bonded molecules)

Which of the following salts is expected to be insoluble in water? A)CsOH B)NH₄NO₃ C)CaCO₃ D)AgClO₄

*according to the solubility rules for salts in water, the only one insoluble would be CaCO₃ Answer=C (solubility)

Which of the following acids could be added to an unknown salt solution and NOT cause precipitation? A)HCl B)HI C)H₂SO₄ D)HNO₃

*according to the solubility rules for salts, all nitrate (NO₃⁻) salts are soluble. Therefore, the addition of nitric acid will not cause precipitation bc it's soluble. Answer=D (solubility)

Which of the following can behave as a Bronsted-Lowry acid but not a Lewis acid? A)CF4 B)NaAlCl4 C)HF D)Br2

*acids want to accept e- pairs or lose H+. Lewis acid accepts a pair of e-'s Bronsted acid donates a H+ *so, Bronsted acids must have a H so it can donate it. Answer=C, the only one here with a H is HF (acid/base equilibria)

Common functional groups, alkyl halide:

*also called haloalkanes *compounds in which one or more hydrogen atoms in an alkane have been replaced by halogen atoms (fluorine, chlorine, bromine or iodine) (stereochemistry of covalently bonded molecules)

Common functional groups, enol or alkenols:

*an alkene with a hydroxyl group attached to one end of the alkene double bond. Notice there are two structures in equilibrium *Generation of enols often involves deprotonation of the 𝜶 carbon (the carbon next to the carbonyl group). When this proton is removed, the result is an anion termed an enolate. (stereochemistry of covalently bonded molecules)

Common functional groups, epoxide:

*an epoxide refers to any molecule that contains the oxirane ring system (a three-membered ring with two carbons and one oxygen) (stereochemistry of covalently bonded molecules)

Common functional groups, thiol:

*an organic compound containing the group —SH. A sulfur-containing analog of an alcohol (stereochemistry of covalently bonded molecules)

Common functional groups, ether:

*an oxygen atom connected to two R groups. (stereochemistry of covalently bonded molecules)

Which of the following fatty acids has the highest melting point? A) (3E, 5E)-deca-3,5-dienoic acid B) (3Z, 5Z)-deca-3,5-dienoic acid

*answer= (3E, 5E)-deca-3,5-dienoic acid. *E double bonds (groups on opposite sides) does not introduce kinks in the molecule. Thus, the molecules can pack tightly together, increasing the mp. *Z double bonds (groups on same side) introduce kinks in the fatty acid chain, making it more difficult for the molecules to pack together, therefore reducing their melting point. (separations and purifications)

Which of the following salts will produce a basic solution when added to pure water? A)KCl B)NaClO C)NH4Cl D)MgBr2

*answer=B Looking at the anions, we have Cl-, ClO-, Cl-, Br₂. Anions that contain Cl-, Br-, or I- are not basic. Here, everything contains those. However, the one that would make the solution the most basic out of these is ClO-, thus NaClO is the salt that will make the solution most basic (acid/base equilibria)

Which of the following is an acidic salt? A)KNO₃ B)SrCl₂ C)CuCl₂ D)Ba(CH₃COO)₂

*answer=C Looking at the cations, we have K+, Sr+, Cu²⁺, Ba²⁺. In order to be acidic, the cation can't be a group I or group II element. So, the most acidic salt must be CuCl2 (acid/base equilibria)

Binary mixtures of equal moles of which of the following acid-base combinations will lead to a complete (99+%) neutralization reaction? A)HCl and NaOH B)HF and NH₃ C)HNO₃ and NaHCO₃ D)all the above

*answer=D. Remember, regardless of the strengths of the acids and bases, all neutralization reactions go to completion. (acid/base equilibria)

Common functional groups, aldehyde:

*consists of a carbonyl center (a carbon double-bonded to oxygen) with the carbon atom also bonded to hydrogen and to an R group (stereochemistry of covalently bonded molecules)

Common functional groups, ketone:

*consists of a carbonyl center (a carbon double-bonded to oxygen) with the carbon atom also bonded to two R groups (stereochemistry of covalently bonded molecules)

Common functional groups, phenol:

*consists of a phenyl group bonded to a hydroxy group (-OH)

Common functional groups, carboxylic acid:

*contains a carboxyl group (COOH) bonded to an R group. *carboxylic acids occur widely; Important examples include the amino acids (which make up proteins) and acetic acid (which is part of vinegar). *Deprotonation of a carboxyl group gives a carboxylate anion. (stereochemistry of covalently bonded molecules)

Common functional groups, enamine:

*derived by the condensation of an aldehyde or ketone with a secondary amine. *If one of the nitrogen substituents is a hydrogen atom, it is the tautomeric form. This usually will rearrange to the imine (stereochemistry of covalently bonded molecules)

Common functional groups, ester:

*derived from the condensation of a carboxylic acid and an alcohol (stereochemistry of covalently bonded molecules)

Isothermal process:

-Constant temperature -cylinder with gas in a water bath to maintain temperature. All energy added (work) must be taken away (heat); all energy lost (work) must be added (heat). -isothermal process.. Thermal energy is gained and lost as heat *For ex, if you apply 300J of work pushing down the piston, 300J of heat energy must leave. *Note: piston should be pushed up or pulled down very slowly, so heat always has time to move in or out of system -on PV graph, going to the left is isothermal compression; going to the right is isothermal expansion -no change in temperature= no change in internal energy ∆T=0, ∆E=0, ∆PV=0 ∆E=Q+W → Q=-W or -Q=W (1st law of thermodynamics) (thermodynamics)

Isochoric/Isovolumetric process:

-Constant volume -heating a gas in a cylinder w a locked piston. Pressure will increase, but no change in volume. Adding heat increases pressure, losing heat decreases pressure -isochoric process.. Thermal energy is used increasing temp (increasing pressure) W=0 (remember work done=area under the curve. Here, we just have a straight line on the graph; area under the curve=0) ∆E=Q+W → ∆E=Q (1st law of thermodynamics) (thermodynamics)

What are the structural determinants of membrane fluidity?

-Degree of saturation (unsaturated fatty acid tails increases membrane fluidity) -Tail length (making the length of fatty acids shorter increases membrane fluidity) -Amount of cholesterol (at low temps, it increases fluidity; at high temps it decreases fluidity) (lipids)

The Rate Constant (k):

-The rate constant, k, is constant for any given reaction at a given temp (in other words, each reaction has its own rate constant). Is an empirically determined value -The k in the rate law is the rate constant. -The rate constant can be expressed mathematically with the Arrhenius equation: k = Ae^(Ea/RT), here A is a constant, Ea is activation energy, T is temperature (in Kelvins), R is universal gas constant. You do not have to memorize this equation. Just understand that: k∝rxn rate k∝1/Ea k∝temp -So, Low Ea, High T → large k → faster reaction. -When activation energy approaches zero, the reaction proceeds as fast as the molecules can move and collide. -When temperature approaches absolute zero, reaction rate approaches zero because molecular motion approaches zero. (kinetics)

Proteins:

-monomer= AA -two AA's connect via a dehydration reaction, forming a peptide bond (carboxyl linked to an amino group) -new AA adds to C-terminus; proteins always read from N → C terminus -20 diff AA's, differ by their R groups Explain primary, secondary, tertiary, and quantaray structure in proteins: -Primary structure= AA sequence -Secondary structure = backbone interactions (H-bonding between the NH and C=O). The two most common secondary structures are alpha helix and beta-pleated sheet *alpha helices are often found going through membrane *the alpha helix is right-handed, with the R groups sticking outward *in β-sheets, R groups stick out above and below the sheet -Tertiary structure= Creates 3D structure of protein. Caused by R group interactions within a polypeptide.Can be: Non-covalent: nonpolar-nonpolar, polar-polar, acidic-basic Covalent: disulfide bond between cysteines -Quaternary structure= R group interactions (disulfide bonds) between diff polypeptides (amino acids, peptides, proteins)

Four classification systems used to organize carbohydrates:

1) (+), d, and (-), l, describes optical activity 2) R and S describes absolute configuration of structure 3) D and L tells us the precursor of a molecule (D or L-glyceraldehyde). Look at the chiral carbon farthest away from the ketone or aldehyde group on the monosaccharide. On the Fischer projection, if the hydroxyl(-OH) group is on the right, then it is classified as D sugar, if the hydroxyl group is on the left, then it is a L sugar. 4) alpha (down) and beta (up) glycosidic-linkages tells us where the OH is positioned on the anomeric carbon *way to remember, alpha (fish swim in the sea); beta (birds fly in the sky) (carbohydrates)

Hybridization of the carbon atom:

1) 2 groups = sp = linear in geometry. A hybrid between one s w one p orbital. **Contains a triple bond 2) 3 groups = sp^2 = trigonal planar in geometry. A hybrid between one s w 2 p orbitals. **Contains a double bond 3) 4 groups = sp^3 = tetrahedral in geometry. A hybrid between one s w 3 p orbitals. **Contains single bonds only (bonding)

How can you apply Le Chatelier's principle to acids and bases?

1) Acids are more soluble in bases. HA → H+ + A- Putting the above in a base will take out the H+, thus, more HA will dissolve according to Le Chatelier's principle. *for ex, putting HCl in a solution containing the base NaOH. NaOH → Na+ + OH- HCl → H+ + Cl- Here, the H+ and OH- combine to form H2O. Thus, H+ concentration decreases. Since one of the product is decreasing in HCl → H+ + Cl-, the equil will shift to the right 2) Bases are more soluble in acids. B + H+ → BH+ Putting the above in an acid will add more H+, and thus, drive more B to dissolve according to Le Chatelier's principle. (solubility)

What are the two types of stereoisomers?

1) Geometric isomers (not optically active bc they do not usually have a chiral center) 2) Optical isomers (rotate plane polarized light. Anything w a chiral center is optically active, except meso compounds or a racemic mixture of enantiomers) *Usually optical isomers is another word for an enantiomer pair.

Nonpolar AA's:

1) Glycine; most simple, R= H 2) Alanine; simple; R= CH3 3) Valine 4) Leucine 5) Isoleucine 6) Phenylalanine (F); aromatic 7) Tryptophan (W); aromatic 8) Methionine; sulfur 9) Proline; alpha-helix breaker *These are all hydrophobic *GAVLIMP TP -hydrophobic residues tend to associate with each other rather than w water, and therefore are found on the interior of folded globular proteins, away from water. The larger the hydrophobic group, the greater the hydrophobic force repelling it from water. (amino acids, peptides, proteins)

Basic AA's:

1) Lysine (K) 2) Arginine (R) 3) Histidine *these are all hydrophilic *A Good Lawyer Aims High -both lysine and arginine are protonated at physiological pH, but histidine is unique in having a side chain with a pKa close to physiological pH. At pH 7.4, physiological pH, histidine may be either protonated or deprotonated (may act as an acid/p+ donor or as a base/p+ acceptor. This explains its prevalence at protein active sites). *way to remember= His goes both ways (amino acids, peptides, proteins)

What makes a molecule more stable?

1) Resonance 2) Induction (e- withdrawing vs e- donating groups) 3) Electronegativity (negative charge on most EN atom; more stable) 4) Size (larger atoms can disperse negative charge better; more stable) *anything that helps minimize charge Reactivity predictions you can make using these fundamentals of stability: -acid strength (higher acidity= more + charge, more EN, larger radii) -base strength (higher basicity= more - charge, less EN, smaller radii) -nucleophile strength (higher nucleophilicity= more - charge, less EN, larger radii) -leaving group ability (better LG= neutral charge, more EN, larger radii) (stereochemistry of covalently bonded molecules)

Polar AA's:

1) Serine 2) Threonine 3) Cysteine; contains sulfur; can create disulfide bonds 4) Tyrosine (Y); aromatic side chain 5) Asparagine (N) 6) Glutamine (Q) *these are all hydrophilic *SomeTimes Cats Try A Growl -the hydroxyl groups of serine, threonine, and tyrosine resides are often modified by the attachment of a phosphate group by an kinase. The result is a change in structure due to the very hydrophilic phosphate group. This modification is important in regulating protein activity. -asparagine and glutamine are the amide derivatives of aspartic acid and glutamic acid. (amino acids, peptides, proteins)

What are the two ways to determine the order of a rate law?

1) a multi-trial experiment in which the concentration of one reagent is changed at a time 2) looking at the rate-determining step in a previously proposed mechanism

Describe two ways to make a buffer

1) add (roughly) equal molar amounts of a weak acid and a salt of its conjugate base (or a weak base and the salt of its conjugate acid) 2) neutralize half of a sample of a weak acid (or base) by a strong base (or acid)

Salt solubility rules:

1) all group I (Li+, Na+, K+. Rb+, Cs+) and ammonium (NH₄⁺) salts are soluble 2) all nitrate (NO₃⁻), perchlorate (ClO₄⁻), and acetate (CH₃COO⁻) salts are soluble 3) all silver (Ag+), lead (Pb²⁺ or Pb⁴⁺), and mercury (Hg₂²⁺ and Hg²⁺) salts are insoluble, except for their nitrates, perchlorates, and acetates (solubility)

Acidic AA's:

1) aspartic acid (D) 2) glutamic acid (E) *these are all hydrophilic *A Good Lawyer Aims High -Aspartic acid and glutamic acid are the only AA's w carboxylic acid functional groups in their side chains, thereby making the side chains acidic. -the terms aspartate and glutamate refer to the anionic (deprotonated) form of each molecule, which is how they are observed at physiological pH. (amino acids, peptides, proteins)

Why are triglycerides more efficient energy storage molecules than carbohydrates?

1) packing= hydrophobicity allows triglycerides to pack together very tightly; they pack much tighter than carbohydrates. Carbohydrates (in the form of glycogen) cannot pack as tightly bc it becomes solvated by water (water H-bonds to their hydroxyl groups). 2) energy content= triglycerides store more energy than carbohydrates (fat has more energy carbon-for-carbon than a carbohydrate). The reason for this is the amount of oxidation that takes place as these compounds are converted to carbon dioxide and water. Carbon for carbon, fats require more oxidation to become CO2 and H2O than do carbohydrates. Because of this, the oxidation of fats takes longer, but it also gives off more energy. (lipids)

What are two common types of covalent bonds between amino acids in proteins?

1) peptide bonds/amide bonds: Formed by the amine group attacking the carbonyl carbon + a dehydration reaction. It is a nucleophilic addition-elimination reaction. Peptide bonds link AA's together into polypeptide chains. 2) disulfide bond/disulfide bridge: the thiol of one cysteine can react w the thiol of another cysteine to produce a disulfide bond. The cysteine's forming the disulfide bond may be located in the same or diff polypeptide chains. Once a cysteine residue becomes disulfide-bonded to another cysteine residue, it is called cystine instead of cysteine. (amino acids, peptides, proteins)

Phase solubility rules:

1) the solubility of solids in liquids tends to increase w increasing temp 2) the solubility of gases in liquids tends to decrease w increasing temp 3) the solubility of gases in liquids tends to increase w increasing pressure (solubility)

Give three reasons why a titration might be performed

1) to determine the concentration of an unknown acid or base 2) to create a buffer 3) to determine the pKa (or pKb) of an unknown weak acid (or weak base), and perhaps thereby identify the acid or base as well

With organic molecules, what three factors affect acid strength by altering conjugate base stability?

1)EN: the atom which is the most electronegative handles negative charge better. For ex, (less acidic) H₃CCH₃ → H₃CCH₂⁻ (less stable; very reactive. Negative charge on C) (more acidic) H₃COH → H₃CO⁻ (more stable; not really reactive. Negative charge on O) 2)resonance: increases stability of the conjugate base 3)induction: depends on the proximity and EN of electron withdrawing groups (stereochemistry of covalently bonded molecules)

In the laboratory, amino acids can be synthesized by:

1)Strecker synthesis 2)Gabriel-Malonic ester synthesis (amino acids, peptides, proteins)

Why do phosphoanhydride bonds store so much energy?

1)The electrostatic repulsion of the positively charged phosphates and negatively charged oxygen stabilizes the products (ADP + Pi) of breaking these bonds. 2)The stabilization of products by ionization and resonance. As the bonds are broken there is an increased stability due to the resonance of that product's structure. 3)The entropy increases. There is a greater stability in the products because there exists a greater entropy; i.e. more randomness. 1 mole of reactants has a higher energy than 2 moles of products. Disorder is favored over order according to the 2nd law of thermodynamics. *linked phosphates are like compressed springs, just waiting to fly open and provide energy (nucleotides and nucleic acids)

The reaction rate is determined by:

1)how frequently the reactant molecules collide In order for a reaction to occur, molecules must collide. To increase molecular collisions, thus speeding up your reaction, you could: -increase temp -increase particle concentration -increase partial pressure (for gases) -decrease volume (for gases) 2)the orientation of the colliding molecules -catalysts can help molecules collide in the correct orientations 3)energy; molecules must collide and create enough energy to overcome their activation energy, Ea -Ea can be lowered by catalysts -Ea can be lowered by increasing temp (kinetics)

Organic molecules are stabilized in two major ways:

1)inductive effects: stabilize charge through 𝜎 bonds 2)resonance effects: stabilize charge by delocalization of electrons through 𝞹 bonds (stereochemistry of covalently bonded molecules)

How do you know which resonance structure is the best (has the lowest energy; is the most stable)?

1)the octet rule is satisfied for all atoms. **most important. 2)the least formal charges 3)negative charges located on more EN atom The best resonance structure (lowest energy; most stable), is called the "Major Structure". The worst resonance structure (highest energy; not stable), is called the "minor structure". The more major structures a molecule has, the more stable the molecule is (stereochemistry of covalently bonded molecules)

What is a neutralization reaction?

A neutralization reaction is when an acid and base react to form a salt (and sometimes water) ~ they neutralize each other Neutralization reactions are: 1)always exothermic (always releases heat) 2)always form a salt, acid + base = salt + water 3)sometimes forms water, for ex, NH₃ + HCl → NH₄Cl, here your forming a salt, NH4Cl, and no water (acid/base equilibria)

What is a nucleophile? What is an electrophile?

A nucleophile is a species that is e- rich and is attracted to something that is e- deficient to donate a pair of e-'s to. It usually has either a fully or a partial negative charge associated w it and/or a lone pair of e-'s. An electrophile is a species that is e- deficient, so it is attracted to an e- rich species. It usually has either a full or a partial positive charge associated w it.

Kinetic control vs thermodynamic control of a reaction:

A reaction can have 2 possible products, kinetic vs thermodynamic product. -Kinetic product = lower activation energy, formed preferentially at lower temperature. -Thermodynamic product = lower (more favorable/negative) ΔG, formed preferentially at higher temperature. *kinetics tells you how fast a reaction will occur. A reaction will occur faster if it has a lower activation energy *thermodynamics tells you whether a reaction will occur; if it is spontaneous or not. Factors favoring a reaction= being exothermic (-∆H), increase in entropy (+∆S) (kinetics)

What is a buffer?

A solution that minimizes the impact of the addition of an acid or base on the pH of the solution

Types of thermodynamics systems:

A thermodynamic system is just a fancy name for the system you are studying 1)isolated system= No exchange of matter or energy between your system and the environment (no exchange of heat or work) 2)closed system= No exchange of matter, but energy can be transferred between system and environment (exchange of heat and/or work). Ex= putting a lid on sause-pan on stove 3)open system= exchange of matter and energy between system and environment (exchange of heat and/or work). For ex, sauce-pan on stove with no lid (thermodynamics)

Coordinate covalent bonds:

A type of 2-electron covalent bond in which the two electrons derive from the same atom. The e-'s are donated from the nucleophile/ligand/lewis base. The electrophile/lewis acid accepts the two e-'s. Some nucleophiles may donate more than one lone pair of e-'s -formed between atoms w either: lone pairs or e- deficient species -e- are localized, not moving -e- are equally shared; but they are donated only from the nucleophile/ligand/lewis base -compounds w coordinate covalent bonds are easily dissociated from each other chelate= a molecule (nucleophile/ligand/lewis base) that can donate more than one e- pair to an electrophile. Oftentimes two diff atoms in one molecule will each donate a pair of e-'s to another molecule *Ex, when hemoglobin binds Fe²⁺ (making the heme unit), each N on hemoglobin donates a pair of e-'s to Fe. So, hemoglobin is a chelate. Often, the mcat will say "Fe²⁺ is ligated" or "Iron (II) is chelated," both mean that hemoglobin has bound its Fe²⁺ ion *intramolecular force

What is a ylide?

A type of zwitterion. -An ylide is a neutral molecule with positive and negative charges on adjacent heteroatoms. -A betaine is a neutral molecule with a positively charged functional group and a negatively charged functional group. *The Wittig reaction employs phosphorus ylides to convert aldehydes and ketones to alkenes. One of the intermediates of the reaction is a 'betaine', a form containing opposite formal charges that are not necessarily adjacent. (nucleotides and nucleic acids)

What is a zwitterion?

A zwitterion is a molecule that has a positive and a negative charge somewhere in the molecule, yet is neutral overall

The pKa's for the three functional groups in aspartic acid are 9.8 for the amino group, 2.1 for the α-carboxyl, and 3.9 for the side chain carboxyl. A) In gel electrophoresis, what pole (- or +) will aspartic acid migrate toward in an electric field at physiological pH? Note: physiological pH is 7.4 B) In gel electrophoresis, what pole (- or +) will aspartic acid migrate toward in an electric field in a pH=1 solution?

A) The amino group will be protonated (NH3+), and both carboxyl groups deprotonated (COO-). This will yield a net charge of -1 per aspartic acid molecule. Thus, aspartic acid will migrate toward the + pole at pH=7.4. B) The amino group will be protonated (NH3+), and both carboxyl groups will be protonated (COOH). This will yield a net charge of +1 per aspartic acid molecule. Thus, it will migrate toward the - pole at pH=1. (amino acids, peptides, proteins)

Given the pKa of H₂CO₃, A)can you find the pKb of CO₃²⁻ ? B)can you find the pKa of HCO₃⁻ ? C)can you find the pKb of HCO₃⁻ ? In solution, H₂CO₃ + H₂O <--> HCO₃⁻ + H₃O⁺

A)No! You could not find the pKb bc your given the pKa of H₂CO₃. The conjugate base of H₂CO₃ is HCO₃⁻, not CO₃²⁻ B)No! You could find the pKb, not the pKa of HCO₃⁻ C)Yes! pKa + pKb =14 (acid/base equilibria)

What is vinegar?

Acetic acid in water! CH3COOH + H2O <--> H3O+ + CH3COO- acetic acid + water <--> hydronium + acetate anion

Amino acid backbones as conjugate acids and conjugate bases:

Acid + Base <---> Conjugate base + Conjugate acid R-COOH + H₂O <---> R-COO- + H₃O⁺ H₂O + R-NH₂ <---> OH- + R-NH₃⁺ *more acidic +H₃N-CH₂-COOH <---> +H₃N-CH₂-COO- <--->H₂N-CH₂-COO- more basic* (acid/base equilibria)

What is the minimum energy required to start a reaction?

Activation energy, Ea

Ionization of water:

Also known as the autoionization of water. Pure water is a neutral solution, has a pH of 7. If water does react with itself, you will get an equal concentration of hydronium and hydroxide ions, thus the pure water will still have a pH=7. H₂O(l) + H₂O(l) <--> H₃O⁺(aq) + OH⁻(aq) or H₂O(l) <--> H⁺(aq) + OH⁻(aq) The equilibrium expression is: Kw= [H3O⁺][OH⁻] or Kw=[H⁺][OH⁻], where Kw= 1x10⁻¹⁴ at 25C At standard conditions, pure water dissociates to achieve [H+]= 10⁻⁷ M and [OH-]= 10⁻⁷ M. So, Kw = [H+][OH-] = (10⁻⁷)(10⁻⁷) = 10⁻¹⁴ (acid/base equilibria)

If you dissolve NH₄Cl in water, what happens?

Ammonium chloride is an acidic salt. It is the salt of a weak base (formed from a WB + SA) It will break into NH₄⁺ and Cl- in water. NH₄⁺ is a stronger acid than water (is not a group I or group II cation) Cl- will not react w water As a result, the solution of this salt will be acidic, and have a pH < 7. NH₄⁺ + H₂O <--> NH₃ + H₃O⁺ (acid/base equilibria)

AA's are _____, meaning they have both acidic (carboxylic acid) and basic (amine) groups present.

Amphoteric *remember, the carboxylic acid group has a pKa= 2, while the amino group has a pKa= 9 *amphoteric= compound that can act as both an acid and base; amphipathic= polar and nonpolar regions; zwitterion= both + and - charged regions (amino acids, peptides, proteins)

Describe Henry's Law with carbonated soft drinks:

An everyday example of Henry's Law is given by one's experience with carbonated soft drinks, which contain dissolved carbon dioxide. Before opening, the gas above the drink in its container is almost pure carbon dioxide, at a pressure higher than atmospheric pressure. After the bottle is opened, this gas escapes, moving the partial pressure of carbon dioxide above the liquid to be much lower, resulting in degassing as the dissolved carbon dioxide comes out of solution. (solubility)

How does the shape of an unsaturated fatty acid differ from that of a saturated fatty acid?

An unsaturated fatty acid is bent, or "kinked," at the cis double bond (lipids)

What is a state function?

