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5D: Structure, Function, and Reactivity of Biologically Relevant Molecules

Nucleic acids, amino acids and proteins, lipids and sugars, and the organic chemistry of every carbonyl, alcohol, acid and aromatic ring in a cell.

38 topics · 155 questions

Each topic is a path, not a menu: work down it in order and every question builds on the one above. Click any of them to watch the answer draw itself.

5D. Nucleotides, Nucleosides and the Sugar Phosphate Backbone

  1. How it worksHow do a sugar, a nitrogenous base and a phosphate assemble into a single nucleotide?
  2. How it worksHow does a phosphodiester bond from the 3-prime to the 5-prime carbon build a backbone?
  3. Worked exampleDraw adenosine monophosphate and outline the nucleoside hiding inside it.
  4. Common mistakeWhy isn't a nucleoside with a phosphate stuck on it still called a nucleoside?
  5. Going furtherWhat changes about the sugar going from RNA to DNA, and why does that swap buy stability?
Your turneasy1 of 3
A single strand of DNA is 30 nucleotides long. How many phosphodiester bonds join its sugar-phosphate backbone together?

5D. Purines, Pyrimidines and Base Pairing

  1. How it worksHow does pairing a two-ring base with a one-ring base keep every rung the same width?
  2. Worked exampleFind how many hydrogen bonds hold a GC pair versus an AT pair and what that predicts about melting.
  3. Common mistakeWhy isn't uracil simply a misspelled thymine with no consequences for the cell?
  4. Going furtherWhat happens to a DNA duplex's melting temperature as its GC content climbs?
Your turneasy1 of 3
A DNA duplex contains 22 GC base pairs and 21 AT base pairs. How many hydrogen bonds hold the two strands together across all of its rungs?

5D. The DNA Double Helix and RNA Structures

  1. How it worksHow do two antiparallel strands wind into a right-handed helix with a major and a minor groove?
  2. Common mistakeWhy isn't RNA merely DNA with one extra oxygen and no other differences?
  3. Worked exampleDraw the hairpin an RNA strand forms when a sequence is followed by its own reverse complement.
  4. Going furtherWhat changes about the helix as the solution dries and B-DNA shifts toward the A form?
Your turneasy1 of 3
A B-form DNA duplex is 1454 base pairs long. Using a rise of 0.34 nanometers per base pair, how long is the duplex along its axis?

5D. Amino Acid Structure and Absolute Configuration

  1. How it worksHow does one alpha carbon carry an amine, an