Another word for a scalar quantity. Path independent. Only care about point A → point B. Do not care about path taken. -scalar quantities: have only magnitude, no direction. Includes length, time, mass, area, volume, speed, density, pressure, temperature, energy, entropy, work, power *includes ∆H (enthalpy), ∆S (entropy), ∆G (free-energy change), ∆U (internal energy change) -vector quantities/not-state functions: have both magnitude and direction. Includes displacement, velocity, acceleration, force, momentum, lift, drag, weight (thermodynamics)

List the following compounds by increasing pKa: I)H₂SO₄ II)NH₃ III)CH3CH2COOH IV)HF A) I < III < II < IV B) I < IV < III < II C) III < I < IV < II D) II < III < IV < I

Answer: B H2SO4 < HF < CH3CH2COOH < NH3 H2SO4 is a strong acid, thus it will have the lowest pKa NH3 is a weak base, thus it will have the largest pKa HF and CH3CH2COOH fall somewhere in the middle. HF is a weak acid, so it will have a lower pKa than CH3CH2COOH (titration)

Which of the following compounds is least acidic? A)CH3COOH, acetic acid (pKa=5) B)H2CO3, carbonic acid (pKa=6) C)H3PO4, phosphoric acid (pKa=2) D)HCO₃⁻, bicarbonate (pKa=10)

Answer: D Highest pKa=least acidic (acid/base equilibria)

Why is ATP know as a "high energy" structure at neutral pH? A) It exhibits a large decrease in free energy when it undergoes hydrolytic reactions B) The phosphate ion released from ATP hydrolysis is very reactive C) It causes cellular processes to proceed at faster rates D) Adenine is the best energy storage molecule of all the nitrogenous bases

Answer= A (nucleotides and nucleic acids)

During adiabatic compression of a gas the temperature: A)increases bc no heat is transferred B)remains constant bc heat is transferred C)remains constant bc no heat is transferred D)decreases bc heat is transferred

Answer= A (thermodynamics)

For the endothermic reaction 2CO2(g) → 2CO(g) + O2(g), which of the following is true? A)ΔH is positive and ΔS is positive B)ΔH is positive and ΔS is negative C)ΔH is negative and ΔS is positive D)ΔH is negative and ΔS is negative

Answer= A (thermodynamics)

The pH of a CH3COOH solution is <7 bc when this compound is added to water A) CH3COOH donates H+, making [H+]>[OH-] B) CH3COOH loses OH-, making [H+]<[OH] C) CH3COOH dissociation increases [H+], thereby increasing Kw

Answer= A CH3COOH donates H+, making [H+] > [OH-] *answer C is not correct bc the only thing that changes Kw or any equil constant is temperature (titration)

Which of the following best describes the strength of the peptide bond in a protein? A)the steric bulk of the R groups prevents nucleophilic attack at the carbonyl carbon B)the e- pair on the nitrogen atom is delocalized by orbital overlap w the carbonyl group C)peptide bonds are never exposed to the exterior or a protein D)the peptide bond is resistant to hydrolysis by many biological molecules

Answer= B (amino acids, peptides, proteins)

Which of the following fatty acids has the highest melting point? A) 4,5-dimethylhexanoic acid B) octanoic acid C) 2,3-dimethylbutanoic acid D) hexanoic acid

Answer= B *these are all fatty acids (hence, they have a carboxylic acid group). Two points to consider in the mp of fatty acids, 1) higher MW=higher melting point, 2)less branching= higher melting point. *choice A and B both have 8 carbons, while choice C and D each have 6 carbons. Eliminate choice C and D since they have a lower MW *choice A is branched, while choice B is not. Less branching= higher melting point. So, the answer is B (lipids)

Which of the following terms best describes the interconversion between α-D-glucose and β-D-glucose? A) tautomerism B) nucleophilic addition C) mutarotation D) elimination

Answer= C (carbohydrates)

The value of the solubility product for copper(I) chloride is Ksp= 1.2x10⁻⁶. Under normal conditions, the maximum concentration of an aqueous CuCl solution will be: A)less than 10⁻⁶ M B)greater than 10⁻⁶ M and less than 10⁻⁴ M C)greater than 10⁻⁴ M and less than 10⁻² M D)greater than 10⁻² M and less than 10⁻¹ M

Answer= C *the equilibrium is CuCl(s) <--> Cu+(aq) + Cl-(aq). If we let x stand for the number of moles of CuCl that have dissolved per liter of saturated solution (which is what we're trying to find), then [Cu²⁺]= x and [Cl-]= x. Substituting these into the solubility product expression gives us: Ksp= [Cu²⁺][Cl-] → Ksp=(x)(x) → Ksp=x² → 1.2x10⁻⁶=x² → √1.2x10⁻⁶ = x → 1x10⁻³ = x. So, the answer is C. Note: here I got the square root of 1.2x10⁻⁶ by raising it to the ½ power. When you raise a power to a power, you just multiply the powers; (-6)(½) = -3 (solubility)

A dipeptide is synthesized w the sequence Asp-Glu. The aspartic acid residue has an observed pKa of 2.1 for its side chain. In free glutamic acid, the side chain has an expected pKa of 2.15. However, in this dipeptide, it is likely that the observed pKa of the glutamic acid side chain will be: A) higher due to a favorable ionic interaction between the deprotonated side chains B) lower due to a favorable ionic interaction between the deprotonated side chains C) higher due to an unfavorable ionic interaction between the deprotonated side chains D) lower due to an unfavorable ionic interaction between the deprotonated side chains

Answer= C *this is a 2x2 question. First, is the ionic interaction between glutamic acid and aspartic acid favorable or unfavorable? It is unfavorable bc both side chains have negative charges, and two negatives repel each other. Eliminate answers A and B. If glutamic acid had a slightly higher pKa, it would be harder to deprotonate it. The repulsion can be avoided somewhat since the group will be deprotonated only at higher pH, and therefore a narrower range of conditions. (amino acids, peptides, proteins)

A graph depicting a titration of a weak acid w a strong base will start at a A) high pH and slope downwards w an equivalence pH below 7 B) low pH and slope upwards w an equivalence pH equal to 7 C) low pH and slope upwards w an equivalence pH above 7

Answer= C Low pH and slope upwards w an equivalence pH above 7 (titration)

Which of the following best describes the secondary structure of a protein? A) various folded polypeptide chains joining together to form a larger unit B) the AA sequence of the chain C) the polypeptide chain folding upon itself due to hydrophobic/hydrophilic interactions D) peptide bonds H-bonding to one another to create a sheet-like structure

Answer= D (amino acids, peptides, proteins)

Which of the following may be considered an example of tertiary protein structure? I) van der Waals interactions between two Phe R-groups located far apart on a polypeptide II) Hydrogen bonds between cysteine residues located far apart on a polypeptide III) Covalent disulfide bonds between cysteine residues located far apart on a polypeptide

Answer= I and III (amino acids, peptides, proteins)

Which of the following AA's is most likely to be found on the exterior of a protein at pH 7? A)leucine B)alanine C)serine D)isoleucine

Answer= Serine *this is the only polar AA listed here (amino acids, peptides, proteins)

Which of these AA's is most likely to be found on the interior of a protein at pH 7? A)alanine B)glutamic acid C)phenylalanine D)glycine

Answer= phenylalanine *alanine's R group is just a methyl *glycine's R group is just a H *at pH of 7, glutamic acid has a charge of -1 (bc carboxylic acid R group has a pKa of 4). Charged things are polar, and would not want to be on the interior of a protein. *phenylalanine has the largest hydrophobic group here, and is therefore more likely to be found on the interior of a protein (amino acids, peptides, proteins)

Suppose you want to raise the temperature of an ideal gas while adding the lowest possible amount of heat and doing no work on the gas. Which process should you use? A)isobaric B)isochoric C)isothermal D)adiabatic

Answer=B (thermodynamics)

Which of the following processes would have a negative ΔS A)the evaporation of a liquid B)the freezing of a liquid C)the melting of a solid D)the sublimation of a solid

Answer=B Liquid → Solid results in a decrease in entropy (thermodynamics)

Which of the following substances does NOT have a heat of formation equal to zero at standard conditions? A)F2(g) B)Cl2(g) C)Br2(g) D)I2(s)

Answer=C Heat of formation, H°f, is zero for a pure element in its natural phase at standard conditions. ALl of the choices are in their standard state, except for bromine, which is a liquid, not a gas, at standard conditions. (thermodynamics)

All of the following are amphoteric, except: A)HCO₃⁻ B)H₂PO₄⁻ C)SO₄²⁻ D)HOOCCOO-

Answer=C. HCO₃⁻, H₂PO₄⁻, and HOOCCOO- can all donate or accept a proton. SO₄²⁻ can accept a proton (basic), but it has no protons to donate, thus it is not acidic. And it can't be amphoteric (titration)

What is an allylic atom?

Anything termed "Allylic" is just the atom that is adjacent to a 𝞹 bond (stereochemistry of covalently bonded molecules)

Basicity vs nucleophilicity:

Basicity= nucleophile donates an electron pair to H+ Nucleophilicity= nucleophile donates an electron pair to any atom other than H+ (usually C) **Trend differences: going down a column on the periodic table, nucleophilicity increases, while basicity decreases. For ex, I- has high nucleophilicity but has low basicity. So, I- can easily donate an e- pair to C, but cannot donate an e- pair to H+ very well. This is bc I- is so large that it cannot find and donate electrons to a tiny little H+. (stereochemistry of covalently bonded molecules)

Why do micelles form?

Because the tails of fatty acids are very hydrophobic and therefore, repelled by water, they aggregate into spheres called micelles.

Buffering system of blood:

Bicarbonate buffer system! Maintaining a constant blood pH is critical. The buffer system that maintains the pH of human blood consists of carbonic acid (H₂CO₃) and its conjugate base, bicarbonate (HCO₃⁻). *When any acidic substance enters the bloodstream, the bicarbonate ions neutralize the hydronium ions forming carbonic acid and water. Thus hydronium ions are removed, preventing the pH of blood from becoming acidic. HCO₃⁻ + H₃O⁺ → H₂CO₃ + H2O *On the other hand, when a basic substance enters the bloodstream, carbonic acid reacts with the hydroxide ions producing bicarbonate ions and water. In this manner, the hydroxide ions are removed from blood, preventing the pH of blood from becoming basic. H₂CO₃ + OH- → HCO₃⁻ + H2O (acid/base equilibria)

In a 1M aqueous solution of boric acid (H3BO3, Ka=5.8x10⁻¹⁰), which of the following species will be present in solution in the greatest quantity? A) H₃BO₃ B) H₂BO₃⁻ C)HBO₃²⁻ D)H₃O⁺

Boric acid is a weak acid (it's not on our list of strong acids), so the equil lies to the left. Also notice how small the Ka value is. They'll be very few H₃O⁺ or H₂BO₃⁻ ions in solution but plenty of undissociated H₃BO₃. Answer=A (acid/base equilibria)

Phenolphthalein vs methyl orange:

Both are types of indicators. *Phenolphthalein has a pKa=9, so it should be used with solutions who have pH values around 9. For ex, when added to a solution whose pH is less than 8, it remains colorless. However, if the solution's pH is above 10, it will turn a deep magenta. Thus, phenolphthalein can be used to differentiate between a solution whose pH is 8 vs one whose pH is 10. *However, the indicator methyl orange could not distinguish between two such solutions. It would be yellow at pH 8 and yellow at pH 10. Methyl orange has a pKa=4, so it changes color around pH=4. *when the pH > pKa of the indicator, it will change color (will become deprotonated) Note: thymol blue and bromocesol green are other indicators (they are polyprotic indicators; can change color more than once) (titration)

Are the two common synthetic techniques to produce amino acids stereo- or non-stereospecific?

Both the Strecker and Gabriel-malonic ester synthesis are non-stereoselective. The Strecker synthesis involves a nucleophilic addition reaction that has a planar starting material, which lead to racemization. The Gabriel-malonic ester synthesis has two identical ester groups that can be converted to the acid group so this leads to a non-stereoselective result as well.

What is a strong acid?

Bronsted-acids can be placed into two big categories, strong and weak. Whether an acid is strong or weak depends on how completely it ionizes in water. Strong acids dissociate completely in water. They have an acid ionization (also called acid dissociation) constant, Ka>1 acids dissociation in water has the form, HA + H₂O <--> H₃O+ + A- Ka= [H3O⁺] [A-] / [HA] If Ka > 1 then products are favored, and the acid is strong *ex, HCl + H2O → H3O⁺ + Cl- If Ka <1 then reactants are favored, and the acid is weak *ex, HF + H2O <--> H3O+ + F- *the larger the Ka value, the stronger the acid; the smaller the Ka value, the weaker the acid *notice that the term Ka is used, not Keq (however, both denote reactions at equil) *if you ever have an equilibrium arrow, you are dealing with a weak acid. You know this bc the reaction is never going to completion. If the acid did completely dissociate (go to completion), it would be a strong acid, thus it would not be at equil and would not have equil arrows. The same is true for bases (acid/base equilibria)

What is a strong base?

Bronsted-bases can be placed into two big categories, strong and weak. Whether a base is strong or weak depends on how completely it ionizes in water. Strong bases dissociate completely in water. They have a base ionization (also called base dissociation) constant, Kb>1 base dissociation in water has the form, B + H2O <--> HB+ + OH- Kb= [HB+] [OH-] / [B] If Kb > 1 then products are favored, and the base is strong If Ka <1 then reactants are favored, and the base is weak *the larger the Kb value, the stronger the base; the smaller the Kb value, the weaker the base *notice that the term Kb is used, not Keq (however, both denote reactions at equil) *if you ever have an equilibrium arrow, you are dealing with a weak base. You know this bc the reaction is never going to completion. If the base did completely dissociate (go to completion), it would be a strong base, thus it would not be at equil and would not have equil arrows. The same is true for acids (acid/base equilibria)

At the beginning of a titration, the solution is behaving as a ______.

Buffer. For ex, if titrating w HF, it is being converted into F-. So, you are forming a solution that contains a weak acid and its conjugate base, (which is a buffer!). *the point of inflection (half equivalence point) is at pH=pKa (or 14-pKb); here, products and reactants of solution are in a 1:1 ratio. *the area around this point is the region where the solution has buffering capacity. The pH of this buffering region is typically pKa +/- 1 (or 14 - pKb +/- 1) Point of inflection: another word for the half-equivalence point on an acid-base titration. At this point: -the [acid]=[conjugate base] or [base]=[conjugate acid] -the pH=pKa -the [titrant] = ½ [weak acid or base] (titration)

How is the pH of a buffered solution calculated?

By using the Henderson-Hasselbalch equation. The pH of the buffer is close to the pKa of the weak acid used, and the exact pH can be determined by taking the ratio of the conjugate base to acid into consideration

Acetic acid:

CH3COOH Weak acid *has a carboxylic acid functional group

Acetic acid will dissociate _____ in a solution containing sodium acetate salt.

CH3COOH, acetic acid, (a weak acid), will dissociate LESS in a solution containing Na(CH3COO), sodium acetate (a basic salt). This is due to Le Chatelier's principle. Since you are increasing the concentration of CH3COO-, the equilibrium position will shift to the left, forming more CH3COOH. CH3COOH <--> CH3COO- + H+ The salt will increase the CH3COO- concentration. Thus, equil will shift to the left. So, less H+ will be present, and pH will increase (become less acidic) This is called the COMMON ION EFFECT. Here, CH3COO- is the common ion. (acid/base equilibria)

What is more basic, CH₃NH₂ or CH₃OH?

CH₃NH₂. The only difference is N and O. Since these two are in the same row, look for less electronegative element (acid/base equilibria)

Cyanide:

CN- (ions in solution)

Carbohydrates can be broken down to ____ via oxidation.

CO2 *this is known as burning or combustion *carbohydrates serve as the principal energy source for cellular metabolism (carbohydrates)

Carbonate:

CO₃²⁻ (ions in solution)

Calcium hydroxide

Ca(OH)₂ Strong base, complete dissociation in water, Kb >1

Acidic AA's:

Can donate a H+ and thus become negatively charged 1) aspartic acid (D) 2) glutamic acid (E) *these are all hydrophilic *A Good Lawyer Aims High (acid/base equilibria)

What three things must be considered to determine whether a reaction will happen, or be spontaneous?

Change in enthalpy, change in entropy, and temperature.

State the three ways to disturb or stress a chemical equilibrium

Change the concentration(s) of reactants/products; change the temperature; or change the volume of the container, thereby changing the pressure

Many proteins fold spontaneously, however some require the assistance of _______.

Chaperone proteins (amino acids, peptides, proteins)

Why do we draw Fischer projections? What do horizontal lines vs vertical lines represent?

Chemists draw chiral molecules in their Fischer projections to illustrate stereochemistry. The conformation of a molecule that is shown in a Fischer projection is the least stable, fully eclipsed form. Horizontal lines= projecting from the plane of the page toward the viewer. Vertical lines= projecting into the plane of the page, away from the viewer (amino acids, peptides, proteins)

The α-carbon of each of the twenty AA's is ________.

Chiral; a stereocenter EXCEPT FOR GLYCINE. It's α-carbon is not chiral (bound to two H's) (amino acids, peptides, proteins)

Chloride:

Cl- (ions in solution)

Hypochlorite:

ClO- (ions in solution)

Chlorite:

ClO₂⁻ (ions in solution)

Chlorate:

ClO₃⁻ (ions in solution)

Perchlorate:

ClO₄⁻ (ions in solution)

What does the term "strong" mean in relation to an acid/base/electrolyte? What about the term weak?

Complete dissociation, K>1 Partial dissociation, K<1 All soluble salts are strong electrolytes, as are strong acids and strong bases. Weak acids and weak bases are weak electrolytes (do not completely dissociate)

What three properties affect the rate of a reaction?

Concentration (or, for gases, partial pressure), temperature, and activation energy

State and describe the three methods of heat transfer.

Conduction: heat is transferred through contact. Convection: heat is transferred by moving masses of fluid. Radiation: heat is transferred by the emission and absorption of electromagnetic waves or photons.

The value of Keq for a given reaction is a _____ at a given temperature.

Constant. The only thing that can change K is temperature! (solubility)

Explain how to convert a Fischer projection to pyranose Haworth and to chair.

Converting an open chain hexose Fischer projection to a cyclic pyranose Haworth= -The OH on carbon 5 attacks the anomeric carbon (carbonyl carbon) -Draw 6 membered ring structure with O in ring. Number in a clockwise fashion -The OH's on RIGHT side in Fischer goes DOWN in Haworth -The OH's on LEFT side in Fischer go UP in Haworth *positions 2, 3, and 4 on Haworth are easy to draw *position 5 on Haworth, if its a D sugar, CH2OH points up. If its an L sugar, CH2OH points down *position 1 on Haworth (the anomeric carbon) can be either alpha (down) or beta (up). Since the carbonyl carbon is sp2 hybridized, if its attacked from one side its alpha; if its attacked from the other side its beta. You cannot determine this, question will have to tell you if alpha or beta. Converting to the chair= -draw chair conformation, with O in chair. Number in a clockwise fashion -The OH's on RIGHT side in Fischer goes DOWN in Haworth -The OH's on LEFT side go UP in Fischer -pay attention to equatorial vs axial (carbohydrates)

What are the relative strength of the diff types of bonds?

Covalent > metallic ~ coordinate covalent *only intramolecular forces form bonds (bonding)

Chromate:

CrO₄²⁻ (ions in solution)

Dichromate:

Cr₂O₇²⁻ (ions in solution)

Hemiacetal sugars exist in equilibrium between the straight chain form and cyclic form, but the equilibrium favors the _______.

Cyclic form. *Cyclic ring structures predominate under normal physiological conditions bc they are lower in energy (thermodynamically favorable), and more stable than their open-chain counterparts. (carbohydrates)

Disaccharides and polysaccharides are broken down into their component monosaccharides by ______.

Enzymatic hydrolysis; the addition of water *hydrolysis of polysaccharides to monosaccharides if favored thermodynamically (energy is released; exothermic). However, it does not occur at a significant rate without enzymatic catalysis. Enzymes increase reaction rate by lowering the activation energy, but do not change the final concentrations of reactants and products. Glycoside + H2O + catalyst → hydrolysis Common catalysts include: amylase for starch and glycosylase for nucleotides. (carbohydrates)

When a reaction is at equilibrium, forward and reverse rates are _____.

Equal. Constant cycling (solubility)

Equilibrium constant Reaction quotient Solubility product Ion product

Equilibrium constant, K Reaction quotient, Q Solubility product, Ksp Ion product, Qsp

FLIP CARD FOR Q Two molecules are enantiomers if they are stereoisomers that are nonsuperimposable mirror images of each other. Here, molecules I and II are enantiomers, as are III and IV. Diasteromers are stereoisomers that are not enantiomers. Thus, each of the following pairs are diastereomeric pairs: I and III, I and IV, II and III, II and IV.

Explain the difference between enantiomers and diasteromers using this drawing

Of the following, which statement best explains why HF is a weak acid, but HCl, HBr, and HI are strong acids? A) F has a greater ionization energy than Cl, Br, or I B) F has a larger radius than Cl, Br, or I C) F- has a larger radius than Cl-, Br-, I- D) F- has a smaller radius than Cl-,Br-, I-

F is smaller than Cl, Br, or I, so eliminate choices B and C. Ionization energy is associated with forming a cation from a neutral atom, and has no bearing here. Answer=D *the more stable an acids conjugate base is, the stronger the acid. Larger anions are better able to spread their negative charge, making them more stable. HF is the weakest of the H-X acids bc it has the least stable conjugate base due to its size (acid/base equilibria)

Fat-Soluble vitamins:

Fat soluble vitamins are absorbed with dietary fat and stored in adipose tissue and in the liver. The four fat soluble vitamins are vitamins A, D, E, and K. All of them have ring structures Vitamin A: Carotene, vision. Vitamin A is a terpenoid. Vitamin D: Cholecalciferol, bone formation. Vitamin D is derived from cholesterol. Vitamin E: A group of compounds, called Tocopherols (methylated phenols). Important antioxidants. Vitamin K: An important coenzyme in the activation of prothrombin, a clotting factor. (lipids)

Fatty acids:

Fatty acid = hydrocarbon chain + carboxylic acid -fatty acids are synthesized two carbons at a time from acetate. Only even numbered fatty acids are made in human cells -fatty acids can be saturated (solids at room temp) or unsaturated (liquids at room temp) *unsaturated fatty acids have one or more double bonds in the hydrocarbon tail. These double bonds are almost always cis/Z. Cis bonds make the chain kinked/bent. The position of the double bond is denoted by the symbol ∆ with the number of the first carbon involved in the double bond (for ex, a Z double bond between carbons 3 and 4 in a fatty acid would be referred to as (Z)-∆^3 or cis-∆^3) -in solution, free fatty acids interact to form micelles (lipids)

Electrostatic energy in ionic bonds:

Felectrostatic= k |q₁q₂| //r^2, where r is the distance between the charged species and k is Coulomb's constant, 9x10⁹ N m²/C² *if q1 doubles (or q2 doubles), the electrostatic force doubles. They are proportional to each other *if r halves, the electrostatic force increases by a factor of 2² = 4 *ions that form ionic bonds have high charge density, that is, the charge to size ratio is high (high charge, small size) (bonding)

What is more acidic, Fe³⁺ or Fe²⁺?

Fe³⁺ bc it has a larger positive charge (acid/base equilibria)

State the first law of thermodynamics. Define internal energy and work. What are the sign conventions of heat and work?

First law: ∆E=Q+W. Internal energy is the thermal or kinetic energy of a system and is a function of temperature. W is the work done by the system; if a gas expands, W is positive; if a gas is compressed, W is negative. If heat is added to the system, Q is positive; if heat is removed from the system, Q is negative.

Formal charge:

Formal charge = valence electrons - sticks - dots formal charges other than 0 must be labeled next to the atom w the formal charge common formal charges: *oxygen w only a single bond: -1 *oxygen w no bonds but has an octet: -2 (why oxygen usually exists as the diatomic O₂ and has a double bond to themselves) *carbon w only 3 bonds: either +1 is carbocation or -1 is carbanion *nitrogen w 4 bonds: +1 *halogen w no bonds but have an octet: -1 (why halogens usually exist as a diatomic and have a single bond to themselves, such as Cl₂) *boron w 4 bonds: -1, for ex BH₄⁻ (bonding)

What types of substances are included in an equilibrium constant (K) expression, and what types of substances are excluded?

Gases and aqueous species are always included. Pure liquids and solids are not part of the K expression.

What is another name for geometric isomers

Geometric isomers are a type of diastereomer. They can also be referred to as cis/trans isomers about a double bond or ring

Maltose is a disaccharide composed of ____ and _____. Is maltose a reducing sugar?

Glucose + Glucose *pyranose + pyranose Maltose is a reducing sugar *It has 1-4-glycosidic linkages. The linkage consists of one acetal and one hemiacetal. Hemiacetal sugars in solution exist in equilibrium between the straight/open chain form and cyclic form. When in the straight chain form, the aldehyde can be oxidized to a carboxylic acid. Maltose is called a reducing sugar bc it is able to act as a reducing agent, while itself being oxidized. (carbohydrates)

What is a glycosidic linkage?

Glycosidic/acetal linkage= linkage involving the hydroxyl group of the anomeric carbon *occurs by a dehydration/condensation reaction (loss of water) *glycosidic linkage can also mean the linkage between the sugar and the base in nucleotides (carbohydrates)

When H binds something more electronegative than C, it has what oxidation state? What happens when it binds something less electronegative than C?

H bonded to something more EN than C (so H bond to FONClBrISC), will have a +1 oxidation state and when put in solution will become H+ For ex, HCl→Cl- + H+ *H with a + charge is an acid When H is bond to something less EN than C, (like a metal hydride) it will have a -1 oxidation state and when put in solution will become H- For ex, NaH →Na+ + H- *H w a - charge is a base

Describe H+ in water

H+ never exists as a proton in water. It is always present as the hydronium ion, H3O+ (ions in solution)

What is the chemical structure for hydrogen peroxide?

H2O2

What is more acidic, H2S or H2O?

H2S. Since S and O are in the same column, look for one with a bigger radii (acid/base equilibria)

Hydrobromic acid

HBr Strong acid, complete dissociation in water, Ka>1

Hydrocyanic acid

HCN Weak acid Note: Cyanide, CN, is a poison that stops the mitochondrial e- transport chain. Cyanide can be present as hydrocyanic acid (hydrogen cyanide), HCN, the gaseous form of cyanide

Which of the following compounds could be added to a solution of HCN to create a buffer? A)HNO₃ B)CaCl₂ C)NaCN D)KOH

HCN is a weak acid, so look for a salt of its conjugate base, CN-. Here, NaCN is such a salt. Answer=C (acid/base equilibria)

Formic acid:

HCOOH Weak acid *has a carboxylic acid functional group

Hydrogen Carbonate (Bicarbonate):

HCO₃⁻ (ions in solution)

Hydrochloric acid

HCl Strong acid, complete dissociation in water, Ka>1

What is more acidic, H₂S or HCl?

HCl. Since Cl and S are in the same row, look for most electronegative element. (acid/base equilibria)

Perchloric acid

HClO₄ Strong acid, complete dissociation in water, Ka>1

Hydrofluoric acid

HF Weak acid Hydrofluoric acid is classified as a weak acid because of its lower dissociation constant compared to the strong acids. It ionizes in aqueous solutions in a similar fashion to other common acids: HF + H2O ⇌ H3O+ + F−

Hydroiodic acid

HI Strong acid, complete dissociation in water, Ka>1

Nitric acid

HNO₃ Strong acid, complete dissociation in water, Ka>1

Hydrogen Phosphate:

HPO₄²⁻ (ions in solution)

Hydrogen Sulfate (Bisulfate):

HSO₄⁻ (ions in solution)

Define heat and temperature. How are they related? In what unit are they measured?

Heat is the transfer of thermal (internal) energy between a system and its environment. It is measured in joules (J). Temperature is a measure of the average kinetic energy of the molecules in a system. It is measured in kelvin (K).

The mathematical formula that describes the relationship between pH, pKa, and the position of equilibrium in an acid-base reaction is known as the _______.

Henderson-Hasselbalch equation pH = pKa + log [base]/[acid] (amino acids, peptides, proteins)

Electron geometry/orbital geometry:

Hybrid orbitals are produced by hybridizing (mixing) e- orbitals to produce geometries that facilitate bonding. The sets of e-'s determine the hybridization. *2 groups = sp = linear in geometry. A hybrid between one s w one p orbital. *3 groups = sp² = trigonal planar in geometry. A hybrid between one s w 2 p orbitals. *4 groups = sp³ = tetrahedral in geometry. A hybrid between one s w 3 p orbitals. count each e- group around the central atom in a molecule to determine its geometry. *Ex, O=C=O, here C has two e- groups surrounding it. It's geometry = linear *Ex, NO₂⁻, here N has three e- groups surrounding it. It's geometry = trigonal planar -molecules which are sp³ hybridized, tetrahedral geometry, are NOT CAPABLE OF FORMING RESONANCE STRUCTURES -weird rule: any atom w a lone pair that's adjacent to an sp² will also be sp² to allow for resonance. Ex, AA's in a peptide bond. (bonding)

How does branching in hydrocarbons affect mp and bp?

Hydrocarbons are nonpolar molecules, so LDF's predominate (all intermolecular interactions are collectively referred to as van der Waals forces) Branching tends to inhibit van der Waals forces by reducing the surface area available for intermolecular interactions. Thus, branching tends to reduce intermolecular interactions between molecules, resulting in a lower mp and bp (easier to melt, easier to boil) (separations and purifications)

Hydrolysis of the peptide bond:

Hydrolysis of the amide bond forms a free amine + carboxylic acid. This is thermodynamically favored (negative ∆G), but kinetically slow. There are two common ways to accelerate the reaction rate (1) using strong acids, (2) proteolytic enzymes. -acid hydrolysis is cleaving of a protein into its constituent AA's using a strong acid and heat. This is a non-specific means of cleaving peptide bonds -proteolysis/proteolytic cleavage by a proteolytic enzyme/protease is a specific means of cleaving peptide bonds. Many proteases will cut only after specific AA's. (amino acids, peptides, proteins)

Acids generate ____ in aqueous solutions.

Hydronium (acid/base equilibria)

Bases generate _____ in aqueous solutions.

Hydroxide (acid/base equilibria)

Determine the hybridization of the central atom on: H₂O, SO₂, NH₄⁺, CO₃²⁻

H₂O, the O is sp³ SO₂, the S is sp² NH₄⁺, the N is sp³ CO₃²⁻, the C is sp² (bonding)

Dihydrogen Phosphate:

H₂PO₄⁻ (ions in solution)

Hydrogen sulfide

H₂S Weak acid

Sulfuric acid

H₂SO₄ Strong acid, complete dissociation in water, Ka>1 This is the only diprotic strong acid there is! Can lose two H+

Hydronium:

H₃O⁺ (ions in solution)

Hydronium ion or proton

H₃O⁺ or H⁺ Strong acid, complete dissociation in water, Ka>1 H₃O⁺ --> H+ + H2O

How does the reaction quotient, Q, help determine if a reaction is at equilibrium?

If K=Q, the reaction is at equilibrium. If Q>K, the reaction will proceed in the reverse direction to reach equilibrium If Q<K, the reaction will proceed in the forward direction to reach equilibrium

Lewis structures for elements in the same column of the periodic table are _________.

Lewis structures for elements in the same column of the periodic table are similar to one another. For ex, SULFUR can be substituted for OXYGEN in lewis structures of oxygen (bonding)

Lithium hydroxide

LiOH Strong base, complete dissociation in water, Kb >1

Give two other names for Lewis bases

Ligand, nucleophile, or chelator

A synonym for hydrophobic is ______.

Lipophilic (lipic-loving) (lipids)

A synonym for hydrophilic is ______.

Lipophobic (lipid-fear/hating) (lipids)

Waxes:

Long chain fatty acids esterified to long chain alcohols. They often form waterproof barriers, most notable in plants. Animals use waxes as a protective barrier, (e.g. earwax) (lipids)

Inductive effects frequently alter the reactivity of molecules. Justify the fact that trichloroacetic acid (pKa= 0.6) is a better acid than acetic acid (pKa= 4.8).

Look at the stability of the conjugate base. Trichloroacetate ion is a more stable conjugate base bc the chlorine atoms withdraw e- density. Bc trichloroacetate anion is more stable than acetate anion, trichloroacetic acid is a stronger acid than acetic acid. (stereochemistry of covalently bonded molecules)

Salts of weak bases and strong acids:

MAKES SOLUTION ACIDIC

The pH scale:

Measures the concentration of H+ or H3O+ ions in solution H2O(l) + H2O(l) <--> H3O+(aq) + OH-(aq) Kw = [H+][OH-] = 10⁻¹⁴ *For an acid, pH = -log[H3O+] Acidic: pH lower than 7, neutral: pH = 7, basic: pH higher than 7 *For a base, pOH = -log[OH-] Most basic: pOH lower than 7, neutral: pOH=7, least basic: pOH higher than 7 Neutral solutions have a pH and pOH of 7 For pure water, pH = -log[10^-7] = 7 pH + pOH = 14 Q: How many more H+ ions does does a solution with pH of 4 have than a solution with a PH of 5? The pH scale is a logarithmic one, meaning that each pH unit has 10 times as many hydrogen ions as the unit above it. So, at pH 4, there are 10 times more hydrogen ions than at pH 5 and 100 times more hydrogen ions than at pH 6. (acid/base equilibria)

Permanganate:

MnO₄⁻ (ions in solution)

What is molar solubility?

Molar solubility, S, is the number of moles of a certain salt that will saturate a liter of water. For ex, maybe NaCl has a molar solubility of 10g/L. This means if you put 10g of NaCl into 1L of water, it will cause the water to be saturated w NaCl *questions will usually give you the Ksp for a solid and ask you to find out how much of it can be dissolved in water; that is, you're asked to determine the salt's molar solubility. (solubility)

What is the molecular geometry of H2O?

Molecular geometry is bent (bonding)

What is the molecular geometry of CO2?

Molecular geometry is linear (something w 2 bonds; 180 degrees) (bonding)

What is the molecular geometry of SF₆?

Molecular geometry is octahedral (something w 6 bonds, 90 degrees) (bonding)

What is the molecular geometry of CH₄?

Molecular geometry is tetrahedral (something w 4 bonds; 109.5 degrees) (bonding)

What is the molecular geometry of CO₃²⁻?

Molecular geometry is trigonal planar (something w 3 bonds; 120 degrees) (bonding)

What is the molecular geometry of H₃O⁺?

Molecular geometry is trigonal pyramidal (something w 3 bonds, 1 lone pair; <109.5 degrees) (bonding)

Molecules w _______ have a dipole moment.

Molecules w asymmetrical partial charge distribution have a dipole moment. For ex, H₂O has a dipole moment bc the molecule is bent and the oxygen side of the molecule is slightly negative (bonding)

Molecules w ______ do not have a dipole moment.

Molecules w symmetrical partial charge distribution do not have dipole moments. For ex, CCl₄ does not have a dipole moment bc the partially negative chlorine atoms are arranged in a tetrahedron. The symmetry cancels out their individual dipole moments *individual bonds in CCl₄ polar = yes *entire molecule of CCl₄ polar = no (bonding)

What is a furanose?

Monosaccharides in a 5 membered ring structure = pentagon shaped. For example, fructofuranose= fructose in a 5 membered ring. Fructose (a ketohexose) forms a furanose when the OH on carbon 5 attacks the carbonyl carbon *furanoses are named due to their resemblance to furan Way to remember, Furanose is a Five membered ring (both start w F) (carbohydrates)

What is a pyranose?

Monosaccharides in a 6 membered ring structure = hexagon shaped. For example, glucopyranose= glucose in a 6 membered ring. Glucose (an aldohexose) forms a pyranose when the OH on carbon 5 attacks the carbonyl carbon *pyranoses are named due to their resemblance to pyran (carbohydrates)

What is a monovalent, divalent, and trivalent atom?

Monovalent= wants to make 1 bond, like H, Li, Na or the halogens, F, Cl, Br, I Divalent= wants to make two bonds Trivalent= wants to make three bonds *How many valence electrons an atom wants to gain or lose (stereochemistry of covalently bonded molecules)

Ammonium hydroxide will dissociate _____ in a solution containing ammonium chloride salt.

NH4OH, ammonium hydroxide, (a weak base), will dissociate/give up a H LESS in a solution containing NH4Cl, ammonium chloride, (an acidic salt). This is due to Le Chatelier's principle. Since you are increasing the concentration of NH4, the equilibrium position will shift to the left, forming more NH4OH. NH4OH <--> NH4+ + OH- The salt will increase the NH₄⁺ concentration. Thus, equil will shift to the left. So, less OH- will be present, and pH will decrease (become more acidic). This is called the COMMON ION EFFECT. Here, NH₄⁺ is the common ion. (acid/base equilibria)

Ammonia

NH₃ Weak base NH₃ + H2O <--> NH₄⁺ + OH-

Ammonium hydroxide

NH₄OH Weak base NH₄OH + H2O <--> NH₄⁺ + OH- *note: ammonia=NH3, ammonium=NH₄+

Ammonium:

NH₄⁺ (ions in solution)

Nitrite:

NO₂⁻ (ions in solution)

Nitrate:

NO₃⁻ (ions in solution)

Which base is a better choice to selectively remove a carboxylic acid from a phenol in the organic layer during an extraction, NaHCO₃ or NaOH

NaHCO₃ bc it will deprotonate only the stronger acid (-COOH) leaving the phenol unaffected

Sodium oxide

Na₂O Strong base, complete dissociation in water, Kb >1

A saturated solution is one in which _____.

No more solute will dissolve. At this point, we have reached the molar solubility of the solute for that particular solvent, and the reverse process of dissolution, called precipitation, occurs at the same rate as dissolving. Both the solid form and the dissolved form of the solute are said to be in dynamic equilibrium. (ions in solution)

Is it possible to have a negative Ka or Kb value?

No!

If the activation energy of polysaccharide hydrolysis were so low that no enzyme was required for the reaction to occur, would this make polysaccharides better for energy storage?

No, bc then polysaccharides would hydrolyze spontaneously (they'd be unstable). The high activation energy of polysaccharide hydrolysis allows us to use enzymes as gatekeepers; when we need energy from glucose, we open the gate of glycogen hydrolysis (carbohydrates)

Do ethers form H-bonds w other ethers?

No, bc they do not have a partially positive H (a donor) *remember, ether= R-O-R (bonding)

Is CCl₄ polar?

No. Although it has bond dipoles which are polar (since it connects two atoms of diff EN), the overall net dipole is 0. The dipoles are symmetrically arranged around the central C atom, leaving the molecule as a whole nonpolar w no dipole moment (bonding)

You crash land on Mars w/out any food but notice that Mars is loaded w edible-looking plants. Martian life has evolved w all L-carbohydrates. Can you metabolize carbohydrates from Mars?

No. Enzyme activity depends on three-dimensional shape, and all animal digestive enzymes have active sites specific for substrate carbohydrates w the D configuration. (amino acids, peptides, proteins)

Are D amino acids ever found in proteins?

No. L-amino acids are the most common in nature, and are the type found in proteins. D-amino acids are less common in nature, and are never found in proteins. (amino acids, peptides, proteins)

Enantiomers:

Non-superimposable mirror images. That means ALL chiral centers in one enantiomer is reversed in the other. Opposite absolute configuration at all chiral centers (if one is R, the other is S) *Each enantiomer has optical rotation of equal magnitude, but opposite sign. Racemic mixture= racemate= 50:50 mix of enantiomers = achiral (no optical activity) *all chemical and physical properties of enantiomers are identical *Resolution= the process of separating enantiomers. Bc enantiomers have identical chemical/physical properties, it is very hard to separate them *the drug Thalidomide for pregnant women was present in R and S forms. One form of these enantiomers caused severe birth defects! (stereochemistry of covalently bonded molecules)

Diastereomers:

Non-superimposable, non-mirror images. More than one chiral center. Opposite absolute configuration at some, but not all chiral centers (for ex, (R)-(R) vs (R)-(S) or (R)-(R)-(S)-(R) vs (R)-(R)-(R)-(R)) *diastereomers have unrelated optical activities *all physical properties are different *diastereomers CAN be physically separated (stereochemistry of covalently bonded molecules)

Nonpolar bonding means ______. Polar bonding means _______.

Nonpolar bonding equal e- sharing Polar bonding means unequal e- sharing; the e- density is higher around the more EN element (bonding)

What is more basic, SCH₃⁻ or OCH₃⁻?

OCH₃⁻. The only difference is S and O. Since these two are in the same column, look for element with smallest radii (acid/base equilibria)

Hydroxide:

OH- (ions in solution)

What is the most basic, OH- or H2O?

OH-, bc it has a larger negative charge (acid/base equilibria)

Le Chatelier's Principle:

ONLY LOOKS AT GASES; Does not look at solids, liquids, or aqueous solutions. Le Chatelier's Principle states that a system at equil will try to neutralize any imposed change (or stress) in order to reestablish equil conditions. Stress can be added to a system by: 1) changing the concentration or partial pressure: -increasing [reactants] or increasing partial pressure of reactants= shift right, wants to make more products -decreasing [reactants] or decreasing partial pressure of reactants= shift left, wants to make more reactants -increasing [products] or increasing partial pressure of products= shift left, wants to make more reactants -decreasing [products] or decreasing partial pressure of products= shift right, wants to make more products 2) volume effects: if you JUST increase the pressure of something, it will have no effect. To stress equil conditions, you must change the pressure and change the volume of something. P and V are inversely related. -decreasing the volume of the reaction container will cause the partial pressures of gases to increase. The reaction will shift toward the side w less moles of gas. -increasing the volume of the reaction container will cause the partial pressure of gases to decrease. The reaction will shift toward the side w more moles of gas. *note: if the same number of moles are on each side, then changing the pressure/volume would have no effect. Each side has the same number of moles, so neither is favored. Adding an inert gas: *if you put an inert gas into a constant volume reaction container, neither the partial pressure or the concentration of products or reactants will change. This is bc an inert gas does not participate in any reactions. *if you put an inert gas into a constant pressure container, BUT one w a moveable piston, adding the inert gas will cause the piston to move up, thus increasing the volume. When volume is increased, partial pressure of the gases decreases. Equil is stressed! The reaction will shift toward the side w more moles. 3) changing the temp: -if endothermic, treat heat as a reactant. You can tell its endothermic bc ΔH term will be + -if exothermic, treat heat as a product. You can tell its exothermic bc ΔH term will be - *after you determine if heat should be treated as a reactant or product, write reaction w ΔH term on that side. *if temp is increased, reaction will always shift to side w/out the ΔH term *if temp is decreased, reaction will always shift to side w the ΔH term NOTE: adding a catalyst does not affect equil. A catalyst will only increase the rate of the forward and reverse rxn. Thus, catalysts do not change equil. (solubility)

What is an aqueous solution?

Occurs when a solution has water as the solvent (ions in solution)

Oxide vs peroxide vs superoxide:

Oxides have O²⁻, peroxides have O₂²⁻ , and superoxides/hyperoxides have O₂¹⁻ *Group 1 metals are very reactive with oxygen and must be kept away from oxygen in order to not get oxidized. For ex, if we denote group 1 alkali metals as X, then the oxide, X₂O, can be formed by just limiting the supply of oxygen. With excess oxygen, the alkali metals can form peroxides, X₂O₂, or superoxides, XO₂. Ex, Cl₂O, Cl₂O₂, ClO₂ (acid/base equilibria)

Peroxide:

O₂²⁻ (ions in solution)

Phosphite:

PO₃³⁻ (ions in solution)

Phosphate:

PO₄³⁻ (ions in solution)

Nine essential AA's:

PVT TIM HALL Phenylalanine (F), valine, threonine, tryptophan (W), isoleucine, methionine, histidine, arginine (R), leucine, lysine (K) (amino acids, peptides, proteins)

Explain the planarity of the peptide bond:

Partial double-bond character (carbonyl <--> amide) inhibits rotation around the peptide bond; thus, the four atoms bound to the carbonyl carbon and amide nitrogen form a plane. A polypeptide chain may be considered as a series of planes with two angles of rotation between each plane. (amino acids, peptides, proteins)

_______ link together the DNA and RNA backbone.

PhosphoDIESTER bonds (nucleotides and nucleic acids)

Phospholipids:

Phospholipid = glycerol + 2 fatty acids + phosphate -major component of cell membranes, forms the lipid bilayer; once the bilayer is formed, it is stabilized by Van der Waals forces between the long tails -amphipathic molecules (both polar and nonpolar regions) -phospholipids are detergents (detergents are like soaps, but stronger) -the phosphate groups on phospholipids can be modified with serine, choline, ethanolamine, etc. Two main classes of phospholipid derivatives: 1)Glycerophospholipids include phosphatidylinositol, phosphatidylserine, and phosphatidylcholine 2)Sphingolipids includes sphingomyelin and others (lipids)

Phosphorus vs phosphoric acid vs phosphate vs pyrophosphate:

Phosphorus= on the periodic table, P Phosphoric acid= H3PO4 Phosphate/orthophosphate= phosphoric acid after it becomes oxidized in solution (loses its hydrogens) Pyrophosphate= two phosphate/orthophosphates linked together via an anhydride linkage. Pyrophosphate is the simplest phosphoric acid anhydride (nucleotides and nucleic acids)

Things w a dipole are said to be what?

Polar! (bonding)

Which requires net energy input, polysaccharide synthesis or hydrolysis?

Polysaccharide synthesis requires energy input (endothermic) (carbohydrates)

All monosaccharides will give a ______ result in a Benedict's test bc they contain an aldehyde, ketone, or hemiacetal, and are therefore reducing sugars.

Positive (carbohydrates)

What is a PV diagram?

Pressure vs Volume diagrams depict thermodynamic processes. They are often used when looking at the 1st law of thermodynamics, ∆E=Q+W and W=P∆V. There are four thermodynamic processes commonly represented on a PV diagram: 1)isobaric: constant pressure 2)isochoric: constant volume 3)isothermal: constant temperature 4)adiabatic: no heat exchange -Work done= area under the curve, given by W=P∆V -Putting heat/thermal energy/Q into the system, this heat will either be used to (1) increase the temperature or (2) to move the piston, thus doing work (thermodynamics)

Primary, secondary, tertiary, quaternary carbons:

Primary carbons are attached to one other carbon Secondary carbons are attached to two other carbons Tertiary carbons are attached to three other carbons Quaternary carbons are attached to four other carbons *hydrogen's are ignored (stereochemistry of covalently bonded molecules)

Prostaglandins:

Prostaglandins belong to a group of molecules known as eicosanoids, derived from 20C fatty acids. Prostaglandins have vastly different roles in different tissues. Their roles include: regulating smooth muscle contraction in the uterus, regulating blood vessel diameter, etc. All prostaglandins have the same general structure, including a 5-membered ring. (lipids)

What effect would a molecule that disrupts H-bonding, like urea, have on protein structure?

Putting a protein in a urea solution will disrupt H-bonding, thus disrupting secondary structure by unfolding α-helices and β-sheets. It would not affect primary structure (no change in peptide bonds). Disruption of 2°, 3°, or 4° structure w/out breaking bonds is denaturation. (amino acids, peptides, proteins)

What is the difference between a disulfide bridge involved in quaternary structure and one involved in tertiary structure?

Quantaray disulfides are bonds that form between chains that aren't linked by peptide bonds. Tertiary disulfides are bonds that are formed between residues in the same polypeptide (amino acids, peptides, proteins)

FLIP CARD FOR QUESTION Answer: It is the farthest one from the anomeric carbon, so it is #6 It is a 5-membered ring, so it is a furanose The anomeric OH is up, so its beta It is D-fructose It has three chiral carbons; four chiral carbons when cyclic

Question: A monosaccharide is represented below in Haworth notation. What number is the carbon that the arrow is point toward? Is it a furanose or a pyranose? Is it the alpha or beta-anomer? Is this a D or L sugar? How many chiral carbons does it have? (carbohydrates)

What are two cases in which solutions of molecules with chiral centers show no observed optical rotation?

Racemic mixtures and meso compounds have an optical rotation of 0°

The addition of a catalyst will affect the ____ of a reaction, but will not affect _____ or ____.

Rate Equilibrium (no change in Keq) or Thermodynamics (no change in ∆G, ∆H, or ∆S) (kinetics)

How does the rate of a chemical reaction change with temperature?

Reaction rate always increases w increasing temperature

What does the Benedict's test indicate?

Reducing sugars, or the presence of an aldehyde or ketone (or a hemiacetal)

Energy is _____ when either a gas condenses into a liquid, or when a liquid freezes into a solid.

Released. *the energy released is the same as the energy of the reverse process (thermodynamics)

To what does the term resolution refer?

Resolution refers to the separation of a mixture of two enantiomers

Thiocyanate:

SCN- (ions in solution)

Sulfite:

SO₃²⁻ (ions in solution)

Sulfate:

SO₄²⁻ (ions in solution)

Acidic salts:

Salts that produce acidic solutions when dissolved in water are called acidic salts. To see if a salt is acidic (and when put into solution will lower the pH), check the cation. Any cations that do not have Group I or Group II elements are acidic. For ex, NH4OH and NaOH. Looking at the cation, we see that NH4 is acidic (not a group I or group II cation), and Na is not acidic (it is a group I cation) (acid/base equilibria)

Basic salts:

Salts that produce basic solutions when dissolved in water are called alkali/basic salts. To see if a salt is basic (and when put in solution will raise the pH), check the anion. Any anions that are not Cl-, Br-, or I- are basic. For ex, HF and HBr₂. Looking at the anion, F- is basic (it's not Cl-, Br-, or I-), and Br₂ is not basic. (acid/base equilibria)

State the second law of thermodynamics. Define entropy

Second law: the entropy of a closed system stays the same or increases during any thermodynamic process (e.g. heat cannot be completely converted to work). Entropy is a measure of the disorder of a system.

Explain the difference between structural isomers, conformational isomers, and stereoisomers

Structural isomers are two molecules that have the same molecular formula but different connectivities. Conformational isomers have the same molecular formula but differ in their rotations about single bonds. Stereoisomers have the same molecular formula and connectivities of atoms, but the groups differ in their spatial arrangements in the molecule

Thiosulfate:

S₂O₃²⁻ (ions in solution)

Identify standard state conditions for temperature and pressure.

T=25C P=1atm

Compare temperature vs heat:

Temperature= thermal (internal) energy of an object due kinetic energy of the molecules. It is measured in kelvin (K). Heat (Q)= transfer of thermal (internal) energy between a system and its environment. It is measured in joules (J) Temperature is an intensive property whereas thermal energy is an extensive property. Temperature (like density) does not depend on the amount of a material present, but thermal energy (like mass) does. For ex, imaging a block of stone at a temp of 300K and containing 20,000J of thermal energy. If you split it in half, each half would still be 300K, but each would only contain 10,000J of thermal energy. (thermodynamics)

The prefix deoxy is commonly used in carbohydrate nomenclature to indicate that _____.

The molecule has a H in place of an OH at a certain position Ex, 2'-deoxyribose in DNA vs ribose in RNA (carbohydrates)

What is an imine?

The nitrogen equivalent to a ketone or aldehyde

What does the order of a rate law say about the reaction mechanism?

The number of molecules colliding in the rate-determining step

What is the difference between α and β-anomers?

The orientation of the C-1 hydroxyl of a pyranose determines which anomer it is. If the hydroxyl is down (under the ring), then it is the α-anomer; if it is up (above the ring), then it is the β-anomer.

What is the isoelectric point of an AA?

The pH at which the molecule is neutral (there is no charge); this structure is referred to as the zwitterion. The isoelectric point of each AA is specific to the unique structure of the side-chain -acidic AA's and proteins w lots of acidic side chains have a lower isoelectric point -basic AA's and proteins w lots of basic side chains have a higher isoelectric point (amino acids, peptides, proteins)

What happens to the pH of a buffer when it is diluted? concentrated?

The pH does not change upon the addition or removal of solvent as the relative concentrations of the acid and conjugate base in solution change proportionately, so their ratio does not change

What is the pH scale, and where do acids and bases fall on the scale?

The pH scale measures the relative acidity and basicity of solutions. Neutral solutions have a pH=7. Acidic solutions have a pH<7 and basic solutions have a pH>7

What does it mean for a reaction to be at equilibrium?

The rate of the forward reaction is equal to the rate of the reverse reaction (or the concentrations of reactants and products do not change w respect to time)

Describe the state of a reaction for which ∆G=0

The reaction is at equilibrium.

What is Ksp?

The solubility product constant. The Ksp is simply the Keq for dissolutions. Here, the reactants and products are the undissolved vs dissolved salts. At equil, the solution is saturated. The ions which go into solution is equal to the rate at which they precipitate out of solution *something w a small Ksp means the reactants dominate in a saturated solution at equilibrium; (does not want to dissociate into ions when in solution; wants to remain in solid form) *something with a large Ksp means the products dominate in a saturated solution at equilibrium; (wants to dissociate into ions when in solution) For ex, *AgCl (s) ↔ Ag+ (aq) + Cl- (aq), the Ksp for AgCl = [Ag+][Cl-] *Ag₂SO₄ (s) ↔ 2Ag+ (aq) + SO₄²⁻ (aq), the Ksp for Ag₂SO₄ = [Ag⁺]²[SO₄²⁻] Ksp values are found in a table: *Ksp for AgCl = 1.8 x 10⁻¹⁰ *Ksp for Ag₂SO₄ = 1.2 x 10⁻⁵ (solubility)

The formation of gases, liquids, and solids is dependent on:

The strength of the intermolecular forces! ionic > H-bond > dipole-dipole > london dispersion force (bonding)

What information is needed to predict the pH at the equivalence point of a titration?

The strengths of the acid and base being mixed. At the equivalence point, the pH=7 if a strong acid is mixed w a strong base. It is <7 if a strong acid is mixed w a weak base and >7 if a strong base is mixed w a weak acid

A solution of glucose may contain both furanose and pyranose rings. How can the same sugar exist in both forms?

The structure that forms depends on which OH attacks the carbonyl carbon (C#1). If OH4 attacks the carbonyl, the result will be a five membered ring. If the OH5 attacks, the result will be a six-membered ring. If you actually counted the structures in solution, you'd find more six-membered rings, since these are inherently more stable due to bond angles. (carbohydrates)

Explain how heat can be transferred following the 0th law of thermodynamics:

The zeroth law of thermodynamics says that heat flows from hot objects to cold objects to achieve thermal equilibrium. There are three mechanisms by which this can be achieved: 1) conduction= heat transfer by direct contact. Requires things to touch. For ex, if you touch a hot metal pan, heat is transferred to your hand 2) convection= heat is transferred by moving masses of fluid, (fluids can be liquid or gas). Need the physical flow of matter. For ex, cooling yourself using a fan; or cooking food in a convection oven involves heating gas molecules (a fluid) which gets transferred to your food 3) radiation= Heat is transferred by the emission and absorption of electromagnetic waves or photons. Does not need the physical flow of matter, can occur through a vacuum (thermodynamics)

What does a low Kd value indicate?

There is tons of products. Kd is the reciprocal of Ka. Reactants → Products Ka= [products]/[reactants], a high Ka means there is tons of products Kd=[reactants]/[products], a low Kd means there is tons of products *Recall that the active site on a protein/enzyme binds a substrate. If there is a low Kd value then the enzyme is binding its substrate tightly (making tons of products!). Note: stronger binding does not always mean a more efficient enzyme (if it binds the substrate and doesn't let go, then it can't catalyze a new substrate). (amino acids, peptides, proteins)

A person who is a lactose malabsorber means what?

They are lactose intolerant. Cannot digest lactose bc their bodies do not make the lactase enzyme (carbohydrates)

How are the common ion and the mechanism of a buffer related?

They are the same concept; an application of Le Chatelier's Principle

In ions, why does resonance occur?

To increase stability. In ions, resonance/electron delocalization helps to "distribute" the charge around. (stereochemistry of covalently bonded molecules)

In molecules, why does resonance occur?

To increase stability. In molecules, resonance/electron delocalization occurs in aromatic rings and conjugated double bonds (stereochemistry of covalently bonded molecules)

Triacylglycerol/Triglycerides:

Triacylglycerol = glycerol + 3 fatty acids *triglyceride is composed of three fatty acids esterified to a glycerol molecule -most fats in our diet are triglycerides -triglycerides are stored in adipose/fat cells and function as an energy source. Triglycerides are more efficient energy storage molecules than carbohydrates. Animals use fat to store most of their energy, storing only a small amount as carbohydrates (via glycogen) -Lipases are enzymes that hydrolyze fats -the reverse of triglyceride synthesis is saponification (lipids)

Is it possible to get a pH outside of the 0-14 range?

Yes. this can happen by: (1) adding very high concentrations of a strong acid (adding a strong acid at a concentration >1M). Or (2) changing the temp. The pH scale is based on standard conditions, which is 25C and 1atm. So, if standard conditions change, pH can go outside the 0-14 range (acid/base equilibria)

Basic solution:

[H3O⁺] < [OH-] (acid/base equilibria)

Acidic solution:

[H3O⁺] > [OH-] (acid/base equilibria)

Enzyme-linked immunosorbent assay (ELISA):

a biochemical technique that utilizes antigen-antibody interactions to determine the presence of either: antigens (for ex, proteins or cytokines), or specific antibodies. *For ex, checking for the HIV virus in a pt's serum: -the experimental wells are coated w antibodies that are specific for the target antigen (anti-HIV antibodies) -a sample of serum is added to the wells -the antibodies immobilize the antigen by binding to it (if it's present in the sample) -any unbound proteins remaining in the sample are washed away -an enzyme-linked antibody that also recognizes the target protein (here, HIV) is added to the wells. Anything unbound is washed away. The wells are filled w a solution that changes color in the presence of the enzyme-linked antibody -a color change indicates the target protein was present in the sample; no color change means the protein was absent (separations and purifications)

Solubility:

a chemical property referring to the ability for a given substance, the solute, to dissolve in a solvent. It is measured in terms of the maximum amount of solute dissolved in a solvent at equilibrium. The resulting solution is called a saturated solution. (solubility)

What is a chiral center?

a chiral center is (usually) a carbon atom bearing four different substituents

Amphoteric compound:

a compound that can act as both an acid and a base. For ex, water. H2O + H2O <--> OH- + H3O⁺, this is called the autoionization of water. When water reacts with itself, one water molecule acts as an acid and the other water molecule acts as a base *way to remember: amPHOTeric, take a PHOTO of acid/base stuff. Important topic on the mcat. Amphipathic is just polar and non polar regions.. phospholipids are not that cool.. do not need to take a photo. (acid/base equilibria)

Amphipathic:

a compound with both polar and nonpolar regions. For ex, phospholipids that make up the cell membrane (polar heads + nonpolar tails) (acid/base equilibria)

Zwitterion:

a compound with no overall electrical charge, but contains separate parts which are positively and negatively charged. An example of a zwitterion is an AA. *An amino acid has both a basic amine group and an acidic carboxylic acid group. There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge. (acid/base equilibria)

Which of the following anions CANNOT behave as a lewis base/nucleophile/ligand? A)F- B)OH- C)NO₃⁻ D)BH₄⁻

a lewis base/ligand is a molecule or ion that donates a pair of nonbonding e-'s. So, in order to even be a candidate Leis base/ligand, a molecule must have a pair of nonbonding e-'s in the first place! Here, BH₄⁻ does not have any nonbonding e-'s. So it cannot behave as a lewis base. All the others could behave as lewis bases/ligands. Answer= D (bonding)

Nucleophilicity:

a measure of how "strong" a nucleophile is. The general trends are: 1) nucleophilicity increases as negative charge increases. For ex, NH2^- is more nucleophilic than NH3 2) Across a row in the periodic table nucleophilicity (lone pair donation) C- > N- > O- > F- since increasing electronegativity decreases the lone pair availability. ***This is the same order as for basicity. 3) Within a group in the periodic table, increasing polarization of the nucleophile as you go down a group enhances the ability to form the new C-X bond and increases the nucleophilicity, so I- > Br- > Cl- > F-. The electron density of larger atoms is more readily distorted i.e. polarized, since the electrons are further from the nucleus. ****Note this is the opposite order to basicity (acidity increases down a group) Way to remember: To increase nucleophilicity, move away from F on the periodic table (stereochemistry of covalently bonded molecules)

Racemic mixture:

a mixture which contains equal amounts of both enantiomers. Another name for racemic mixtures is racemate. Racemic mixtures do not rotate polarized light, so they are optically inactive. *resolution= a way to separate enantiomers (R from S) in a racemic mixture (stereochemistry of covalently bonded molecules)

Achiral:

a molecule that can be superimposed on its mirror image, has a plane of symmetry. It is not optically active. (stereochemistry of covalently bonded molecules)

Chiral:

a molecule that cannot be superimposed on its mirror image, has no plane of symmetry *your right and left hand are chiral to each other. They are mirror images. If you flip your right hand to the back side and place on palm of left hand, the two can never be superimposed *to identify a molecule that may be chiral, first locate a chiral center *carbon chiral center will be: 1) sp³ hybridized 2) tetrahedral geometry 3) have 4 different substituents attached to it *chiral center is also called a stereocenter, stereogenic center, or asymmetric center *chiral centers can be assigned an absolute configuration *chiral molecules are optically active *a compound will have a total of 2^# of chiral centers = stereoisomers. If it is meso, you will get less stereoisomers (possibly you will get an odd number of stereoisomers!) (stereochemistry of covalently bonded molecules)

For each of the following chromatographic techniques, name the property or properties that is(are) key to the function of the technique: (a) TLC, (b) GC, (c) SEC, (d) affinity chromatography, and (e) ion exchange chromatography

a) polarity b) polarity and bp c) size d) intermolecular forces e) charge and size

Will adding 5x10⁻⁶ M CaCl₂ precipitate 1x10⁻⁵ M Na₃PO₄? Ca₃(PO₄)₂(s) ⇌ 3Ca²⁺(aq) + 2PO₄³⁻(aq), Ksp= 2x10⁻³³

a)whenever a question gives you their adding/removing something and they give you a concentration, you know that are messing up the equil state; thus, you are calculating Q b)writing the Qsp, you get Qsp= [Ca²⁺]³ [PO₄³⁻]² *never include solids or liquids in K or Q equations c)fill in values given into the equation, Qsp=[5x10⁻⁶]³ [1x10⁻⁵]² d)to make your life easier, round the number in front of power of ten to 1. Here, Qsp=[1x10⁻⁶]³ [1x10⁻⁵]² e)after solving, we get Qsp=1x10⁻²⁸ f)since Qsp > Ksp, it will precipitate out of the solution, so the answer to the question is yes. (solubility)

Water can act as both an ________.

acid and a base! It is amphoteric compound Acid + Base <---> Conjugate base + Conjugate acid H2O + H2O <---> OH- + H3O+ (acid/base equilibria)

Acids:

acids want to accept e- pairs or lose H+ positively charged things want to accept e-'s or lose H+, thus becoming neutral or negatively charged 1)Bronsted Acid= donates a H+ 2)Lewis Acid/Electrophile= accepts an e- pair 3) Arrhenius= produces H3O+ in water (acid/base equilibria)

Name three functional groups that have delocalized electrons

all carbonyl containing groups: ester, amide, carboxylic acid, acid anhydride, acid halide, aldehyde, ketone

Anomers:

epimers that form as a result of ring closure *on the mcat, anomers are looked at when talking about sugar chemistry For ex, linear/open-chain (D-glucose) exists in equilibrium w cyclic glucose (glucopyranose). Cyclization occurs when the C-5 hydroxyl group attacks the carbonyl (C=O) carbon, C-1. This converts a carbon w three substituents to a carbon w four substituents; thus, a new chiral center is formed, (C-1), and it can assume one of two possible forms: -with the hydroxyl up, it is 𝛽 -with the hydroxyl down, it is 𝝰 This 𝛽 and 𝝰 hydroxide position distinguishes the two anomers. *This carbon is known as the anomeric carbon (stereochemistry of covalently bonded molecules)

Isomers:

some molecular formula, different structures; same in writing, different in drawing. Includes: 1) Constitutional isomers 2) Conformational isomers 3) Stereoisomers (enantiomers vs diastereomers; If its an enantiomer, it may be a meso compound; if its a diastereomer, it may be an epimer or geometric isomer; if its an epimer, it may be an anomer) (stereochemistry of covalently bonded molecules)

What is an inert gas?

something that does not participate in any reactions, like Ar or He. The group 8 elements (noble gases). (solubility)

Explain the difference between sp, sp², and sp³ hybridized carbon atoms

sp-hybridized carbon atoms have two groups bonded to them and have a 180° bond angle between those groups. sp²-hybridized carbons have three groups bonded 120° apart. sp³-hybridized carbons have four groups bonded 109.5° apart

Electrophiles:

species that are e- deficient. They often have a full or partial positive charge or an incomplete octet. Since electrophiles are e- pair acceptors, they are also known as lewis acids. When an electrophile accepts a pair of electrons from a nucleophile (a lewis acid/lewis base reaction), a new covalent bond forms between the two species (coordinate covalent bond). *electrophiles= electron loving *electrophilicity is a measure of how strong an electrophile is *the pic shows some common electrophiles (stereochemistry of covalently bonded molecules)

Nucleophiles (Nu-):

species that have unshared pairs of electrons or 𝝅 bonds and, frequently, a full or partial negative charge. Since nucleophiles are e- pair donors, they are also known as Lewis bases. When a nucleophile donates an e- pair, it is said to "attack" the other atom. *nucleophiles= nucleus loving *the pic shows some common nucleophiles (stereochemistry of covalently bonded molecules)

The internal energy for an ideal gas is proportional to its _______.

temperature (thermodynamics)

What are the two common names for the bond linking two amino acid residues together in a protein?

the amide bond or the peptide bond

What is the most stable conformation of methylcyclohexane?

the chair form w an equatorial methyl group

Henry's Law:

the solubility of a gas is proportional to the partial pressure of that gas. If you increase the partial pressure of a gas (by applying force and pushing down a piston, thus decreasing the volume), then solubility of the gas into the solution will increase. So, decreasing volume causes an increase in partial pressure, thus increasing solubility Pressure₁/Pressure₂ = Solubility₁/Solubility₂ P is the partial pressure of the solute at the solution's surface, solubility is the solute concentration in solution. The partial pressure of a solute just above the solution's surface is directly proportional to its concentration. For ex, if partial pressure increases by a factor of 3, then the concentration of solute in solution will also increase by a factor of 3 (solubility)

Thermodynamics:

the study of the relationship between heat, work, and other forms of energy (thermodynamics)

Bond order:

the total number of bonds between adjacent atoms. So, a single bond has a bond order of 1, while a triple bond has a bond order of 3. -The higher the bond order, the shorter and stronger the bond is. For ex, triple bonds are held more tightly than a single bond Bond order in RESONANCE STRUCTURES gets more complicated. It is an average of bond order between the diff resonance structures, so: bond order = total # of bonds in one resonance structure // total # of resonance structures (bonding)

Blotting:

the transfer of DNA or proteins from an electrophoresis gel to a nitrocellulose or PVDF membrane. Once transferred, further experiments can be run to isolate or detect a particular nucleic acid fragment or protein (called "probing"). Blotting is classified by the type of molecule being probed (southern blotting, northern blotting, western blotting). (separations and purifications)

Define conjugate pair

two molecules/ions that differ by one H+

Metallic bonds:

type of covalent bonding which specifically occurs between atoms of metals, in which the valence electrons are free to move through the lattice. -formed between metals + metals, two things w relatively low electronegativity *the diff between electronegativities in the two elements must be small (they must have similar electronegativities) in order for them to equally share their e-'s -e- are delocalized, moving -e- are equally shared, donated from all the atoms -compounds w metallic bonds are conductors and malleable/ductile/soft (moldable) *since the e-'s are moving, they are conductors (can conduct electricity) and malleable (able to be hammered/pressed out of shape). *way to remember, Malleable = Metallic, both start w M (bonding)

Meso compound:

when there is an internal plane of symmetry in a molecule that contains chiral centers, the compound is called a meso compound. Meso compounds are not optically active. They have multiple chiral centers, but are not chiral molecules. This is bc of internal cancelation (the R and S on each plane of symmetry cancels the other out) *notice that on a molecule, at each chiral center, they have the same atoms attached. Just opposite configurations, one is R and one is S. *meso compounds are achiral and optically inactive *meso compounds reduce the total number of stereoisomers (bc they are the same molecule) (stereochemistry of covalently bonded molecules)

The term chemical equilibrium applies to a system:

where individual molecules are still reacting, but there is no net change in the system (solubility)

Gibbs free energy:

ΔG = ΔH - TΔS, Higher temps, higher ΔS, or low ΔH is favorable -ΔG = spontaneous in the forward direction, exergonic rxn, gives off energy; breaking things down +ΔG = non-spontaneous in the forward direction, endergonic rxn, requires energy; building things up ΔG = 0, reaction is at equilibrium -while values of ΔH are usually given in kJ, values of ΔS are usually given in J. When using the equation ΔG = ΔH - TΔS, make sure your ΔH and ΔS are both expressed in the same units -do not assume that an exothermic reaction is spontaneous, bc a large, negative ΔS can cause it to become nonspontaneous -do not assume that an endothermic reaction is nonspontaneous, bc a large, positive ΔS can make it spontaneous -do not assume that spontaneous reactions will occur quickly, bc it may take millions of years for it to happen, depending on its kinetics (thermodynamics)

A gas is observed to undergo condensation. The ΔH is ______ and ΔS is _______.

ΔH is negative and ΔS is negative (thermodynamics)

At equilibrium, what is true of ∆G, rate, and Q?

∆G=0 rateforward=ratereverse Q=Keq

Using the average bond dissociation energies listed below, calculate ∆Hrxn for the combustion of methane, CH4(g) + 2O2(g) → CO2(g) + 2H2O(l) C-H, 413 kJ/mol O-H, 467 kJ/mol C=O, 799 kJ/mol C=N, 615 kJ/mol H-Cl, 427 kJ/mol O=O, 495 kJ/mol

∆Hrxn = ∑ BDE bonds broken - ∑ BDE bonds formed ∆Hrxn= [(4)(413) + (2)(495)] - [(2)(799) + (4)(467)] → -824 kJ/mol *note that all the bond dissociation energies listed here are positive values bc energy input is required to break bonds (thermodynamics)

What is the ∆H° for the following reaction under standard conditions if ∆H°f of CH4(g)= -75 kJ/mol ∆H°f of CO2(g)= -393 kJ/mol ∆H°f of H2O(l)= -286 kJ/mol Reaction: CH4(g) + 2O2(g) → CO2(g) + 2H2O(l)

∆Hrxn= ∑ (n)(∆H°fproducts) - ∑ (n)(∆H°freactants), where n is the number of moles ∆Hrxn= [-393 + (2)(-286)] - [-75 + (2)(0)] → -890 kJ/mol = ∆Hrxn (thermodynamics)

Basic AA's:

can accept a H+ and thus become positively charged 1) Lysine (K) 2) Arginine (R) 3) Histidine (H) *these are all hydrophilic *A Good Lawyer Aims High (acid/base equilibria)

Diprotic acid:

capable of donating 2H⁺ cations. For ex, carbonic acid (H₂CO₃). Since it can donate more than one H⁺, it is considered a polyprotic acid. (acid/base equilibria)

Triprotic acid:

capable of donating 3H⁺ cations. For ex, phosphoric acid (H₃PO₄). Since it can donate more than one H⁺, it is considered a polyprotic acid. (acid/base equilibria)

Polyprotic:

capable of donating more that one H⁺ cation. Can be diprotic, triprotic, etc (acid/base equilibria)

What functional groups can be manipulated in an extraction to alter the solubility of a molecule?

carboxylic acids, phenols (ArOH), and amines

Experimental rate/average reaction rate:

change in the concentration of reactants or products / change in time rate=-∆reactants/∆time or rate=∆products/∆time -this is not a rate law, so include solids, liquids, gases; can look at either reactants or products -if using reactants to calculate rate, you must put a negative in front of ∆reactants. This is bc you are looking at the rate of disappearance of reactants, so your answer will be negative, and you can't have negative rates. -remember, experimental rate/average rate is NOT a rate law! (kinetics)

What is the only way to change the value of the equilibrium constant, K?

change the temperature

Electrophoresis separates amino acids based on what property?

charge

Molecules that form ionic bonds have a high ______.

charge to size ratio. In other words, the factors playing into the strength of an ion's charge density are: the charge of the ion (e.g. 2+ for Mg, 1+ for Na) and the effective volume which that charge acts over, which is where the ionic radius comes in. (bonding)

Least stable cyclohexane conformation:

completely eclipsed (boat conformation), w bulky groups in the axial position (stereochemistry of covalently bonded molecules)

Most stable cyclohexane conformation:

completely staggered (in chair conformation), w bulky groups in the equatorial position (stereochemistry of covalently bonded molecules)

Partial ionic character:

covalent bonds between atoms w dissimilar electronegativities have a partial ionic character. Polar covalent vs nonpolar covalent The more electronegative atom is slightly negative, while the less electronegative atom is slightly positive. Partial ionic character allows dipole-dipole interactions to occur (bonding)

Cysteine vs cystine:

cysteine= side chain containing the thiol group cystine= two cysteines linked together via a disulfide bond (amino acids, peptides, proteins)

Geometric isomers:

diastereomers (same molecular formula, same connectivity), but differ in orientation of substituents around a ring or a double bond *when both sides of the double bond contains the same 2 groups, then cis and trans is used. Cis=same side, trans=opposite sides *when different groups are attached to either size, Z and E is used. Z is when higher priority groups are on the same side, E is when higher priority groups are on opposite sides (highest priority group= highest atomic number) (stereochemistry of covalently bonded molecules)

Epimers:

diastereomers that differ in absolute configuration at ONLY ONE chiral center (only one stereocenter is inverted). All epimers are diastereomers, but not all diastereomers are epimers *In epimers the chiral carbon atoms whose absolute configuration makes the two compounds different are called the epimeric carbons (stereochemistry of covalently bonded molecules)

Monoprotic acid:

donates only one H+, for ex, HCl (acid/base equilibria)

Calculate the DOU for each of the following: 1)C₅H₅Br₃ 2)C₆H₁₂O₆ 3)C₁₀H₁₇NO₂ 4)C₃H₈O

dou= (2n+2) - x / 2 *for C₅H₅Br₃, dou= ((2)(5)+2) - 8/2 → 2 *for C₆H₁₂O₆, dou= ((2)(6)+2) - 12/2 → 1 *for C₁₀H₁₇NO₂, dou= ((2)(10)+2) - 16/2 → 3 *for C₃H₈O, this is saturated. We can see this by: dou=((2)(3)+2)-8 → 0 (stereochemistry of covalently bonded molecules)

π bonds:

double and triple bonds. They make up the second bond in a double bond, and both the second and third bond in a triple bond (bonding)

Inductive effects:

electrons in a 𝜎 bond shift toward the more EN atom. *electronegative substituents WITHDRAW electron density (for ex, O, halogens) *electropositive substituents DONATE electron density (for ex, alkyl group) Note: alkyl substituents are always electron donating (stereochemistry of covalently bonded molecules)

Oxygen vs Oxide

oxygen= O oxide= O²⁻ (bonding)

Rank the following compounds from the most acidic to least acidic: PhOH, p-(NO₂)PhOH, p-(MeO)PhOH, p-(Cl)PhOH, p-(Me)PhOH

p-(NO₂)PhOH > p-(Cl)PhOH > PhOH > p-(Me)PhOH > p-(MeO)PhOH All these structures are p-substituted phenols, so the substituent must be the controlling factor. The effect the substituent exerts on the benzene ring will influence the stability of the phenolate ion. A strong electron withdrawing group will stabilise the phenolate making the phenol more acidic whereas a strong electron donor will destabilise the phenolate making the phenol less acidic. A nitro group is strongly withdrawing due to resonance, a chloro group is weakly electron withdrawing due to inductive effects, a methyl group is a weak electron donor and a methoxy group a strong electron donor. **methoxy groups are always electron donating

How is the pH of a strong acid calculated?

pH=-log[H+], since strong acids completely dissociate

What does pI represent?

pI represents the pH at which the most zwitterion is present

pKa and pKb:

pKa and pKb is the negative log of the Ka and Kb. It gives us easier numbers to look at (instead of negative powers of 10). pKa= -logKa pKb= -logKb Additionally, pKa +pKb =14, if given the pKa of something, you can calculate the pKb of its conjugate base by using this equation (the same is true in the reverse, if given the pKb) *larger Ka = smaller pKa = strong acid *small Ka = large pKa = weak acid *large Kb = small pKb = strong base *small Kb = large pKb = weak base Ex: acetic acid (CH3COOH) has a Ka of 1.75x10⁻⁵, and hypochlorous acid (HClO) has a Ka of 2.9x10⁻⁸. Since Ka of acetic acid > Ka of hypochlorous acid, there will be more molecules of acetic acid than hypochlorous acid (more ions in solution). Acetic acid is a stronger acid than hypochlorous acid. The pKa of acetic acid is 4.8, and the pKa of hypochlorous acid is 7.5. The acid with the lower pKa value is the stronger acid. (acid/base equilibria)

Hydrogen bond acceptor:

partially negative atoms. Includes F: O: N: (bonding)

Hydrogen bond donor:

partially positive H. Includes hydrogens that are bonded to either F, O, or N. (bonding)

Do polar molecules or nonpolar molecules have lower Rf values in a TLC experiment?

polar molecules have lower Rf values

Explain the difference between primary, secondary, tertiary, and quaternary protein structure.

primary= AA sequence secondary= the initial folding of the polypeptide chain stabilized by H-bonding into an α-helix or a β-sheet. tertiary= interactions between AA side chains, stabilized by hydrophobic/hydrophilic interactions quaternary= interaction between polypeptide subunits

Intermolecular forces are the ___________.

relatively weak interactions that take place between molecules (bonding)

Covalent bond:

results when there is a sharing of electrons between two atoms, resulting in the overlap of their e- orbitals -formed between nonmetals + nonmetals, two things w relatively high electronegativity *however, the diff between electronegativities in the two elements must be small (they must have similar electronegativities) in order for them to equally share their e- -e- are localized, not moving -e- are equally shared (donated from both atoms) -compounds with covalent bonds are INSULATORS (dielectric) and RIGID (unable to bend) *way to remember, oRbitals overlap; Rigid covalent bonds can be: 1)polar covalent bonds= if ΔEN > 0 between the two atoms, the bond is polar covalent and e- are not shared equally. The covalent bond has partial ionic character. For ex, C-F is a polar covalent bond. F is more EN than C, so F pulls the shared e-'s closer to it, creating a dipole. F is slightly negative while C is slightly positive 2)nonpolar covalent bonds= if ΔEN ~ 0 between the two atoms, the bond is nonpolar covalent and e- are shared equally. The covalent bond does not have partial ionic character. For ex, F2 is a nonpolar covalent bond. The e-'s are shared equally between the two atoms. No diff in EN, no dipole moment *intramolecular force (bonding)

What is the pKa of the carboxylic acid of an amino acid? What is the pKa of the protonated amino group?

roughly 2 roughly 10

Explain the difference between σ and π bonds

sigma bonds are the result of end-to-end overlap of orbitals and make single bonds. Pi bonds are the result of side-to-side overlap of orbitals and result in double and triple bonds

Sigma bonds:

single bonds. They also make up the 1st bond of double and triple bonds (bonding)

What is a hexose?

A monosaccharide containing 6 carbon atoms *a hexose can be further classified as either an aldose or ketose (carbohydrates)

If pH > pKa, then _____.

In deprotonated form (acid/base equilibria)

If pH < pKa, then _____.

In protonated form (acid/base equilibria)

Steroids:

Includes cholesterol and derivatives -all steroids have three 6C rings + one 5C ring, (it is polycyclic- contains several rings) -steroids are made from the cyclization of squalene, a terpene -cholesterol is the primary steroid hormone precursor. Two examples are testosterone (an androgen; male sex hormone) and estradiol (an estrogen; female sex hormone) *steroids are hydrophobic and diffuse through the lipid bilayer; receptors for steroid hormones are located within cells rather than on the cell surface -cholesterol is the vitamin D precursor -cholesterol is important in maintaining cell-membrane fluidity (at low temps, it increases fluidity; at high temps it decreases fluidity)) -cholesterol is obtained from our diet and synthesized in the liver. It is carried in the blood packaged w fats and proteins into lipoproteins. Low density, LDL: BAD. Moves cholesterol → tissues High density, HDL: GOOD. Moves cholesterol → liver, exits the body -cholesterol is important in making bile salts (one of the main components of bile. Bile is a greenish-yellow fluid made by the liver and stored in our gallbladder.) (lipids)

What is the difference between an intermediate and a transition state?

Intermediates are found at local energy minima along a reaction coordinate while transition states are at local energy maxima along a reaction coordinate. Transition states are the highest energy species in a reaction bc bonds are breaking and forming, so cannot be isolated from a reaction.

If a gas undergoes a series of reversible processes such that the final thermodynamic state is equal to the initial state (i.e. complete cycle), what is true about the relationship between internal energy, work, and heat?

Internal energy, ∆E, depends on temperature. If initial state=final state, then initial temperature=final temperature, so ∆E=0. Since ∆E=Q+W, then Q=W

What are the relative strengths of the diff types of intermolecular forces?

Ionic > H-bond > dipole-dipole > london dispersion force (bonding)

How is the formation of micelles thermodynamically unfavorable?

It is thermodynamically unfavorable bc it increases order (decreasing entropy) *Water forms a solvation shell around micelles (water interacts w the polar carboxylic acid head groups). This solvation shell increases order, thus decreasing entropy, which is unfavorable according to the second law of thermodynamics (lipids)

Why is Kw used rather than Keq?

It is used to emphasize that you are looking at the equilibrium expression for the autoionization of water. (acid/base equilibria)

Why are standard/normal AA's sometimes called α-amino acids?

It simply refers to the fact that there is an α-carbon with an amino group + H + R group attached to it (amino acids, peptides, proteins)

How will a catalyst affect a system that is at equilibrium?

It won't do anything, as a catalyst only helps a reaction get to equilibrium more quickly by increasing the reaction rate.

If a single polypeptide folds once and forms a β-pleated sheet w itself, would this be a parallel or antiparallel β-pleated sheet?

It would be antiparallel bc one participant in the β-pleated sheet would have a C to N direction, while the other would be running N to C. (amino acids, peptides, proteins)

How do you calculate the isoelectric point of an AA?

Just average the pKa's of the functional groups, (pKa1 + pKa2 + ...)/# of functional groups On a molecule of glycine, if the pKa of the amine group is 9.6, and the pKa of the carboxyl group is 2.3, what is the isoelectric point of glycine? (9.6+2.3)/2 → ~6 *here, we don't have to worry about the pKa of the R group bc it is just a H. So, we just average the pKa's of the amine and carboxyl groups. (amino acids, peptides, proteins)

Which of the following is most likely an ionic compound? A)NO B)HI C)ClF D)KBr

KBr (bonding)

Potassium hydroxide

KOH Strong base, complete dissociation in water, Kb >1

Ka and Kb:

Ka (the acid dissociation constant) and Kb (the base dissociation constant) is used to look at acid-base conjugate pairs. At standard conditions (25C and 1atm): H2O(l) + H2O(l) <--> H3O⁺(aq) + OH-(aq) *this is saying if you took H2O (acting as a base) and H2O (acting as an acid), you will form H3O⁺ and OH-. If you write the equilibrium expression for this, you would get K=[H3O+][OH-], you wouldn't include H2O bc it's a liquid. From this, we know that this is just the Kw (the ion product constant of water), bc Kw= [H3O+][OH-]. And the Kw at 25C is 1x10⁻¹⁴. Thus, we can write: KaKb = Kw = 1x10⁻¹⁴ *larger Ka = smaller pKa = strong acid *small Ka = large pKa = weak acid *large Kb = small pKb = strong base *small Kb = large pKb = weak base *way to remember, large Ka or large Kb means it is good at what it does.. It is a good acid or a good base. (acid/base equilibria)

Are animal amino acids in the D or in the L configuration?

L

All animal amino acids have ___ configuration.

L *its amino group is on the left in Fischer notation; all animal AA's are derived from L-glyceraldehyde *way to remember: we "Like" L amino acids (amino acids, peptides, proteins)

In Fischer projections, what is meant by the L and D configuration?

L-configuration means the penultimate carbon (second to last) has its amino or hydroxyl group on the left. D-configuration means the penultimate carbon has its amino or hydroxyl group on the right. A molecule in its D and L configuration is an enantiomeric pair. *Note: L and D are enantiomers, NOT epimers. So, every chiral C center inverts. (amino acids, peptides, proteins)

Common functional groups, alkyne:

*unsaturated hydrocarbon, has a triple bond (stereochemistry of covalently bonded molecules)

Unstable molecules are ________. Stable molecules are _________.

*unstable molecules are higher in energy and more reactive. Bad LG's. *stable molecules are lower in energy and less reactive. Good LG's. (stereochemistry of covalently bonded molecules)

How much 0.1M NaOH solution is needed to neutralize 40mL of a 0.3 M HCl solution?

*use the formula (a)[A](Va) = (b)[B](Vb), where a is the number of acidic hydrogens per formula, A is the molarity of the acid, Va if the volume of acid, b is the number of H+ ions the base can accept, B is the molarity of the base, Vb is the volume of base *so, Vb= (a)[A](Va)/(b)[B] → Vb= (1)(0.3 M)(40mL) // (1)(0.1 M) → 120mL (acid/base equilibria)

Of the following, which is the weakest electrolyte? A)NH₄I B)LiF C)AgBr D)H₂O₂

*when ionic substances dissolve, they dissociate into ions. Free ions in a solution are called electrolytes bc the solution can conduct electricity *all ionic compounds, whether soluble or not, are defined as strong electrolytes. So, NH₄I, LiF, and AgBr are all strong electrolytes. H2O2, hydrogen peroxide, is a covalent compound that does not produce many ions upon dissolution and thus is a weak electrolyte. Answer= D Note: There is a couple different ways to determine if a bond is ionic or covalent. By definition, an ionic bond is between a metal and a nonmetal, and a covalent bond is between 2 nonmetals. So you usually just look at the periodic table and determine whether your compound is made of a metal/nonmetal or is just 2 nonmetals. The exception is a compound made with ammonium (NH4+) Since ammonium is an ion, it forms ionic compounds. (ions in solution)

How do antacids, like tums, work?

*you take an antacid to relieve excess stomach acid, HCl. The antacid is a weak base, usually carbonate (CO3^2-), that reacts in the stomach to neutralize acid. (acid/base equilibria)

Wittig Reaction:

-A ketone or aldehyde reacts with wittig reagent (phosphorus bound to 3 phenyl groups), forming a new C=C (generates alkenes). -What is wittig reagent? *three phenyl groups + phosphorus + R Ph3P-R The carbon attached to P can become deprotonated, giving phosphorus a + charge and the carbon a - charge. This is a YLIDE (a zwitterion that has both + and - charges on adjacent heteroatoms (diff atoms)). -this phosphorus ylide reacts with the carbonyl group of an aldehyde or ketone forming a new alkane Carbonyl + phosphorus ylide → alkene C=O + Ph3P=C' → C=C' https://www.youtube.com/watch?v=5TTqyVExV9Y (nucleotides and nucleic acids)

Transition state, (TS):

-Activated complex = what's present at the transition state. -In the transition state, bonds that are going to form are just beginning to form, and bonds that are going to break are just beginning to break. -The transition state is the peak of the energy profile. -The transition state can go either way, back to the reactants, or forward to form the products. -You CANNOT isolate the transition state. Don't confuse the transition state with a reaction intermediate, which is one that you can isolate. (kinetics)

Constitutional isomers:

-Also called structural isomers. -Constitutional/structural isomers are compounds that have the same molecule formula, but have their atoms connected together differently. Bc of this, they have diff chemical properties (how reactive they are) and diff physical properties (mp, bp, density, solubility, etc) Two types of constitutional isomers: 1)positional isomers= structural isomers that have the same functional groups positioned differently 2)functional isomers= structural isomers that have different functional groups (stereochemistry of covalently bonded molecules)

Buffer:

-Buffers are solutions that resist changes in pH upon addition of small amounts of acid or base. Buffers are composed of a WA + its conjugate base. Or WB + its conjugate acid. -In order to be an effective buffer, the number of moles of the weak acid and its conjugate base must be large compared to the number of moles of strong acid or base that may be added. The best buffering will occur when the ratio of [HA] to [A-] is about 1:1. Buffers are considered to be effective when the ratio is anywhere between 10:1 and 1:10. -The pH of a buffer is calculated by using the Henderson-Hasselbalch equation, pH=pKa+log [A-]/[HA] -The pH of a buffer system should be close to the pKa of the WA used in the buffer (this ensures the buffer is in 50% protonated form and 50% deprotonated form). If we want to buffer an acidic solution, use an acid with a small (acidic) pKa. To buffer a basic solution, use an acid with a large (basic) pKa. Buffers are generally good over the range pH = pKa ± 1. -Buffering capacity is the concentration of acid/base that can be absorbed. A higher concentration of buffer resists changes in pH better (that is, the solution has a higher buffering capacity). The more A- and HA molecules available, the less of an effect the addition of a strong acid or base will have on the pH of the solution. Note: A buffer system consists of an equilibrium between an acidic species and a basic species. Note the "equilibrium", you can't just dump HCl and NaOH together and expect buffering, because neutralization will occur and the acidic species and the basic species won't be at an equilibrium. Q: how does adding water change the buffering capacity? Adding water will dilute the buffer, thus buffering capacity will decrease. However, adding water (or allowing water to evaporate) has no effect on the pH. How buffers are prepared: 1)mixing a large volume of a weak acid w the salt of its conjugate base (for ex, acetic acid + sodium acetate, CH3COOH + NaCH3COO. Since acetic acid is a WA it will partially dissociate to give a little bit of acetate ion (CH3COO-). However, the salt, NaCH3COO is soluble and will dissociate to give Na+ and CH3COO-. This common ion will shift the equil to the left, so the concentrations of CH3COOH and CH3COO- will be in equal. 50% is protonated and 50% is deprotonated) CH3COOH + H2O <--> H3O+ + CH3COO- 2)mixing a large volume of a weak base w the salt of its conjugate acid (for ex, ammonia + a salt containing the ammonium ion, NH3 + NH₄⁺.) (acid/base equilibria)

Enzyme/Catalysts:

-Catalysts speed up a reaction without getting itself used up. -Catalysts/enzymes decrease the activation energy (Ea) of a reaction by lowering the energy of the transition state -Catalysts/enzymes alter kinetics, not thermodynamics. -Catalysts/enzymes help a system to achieve its equilibrium faster, but does not alter the position of the equilibrium. -Catalysts/enzymes increase k (rate constant, kinetics), but does not alter Keq (equilibrium). *catalysts/enzymes do not change Keq bc they work to lower the activation energy for BOTH forward and reverse reactions. -Catalysts/enzymes do not alter the spontaneity of a reaction, ∆Gcatalyzed=∆Guncatalyzed *note: enzymes are just biological catalysts (kinetics)

Isobaric process:

-Constant pressure -heating gas in a cylinder, the volume of gas expands, pushing the piston upward. Pressure is held constant bc weight of the piston is held constant -isobaric process.. thermal energy is used for work (increasing volume) ∆E=Q+W W=P∆V And, ∆E=Q+P∆V *if putting thermal energy (heat) into the system, the gas is doing work moving the piston up, so ∆E should be decreasing -on PV graph, going to the left is isobaric expansion; going to the right is isobaric compression (1st law of thermodynamics) (thermodynamics)

Conformational Isomers Newman Projections:

*Conformers about a single bond 1)ECLIPSED: a sigma bond on one carbon directly lines up w a sigma bond on an adjacent carbon. Eclipse conformations can be: -Syn-Periplanar: highest torsional strain, most unstable, bulky groups eclipse each other -Anticlinal eclipsed: high torsional strain, unstable, bulky groups eclipse hydrogens 2)STAGGERED: a sigma bond on one carbon bisects the angle formed by two sigma bonds on the adjacent carbon. Staggered conformations can be: -Gauche: low torsional strain, stable, bulky groups 60° staggered -Anti: lowest torsional strain, most stable, bulky groups 180° staggered Note: single bonds will rotate such that is achieves the most stable conformation (remember, all sigma bonds can rotate). *the eclipse, syn-periplanar conformation is highest in energy due to steric interactions. The staggered, anti conformation is lowest in energy. However, sometimes the staggered, gauche conformation can be lowest in energy. This is bc sometimes the atoms can H-bond w each other, resulting in a lower energy state (for ex, if substituents were OH or NH₂, could form H-bonds) (stereochemistry of covalently bonded molecules)

Strong acid titrated w a strong base:

*For ex: HCl, (strong acid), being titrated w NaOH, (strong base) or H+, (strong acid), being titrated w OH- (strong base) *equivalence point always occurs at pH=7. Equivalence point is when moles of acid = moles of base. For ex, HCl, (strong acid), being titrated w NaOH, (strong base), you would only have Cl-, Na+, and H2O in solution. No OH- or H+. *graph shape is flat on top and bottom (titration)

Weak base titrated w a strong acid:

*For ex: NH3 (a weak base) being titrated w HCl (a strong acid) or a more general example, A- (a weak base) being titrated w H+ (a strong acid). *equivalence point is dominated by the strong acid. At the equivalence point, the pH<7. Equivalence point occurs when moles of base=moles of acid. For ex, NH3 (a weak base) being titrated w HCl (a strong acid), you would only have NH4^+ and Cl- (forming a salt, NH4Cl). No H+. *half-equivalence point occurs during the buffering region. Here, pH=pKa, products and reactants are present in equal concentrations. For ex, NH3 (a weak base) being titrated w HCl (a strong acid), half-equivalence point is when NH3=NH4^+ *at the half-equivalence point, the concentration of acid added is equal to ½ the concentration of base (you have added enough acid, for ex HCl, to neutralize half of your weak base, for ex NH3). *graph shape: tail at the top (characteristic of a weak base), w a bottom that is flat (characteristic of a strong acid) (titration)

Strong base titrated w a strong acid:

*For ex: NaOH, (strong base) being titrated w HCl, (strong acid) or OH, (strong base), being titrated w H+, (strong acid). *equivalence point always occurs at pH=7. Equivalence point is when moles of base = moles of acid. For ex, NaOH, (strong base), being titrated w HCl, (strong acid), you would only have Na+, Cl-, and H2O in solution. No OH- or H+ *graph shape is flat on top and bottom (titration)

Weak acid titrated w a strong base:

*For ex: acetic acid, (a weak acid) being titrated w NaOH (a strong base) or a more general example, HA (a weak acid) being titrated w OH- (a strong base). *equivalence point is dominated by the strong base. At the equivalence point, the pH>7. Equivalence point occurs when moles of acid=moles of base. For ex, acetic acid, (a weak acid) being titrated w NaOH (a strong base), you would only have CH3COO-, Na+, and H2O. No H+ or OH- *half-equivalence point occurs during the buffering region. Here, pH=pKa, products and reactants are present in equal concentrations. For ex, acetic acid, (a weak acid) being titrated w NaOH (a strong base), half-equivalence point is when CH3COOH=CH3COO- *at the half-equivalence point, the concentration of base added is equal to ½ the concentration of acid (you have added enough base, for ex NaOH, to neutralize half of your weak acid, for ex acetic acid). *graph shape: bottom has a tail (characteristic of a weak acid), while the top is flat (characteristic of a strong base) (titration)

Common functional groups, acetal:

*Formation of an acetal occurs when the hydroxyl group of a hemiacetal becomes protonated and is lost as water. The carbocation that is produced is then rapidly attacked by a molecule of alcohol. Loss of the proton from the attached alcohol gives the acetal. (stereochemistry of covalently bonded molecules)

Conventions for writing E and Z:

*If only 1 double bond: (E/Z)-molecule, where E/Z is the geometric configuration across the double bond, and molecule is the name of the compound. For example, (Z)-2-chloro-2-butene. *If more than 1 double bond: (#E/Z, #E/Z)-molecule, where # is the carbon number in ascending order, and molecule is the name of the compound. (stereochemistry of covalently bonded molecules)

How does intermolecular H-bonding affect mp and bp?

*Increased intermolecular H-bonding holds molecules together better, thus leading to an increase in mp and bp. The more H-bond donors and H-bond acceptors there are in a molecule, the higher the bp and mp will be. *remember, for H-bonding, you need a donor (a hydrogen bonded to a F, O, N), and an acceptor (a lone pair of electrons on a F, O, N) *Note: Intramolecular H-bonding within the same molecule can sometimes lead to a decrease in the amount of intermolecular interactions that can occur between molecules. Thus, mp and bp could decrease. (separations and purifications)

Common functional groups, lactam:

*Lactams are cyclic amides. Consisting of a ring containing two or more carbon atoms and a single nitrogen atom (stereochemistry of covalently bonded molecules)

Common functional groups, lactone:

*Lactones are cyclic esters. Composed of a ring containing two or more carbon atoms and a single oxygen atom *γ and δ-lactones, containing five and six-membered rings, respectively, are the most common. (stereochemistry of covalently bonded molecules)

Recrystallization:

*Recrystallization = barely dissolving your compound, then let it recrystalize out of solution = compound ends up being more pure. *Barely dissolving = use just enough to fully dissolve your compound under warm temperature = saturated solution. *Recrystalize = solution cools, solubility decreases, compound comes out of solution. *Solvent choice = choose a solvent in which your compound is soluble in at warm temperature, but not at cool temperature. Also, choose a solvent in which impurities are highly soluble. *Impurities should remain dissolved in the solvent even when your compound recrystalizes out. (separations and purifications)

Which is more polar, CCl₂H₂ or CClH₃?

-in CCl₂H₂, the bond dipoles point out/downward, while the net dipole points straight down -in CClH₃, the bond dipole points straight down, the same direction as the net dipole *So, CClH₃ is a more polar molecule If the net dipole points the same way as the bond dipoles, this will often be more polar. Vs if the net dipole does not point the same way as the bond dipoles. (bonding)

Titration of a polyprotic acid with a strong base:

*for ex: H2CO3 (a polyprotic acid) being titrated w NaOH (a strong base) or a more general example, H2A (a diprotic acid) being titrated w OH- (a strong base). *will have multiple equivalence points and multiple half-equivalence points (thus, multiple pKa's). There are multiple deprotonation steps. *like monoprotic acids, each half-equivalence point is when [acidic species]=[conjugate base of the acidic species], thus pH=pKa. For ex, H2CO3 (a polyprotic acid) being titrated w NaOH (a strong base), the 1st pKa is when [H2CO3]=[HCO₃⁻]. The 2nd pKa is when [HCO₃⁻]=[CO₃²⁻] *multiple equivalence points, occurs when moles of base=moles of acid. For ex, H2CO3 (a polyprotic acid) being titrated w NaOH (a strong base), the first equivalence point is when you primarily have HCO₃⁻ in solution. The second equivalence point is when you primarily have CO₃²⁻ in solution. *Amino acids are polyprotic acids *any diprotic acid, unless it's sulfuric acid (H2SO4), is a weak acid. Thus, the equivalence points are dominated by the strong base. At the equivalence point, the pH>7. (titration)

Common functional groups, acid anhydride:

*functional group consisting of two acyl groups bonded to the same oxygen atom. *note: an acyl group is just R-C=O (stereochemistry of covalently bonded molecules)

Common functional groups, imine:

*functional group containing a carbon-nitrogen double bond. The nitrogen atom can be attached to a hydrogen or an R group. If this group is not a hydrogen atom, then the compound can sometimes be referred to as a Schiff base. (stereochemistry of covalently bonded molecules)

Common functional groups, amine:

*functional group that contains a basic nitrogen atom with a lone pair. Amines are derivatives of ammonia, wherein one or more hydrogen atoms have been replaced by an R group (stereochemistry of covalently bonded molecules)

Explain how to convert a Fischer projection to a furanose Haworth:

*furanose (5-membered ring) can be formed from linear hexoses or pentoses -The OH on carbon 5 attacks the anomeric carbon (carbonyl carbon) -Draw 5 membered ring structure with O in ring. Number in a clockwise fashion -The OH's on RIGHT side in Fischer goes DOWN in Haworth -The OH's on LEFT side in Fischer go UP in Haworth *positions 3 and 4 on Haworth are easy to draw *position 5 on Haworth, if its a D sugar, CH2OH points up. If its an L sugar, CH2OH points down *position 2 on Haworth (anomeric carbon) has a CH2OH attached and an alpha (down) or beta (up) OH. Since the carbonyl carbon is sp2 hybridized, if its attacked from one side its alpha; if its attacked from the other side its beta. You cannot determine this, question will have to tell you if alpha or beta. Note: furanoses (5 membered rings) do not have chair conformations. Chair only happens for pyranoses (6 membered ring) (carbohydrates)

Conventions for writing R and S in molecular naming:

*if only 1 chiral center: (R/S)-molecule. So, R or S is written in front of the molecule name. For ex, (R)-2-hydroxyl-propanal *if more than 1 chiral center: (#R/S, #R/S)-molecule. Where # is the carbon number (in ascending order), R/S is the absolute configuration, and molecule is the name of the compound. For ex, (2R, 3S)-2,3,4-hydroxyl-butanal (stereochemistry of covalently bonded molecules)

Isoelectric vs Isotope vs Isomers:

*isoelectric= same e- configuration, same number of valence e-'s. For ex, F- and Ne *isotope= same element (same # of p+), diff number of neutrons. For ex, carbon-12 and carbon 13 *isomers= same molecular formula, different structures (stereochemistry of covalently bonded molecules)

Common functional groups, phenyl:

*phenyl ring *Phenyl groups are closely related to benzene and can be viewed as a benzene ring, minus a hydrogen, which has been replaced by some other functional group (usually an R group). (stereochemistry of covalently bonded molecules)

Common functional groups, alkane:

*saturated hydrocarbon, R₃C𑁋CR₃ (stereochemistry of covalently bonded molecules)

A 0.01M solution of HCl will have what concentration of H+ ions?

*since HCl is a strong acid, it will dissociate completely in solution. Thus, it will have a [H+] = 0.01M or [H+]= 1x10⁻² and a pH=2 (acid/base equilibria)

Lewis electron dot structures: Draw NO₂⁻ lewis structure

*steps for drawing a lewis structure (using NO₂⁻ as an ex): 1) count the number of valence e-. Negative charges count as extra e-, positive charges count as removed e-. Here, N = 5 valence e- and O₂ = 12 valence e-. Total, there is 18e- 2) put the atom which is the least electronegative in the center. C always goes in the center, H never does Here, O N O 3)connect each of the outer atoms to the central atom w one line. Subtract these e- from the total O-N-O, 14 total e- left 4) add pairs of e- as dots to all non-H OUTER atoms until each has 8e. Start w the most electronegative atom first. If there are no remaining e-, you are done. 5) if there are remaining e-, add them in pairs, if possible, to the central atom 6) if there are missing octets on a F, O, N, C form double bonds (or triple bonds) by taking lone pairs from any atom w an octet and sharing them w the electron deficient atom. F, O, N, C must obey the octet rule. EXCEPTIONS/DO NOT OBEY OCTET RULE: A) Boron column: they usually form 3 bonds and have a six-tet vs octet B) large elements, 3rd row and below: P, S, Cl do not have to follow octet rule *While elements in the first two periods only have access to the 1s, 2s, and 2p energy sublevels, elements in the third period or higher have access to d orbitals. 7) resonance structures are possible if there are equivalent locations for the multiple bonds 8) assign formal charges if necessary, formal charge = #valence - sticks - dots *the best lewis structures have an octet of e- and a formal charge of zero on all atoms. For dot structures that must have formal charges, the best structures have negative formal charges on the more electronegative element (bonding)

Of the following, which acid has the weakest conjugate base? A)HClO4 B)HCOOH C)H3PO4 D)H2CO3

*strong acid → weak conjugate base, here the only strong acid is perchloric acid, HClO4 Answer=A (acid/base equilibria)

Of the following anions, which is the strongest base? A)I- B)CN- C)NO₃⁻ D)Br-

*strong base → weak conjugate acid. So, which of the anions has the weakest conjugate acid? I- → HI, strong acid CN- → HCN, weak acid NO₃⁻ → HNO3, strong acid Br- → HBr, strong acid *HCN is a weak acid, thus CN- must be the strongest base. Answer= B (acid/base equilibria)

Common functional groups, alkene:

*unsaturated hydrocarbon, has a double bond, R₂C=CR₂ (stereochemistry of covalently bonded molecules)

Calculate the pH of a 0.20 M NaOH solution

0<pOH<1 14>pH>13 This is a SB

Describe the isomers that are possible in carbohydrates.

-Due to the fact that carbohydrates contain multiple chiral centers, many stereoisomers are possible including enantiomers, diastereoisomers, and epimers. Remember, to determine the number of stereoisomers, take 2^n, where n is the number of chiral centers -Two carbohydrates are said to be enantiomers if they are nonsuperimposable mirror images of one another. All D and L configurations of a particular carbohydrate are enantiomers of each other (opposite configurations at every chiral C; R vs S). For ex, D-glucose and L-glucose are enantiomers of each other. *note: 2^n= stereoisomers. Half of the stereoisomers will be in D form, half will be in L form -Two carbohydrates are diastereomers if they have opposite configurations at some chiral centers, but not all. All D-aldohexoses are diastereomers. All L-aldohexoses are diastereomers. All D-ketopentoses are diastereomers. All L-ketopentoses are diastereomers. -epimers= opposite configurations at one chiral center (for ex, galactose is the C4 epimer of glucose) -anomers= different configuration in the chiral, anomeric carbon when the molecule is in cyclic form. OH down is alpha, OH up is beta (carbohydrates)

What is the Fischer projection vs Haworth vs chair?

-Fischer= A way of representing an acyclic (open chain) carbohydrate. Vertical lines point away from the viewer and horizontal lines point toward the viewer. -Haworth= A way of representing a cyclic (closed chain) carbohydrate. Substituents can either point up or down on this ring. -Chair= The most stable conformation of cyclohexane (resembles a chair) What is the anomeric carbon? The carbonyl carbon in a sugar molecule. It will be either an aldehyde or ketone. The anomeric carbon is given the #1 position when numbering for hexoses, and the #2 position when numbering in pentoses. The -OH group on the anomeric carbon can be either up (beta) or down (alpha) *when converting from linear Fischer to cyclic haworth, the carbon 5 OH always attacks the anomeric carbon (carbohydrates)

Common reactions with monosaccharides:

-Hemiacetal formation = -OH attacks carbonyl group = produces ring form. -Acetal formation = another -OH attack on the same carbonyl group = produces polysaccharides if the -OH is from another monosaccharide. -Mutarotation = equilibrium between the α and β anomers. -Strong oxidation turns aldehyde and terminal hydroxyls to carboxylic acids, and other hydroxyls to ketones. The strongest kind of oxidation turns everything to CO2, and this occurs in cellular respiration. -Mild oxidation is more selective. Tollens agent (the test for aldoses, silver reagent) selectively oxidizes the aldehyde to carboxylic acid. Nitric acid oxidizes both the aldehyde and the terminal hydroxyl to carboxylic acids, but leaves the other hydroxyls alone. -Reduction turns monosaccharides into polyalcohols (sugar alcohols). (carbohydrates)

Describe hemiacetal vs acetal sugars in solution

-Hemiacetal sugars exist in equilibrium between the straight chain form and cyclic form. When in the straight chain form, the aldehyde or ketone can be oxidized to a carboxylic acid. Hemiacetals are reducing sugars bc they act as a reducing agent, while itself being oxidized. -acetal sugars do NOT exist in equilibrium between the straight chain form and cyclic form. They are present only in the cyclic form (need an enzyme to convert to straight chain). In the cyclic form, there is no free aldehyde or ketone, so cannot be oxidized. Acetals are non-reducing sugars. (carbohydrates)

Compare the R groups in acidic vs basic AA's:

-If the R group contains carboxylic acid, then it's an acidic AA. There are two acidic AA's, aspartic acid and glutamic acid. The acidic AA donates a proton, becoming negatively charged. -Basic AA's have an amine in their R group. There are three basic AA's, lysine, arginine, and histidine. The basic AA accepts a proton, becoming positively charged. (amino acids, peptides, proteins)

Adiabatic process:

-No heat exchange -gas is in an insulated cylinder. Move piston up or down quickly so there's only work and no time for heat exchange -adiabatic process.. Thermal energy used as work (increase volume=decreased pressure and vice versa) Q=0, W≠0 (temperature can change bc of work) ∆E=Q+W → ∆E=-W or -∆E=W -Looks like isothermal graph; adiabatic is more steep than isothermal graph (1st law of thermodynamics) (thermodynamics)

Calculating enthalpy - Hess's law of heat summation:

-One of the three ways to calculate ∆Hrxn -Hess's law problems will require you to combine two or more reactions and their enthalpies to find the enthalpy of an overall reaction -reversing the direction of a reaction changes the sign of ∆H -if an equation is multiplied by a coefficient, then ∆H must be multiplied by that same number -add reactions together to cancel out intermediate species (thermodynamics)

Calculating enthalpy - summation of bond enthalpies:

-One of the three ways to calculate ∆Hrxn -The enthalpy of a reaction can be estimated by summing the total enthalpy required to break the bonds in the reactants w the energy released by forming the bonds in the products. -If a question provides a list of bond dissociation enthalpies, ∆Hrxn can be determined by: ∆Hrxn = ∑ BDE bonds broken - ∑ BDE bonds formed (thermodynamics)

Calculating enthalpy - heat of formation:

-One of the three ways to calculate ∆Hrxn -The ∆H°f is the amount of energy associated with forming ONE MOLE of a compound from its constitutive elements in their standard states -the ∆H°f of any element in its standard state is defined as 0 (for ex, ∆H°f =0 for O2) -If a question provides a list of ∆H°f values, ∆Hrxn can be determined by: ∆Hrxn= ∑ (n)(∆H°fproducts) - ∑ (n)(∆H°freactants), where n is the number of moles (thermodynamics)

Reaction intermediates:

-Reaction intermediates are produced in an early step of the reaction mechanism, and are later used up so they don't appear as products of the overall reaction -The intermediate is at a local minimum in terms of energy, but has more energy than the reactant or product -You CAN isolate an intermediate. Don't confuse the intermediate with the transition states (kinetics)

Activation energy, Ea:

-The energy required to produce the transition state -If you have a high activation energy, that means the rate of the reaction is more slow vs if you have a low activation energy (kinetics)

Three classification systems used to organize AA's:

1) (+), d, and (-), l, describes optical activity 2) R and S describes absolute configuration of structure 3) D and L tells us the precursor of a molecule (D or L-glyceraldehyde) (amino acids, peptides, proteins)

Rate Law:

-The rate law gives the rate in terms of the initial concentrations of reactants and the rate constant, k, for the process. aA + bB → cC + dD -If the above reaction is single-step, then rate = k[A]a[B]b -If the above reaction is the rate-determining step of a multi-step reaction, then the rate of the multi-step reaction = k[A]a[B]b -If the above reaction is a multi-step reaction, then rate = k[A]x[B]y, where x and y are unknowns that correspond to the rate-determining step. -Rate laws only include the slow-step of a reaction. They only look at rate in terms of reactants (not products). They never include solids or liquids/solvents. Only includes gases. -To determine the rate law, you refer to a table of rates vs reactant concentrations, which will be given on the mcat. -For ex, using the above equation and table on the left, rare = k[A]x[B]y[C]z -From this table, a 2x increase in [A] corresponds to a 4x increase in the rate. 2^x = 4, so x = 2. -A 2x increase in [B] corresponds to a 2x increase in the rate. 2^y = 2, so y = 1. -A 2x increase in [C] corresponds to 1x (no change) in rate. 2^z = 1, so z = 0. -So, the rate = k[A]2[B]1[C]0 → rate = k[A]2[B] -Reaction order = sum of all exponents of the variables in the rate law. For ex, the reaction order here is third order. -The individual reaction order of the reactants in a rate law follows their stoichiometry. For ex, the individual reaction order for A is second order. -Do not confuse the rate law with the experimental rate/average reaction rate. (kinetics)

Rate-determining step:

-The slowest-step of a multi-step reaction -The rate-determining step is the transition state with the highest energy -The rate of the whole reaction=the rate of the rate determining step -The rate law corresponds to the components of the rate determining step (kinetics)

Compare thermodynamics vs kinetics:

-Thermodynamics will tell you where a system starts and finishes but NOTHING about the path traveled to get there. Thermodynamics tells you IF a reaction is spontaneous or not (either -ΔG or +ΔG), it tells you nothing about the speed/kinetics of a reaction. Just bc a rxn is spontaneous (thermodynamically favorable, -ΔG), the rxn may proceed very very slowly Ex, how does the ΔG for a rxn burning (oxidizing) sugar in a furnace compare to the ΔG when sugar is broken down (oxidized) in the human body? ΔG is the same in both cases! It does not depend on the path traveled. *words relating to thermodynamics: stability, equilibrium, spontaneity/∆G, entropy/∆S, enthalpy/∆H, etc -Kinetics tells you how fast a reaction occurs. It tells you nothing about the spontaneity of a reaction. *words relating to kinetics: rate, mechanism, catalyst, intermediates, activated complexes/transition states, activation energy/Ea, etc (thermodynamics)

A(s) + B(aq) <--> C(l) + D(aq). What will induce the reaction to move forward? What will induce the reaction to move backward?

-To move forward: Add B. Remove D. Adding or removing solids or liquids to a reaction at equilibrium doesn't do anything that will knock the system off its equilibrium. So, altering A and C won't make a difference. -To move backward: Remove B. Add D.

A(s) + B(aq) <--> C(l) + D(g). What will induce the reaction to move forward? What will induce the reaction to move backward?

-To move forward: Add B. Remove D. Or remove/decrease pressure (reaction will go to side with more moles of gas) -To move backward: Remove B. Add D. Or add/increase pressure (reaction will go to side with less moles of gas)

A(s) + B(aq) <--> C(l) + D(aq), ΔH<0. What will induce the reaction to move forward? What will induce the reaction to move backward?

-To move forward: Add B. Remove D. Removing heat by cooling the reaction. -To move backward: Remove B. Add D. Add heat by heating the reaction.

Describe AA's at low vs high pH

-at low pH, AA's exist in the cationic form -at high pH, AA's exist in the anionic form -at pH=isoelectric point (pI), AA's exist in the zwitterion form (also called a dipolar ion), which is overall neutral (amino acids, peptides, proteins)

Describe different types of protein motors:

-flagella (bacteria and sperm) -ATP synthase (mitochondria, chloroplasts) -motile cilia (trachea) -myosin (muscle) -kinesin/dynein (intracellular transport) -actin polymerization (Listeria bacteria make a protein that allows them to polymerize actin, making them mobile) (amino acids, peptides, proteins)

Fluorine vs Fluoride:

-fluorine= F -fluoride= F- (bonding)

List common monosaccharides:

-glyceraldehyde (3 C sugar) -dihydroxyacetone (3 C sugar) -Glucose (6 C sugar) *blood sugar is based on glucose levels; glucose is also the product of photosynthesis in plants -Fructose (6 C sugar) *fructose is the sugar in fruits, it is sweeter than glucose -Galactose (6 C sugar) -Ribose (5 C sugar) *the sugar that makes up RNA -Deoxyribose (5 C sugar) *the sugar that makes up DNA (carbohydrates)

What is the Benedict's test?

-hemiacetal sugars in solution exist in equilibrium between the straight chain form and cyclic form. The equilibrium favors the cyclic form. -when a sugar is in its straight chain form, it will have an aldehyde or ketone present (aldose or ketose sugar) -this aldehyde or ketone can be oxidized to a carboxylic acid -Benedict's test uses a copper reagent to oxidize the sugar's aldehyde or ketone to the carboxylic acid. -any carbohydrate that can be oxidized by Benedict's reagent is referred to as a reducing sugar bc it reduces the copper Cu^2+ to Cu^+ while itself being oxidized -Benedict's test is useful bc it distinguishes hemiacetals from acetals. Only hemiacetals are in equilibrium with the carbonyl (straight/open chain) form. For ex, if you had a while powder that you knew to be composed of glucose, you would be able to say whether the glucose existed in the free monosaccharide form or was in the form of glycogen. How? Well, if it's in the monosaccharide form, there will be many hemiacetals, and Benedict's test will be strongly positive (very red in color). However, if the powder consists only of glycogen, Benedict's test will be only weakly positive, bc all the glucose units in a glycogen polymer are tied up in acetal linkages (except the very first one in the chain, the one which was attacked during polymerization). Summary: all aldehydes, ketones, and hemiacetals give a + result in Benedict's test for reducing sugars; acetals give a negative result bc they do not react w Cu^2+, and they are not in equilibrium with the open-chain (carbonyl) form. (carbohydrates)

Hydrophilic vs hydrophobic AA's:

-hydrophilic: if the R group contains acids, bases, amines, or alcohols. -hydrophobic: if the R group doesn't contain any of the stuff listed above (tryptophan is an exception). (amino acids, peptides, proteins)

What does a catalyst do, and how does it do it?

A catalyst increases the rate at which a reaction reaches equilibrium by lowering the activation energy.

Lipids:

-monomer= hydrocarbon -can be saturated (packs tightly at room temp, margarine) or unsaturated (does not pack tightly at room temp, olive oil) -fatty acid= hydrocarbon chain + carboxylic acid -four types of lipids: 1)triglyceride= glycerol + 3FA's (energy storage; most fats in our diet are triglycerides) 2)phospholipids= glycerol + 2FA's + phosphate (phospholipid bilayer. Phospholipids are amphipathic - have both polar and nonpolar regions) 3)terpenes= multiple isoprenes put together (precursor to earwax, cholesterol, steroid hormones. Can also form terpenoids, such as Vit A). *2 isoprene = monoterpene *6 isoprenes = triterpene; also called Squalene 4)cholesterol= three 6-C rings + one 5-C ring (cell membrane fluidity, steroid hormone precursor, Vit D precursor, bile salts. When cholesterol is carried in the blood w fats/proteins, it's called a lipoprotein) *note, bile salts are one of the main components of bile. Bile is a greenish-yellow fluid made by the liver and stored in our gallbladder. Other lipids include: sphingolipids, waxes, fat-soluble vitamins, and prostaglandins (lipids)

Carbohydrates:

-monomer= monosaccharide/simple sugar (CnH2nOn); Carbs have 2x as many H compared to O or C **Common monosaccharides: -Glucose (6 C sugar) -Fructose (6 C sugar) -Galactose (6 C sugar) -Ribose (5 C sugar) -Deoxyribose (5 C sugar) **Monosaccharide + Monosaccharide = Disaccharide C6H12O6 + C6H12O6 = C12H22O11, notice a molecule of water is lost upon formation *Common disaccharides: -Maltose (glucose + glucose) -Sucrose (glucose + fructose) -Lactose (glucose + galactose) **Many monosaccharides put together = polysaccharide *Common polysaccharides (these are all glucose polymers): -Glycogen= sugar storage in animals; alpha linkages; branched -Starch= sugar storage in plants; alpha linkages -Cellulose= structural molecule in plants; beta linkages *polysaccharides are important for: energy, cell surface markers, structural in plants *carbs can be linked by either alpha or beta glycosidic-linkages; the human body can only digest alpha-glycosidic linkages (OH on C1 is below the glucose ring). Lactose has beta glycosidic-linkages, but we can digest it bc we have lactase (a specific enzyme which breaks lactose down) (carbohydrates)

How does double bonds and triple bonds affect bond length, bond energy, and rigidity?

-multiple bonding decreases bond length -multiple bonding increases bond energy -multiple bonding increases rigidity in molecular structure *single bonds can rotate, but double and triple bonds can't *even partial double bonds, like those found in the peptide bond, prevents free rotation (stereochemistry of covalently bonded molecules)

4 biologically important macromolecules:

-proteins -carbs -lipids -nucleic acids *All these macromolecules are polymers (made from monomers) -enzymes that make them = polymerase (they undergo polymerization reactions) *polymerization reactions are often run via dehydration synthesis/condensation **the opposite of dehydration synthesis/condensation = hydrolysis (amino acids, peptides, proteins)

Resonance effects:

-resonance stabilization occurs in molecules w 𝞹 bonds. Resonance stabilization= delocalization of electrons and/or charge -It occurs when a +/- charge or lone e- pair is adjacent to (one atom away) from a 𝞹 bond -delocalization can only occur if there is an empty p orbital. For ex, if something is sp² hybridized, it has an unoccupied p orbital. Thus, moving e-'s between the p orbitals results in greater stability. *resonance cannot occur if something is sp³ hybridized, bc there is no empty p orbital! Remember: weird exception, any atom w a lone pair adjacent to an sp² atom will also be sp² to allow for resonance (stereochemistry of covalently bonded molecules)

Saturated and unsaturated organic molecules:

-saturated organic molecules contain no 𝛑 bonds and no rings; all carbons have the maximum number of H atoms attached *a saturated compound with n carbon atoms has exactly 2n+2 H atoms -unsaturated organic molecules have at least one 𝛑 bond or a ring; a degree of unsaturation (DOU) is introduced each time an H₂ is removed. For ex, if a molecule has 1 DOU, it must have one 𝛑 bond or be a ring shape *an unsaturated compound with n carbon atoms has fewer than 2n+H atoms Note: you can determine quickly if a molecules is saturated or not by looking at the number of H atoms in relation to the number of C atoms. For ex: C₇H₁₆ is saturated. 2n+2 = number of H atoms if molecule is saturated; (2)(7)+2 = 16. And C₇H₁₄ is unsaturated (H₂ is removed); here only 14H, not 16H (stereochemistry of covalently bonded molecules)

Compare starch vs glycogen:

-starch= glucose molecules joined by 1,4-glycosidic linkages= energy storage in plants -glycogen= glucose molecules joined by 1,4-glycosidic linkages and 1,6-glycosidic linkages via branching= energy storage in animals (stored in the liver) (carbohydrates)

Terpenes:

-terpenes are made from the polymerization of isoprene; terpenes are hydrocarbons -terpenes contain double bonds, which gives the molecule the ability to undergo cyclization -2 isoprene units= monoterpene -4 isoprene units= diterpene -6 isoprene units= triterpene; squalene -squalene is the precursor of cholesterol/steroid hormones. A self-cyclization reaction converts squalene to different steroids -terpenoids are terpenes with different functional groups. Vitamin A and vitamin E are both terpenoids (lipids)

∆E or ∆H of a reaction:

-the difference between the enthalpy of the reactants vs products. May be given as ∆H or ∆E -exothermic reaction, heat energy given off, -∆H -endothermic reaction, heat energy consumed, +∆H (kinetics)

List the laws of thermodynamics:

-zeroth law= heat flows from hot objects to cold objects to achieve thermal equilibrium -1st law= law of conservation of energy, the energy of the universe is constant -2nd law= disorder, entropy, ΔS, in the universe is always increasing (spontaneous rxns increase disorder of the universe) -3rd law= The entropy of a system approaches a constant value as its temperature approaches absolute zero. Thermodynamics overview: ΔG = ΔH - TΔS *note: ΔG ≈ ΔH *note: ΔG ↓ when ΔS ↑ ΔH is enthalpy; negative is favorable, giving off heat. *Negative ΔH = exothermic reaction (heat liberated). Positive ΔH = endothermic reaction (heat needed) ΔS is entropy; positive is favorable, disorder increasing Higher temps, higher ΔS, or low ΔH is favorable. -ΔG = spontaneous, exergonic rxn, gives off energy; breaking things down +ΔG = non-spontaneous, endergonic rxn, requires energy; building things up -when ΔG = 0, you are at equilibrium -The body uses reaction coupling to couple endergonic rxns w a favoriable rxn (for ex, using ATP, ΔG= -12) -additionally, enthalpy can be defined by: ΔH = ΔE + PΔV E is the bond energy, P is pressure, V is volume (thermodynamics)

Gabriel-Malonic ester synthesis:

1)the reaction starts out w malonic ester that has a LG at the α position. N is present in the form of phthalimide (here, the negatively charged N is protected/its reactivity is decreased so we only end up w one product and not multiple). In the first step of the reaction, the N on phthalimide attacks the α position on malonic ester via an SN2 reaction, yielding N-phthalimidomalonic ester. This gives us the N that will ultimately be the α-nitrogen of our AA. 2)in the next step, a base + an R (w a good LG) is added (here, the R group will become the R group on your new AA). The base deprotonates the α-carbon, allowing the desired AA side chain to be attached. 3)now that the desired groups are added (the amino group + R group), we can begin kicking off protecting groups. -Adding H3O+ will result in acid hydrolysis, turing the ester into a carboxylic acid and unprotecting the N yielding the α-amine. -finally, we add heat for decarboxylation, removing the second carboxylic acid, yielding the final amino acid product, which will be a racemic mixture (both L and D AA's present) *notice that the final AA product is in its cationic form (this occurs bc we added H3O+. At low pH, AA's exist in their cationic form) Summary: -start out w the backbone (carboxyl group) -next, add the amino group -finally, add the appropriate R chain (amino acids, peptides, proteins)

Strecker synthesis:

1)you start out w an aldehyde, where the R group on the aldehyde will become the R group on your new AA. So, you should choose the R group on your aldehyde carefully, (for ex, if you want to synthesize glycine, you would start out w formaldehyde). In the first step, your putting the aldehyde w ammonium chloride. This results in an imine intermediate 2)In the next step, HCN is added. CN- acts as a nucleophile, attacking the imine-carbon. This results in an α-amino nitrile. 3)adding H3O+ results in acid catalyzed hydrolysis of the nitrile group, yielding the final amino acid product, which will be a racemic mixture (both L and D AA's present) *notice that the final AA product is in its cationic form (this occurs bc in step 3 we added H3O+. At low pH, AA's exist in their cationic form) Summary: -start out w an aldehyde that has appropriate R chain -next, add the backbone. First the amino group then the carboxyl group *this is the reverse of the Gabriel AA synthesis (amino acids, peptides, proteins)

Calculate the pH of a 0.030 M HNO₃ solution.

1<pH<2 This is a SA

What is a leaving group?

A LG is a stable species that detaches itself from a molecule w its e- pair during the course of a reaction

What is a Lewis acid? What is a Lewis base?

A Lewis acid is an e- pair acceptor, or an electrophile. A Lewis base is an e- pair donor, or a nucleophile

Which of the following anions CANNOT behave as a Lewis base/ligand? A)F- B)OH- C)NO₃- D)BH₄-

A Lewis base/ligand is a molecule that donates a pair of nonbonding e-'s. So in order to even be a candidate Lewis base/ligand, a molecule must have a pair of nonbonding e-'s in the first place. F-, OH- and NO₃⁻ all have pairs of nonbonding e-'s. So, the answer is BH₄-, since it has no lone pairs. Answer= D

What is the difference between a reducing agent vs a base? What about an oxidizing agent vs an acid?

A base and a reducing agent (or an acid and an oxidizing agent) are very different concepts that apply to different phenomena. With reducing and oxidizing agents, the electrons are irreversibly transferred. They actually move from orbitals of the reducing agent (which will be oxidized) into orbitals of the oxidizing agent (which will be reduced). This transfer is thermodynamically favorable and thus the electrons won't just 'go back' With acids and bases, bonds are formed, which is a reversible process. Brønsted theory: an acid is a compound that can transfer a H+ ion onto another compound. The lewis theory realizes, that the acidic transfer reagent does not need to be hydrogen. Instead, anything with an unoccupied low-energy orbital can function as a Lewis acid; most notably boron compounds and metal cations. Upon creation of a Lewis acid-base pair, a coordinate bond is formed (one atom is donating both of the shared e-'s in a bond). The key concept is that the interaction is fully reversible and that upon dissociation the Lewis base keeps its lone pair.

Salts of weak acids and strong bases:

A chromatography technique where compounds are separated based on differing charge states. Ion exchange chromatography is commonly used to separate mixtures of proteins. At any pH, proteins in a mixture may exist in a variety of charged states *a mobile liquid phase containing the analyte is passed through a column packed w a solid stationary phase. Here, the solid stationary phase uses a polymeric resin w either positively or negatively charged moieties on the polymer surface *cation exchange resin= a column containing negatively charged groups; will bind cations in your sample. Proteins w isoelectric points greater than the pH of the mobile phase will be positively charged and elute slowly compared to those with isoelectric points below the solution pH *anion exchange resin= a column containing positively charged groups; will bind anions in your sample. Proteins w isoelectric points smaller than the pH of the solution will be negatively charged and will elute slowly. *once most of the species have been eluted through the column, the column is then treated w a concentrated solution to displace all species that are bound onto the column **if the isoelectric points of the proteins to be separated are known, the pH of the mobile phase can be buffered to a specific pH, thereby ensuring different charge states and hence good separation (separations and purifications)

Ion exchange chromatography:

A chromatography technique where compounds are separated based on differing charge states. Ion exchange chromatography is commonly used to separate mixtures of proteins. At any pH, proteins in a mixture may exist in a variety of charged states *a mobile liquid phase containing the analyte is passed through a column packed w a solid stationary phase. Here, the solid stationary phase uses a polymeric resin w either positively or negatively charged moieties on the polymer surface *cation exchange resin= a column containing negatively charged groups; will bind cations in your sample. Proteins w isoelectric points greater than the pH of the mobile phase will be positively charged and elute slowly compared to those with isoelectric points below the solution pH; pH<pI= protonated, positively charged. *anion exchange resin= a column containing positively charged groups; will bind anions in your sample. Proteins w isoelectric points smaller than the pH of the solution will be negatively charged and will elute slowly; pH>pI= deprotonated, negatively charged. *once most of the species have been eluted through the column, the column is then treated w a concentrated solution to displace all species that are bound onto the column **if the isoelectric points of the proteins to be separated are known, the pH of the mobile phase can be buffered to a specific pH, thereby ensuring different charge states and hence good separation (separations and purifications)

Column chromatography (flash chromatography):

A chromatography technique where compounds are separated based on differing polarities. Column chromatography is good when you have a large sample/need to separate bulk compounds. *a chromatography column is filled w silica gel (SiO₂). The materials to be separated are dissolved in solvent, loaded onto a column packed w stationary phase, and allowed to travel to the bottom of the column where they are collected. *silica gel=stationary phase *solvent= mobile phase *the flow of solvent (along w the separated compounds) is collected from the bottom. *Polar compounds will spend more time adsorbed on the polar solid phase (the stationary phase), and travel more slowly down the column. *the faster a component travels = less polar, it is attracted to the mobile phase; the slower a component travels= more polar, it is attracted to the stationary phase *Compounds leave the column and are collected in order from least polar to most polar (separations and purifications)

Paper chromatography:

A chromatography technique where compounds are separated based on differing polarities. Paper chromatography is the same as TLC; TLC just uses a different stationary phase than paper chromatography. Paper chromatography uses a paper stationary phase, while TLC uses silica or alumina as the stationary phase *paper=stationary phase *solvent= mobile phase *paper chromatography was classically used to separate pigments in dyes. Pigments in dyes stick to paper, solvent tries to wash them along, those w greater affinity for paper stays behind, those w greater affinity to solvent gets washed away *the farther a component travels = less polar, it is attracted to the mobile phase; the less a component travels= more polar, it is attracted to the stationary phase *Rf=distance traveled by pigment/distance of solvent front (separations and purifications)

Thin-Layer Chromatography (TLC):

A chromatography technique where compounds are separated based on differing polarities. TLC is good for separating very small amounts of material in order to assess how many compounds make up the mixture *In TLC, a plate is coated w a specific polar stationary phase. This adsorbent material is usually silica (SiO₂) *After the sample has been applied on the plate, the plate is placed upright in a sealed container w a shallow layer of solvent. The solvent (known as the mobile liquid phase) is drawn up the plate via capillary action. This process is known as developing or running. Because different analytes ascend the TLC plate at different rates, separation is achieved. *the more polar components of the mixture interact more w the polar stationary phase and travel at a slower rate. *The less polar components have a greater affinity for the solvent that the stationary phase and travel w the mobile solvent at a faster rate than the more polar components *After the experiment, the spots are visualized. Often this can be done simply by projecting ultraviolet light onto the sheet. *once the components have been visualized, Rf values can be determined. This "ratio to front" is simply the distance traveled by an individual component divided by the distance traveled by the solvent front, Rf=distance traveled by pigment/distance of solvent front *Rf values are never greater than 1 *If Rf=0, that means the pigment has not moved *If Rf=1, that means the pigment moved as far as the solvent front (nonpolar) Note: TLC is just advanced paper chromatography (separations and purifications)

What is a carbanion?

A molecule w a full negative charge on carbon; usually present as reaction intermediates. Carbanions in order from most stable to least stable: methyl > 1° > 2° > 3° methyl= CH₃⁻ 3°= R₃C⁻ 2° = R₂CH⁻ 1° = RCH₂⁻ Stability has to do with: Inductive effects: carbanions are stabilized by electron-withdrawing groups. If you have a carbanion, you want to pull e- density away from the central C atom. This can be accomplished best if you have less alkyl groups (less R groups, less e- donating groups), or more e- withdrawing groups (like F or Cl).. or less strong e- donating groups (like H) NOTE: alkyl substituents are ALWAYS e- donating groups. (stereochemistry of covalently bonded molecules)

What is a triose?

A monosaccharide containing 3 carbon atoms *can be further classified as either an aldose or ketose (carbohydrates)

What is a threose?

A monosaccharide containing 4 carbon atoms *can be further classified as either an aldose or ketose (carbohydrates)

Affinity chromatography:

A chromatography technique where compounds are separated based on highly specific binding interactions between antigen and antibody, enzyme and substrate, or receptor and ligand. Affinity chromatography is good for purifying proteins or nucleic acids from biochemical mixtures (like cell lysates, growth media, blood, etc). *The high selectivity of affinity chromatography is caused by allowing the desired molecule to interact with the stationary phase and be bound within the column in order to be separated from the undesired material which will not interact and elute first. The molecules no longer needed are first washed away with a buffer while the desired proteins are let go in the presence of the eluting solvent (of higher salt concentration). This process creates a competitive interaction between the desired protein and the immobilized stationary molecules, which eventually lets the now highly purified proteins be released. *Ex, purifying a protein of interest using an antibody: To your cell lysate sample, you add an antibody against the protein of interest. To isolate the antigen-antibody complex, a protein linked to a bead is added, this will bind the complex, so now you have: protein of interest-antibody-protein-solid support bead, all bound. The target is then isolated after centrifuging the sample and decanting the supernatant Note: not all proteins of interest have a commercial antibody available. In this case, researchers can use an affinity tag (using recombinant technology, a small affinity tag is added to the N-terminus or C-terminus of the protein) (separations and purifications)

Size exclusion chromatography:

A chromatography technique where compounds are separated based on molecular size. It is good for separating large polymers from small oligomeric fragments, or the separation of full proteins from smaller peptide chains. *the materials to be separated are dissolved in solvent, loaded onto a column packed w stationary phase, and allowed to travel to the bottom of the column where they are collected. The stationary phase consists of chemically inert porous polymer beads. The sizes of the pores in the beads are carefully controlled to allow permeation of small molecules in the eluent, while excluding larger ones. The exclusion of large molecules from the pore creates a more direct path down the column for large species than the more complicated pathway taken by compounds small enough to permeate the beads. The overall result is the quick elution of large molecules and longer retention of smaller species (separations and purifications)

Gas chromatography:

A chromatography technique where compounds are separated based on their differing volatilities. Volatility is another word for bp. *the sample is loaded into the chromatograph. It is then vaporized by a heater in the injection port and carried along by a stream of inert gas (typically helium). The vaporized sample is quickly moved by the inert gas stream into a column composed of particles that are coated w a liquid absorbent. As the components of the sample pass through the column, they interact differently w the absorbent based on their relative volatilities. As each component exits the column, it is burned, and the resulting ions are detected by an electrical detector that generates a signal that is recorded by a chart recorder. The chart recorder printout enables you to determine the number of components and their relative amounts. *Good to use if analyte can be promoted to gas phase. *Gas-liquid chromatography (GLC) is the same thing as gas chromatography (GC). *The gas part is the mobile phase, the liquid part is the stationary phase coated to the inside walls of the column. *Substrate equilibrates between mobile (gas) and stationary (liquid coat) phase. *Those with greater affinity for the stationary phase comes out of the column slower. Polar substrate has more affinity for polar stationary phase, and hydrophobic substrate has more affinity for hydrophobic stationary phase. *the less volatile components will spend more time dissolved in the liquid stationary phase than the more volatile component that will be carried along by the carrier gas at a faster rate. The more volatile components emerge from the column first. (separations and purifications)

High performance liquid chromatography (HPLC):

A chromatography technique where compounds can be separated based on differing polarities or different charge states. It is similar to column chromatography, however, the mobile phase is forced through the stationary phase at very high pressures. Both speed and efficiency of the separation is increased. Making this technique an improvement over column chromatography. *the sample to be separated is injected by syringe, then the mobile phase carries the sample to the column.. The sample is separated into its constituent components, which are detected and analyzed as they exit the column. *the stationary phase= silica gel which has been bonded to a nonpolar group, creating a relatively nonpolar stationary phase *the mobile phase= solution which is polar **the order of elution will be the reverse of what we see on TLC/paper chromatography, column chromatography, or ion exchange chromatography. Instead, the more polar compounds elute first, since they have high affinity for the mobile phase. The less polar compounds are slowed by their interactions w the nonpolar stationary phase, and therefore elute last (separations and purifications)

What is a complex ion?

A complex ion has a metal ion at its center with other molecules or ions surrounding it via coordinate covalent bonds. The metal ion acts as a lewis acid; it accepts a pair of electrons from a lewis base/nucleophile/ligand Metal+ + Lewis base: → Complex ion *The Lewis base can be charged or uncharged. *The Keq for this reaction is called Kf, or the formation constant. For ex: normally AgCl in water is only slightly soluble. Some will dissolve (giving a saturated solution), but most will remain undissolved (Ksp= 1.8x10⁻¹⁰) AgCl(s) <--> Ag+ + Cl-, here equilibrium lies to the left. *But, if we add some NH₃ to the solution, we get: Ag⁺(aq) + 2NH₃(aq) <--> Ag(NH₃)₂⁺(aq). The formation of Ag(NH₃)₂⁺ is a complex ion. Ag+ is a metal that acts as a lewis acid; it accepts an e- pair from NH₃, a lewis base; (Kf= 1.6x10⁷) tons of Ag(NH₃)₂⁺ is formed; equil lies to the right *We see that ammonium removes silver ions from solution. If you are decreasing Ag+, then equilibrium will shift to the right to make more products AgCl(s) <--> Ag+ + Cl-, equil shift to the right Thus more AgCl can dissolve bc of formation of complex ion (solubility)

Free radical:

A free radical is a chemical species with an odd number of valence electrons. Consequently, it violates the octet rule. One important example is nitrogen dioxide (NO₂), where N forms a 7-tet (bonding)

What is a hydride? How does it differ from a proton? How does it differ from a hydrogen atom?

A hydride is H:⁻ A proton is H⁺ A hydrogen is H∙ (the hydrogen atom is a hydrogen radical)

What is a pentose?

A monosaccharide containing 5 carbon atoms *a pentose can be further classified as either an aldose or ketose (carbohydrates)

Explain the structure of ATP and what bonds are present.

Adenosine triphosphate (ATP) consists of the base adenine, the monosaccharide ribose and three phosphate groups. -PHOSPHOESTER bonds link the phosphate to the sugar in ATP. *The first phosphate group is connected to the ribose with a phosphate ester bond i.e. phosphate condensed with a hydroxyl (OH) group. This is a fairly stable bond and does not qualify as a high-energy bond. Adenosine monophosphate (AMP) therefore doesn't carry enough energy to power cellular processes. -The bond between two phosphate groups is a PHOSPHOANHYDRIDE bond. This bond is less stable and is considered a high-energy bond. Adenosine diphosphate (ADP) can provide more energy than AMP. *In ATP there are three phosphate groups with two high-energy bonds. The bond with the outermost phosphate group has the most potential energy and is prone to hydrolysis. ATP is therefore a very good provider of energy for cellular processes. Note: ATP is the universal short-term energy storage molecule. Energy extracted from the oxidation of food is immediately stored in the phosphoanhydride bonds of ATP. This energy will later be used to power cellular processes. ATP may also be used to synthesize glucose or fats, which are longer-term energy storage molecules (nucleotides and nucleic acids)

Using R for the side chain, write the general structure of an amino acid.

All R groups are attached to the same α C

Draw three different D-aldopentoses in their Fischer projections. Which ones can form pyranoses?

All aldopentoses can form pyranoses

Optical activity:

All chiral molecules rotate plane-polarized light, and are optically active. *light is an EM wave *EM waves are waves of electric and magnetic fields (in phase, but perpendicular to each other and also to the direction of propagation) *normal light has the EM fields in all directions (in a 360° circle perpendicular to the direction of propagation) *polarized light has EM fields all in one direction *specific rotation= chiral molecules containing a SINGLE enantiomer will rotate polarized light (to varying degrees) either to the left or to the right. This is why chiral molecules are said to be "optically active" *right rotation: (+) or d, dextrorotatory (clockwise rotation) *left rotation: (-) or l, levorotatory (counter-clockwise rotation) *optical activity is a physical property that must be measured in lab. You cannot tell optical activity by just looking at a structure. *a PAIR of enantiomers will rotate plane-polarized light w equal magnitude, but in opposite directions. Racemic mixture= a mixture that contains equal amounts of the two enantiomers. Two enantiomers rotate light in opposite directions, so a 50:50 mixture will have a specific rotation of 0°. The mixture as a whole is not optically active (achiral) Note: (+) or (-) does not correspond to R or S configurations. And, d or l does not correspond to D and L. The upper case letters denote absolute configurations on sugars (stereochemistry of covalently bonded molecules)

Resolution:

Allows you to separate enantiomers in a racemic mixture *Step 1: you have a racemic mixture of enantiomers (contains 50% R form and 50% S form). To this mixture, you add a chiral compound that will react with each enantiomer. This will convert the enantiomers to diastereomers. Since diastereomers have diff chemical/physical properties, they can be separated. *Step 2: You separation the diastereomers by chromatography or some other means Step 3: once separated, you will have one flask containing one diastereomer, and one flask containing the other diastereomers. Then, you convert the diastereomers back to enantiomers. Now, you have successfully separated the R enantiomer from the S enantiomer!) This is necessary in drug development. Drugs contain only one form of an enantiomer, either R or S. **Summary: conversion of the racemic mixture into a pair of separate diastereomers temporarily before converting back to the pure, chiral enantiomers (separations and purifications)

London dispersion:

Also called "induced-dipole-induced dipole forces" or "Van der Waals' forces" or just "dispersion forces." A type of intermolecular force where an instantaneous dipole in a nonpolar molecule may induce a dipole in a neighboring nonpolar molecule. The force is produced by collisions that produce temporary but small dipoles by deforming the e- cloud -dispersion forces result from induced and instantaneous dipoles -all molecules have london dispersion forces, however, they are the predominant force that holds nonpolar molecules together (for polar molecules, dipole forces predominate) -thus, formed between a nonpolar molecule + nonpolar molecule -a molecule w more e-'s/larger size generates a stronger london dispersion force. For ex, F₂ has only the n=2 shell. It has less e-'s, and is smaller in size compared to I₂. I₂ is able to distort its e-'s more easily (thus moving them around).. It generates a stronger london dispersion force. Similarly, decane (C₁₀H₂₂) has a stronger dispersion force than ethane (C₂H₆) -dispersion forces are very weak and are easily cleaved *intermolecular forces (bonding)

What is a carbocation?

Also called a carbonium ion. It is a molecule with a full positive charge on carbon; usually present as a reaction intermediate. Carbocations are ALWAYS sp² hybridized (has 3 bonds). Carbocations in order from most stable to least stable: 3° > 2° > 1° > methyl 3°= R₃C⁺ 2° = R₂CH⁺ 1° = RCH₂⁺ methyl= CH₃⁺ Stability has to do with: Induction effects: carbocations are stabilized by electron-donating groups. If you have a carbocation w 3 alkyl groups surrounding it (3 R groups), it will be more stable than a carbocation w only 1 alkyl group surrounding it (1 R group). The one w 3 R groups surrounding it can donate more e- density to help w the + charge on the central C, making it more stable NOTE: alkyl substituents are ALWAYS e- donating groups. (stereochemistry of covalently bonded molecules)

Acetate:

Also called acetate ion CH3COO- (ions in solution)

Northern blotting:

Also called an RNA blot. It is a technique used to study gene expression by detection of RNA in a sample. This technique allows you to determine whether specific gene products (normal or pathogenic) are being expressed (if their mRNA is present in a cell, they are probably being translated to protein) (separations and purifications)

Hydration:

Also called solvation. Occurs when water forms a shell around ions in solution. The oxygen atom on water is partially negative, so it surrounds cations. The hydrogen atom on water is partially positive, so it surrounds anions. (ions in solution)

Ring strain:

Cycloalkanes tend to be unstable and high in energy. The spatial orientation of the atoms often creates ring strain, which weakens C-C bonds and increases reactivity. *cyclopropane has the highest ring strain *cyclobutane has the second highest ring strain *cyclohexane has the least ring strain. Any ring with greater or equal to 14 carbon atoms has the next lowest ring strain *ring strain consists of Angle (Baeyer or Bayer) strain and Torsional strain 1) Angle (Baeyer) strain is caused by deviation from the ideal sp³ tetrahedral bond angle of 109.5 degrees 2) Torsional strain is caused by the molecule having eclipsed conformations instead of staggered ones -cyclopropane has both angle (Baeyer) strain and torsional strain *in cyclopropane, all atoms are sp³ hybridized and have 60 degree bond angles (we know this bc there is 180° in a triangle). Since bond angles are less than 109.5 degrees, the C atoms are compressed like a spring and forced to fit together. Bc of this, the C bonds are highly reactive. If we allow cyclopropane to undergo a hydrogenation reaction (give back H₂), it will form linear propane, which is more stable/lower in energy *similarly, in cyclobutane, all atoms are sp^3 hybridized and have 90 degree bond angles (we know this bc there is 360° in a square). If we allow cyclobutane to undergo a hydrogenation reaction, it will form linear butane, which is more stable/lower in energy -cyclohexane, in the chair conformation, has no angle (Baeyer) or torsional strain. All angles are approximately 109.5 degrees, with staggered conformation. Cyclohexane is very stable, that's why it's often seen in nature. (stereochemistry of covalently bonded molecules)

Oxalate:

C₂O₄²⁻ (ions in solution)

Pyridine

C₅H₅N Weak base Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It is structurally related to benzene, with one carbon replaced by a nitrogen atom.

All naturally occurring carbohydrates have ___ configuration.

D *its hydroxyl group is on the right in Fischer notation; all animal carbohydrates are derived from D-glyceraldehyde *way to remember: when I eat carbohydrates, I think Damn, I'm fat. Damn, carbohydrates. (amino acids, peptides, proteins)

In the human body, what are the only type of sugars we have?

D-carbohydrates Note: the D/L configuration is assigned based on the chirality of the carbon atom farthest from the carbonyl group (carbohydrates)

What does it mean to denature a protein?

Denature= loss of native 3D structure; disruption of a protein's shape w/out breaking peptide bonds. Proteins are denatured by: urea (which disrupts H-bonds), extremes of temperature, salt concentration (tonicity), or by extremes of pH. (amino acids, peptides, proteins)

The process of forming a solution by dissolving one substance into another is known as ___.

Dissolution (ions in solution)

______ and _______ separate compounds based on boiling point.

Distillation and gas chromatography (separations and purifications)

Thermodynamics states that free energy must decrease for a reaction to proceed spontaneously. At equilibrium, hydrolysis of peptide bonds is more thermodynamically favorable than peptide bond formation. With this being said, how are peptide bonds formed and maintained inside cells?

During protein synthesis, stored energy in the form of ATP is used to force peptide bonds to form. Once the bond is formed, even though its hydrolysis is thermodynamically favorable, it remains stable bc the activation energy for the hydrolysis reaction is so high. In other words, hydrolysis is thermodynamically favorable but kinetically very slow. So the peptide bond is stable. (amino acids, peptides, proteins)

Resonance is another word for _______.

Electron delocalization. More resonance= more stability. The delocalization of electrons makes makes a molecule more stable. The molecule will spend most of its time in the most stable resonance structure. (bonding)

What are delocalized electrons?

Electrons that are not fixed in position. Resonance structures result from electrons not being fixed in position (that's why you "push" electrons when drawing resonance structures) (stereochemistry of covalently bonded molecules)

What is the first law of thermodynamics?

Energy is never created or destroyed, just transformed from one form into another. When energy passes, as work or as heat into or out from a system, the system's internal energy changes in accord with the law of conservation of energy. ∆E=Q+W *∆E is the same thing as ∆U, which is the change in internal energy *Q is the contribution from heat (thermal energy). +Q means heat is absorbed into the system (heating it). -Q means heat is released from the system (cooling it). *W is the contribution from work. +W means work was done on the system (compression). -W means work was done by the system (expansion) *work done by a gas is given by: W=P∆V, where P is pressure and ∆V is change in volume -pressure vs volume diagrams are often used when looking at 1st law problems (thermodynamics)

What is enthalpy?

Enthalpy, H, is energy stored within chemical bonds. The change in enthalpy ∆Hrxn is a measure of the heat energy that is released or absorbed when bonds are broken and formed during a reaction. -forming bonds is always exothermic, energy released, -∆H *this is why ∆H°formation values are always listed as negative -breaking bonds is always endothermic, energy needed, +∆H *this is why bond dissociation values are always listed as positive -the enthalpy change, ∆H, is also called the "heat of reaction" ∆Hrxn can be calculated three ways: 1)summation of bond enthalpies 2)heat of formation, ∆H°f 3)Hess's law of heat summation Note: when calculating, always use standard state conditions (not STP) (thermodynamics)

Is freezing water spontaneous?

Enthalpy: -going from a solid → liquid → gas, heat is needed, endothermic, +ΔH -going in the opposite direction, heat is released, exothermic, -ΔH Entropy: Disorder is decreasing, -ΔS ΔG = ΔH - TΔS Here, we have ΔG= negative - (positive)(negative) Answer: freezing water is spontaneous at a low temperature; freezing water is nonspontaneous at a high temperature (thermodynamics)

Which has a higher lattice energy, NaCl or LiF?

Lattice energy= the energy required to break the ionic bond. Felectrostatic= k |q1q2| // r^2 NaCl is larger in size compared to LiF. So, NaCl has a smaller Felectrostatic and thus a smaller lattice energy. Answer= LiF has the higher lattice energy (is harder to break)

Conformational Isomers Chair Structures:

If cyclohexane were planar, it would have bond angles of 120°. This would produce considerable strain on sp³ hybridized carbons (since ideal bond angles are 109.5°). So, cyclohexane develops a "puckered" shape. This is referred to as the chair conformation. Four carbons of the ring are in the plane of the page, one carbon is above the plane, and one carbon is below the plane. There are two chair conformations for cyclohexane, which easily interconvert at room temp. As one chair conformation flips to the other chair conformation, it must pass through several less stable conformations (called half-chair conformations) that reside as energy maximum (boat) and local energy minimum (twist boat). The hexose ring will twist and turn to achieve the most stable conformation. Conformers of Cyclohexane: 1)chair: most stable, everything staggered 2)twist boat 3)boat 4)half-chair 5)planar: least stable, everything is eclipsed *all the conformations between chair and planar are partially eclipsed -torsional strain= the strain due to eclipsing of groups across a single bond -steric interactions: substituents can be in either axial or equatorial position a) axial position= substituents lie straight up or straight down; most unstable bc the axial groups are oriented w a high degree of clashing; called 1,3-diaxial interaction b) equatorial position= substituents lie in equator of the ring; most stable bc equatorial groups are oriented away from one another; bulky groups like to be in equatorial position -when drawing a chair conformation, you can tell if substituents will be in axial or equatorial position by looking at if they are "up" or "down" on cyclohexane structure. -if substituents are both facing the same direction (both up or both down), they are cis -if substituents are not facing the same direction (one is up and one is down), they are trans *cis and trans has nothing to do w axial vs equatorial. Only has to do w up vs down when converting between the two chair conformations for cyclohexane: *take position 1 at right point and flip it down. Take position 4 at left bottom point and flip it up *fill in remaining #'s clockwise *axial become equatorial and equatorial become axial. Direction stays the same (up vs down) (stereochemistry of covalently bonded molecules)

What is a ketose?

If the carbonyl group is a ketone, the sugar is a ketose For ex, ketopentose is a five carbon sugar with a ketone group. Ketohexose is a six carbon sugar with a ketone group *In Fischer projections, ketose are distinguished by looking at the anomeric carbon. You can see that its a ketose quickly by noticing that the carbonyl (C=O) group is in the middle of the carbon chain *in Haworth projection, ketoses are distinguishable by looking at the anomeric carbon. If it does not have a H attached, it is in the ketose form *the most common ketoses are ribulose (a ketopentose) and fructose (a ketohexose) (carbohydrates)

What is an aldose?

If the carbonyl group is an aldehyde, the sugar is an aldose. For ex, aldopentose is a five carbon sugar with an aldehyde group. Aldohexose is a six carbon sugar with an aldehyde group. *in Fischer projections, aldoses are distinguishable by looking at the anomeric carbon. You can see its an aldose quickly by noticing that the carbonyl (C=O) group is located at the end of the carbon chain *in Haworth projection, aldoses are distinguishable by looking at the anomeric carbon. If it has a H attached, it is in the aldose form *the most common aldoses are ribose (a aldopentose) and glucose or galactose (an aldohexose) (carbohydrates)

Degree of unsaturation:

If the value of 2n+2 and x are different, this tells you automatically that you have an unsaturated molecule. To find the degree of unsaturation in a molecule, use the formula: dou= (2n+2) - x / 2, where n represents the number of carbon atoms, and x represents the number of hydrogens + halogens *halogen atoms, like F, Cl, Br, I: treat as if they are hydrogens *oxygen atoms: ignore (since the number of oxygen molecules has no effect) *nitrogen atoms: subtract the number of N atoms from x Note: you divide by 2 in this formula bc two H's must be removed to form 1DOU (stereochemistry of covalently bonded molecules)

How can the D or L form of a sugar be determined by structure?

In a Fischer projection, the -OH group of the last chiral center will be on the right-hand side of the structure. This stereo center will also have an R-configuration.

Neutralization reactions with a strong acid and strong base:

In all neutralization rxns, protons and hydroxide react to form a salt. With a strong acid + strong base, equimolar amounts will result in a solution that is pH neutral, where [H₃O⁺] = [OH-]. For ex, HCl (acid) + NaOH (base) → NaCl (salt) + H2O (water), protons from the acid and hydroxides from the base, if present in equal amount, will react to form water. You will also generate an ionic salt, NaCl. All the hydronium and hydroxide has been neutralized. The resulting solution is pH neutral. *note: here, you use equimolar amounts of HCl and NaOH to form a neutral solution. This is bc HCl gives one hydronium ion and NaOH gives one hydroxide ion. If, however, you were using HCl and Ca(OH)₂, then you would need twice as much acid as base to form a neutral solution. This is bc HCl give one hydronium ion and Ca(OH)₂ gives you two hydroxide ions (acid/base equilibria)

Neutralization reactions with a strong acid and weak base:

In all neutralization rxns, protons and hydroxide react to form a salt. With a strong acid + weak base, a small volume of strong acid and a large volume of weak base will be needed to get a solution that is pH neutral, where [H₃O⁺] = [OH-]. For ex, if your strong acid and weak base are present in equal amounts: HCl (strong acid) + NH₃ (weak base) <--> NH₄⁺ + Cl-, if a strong acid like HCl reacts with a weak base like ammonia, the resulting solution will at first be weakly acidic bc the strong acid will completely protonate the base, forming the ammonium ion (you will also get some salt, NH₄Cl). Since the ammonium ion is weakly acidic, it will generate hydronium ion in solution, NH₄⁺ + H₂O <--> NH₃ + H₃O⁺, which makes the solution acidic. Thus, to get a neutral solution, you need to add a higher concentration of the weak base (acid/base equilibria)

Neutralization reactions with a weak acid and strong base:

In all neutralization rxns, protons and hydroxide react to form a salt. With a weak acid + strong base, a large volume of weak acid and a small volume of strong base will be needed to get a solution that is pH neutral, where [H₃O⁺] = [OH-]. For ex, if your weak acid and strong base are present in equal amounts: CH₃COOH (weak acid) + NaOH (strong base) <--> CH₃COO- + H₂O, if a weak acid like acetic acid reacts with a strong base like sodium hydroxide, the resulting solution will at first be weakly basic bc hydroxide from the strong base will completely deprotonate the weak acid, forming the acetate ion. Since the acetate ion is weakly basic, it will generate hydroxide ion in solution, CH₃COO- + H₂O <--> CH₃COOH + OH-, which makes the solution basic. Thus, to get a neutral solution, you need to add a higher concentration of the weak acid (acid/base equilibria)

Neutralization reactions with a weak acid and weak base:

In all neutralization rxns, protons and hydroxide react to form a salt. With a weak acid + weak base, it is difficult to predict what volume of weak acid and weak base you should add to get a solution that is pH neutral. If your weak acid and weak base are present in equal amounts, your solution might be acidic, basic, or neutral depending on which is slightly weaker, the acid or the base. For ex, CH₃COOH (weak acid) + NH₃ (weak base) <--> CH₃COO- + NH₄⁺ (acid/base equilibria)

What is a heteroatom?

In chemistry, a heteroatom is, strictly, any atom that is not carbon or hydrogen. For ex, O, N, S, P, Cl, Br, I, etc. (stereochemistry of covalently bonded molecules)

Radioimmunoassay (RIA):

Similar to ELISA, but uses radiolabeled antibodies rather than enzyme-linked antibodies. Thus, the presence of target proteins or antibodies is assayed by measuring the amount of radioactivity instead of a color change. RIA's are used in the medical field often to measure the amount of hormones or drugs in a pt's serum *For ex, if checking for the concentration of insulin in a pt's serum: 1)a known amount of radiolabeled antigen (for ex, insulin that was synthesized in lab), is incubated w a known amount of antibody that is specific to the antigen 2)the insulin:antibody complexes are isolated 3)the total amount of radioactivity is measured 4)unlabeled insulin (also called cold insulin) is mixed into the solution in increasing amounts. The cold insulin completes w the labeled insulin (hot insulin) for the antibody. As more cold insulin is added, less total radioactivity is recovered and measured. This competition assay helps formulate a standard curve *steps 1-3 are repeated using pt serum instead of the cold insulin. The standard curve is used to extrapolate the amount of insulin that is circulating in a pt's serum (separations and purifications)

Sphingolipids:

Similar to phospholipids except the backbone is sphingosine instead of glycerol. The only significant sphingolipid in humans is sphingomyelin, an important component of the myelin sheath around neurons (lipids)

How does soap help to remove grease from your hands?

Soaps are the sodium salts of fatty acids (RCOO- Na+). They are amphipathic, which means both hydrophilic and hydrophobic. Grease is hydrophobic. It does not wash off easily in water bc it is not soluble in water. Scrubbing your hands with soap causes micelles to form around the grease particles. Thus, the grease dissolves in the center of the micelle, allowing you to wash it away. (lipids)

If you dissolve Na(CH3COO) in water, what happens?

Sodium acetate is a basic salt. It is the salt of a weak acid (formed from a WA + SB). It will break into Na+ and CH3COO- in water. Na+ is a group 1 cation and does not react w water. CH3COO- is a stronger base than water (anion does not contain Cl-, Br, or I-) Therefore, a solution of the salt will be basic, and have a pH > 7. CH3COO- + H2O <--> CH3COOH + OH- (acid/base equilibria)

Acid strength trends:

Something is a stronger acid if: 1) More positively charged: larger positive charge means it is more acidic; they want to accept e-'s or lose H+ badly. For ex, NH₄⁺ is more acidic that neutral NH₃. Fe³⁺ is more acidic than Fe²⁺ 2) comparing two elements in the same row/period, the more electronegative element is more acidic. As an example, comparing H2O and CH₄. Both have H, the only difference is oxygen and carbon. Since O and C are in the same row, and O is more electronegative, H₂O is a stronger acid than CH₄ 3) comparing two elements in the same family/column/group, the element w a larger atomic radii is more acidic. This is bc as radii increases, the e-'s are not held as tightly to the nucleus (can accept e- pairs easier, or lose H+ better) (acid/base equilibria)

Base strength trends:

Something is a stronger base if: 1) more negatively charged: larger negative charge means it is more basic; it wants to donate e- pairs or accept H+ badly. For ex, OH- is more basic than H₂O. And CO₃²⁻ is more basic than HCO₃⁻ 2) comparing two elements in the same row/period, the less electronegative element is more basic. For ex, comparing NH3 and HF, N is less electronegative than F, so NH₃ is more basic 3) comparing two elements in the same family/column/group, the element w a smaller atomic radii is more basic. For ex, comparing F- and I-, F- is smaller in size, so it is more basic (acid/base equilibria)

Inductive and resonance effects contributes to ____ of a molecule.

Stability (stereochemistry of covalently bonded molecules)

Four types of acids and four types of bases:

Strong acid → weak conjugate base Strong base → weak conjugate acid Weak acid → Stronger conjugate base Weak base → Stronger conjugate acid *In order from strongest acid to weakest acid: strong acid > weak acid = stronger conjugate acid >>>>> weak conjugate acid, the weak conjugate acid (derived from a strong base) is not even acidic... Acts more like a base. *In order from strongest base to weakest base: strong base > weak base = stronger conjugate base >>>>> weak conjugate base, the weak conjugate base (derived from a strong acid) is not even basic... Acts more like an acid. For ex, when looking at the strong acid HCl in water, HCl + H2O → H3O+ + Cl-, here Cl- does not act as a base. It does not want to donate e-'s or accept a H+ (acid/base equilibria)

List important organic functional groups in order from most acidic to least acidic:

Strong acids (HClO4, HI, HBr, HCl, HNO3, H2SO4) > sulfonic acids (R−S(=O)₂−OH) > carboxylic acids > phenols > alcohols and water > aldehydes and ketones (α hydrogens) > sp hybridized CH bonds > sp² hybridized CH bonds > sp³ hybridized CH bonds (stereochemistry of covalently bonded molecules)

List the strong acids:

Strong acids which dissociate completely in water, (Ka > 1), includes: 1)Perchloric acid, HClO₄ 2)Hydroiodic acid, HI 3)Hydrobromic acid, HBr 4)Sulfuric acid, H₂SO₄ *note: this is the only diprotic strong acid there is! Can lose two H+ 5)Hydrochloric acid, HCl 6)Nitric acid, HNO₃ 7)Hydronium ion, H₃O⁺ or H+ *strong acids completely dissociate in solution *complete dissociation occurs bc the conjugate base anion is highly stable *any acid that is not listed above is considered to be a weak acid *acids always decrease in oxidation state (acid/base equilibria)

Name the strong acids and strong bases

Strong acids= HClO₄, HI, HBr, HCl, HNO₃, H₂SO₄ Strong bases= group 1 hydroxides and oxides; Ba/Sr/Ca hydroxides; metal amides

List the strong bases:

Strong bases which dissociate completely in water, (Kb > 1), includes: NaOH, Na₂O, Ca(OH)₂, CaO, Hydride (H-), AMide (NH₂⁻), KOH Now Now Cow Cow, HAM OHK? 1) All group 1 hydroxides, (OH-), for example: Lithium hydroxide, LiOH --> Li+ + OH- Sodium hydroxide, NaOH Potassium hydroxide, KOH Rubidium hydroxide, RbOH Cesium hydroxide, CsOH 2) Group 1 oxides, (O²⁻), for example: Lithium oxide, Li₂O --> 2Li+ + O²⁻, and O²⁻--> 2OH- Sodium oxide, Na₂O *oxides are diprotic (will bind two H+) 3) Some group 2 hydroxides, (OH-), for example: Calcium Hydroxide, Ca(OH)2 --> Ca^2+ + 2OH- Strontium hydroxide, Sr(OH)2 Barium hydroxide, Ba(OH)2 4) anything that produces a hydride, (H-), for example: Sodium hydride, NaH --> Na+ + H-, and H- --> OH- 5) anything that produces an amide, (NH₂⁻) for example: metal amides like Sodium amide, NaNH₂ --> Na+ + NH₂⁻, and NH₂⁻ --> NH3 6) anything that produces a carbanion, (R-), for example: Butyllithium, LiC₄H₉ --> Li+ + C₄H₉⁻, and C₄H₉⁻--> C4H10 *strong bases completely dissociate in solution *complete dissociation occurs bc the conjugate acid cation is highly stable *bases always increase in oxidation state (acid/base equilibria)

What is the 2nd law of thermodynamics?

The 2nd law states that disorder/entropy in the universe is always increasing. ΔS is entropy; positive is favorable, disorder increasing ΔG = ΔH - TΔS, Higher temps, higher ΔS, or low ΔH is favorable -entropy has units of J/K -molar entropy has units of J/mol⋅K -reactions that produce more moles of gas have a greater increase in entropy -an isolated system will increase in entropy over time -an open system can decrease in entropy, but only at the expense of a greater increase in entropy of its surroundings -the universe as a whole is increasing in entropy Three things can change entropy: 1) increasing the number of particles increases entropy *if you have a classroom w 5 people vs if you have a classroom w 500 people. The classroom w 500 people has much more disorder (higher entropy!) 2) changing phases from solid → liquid → gas increases entropy 3) increasing the temperature increases entropy The 2nd law also states that during any thermodynamic process heat cannot be completely converted to work. For ex, when you heat a steam engine- some heat is used for useful work and some heat is lost to the environment. No machine is 100% efficient. And heat always flows from hot to cold areas. (thermodynamics)

What rules should be followed when prioritizing substituents on a chiral center to assign absolute configuration?

The Cahn-Ingold Prelog rules, which state to find the first point of difference in the substituents, and assign highest priority based on atomic number (and atomic mass in the case of isotopes). Triple bonds are higher priority than double bonds, which are higher priority than single bonds bc multiple bonds count as bonds to multiple atoms

What two pieces of information are needed to calculate the pH of a weak acid?

The Ka and molarity of the acid pH= -1/2 log(Ka[WA])

What are two common techniques to synthesize amino acids?

The Strecker and Gabriel-malonic ester synthesis

In an extraction, why are organic acids soluble in an aqueous basic solution?

The acid gets deprotonated to form a salt, and salts (charged species) are water soluble

Which of the two functional groups of an amino acid is more basic?

The amino group

What is the enthalpy of formation?

The amount of energy associated with forming one mole of a compound from its constituent elements in their standard states.

In carbohydrates in their pyranose form, the anomeric carbon is part of what functional group?

The anomeric carbon is part of a hemiacetal.

What equilibrium exists in water that is shifted by the addition of an acid or a base, and what is the value of K for this reaction at standard conditions?

The autoionization of water, for which Kw=10⁻¹⁴ at standard conditions (1atm and 25C)

Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions w neighboring alkyl chains in a bilayer membrane?

The bent shape of the unsaturated fatty acid means that it doesn't fit in as well and has less contact w neighboring groups to form van der Waals interactions. Unsaturation makes the membrane less stable, less solid. (lipids)

What is the conjugate base of HBrO (hypobromous acid)? A)H+ B)H2BrO2 C)H2BrO+ D)BrO-

The conjugate base of HBrO is BrO- (acid/base equilibria)

Explain the dissociation of carbonic acid:

The dissociation of carbonic acid, a weak acid is: H₂CO₃ + H₂O <--> H₃O⁺ + HCO₃⁻ Here, a weak acid, H₂CO₃, makes a stronger conjugate base, HCO₃⁻. Carbonic acid is said to be POLYPROTIC bc it has more than one proton to donate. So, HCO₃⁻ + H₂O <--> H₃O⁺ + CO₃²⁻ Here, HCO₃⁻ is now acting as an acid (it gives a H+) *whenever a substance acts as either an acid or a base, it is AMPHOTERIC *the conjugate base of a weak polyprotic acid is always amphoteric, bc it can either donate or accept another proton *also, notice that HCO₃⁻ is a weaker acid than H₂CO₃. In general, every time a polyprotic acid donates a proton, the resulting species will be a weaker acid than its predecessor (acid/base equilibria)

Ribonuclease has eight cysteines that form four disulfide bonds. What effect would a reducing agent have on its tertiary structure?

The disulfide bridges would be broken. Tertiary structure would be less stable, but the protein shape would not change. Disulfides only "lock" into place tertiary protein structures that first form on its own. If disulfide bonds were broken, the shape would just be less sturdy. Like a concrete wall w/out the rebar. (amino acids, peptides, proteins)

Mutarotation:

The equilibrium between the alpha and beta anomers (the interconversion between two anomers) (carbohydrates)

Explain α and β carbons in organic molecules:

The first carbon atom after the carbon that attaches to the functional group is called the alpha carbon (Cα). The second is called the beta carbon (Cβ), the third is called the gamma carbon (C𝛾). The system continues naming in alphabetical order with Greek letters. (stereochemistry of covalently bonded molecules)

How does molecular weight in hydrocarbons affect mp and bp?

The greater the MW of a compound, the more surface area there is to interact, the greater the number of van der Waals interactions, and the higher the mp and bp. For ex, hexane (a six-carbon alkane) has a higher mp and bp than propane (a three-carbon alkane) **small hydrocarbons (1 to 4 carbons) tend to be gases at room temp **intermediate hydrocarbons (5 to 16 carbons) tend to be liquids at room temp **large hydrocarbons (> 16 carbons) tend to be (waxy) solids at room temp (separations and purifications)

Extraction:

Two types of extraction: 1) Liquid-liquid extraction: First, pour your solution in the separatory funnel, and shake it. Then you let it settle; 2 diff layers will form. One with a higher density will be on the bottom, while the one w the lower density will be on top. -thus, organic compounds can be separated via extraction based on their differing solubility in aqueous or organic solvents. The aqueous phase includes substances that are highly polar or charged, including inorganic salts, strong acids and bases, and polar low molecular weight compounds (less than 5 carbons), such as alcohols, amines, and carboxylic acids. The organic phase includes substances that are insoluble or neutrally charged (like hydrocarbons). 2) acidic or basic extractions: organic acids (COOH's and PhOH's) and bases (amines) can undergo acid-base reactions to generation ions, which will preferentially dissolve in the aqueous layer during an extraction a) extraction of carboxylic acids: using a dilute weak base (like 5% sodium bicarbonate, NaHCO3), converts carboxylic acids into their anionic salts (which are soluble in the aq layer) b) extraction of phenols: using a dilute strong base (like 10% NaOH), will convert phenols into their anionic salts. *Note: this will also convert carboxylic acids to their anionic salts c) extraction of organic amines: using a dilute strong acid (like 5% HCl), will protonate basic functional amine group, forming a cationic salt. (separations and purifications)

What is standard state conditions?

Used for thermodynamic calculations -all gases are at 1atm pressure -temp = 25C or 298K -all aqueous reactants in the solution are present at 1M concentrations -substances are present in their standard states (standard states means how something naturally exists at room temp. For ex, mercury is liquid at room temp. That is its standard state) -the energy of formation of an element in its standard state is zero -values that have been determined under standard state are given a ° subscript (for ex, ∆H°) (thermodynamics)

Conjugate acid and conjugate base:

Used when talking about Bronsted acids and bases. When an acid donates a H+, the remaining structure is called the conjugate base. When a base accepts a H+, the new species is called the conjugate acid. H-Acid + Base- → Acid- + H-Base Acid: proton donor Base: proton acceptor Conjugate base: acid after losing its proton Conjugate acid: base after gaining its proton *IF YOU EVER NEED TO WRITE A CB OR CA, JUST ADD OR REMOVE A HYDROGEN (acid/base equilibria)

Shape/molecular geometry:

VSEPR theory, used to predict the molecular geometry/shape of molecules. The angles between e- groups around the central atom are maximized for greatest stability. VSEPR stand for "valence shell electron-pair repulsion" -the VSEPR number (also called steric number)= the total number of bonds + unbonded electron pairs -this will also tell you the hybridization *radicals also count as an e- pair *when calculating the VSEPR number, always look at the central atom -the number of unbonded e- pairs/lone pairs determines the bond angles A) 2 groups, VSEPR is 2 = sp = a hybrid between one s w one p orbital. e- geometry/orbital geometry: linear, bond angles are 180 degrees shape/molecular geometry: linear (something w 2 things bonded to it; 180 degrees), Ex= CO₂ B) 3 groups, VSEPR is 3 = sp² = a hybrid between one s w 2 p orbitals. e- geometry/orbital: trigonal planar shape/molecular geometry is either: -Trigonal planar (something w 3 things bonded to it; 120 degrees), Ex= CO₃²⁻ -Bent (something w 2 things bonded to it and 1 lone pair; <120 degrees), Ex= O₃ C) 4 groups, VSEPR is 4 = sp³ = a hybrid between one s w 3 p orbitals. e- geometry/orbital geometry: tetrahedral shape/molecular geometry: -Tetrahedral (something w 4 things bonded to it; 109.5 degrees), Ex= CH₄ -Trigonal Pyramidal (something w 3 things bonded to it, 1 lone pair; <109.5 degrees), Ex= H3O⁺ -Bent (something w 2 things bonded to it, 2 lone pairs; <<109.5 degrees), Ex= H2O D) 5 groups, VSEPR is 5 = sp³d = hybrid between one s, three p orbitals, and one d orbital e- geometry/orbital geometry: trigonal bipyramidal (something w 5 things bonded to it; 90 and 120 degrees) shape/molecular geometry: -Trigonal Bipyramidal (something w 5 things bonded to it; 90 degrees and 120 degrees), Ex= PF₅ -Seesaw (something w 4 things bonded to it, one lone pair; 90 degrees and 120 degrees), Ex= TeCl₄ -T-shaped (something w 3 things bonded to it, two lone pairs; 90 degrees), Ex= ClF₃ -Linear (something w 2 things bonded to it, three lone pairs; 90 degrees and 120 degrees), Ex= I₃⁻ E) 6 groups, VSEPR is 6 = sp³d² = hybrid between one s, three p orbitals, and two d orbitals e- geometry/orbital geometry: octahedral (something e 6 things bonded to it; 90 degrees) shape/molecular geometry: -Octahedral (something w 6 things bonded to it; 90 degrees), Ex= SF₆ -Square Pyramidal (something w 5 things bonded to it, one lone pair; 90 degrees), Ex= SbCl₅²⁻ -Square Planar (something w 4 things bonded to it, two lone pairs; 90 degrees), Ex= ICl₄⁻ -T-shaped (something w 3 things bonded to it, three lone pairs; 90 degrees) -Linear (something w 2 things bonded to it, four lone pairs; 90 degrees) (bonding)

Compare an alkyl vs aryl vs acyl vs acetyl

Way to remember: ALkyl= ALkane aRyl= Ring aCYL= Carbonyl + alkYL group aCETyl= Carbonyl + mEThyl *note: aryl is any functional group derived from an aromatic ring, usually an aromatic hydrocarbon by removal of a H atom (such as phenyl and naphthyl)

List common weak acids:

Weak acids do not dissociate completely in water, equation will have equilibrium arrows, Ka <1 1) Formic acid, HCOOH 2) Acetic acid, CH3COOH 3) Benzoic acid, C6H5COOH 4) Hydrofluoric acid, HF 5) Hydrocyanic acid, HCN 6) Hydrogen sulfide, H2S 7) Water, H2O 8) carbonic acid, H2CO3 9) phosphoric acid, H3PO4 *weak acids partially dissociate in solution *partial dissociation occurs bc the conjugate base is somewhat stable (acid/base equilibria)

List common weak bases:

Weak bases do not dissociate completely in water, equation will have equilibrium arrows, Kb <1 1) Ammonia, NH3 2) Amine, NR3 3) Pyridine, C5H5N 4) Ammonium hydroxide, NH4OH 5) Water, H2O *weak bases partially dissociate in solution *partial dissociation occurs bc the conjugate acid is fairly/somewhat stable *dissociation of weak acids and bases (acid/base equilibria)

When is the entropy of a substance equal to zero?

When a pure element is solid at 0K

When does pH=pKa for a buffer? What is this point called in a titration?

When the concentrations of the weak acid and its conjugate base are equal (this occurs at the half-equivalence point in a titration experiment)

What is a Halide in solution? What is a hypohalide?

X- and XO- (ions in solution)

Is it possible to separate enantiomers by biological means?

Yes. Enzymes are highly specific and can differentiate between enantiomers. For example, if an enzyme digests or modifies all L-amino acids, then you'd be able to use that enzyme to separate a D/L racemic mixture. *Note: in nature, all proteins are made up of L-amino acids. remember, sugars and amino acids can be in either L or D forms (separations and purifications)

Southern blotting:

a procedure for identifying specific sequences of DNA, in which fragments separated on a gel are transferred directly to a second medium on which detection by hybridization may be carried out. Steps for southern blotting: 1)separate the DNA fragments on an electrophoresis gel; restriction endonuclease may be used prior to gel electrophoresis to cut the DNA into smaller pieces; prior to electrophoresis or after, the DNA is denatured to ssDNA. This is necessary for later hybridization to the probe. 2)transfer the fragments to a nitrocellulose membrane (via blotting) 3)add a labeled probe to the membrane (in buffer solution). Hybridization probes are short ss sequences of nucleic acid (usually DNA) that are: -complementary to (and thus will base-pair) with your target DNA -constructed with radiolabeled nucleotides, which allows visualization of the target sequence *probes are often engineered to complement mutations or certain gene rearrangements, making Southern blotting a useful diagnostic tool. 4)after hybridization, excess probe is washed from the membrane and the pattern of hybridization is visualized on X-rayfilm by autoradiography. (separations and purifications)

Western blotting:

a procedure used to detect and analyze proteins. Western blotting is used as a diagnostic tool in medicine, for ex, you can determine whether cancer cells express certain tumor promoting growth receptors on their surface. Steps for western blotting: 1)cells are collected and solubilized in detergent to release their cytoplasmic contents 2)cell lysates, which contain hundreds of diff proteins, are denatured (denaturation occurs by SDS). Lysates and a ladder are loaded onto a gel. The ladder is used so protein size can be compared to a standard. 3)an electric current is applied. Bc of the detergent used, the proteins are all negatively charged. Therefore, they migrate toward the positive electrode. -larger charge=more electrical force=travels faster (AA's will have diff charges due to diff isoelectric points) -smaller protein=squeezes through easier=travels faster -structure plays no role bc SDS has denatured the protein *gel electrophoresis= SDS-PAGE 4)the separated proteins from the gel are transferred to a nitrocellulose or PVDF membrane. 5)the membrane is probed for the target protein. Probing for proteins in western blotting is diff than probing in southern or northern blotting in that antibodies are used as probes, not nucleic acids. A primary antibody is used first, which will recognize only the target protein. Then, an enzyme-linked secondary antibody is used that recognizes the constant region of the primary antibody. The enzyme on the secondary antibody will fluoresce when a detection substrate is added, and this light can be photographed. The target protein will show up as a band w an intensity that is proportional to the abundance of the protein in the sample (separations and purifications)

What is a racemic mixture?

a racemic mixture is a 50/50 mixture of two enantiomers

What is a salt in chemistry?

a salt is an ionic compound, consisting of a cation and an anion Salt= cation+anion In water, the salt dissociates into ions and depending on how these ions react with water, the resulting solution can be either acidic, basic, or pH neutral. For the CATION of a salt, there are two possibilities: 1) doesn't react w water; It is not an acidic salt. Solution will not be acidic. Group 1 cations (Na+, Li+, K+) and LARGER Group 2 cations are not acidic *can become hydrated, but does not react w water. Remember, a SB --> WCA. The WCA is very stable; does not want to react with anything. 2) is a stronger acid than water; reacts w water. It is an acidic salt; Solution will be acidic. Cations that do not contain Group 1 or Group 2 elements are acidic. *remember, WA --> stronger CB and WB--> stronger CA. The stronger CB or CA can react w water. For the ANION of a salt, there are two possibilities: 1) doesn't react w water; salt is not basic. Cl-, Br-, and I- do not want to react with anything *Remember, SA--> very WCB. The WCB is stable, does not want to react w anything. 2) reacts w water; salt is basic. Remember, WA --> stronger CB. The stronger CB can react w water. Primarily, anions that are not Cl-, Br-, or I- are basic. *salts are formed by a neutralization reaction with an acid and a base. *the reaction of a salt with water is called a hydrolysis reaction (this is a more general use of the term since the water molecule may or may not be split) *Salts that produce acidic solutions when dissolved in water are called acidic salts. Salts that produce basic solutions when dissolved in water are called alkali/basic salts. Neutral salts produce neither an acidic or basic solution, for ex, NaCl. (acid/base equilibria)

Indicators:

a weak acid that undergoes a color change when its converted to its conjugate base. HA + H2O <--> H3O+ + A-, here when the indicator is in its nonionized form, HA, it will be of one color. When its in its ionized form, A-, it will be a different color. Indicators behave just like weak acids/bases. And, Ka= [H3O+][A-] / [HA] *HOW TO SELECT AN INDICATOR: Choose an indicator that has a pKa within approximately +/- 1pH unit of the acid in question. This will result in either the indicator being protonated or deprotonated. Allowing the indicator to do its job (determining pH of the solution!) *note: the indicator is present in such a small amount that is doesn't affect the solution's pH (titration)

What must be present in order for resonance to occur?

a π bond so that electrons can be delocalized

Acid base titrations:

an acid base titration is an experimental technique used to determine the identity of an unknown acid (or base) by determining its pKa (or pKb); or it can be used to determine the concentration of an unknown acid or base The procedure consists of adding a strong acid (or a strong base) w a known identity and concentration, (the titrant), to a solution containing the unknown base (or acid). When the titrant is added in small, discrete amounts, the pH of the solution is recorded w a pH meter. Important points: *Buffering region= section of the titration curve where the pH changes very gradually. On a titration curve, this is where the graph is flat (occurs when titrating WA w SB or WB w SA) *Half-equivalence point (also called the point of inflection)= at exactly one-half the volume of the equivalence point, the measured pH is equal to the pKa (there is equal concentrations of HA and A-) *Equivalence point= point in titration at which the amount of titrant added is just enough to completely neutralize the analyte solution. At the equivalence point in an acid-base titration, moles of base = moles of acid, and the solution only contains salt and water. *For ex, the titration of a weak acid, HF, with a strong base, NaOH: When no titrant is added, the pH of the solution is just the pH of HF. Then, as NaOH is added, an equivalent amount of HF will be neutralized, NaOH + HF → Na+ + F- + H2O. As HF is neutralized, the pH will increase some, but not a ton at first. This is bc you have both HF and F-, which is acting as a buffer (BUFFERING REGION). In the buffering region, when you have equal amounts of HF and F-, this is the HALF-EQUIVALENCE POINT (pH of the solution=pKa of HF. We know this bc pH=pKa[products/reactants], since products and reactants are in a 1:1 ratio, you are left w pH=pKa). As you continue adding NaOH, the solution suddenly loses its buffering capacity, and the pH increases dramatically. The ACID-BASE EQUIVALENCE POINT occurs when just enough NaOH has been added to neutralize all HF. At this point, you simply have Na+, F- , and H2O in solution (no OH- or H+). After the equivalence point, as we continually add NaOH, the concentration of OH- rises and remains in solution (there is no H+ for it to react w). Thus, the pH continues to increase, until the OH- concentration in solution is not that much different than the OH- concentration in the titrant. From here on, the pH doesn't change very much and the curve levels off. Four types of acid base titrations: 1)SA titrated w a SB 2)SB titrated w a SA 3)WA titrated w a SB 4)WB titrated w a SA (titration)

To what does the term unsaturated refer?

an unsaturated molecule contains one of more rings or π bonds, such that it does not contain the maximum possible amount of hydrogen

Polyatomic ions:

another word for a molecular ion, made up of >2 atoms (ions in solution)

Are molecules with five or fewer carbon atoms that also bear a polar functional group more soluble in the aqueous or the organic layer in an extraction?

aqueous

Bases:

bases want to donate e- pairs or accept H+ negatively charged things want to donate e-'s or accept H+, thus becoming neutral or positively charged 1)Bronsted Bases= accepts a H+ 2)Lewis Base/Nucleophile/Ligand= donates an e- PAIR 3)Arrhenius= produces OH- in water *chelate: donates more than one e- pair. Reactions where something donates both e-'s to make a chemical bond is called a coordinate covalent bond/coordinate complex. Acid/base reactions produce coordinate covalent bonds (base donates both e-'s, while acid accepts both e-'s, forming a bond) (acid/base equilibria)

Ionic bonds:

forms when e-'s transfer completely from one atom to another, resulting in oppositely charged species that attract each other via electrostatic interaction -formed between metal + nonmetal *a metal donates an e- to a nonmetal. They are held together by electrostatic interaction between a cation and an anion, but are two separate entities (no sharing of e-'s). Felectrostatic= k q₁q₂/r^2 -the diff between electronegativities in the two elements must be LARGE (they must have very diff electronegativities). This is why e- are not shared! -the strength of the ionic bond is proportional to the charges on the ions, and inversely proportional to atomic size. Strengthionicbond ∝ charge ∝ 1/radii ∝ 1/distance The ionic bond strength decreases as ions get farther apart, or as the ionic radii increase. We can use this to estimate the relative strength of diff ionic bonds For ex, MgS vs NaCl. In MgS, the magnesium ion has a charge of +2, while the sulfide ion has a charge of -2. For NaCl, the charges are +1 for sodium and -1 for chloride. Therefore, the MgS bond is ~4x as strong. -LARGE charges and SMALL ions/small atomic size = strongest ionic bonds -ionic bonds are the strongest intermolecular force. In SOLID form (not in a aq solution): -an ionic solid is held together by the electrostatic attraction between cations and anions in a lattice structure (crystal lattice) -e- are localized (not moving) -e- are transferred to more electronegative atom -compounds w ionic bonds, when not in an aq solution, are insulators (do not conduct electricity) and are brittle/hard (not malleable or ductile; cannot be shaped without cracking/breaking)) In DISSOCIATED/ELECTROLYTE form (in an aq solution): -e- are localized (not moving) -e- are transferred to more electronegative atom -compounds w ionic bonds, when in an aq solution, are conductors (conduct electricity) *intermolecular forces (bonding)

Sucrose is a disaccharide composed of ____ and _____. Is sucrose a reducing sugar?

glucose + fructose *pyranose + furanose Sucrose is not a reducing sugar *It has 1,2-glycosidic linkages (linked together by the hydroxyl groups on the two anomeric carbon; making two acetals). Only hemiacetals are in equilibrium with their straight/open chain forms. Acetals are quite stable, and only exist in the cyclic form. Thus, there is no aldehyde or ketone that can be oxidized. Sucrose is a non-reducing sugar bc it cannot act as a reducing agent. (carbohydrates)

Lactose is a disaccharide composed of ____ and _____. Is lactose a reducing sugar?

glucose + galactose *pyranose + pyranose Lactose is a reducing sugar *It has 1-4-glycosidic linkages. The linkage consists of one acetal and one hemiacetal. Hemiacetal sugars in solution exist in equilibrium between the straight/open chain form and cyclic form. When in the straight chain form, the aldehyde can be oxidized to a carboxylic acid. Lactose is called a reducing sugar bc it is able to act as a reducing agent, while itself being oxidized. (carbohydrates)

Stereoisomers:

have the same molecular formula, same connectivity, but have different 3-D arrangements across one or more asymmetric (chiral) centers. They cannot be interconverted by rotation around σ bonds. *you can't have stereoisomers if you don't have a chiral center *a compound will have a total of 2^# of chiral centers = stereoisomers, if it is not meso *stereoisomers have the same chemical properties Types of stereoisomers: 1)enantiomers (non-superimposable mirror images (R/S)); meso 2)diastereomers (non-superimposable non-mirror images); epimers or anomers (D/L and 𝜶/β); geometric isomers (cis/trans, Z/E) (stereochemistry of covalently bonded molecules)

Conformational isomers:

have the same molecular formula, same connectivity, same stereochemistry, but can rotation about a σ bond to switch between different conformations. *In truth, conformational isomers are not really isomers bc you don't have to break any bonds to convert from one conformation to another. They are more accurately called conformers *Identical chemical and physical properties; cannot be isolated. *conformational isomers are visualized using Newman projections (eclipsed vs staggered) OR Chair conformations (when looking at cyclohexane) (stereochemistry of covalently bonded molecules)

R and S configurations:

if a molecule has a chiral center, it can be assigned an absolute configuration (R/S). This allows you to visualize how the substituent groups are oriented in space on a chiral center. Rules for assigning R/S configurations: 1)assign priority (1-4) to atoms directly bonded to chiral center -atom w highest atomic number has highest priority (for ex, Cl > O) -heavier isotopes have higher priority (for ex, T (tritium) > D (deuterium) > P (protium)) -if two atoms on a chiral center are identical, move to the next atom to find the first point of difference; the atom w the higher atomic # takes priority -multiply-bonded atoms count as 2x single bonded atoms 2)ensure lowest priority substituent is oriented away -if lowest priority group is not pointing away, exchange two groups so the lowest priority group is pointing away 3)trace an arc from group 1 to 2 to 3 -clockwise= R -counter-clockwise= S 4)if you had to change two groups on chiral center, invert the configuration. R --> S and S --> R (stereochemistry of covalently bonded molecules)

Chelate:

in reference to coordinate covalent bonds, a chelate is a molecule (nucleophile/ligand/lewis base) that can donate more than one e- pair to an electrophile. Oftentimes two diff atoms in one molecule will each donate a pair of e-'s to another molecule (bonding)

Intermolecular forces:

intEr = Exit, outside external forces between molecules, occurs when opposite charges attract each other. *The strength of an intermolecular force depends on: (1) charge. Larger charges correspond to stronger attractive forces. For ex, +3 and -3 will be more attracted to each other than +1 and -1. *types of intermolecular forces: -ionic bonds -dipole-dipole -london dispersion -H-bonds (bonding)

Intramolecular forces:

intrA = Arrive at the center internal forces between molecules; bonding. Chemical bonds are formed when e- are shared between two atoms as their orbitals overlap. *Types of intramolecular forces include: -covalent bonds -metallic bonds -coordinate covalent bonds (bonding)

Name the various intermolecular forces, from strongest to weakest

ionic bond > hydrogen bonds > dipole-dipole forces > LDF

Define isobaric, isochoric, isothermal, and adiabatic

isobaric= constant pressure; isochoric= constant volume; isothermal= constant temperature; adiabatic= no heat is exchanged between the system and its environment

Leaving groups:

leaving groups are more likely to dissociate from their substrate if they are more stable in solution. -when a LG breaks off, it takes a pair of e-'s w it. To make this more stable, a good LG should have: 1) resonance 2) larger size (larger size= better LG bc negative charge is more spread out) 3) if possible, a neutral LG is better than a charged LG *this can be accomplished by adding an acid catalyst. For ex, an alcohol functional group is unlikely to dissociate from a molecule (OH- is not stable in solution). However, treating the compound w an acid protonates a lone pair of electrons on the oxygen, thereby making the functional group OH₂⁺. This altered group can dissociate as a neutral water molecule, H2O. This is the reason why organic reactions are often acid catalyzed bad leaving groups: 1)strong bases (HO-, RO-, NH₂⁻, etc); small atoms that don't have resonance *if you have an acid catalyst, this will convert a bad LG to a good LG *LG tendency is inversely proportional to basicity, LG ∝ 1/basicity *the best LG is a very weak base 2) H and alkanes are (almost) never leaving groups. You don't want to put a negative charge on a C or H (stereochemistry of covalently bonded molecules)

Tertiary carbocations are ______ than primary carbocations.

more stable (stereochemistry of covalently bonded molecules)

Thermal expansion:

most materials expand as their temperature increases. This is why bridges have expansion slots. If the bridge got longer in response to an increase in temperature but had no room to expand, it would buckle and crack (thermodynamics)

Instantaneous dipoles:

nonpolar molecules have randomly fluctuating dipoles that tend to align w one another from one instant to the next (bonding)

What are the three kinds of covalent bonds?

normal (which can be polar or non polar), metallic, and coordinate covalent bonds

Keq, the equilibrium constant:

the equilibrium constant, K, describes the position of the equilibrium. *a reaction will tends towards its own equil, and for a given temp, will have an equil constant (Keq). For example, aA + bB <--> cC + dD, the equil expression is given by: Keq= [C]^c [D] ^d / [A]^a [B]^b Rules: 1) when calculating Keq, you must use the equil concentrations. If you use reactant or product concentrations not in equil, your calculating Q, not Keq 2) when calculating Keq, do not include liquids or solids. Only gases and aqueous solutions are included 3) the value of Keq for a given reaction is a constant at a given temp. If the temp changes, then a reactions Keq value will change. **the only thing that can change K is temp 4) you can have Kc, Ksp, Ka, Kb, Kp, Kd, Kaff. These are all the same as Keq, they just describe specific types of reactions. Note: Kc=concentration equilibrium, Ksp=solubility equilibrium, Ka=acid equilibrium, Kb=base equilibrium, Kp=pressure equilibrium, Kd=dissociation equilibrium, Kaff= equilibrium affinity constant 5) a K value tells you the reaction is in equilibrium. When K>1 it tells you at equil products are favored. When K<1 it tells you when at equilibrium reactants are favored. When K=1, it tells you at equil, neither reactants or products are favored. (solubility)

What is the equivalence point of a titration?

the equivalence point has been reached when the same number of moles of acid and base have been mixed [moles of acid]=[moles of base]

Ksp vs Qsp:

the ion product, Qsp, is the reaction quotient for a solubility reaction. That is, while the Ksp is equal to the product of the concentrations of the ions in solution when the solution is saturated, (when it's at equil), the ion product, Qsp, has exactly the same form as the Ksp expression, but the concentrations don't have to be at equil. The Qsp allows you to make predictions about what the reaction will do. -if Qsp>Ksp, the reaction will shift left, excess salt will precipitate out of solution -if Qsp=Ksp, the reaction is at equil; the solution is saturated -if Qsp<Ksp, the reaction will shift right, precipitate is not formed, more salt can be added/dissolved to solution (solubility)

Lattice energy:

the lattice energy, ΔHlattice, (enthalpy final - enthalpy initial), is the energy required to break the ionic bond. When bonds are broken, this is ALWAYS an endothermic process (energy is required). The lattice energy tells you the ionic bond strength. It is proportional to the electrostatic attraction between the ions Felectrostatic ∝ Elattice -the larger the magnitude of the lattice energy, the stronger the ionic bond (harder to break) -the smaller the magnitude of the lattice energy, the weaker the ionic bond (easier to break) -remember, ionic bonds when not in solution form crystal lattice structures *In summary, lattice energy = the energy required to convert the crystal into infinitely separated gaseous ions in vacuum, an endothermic process. For ex, the lattice energy of NaCl is +786 kJ/mol. **breaking bonds is always an endothermic process (heat needed) **forming bonds is always an exothermic process (heat released) *way to remember, "when you break up with boyfriend, it takes your energy; requires energy" (bonding)

The anomeric forms of a sugar differ by __________.

the position of the OH group on the anomeric carbon; OH down= alpha, OH up=beta (carbohydrates)

Distillation:

the process of raising the temperature of a liquid until it can overcome the intermolecular forces that hold it together in the liquid phase. The vapor is then condensed back to the liquid phase and subsequently collected in another container. *Separates liquids based on boiling point. The stuff with the lower boiling point is boiled off and collected; the higher boiling point stuff remains behind. Three types of distillation: 1) Simple distillation = done with a normal column = can separate two liquids if the difference in boiling point is large. For ex, to purify fresh drinking water away from a salt water solution; the more volatile water can be boiled away, then condensed and collected, leaving behind the nonvolatile salts 2) Fractional distillation = done with a fractionating column = can separate two liquids with smaller differences in boiling point. The fraction distillation column is packed with a material, such as glass beads. This allows the liquid mixture to be subjected to many vaporization-condensation cycles as it moves up the column toward the condenser. As the cycle progresses, the composition of the vapor gradually becomes enriched in the lower bp component. 3) Vacuum distillation = done under lower pressure (vacuum) = lowers the boiling point for all liquid components so you don't have to crank up the temperature so high (chemical might decompose). (separations and purifications)

Solvation:

the process that occurs when solvent molecules surround solute molecules. If the solvent is water, the process is called hydration (ions in solution)

Q, the reaction quotient:

the reactant quotient, Q, describes the distance from equilibrium. It is calculated the same way as K, except we look at reactant and product concentrations when not at equilibrium. For ex, A(s) + 2B(g) <--> 2C(aq) + D(aq), so Q=[C]²[D]/[B]² Rules: 1) reactions will strive to reach a state where Q=Keq -if Q<Keq, the reaction will proceed in forward direction; wants to increase [products] -if Q>Keq, the reaction will proceed in the reverse direction; wants to increase [reactants] -when Q=Keq, the reaction is at equil *way to remember: shark's mouth tells you which way reaction goes; > reaction goes right towards reactants; < reaction goes left, towards products 2) when calculating Q, do not include liquids or solids. Only gases and aqueous solutions are included. (solubility)

Chromatography:

the separation of a mixture by passing it in solution through a medium in which the components move at different rates. The mixture is dissolved in a fluid called the MOBILE PHASE, which carries it through a structure holding another material called the STATIONARY PHASE. The various constituents of the mixture travel at different speeds, causing them to separate. The separation is based on differential partitioning between the mobile and stationary phases. Types of chromatography: 1) Paper chromatography or TLC (mobile phase=nonpolar; stationary phase=polar) 2) Column (flash) chromatography (mobile phase=nonpolar; stationary phase=polar) 3) Ion exchange chromatography (mobile phase; stationary phase= + or - charged resin) 4) High performance liquid chromatography (mobile phase=polar; stationary phase=nonpolar) 5) Size exclusion chromatography (mobile phase; stationary phase=porous polymer beads) 6) Affinity chromatography (mobile phase; stationary phase=agarose bead w receptor/antibody/substrate) 7) Gas chromatography (mobile phase=gas; stationary phase= liquid) (separations and purifications)

Dipole-dipole:

type of intermolecular force involving the attraction between the positive end of one polar molecule and the negative end of anther polar molecule (partial ionic character). H-bonds are the strongest dipole-dipole force -form bc of differences in electronegativity. The larger the difference in electronegativity, the larger the dipole moment. -formed between a polar molecule + polar molecule -all polar molecules exhibit dipole-dipole interactions. -bond dipole= looking at one bond-dipole in a molecule -molecular/net dipole= putting all bond dipoles together and coming up w a molecule/net dipole to determine if molecule is polar or not *the force of the dipole-dipole interaction is aligned along the molecular/net dipole -the more polar a molecule, (strong molecular/net dipole), corresponds to stronger dipole-dipole forces -dipole-dipole forces are easily cleaved -dipole-dipole interactions increase the bp, though not as significantly as H-bonding Dipole moment is calculated by: μ=Qr, where μ is the dipole moment, Q is the partial charge, and r is distance between the charges. Hence, dipole moment is proportional to CHARGE and DISTANCE: 1) the greater the electronegativity diff, the greater the charge distribution, and hence greater the dipole moment 2) the larger the distance separating the partial charges, the larger the dipole moment. Large distance means there is more of a net dipole, stronger dipole-dipole forces, molecule is more polar. *intermolecular forces (bonding)

Ion-dipole:

type of intermolecular force, similar to dipole-dipole interactions. However, it is stronger than dipole-dipole interactions bc it is no longer an interaction involving just partial charges. Instead, it is an interaction between a full charge (ion) and a partial charge (dipole) -ion dipole interactions get stronger when you have larger charge magnitude of the ion, and large polarity of the dipole molecule (bonding)

H-bonds:

type of intermolecular force; the strongest type of dipole-dipole force. H-bonds are formed between a slightly positive hydrogen and a slightly negative atom. -formed between a polar molecule + polar molecule -the more polar a bond is, the stronger the H-bond. The H-F bond is the most polar, followed by the H-O bond, and lastly the H-N bond -the H-bond force is aligned along the bond dipole, not the molecular/net dipole. This is what makes H-bonding so strong. -the more paired donors and acceptors = a stronger force (stronger H-bond) -H-bonding increases the bp a molecule can H-bond to itself if it contains: hydrogen bond donor (N-H, O-H, F-H) AND a hydrogen bond acceptor (N:, O:, F:) a molecule can H-bond w water if it contains: hydrogen bond donor (N-H, O-H, F-H) OR a hydrogen bond acceptor (N:, O:, F:) *intermolecular forces (bonding)

Rank the four possible types of alkyl carbocations from least stable to most stable

unsubstituted (methyl) < primary < secondary < tertiary

Henderson-Hasselbalch equation:

used to determine the pH of a buffer solution. 1) Henderson-Hasselbalch equation for acids: pH=pKa + log ([base]/[acid]) *to design a buffer solution, choose a weak acid whose pKa is as close to the desired pH as possible. An ideal buffer would have [weak acid] = [conjugate base], so pH=pKa. 2)Henderson-Hasselbalch equation for bases: pOH=pKb + log ([acid]/[base]) *to design a buffer solution, choose a weak base whose pKb value is as close to the desired pOH as possible (acid/base equilibria)

Electrophoresis:

used to separate things by size or by charge. -a gel is made out of either acrylamide or agarose. The more acrylamide or agarose you use, the smaller the pores -the mold used to pour the gel creates wells in the gel into which samples can be loaded. An electrical current is applied such that the end of the gel w the wells is negatively charged and the opposite end is positively charged. This causes the samples to migrate toward the positive pole, according to size; smaller things migrate faster and larger things migrate slower. -For ex, here are the steps for separating DNA fragments by size: 1)isolate the DNA from cells 2)expose the DNA to a restriction endonuclease, which cleaves the strands of DNA into smaller fragments of varying size 3)add a loading dye to the DNA sample. This makes the sample visible as it is being loaded into the gel 4)load your sample into the gel wells and apply the electrical current (called "running a gel"). Each strand of DNA in your sample migrates toward the positive electrode at various speeds. You run the samples alongside a "standard" lane, which contains fragments of known size (used like a ruler). 5)after electrophoresis, visualize the bands of DNA in the gel. This is often done using a dye that binds to nucleic acids and fluoresces them when exposed to UV light. The size of each DNA band can be approximated by comparing it to the ladder *in addition to determining their sizes, fragments of DNA (or RNA) in an electrophoresis gel can be transferred to a membrane in a process called "blotting." (separations and purifications)

How many bonds does B like to make?

valence e-= 3 usual # of bonds= 3 or 4 (bonding)

How many bonds does Si like to make?

valence e-= 4 usual # of bonds= 4

How many bonds does C like to make?

valence e-= 4 usual # of bonds= 4 (bonding)

How many bonds does N like to make?

valence e-= 5 usual # of bonds= 3 (bonding)

How many bonds does P like to make?

valence e-= 5 usual # of bonds= 3 or 5

How many bonds does O like to make?

valence e-= 6 usual # of bonds= 2 (bonding)

How many bonds does S like to make?

valence e-= 6 usual # of bonds= 2 or 6

How many bonds does Cl like to make?

valence e-= 7 usual # of bonds= 1

How many bonds does F like to make?

valence e-= 7 usual # of bonds= 1 (bonding)

Induced dipoles:

when a polar molecule interacts w a nonpolar molecule, then the polar molecule induces a dipole in the nonpolar molecule (bonding)

D and L configurations:

when looking at Fischer projections, a sugar can be categorized as being either D or L depending on the orientation of the hydroxyl group on the highest numbered chiral center. When the hydroxyl group is on the right, the molecule is a D sugar. When the hydroxyl group is on the left, the molecule is an L sugar *most sugars are epimers (they differ in absolute configuration at single chiral center; one stereocenter is inverted; R vs S) (stereochemistry of covalently bonded molecules)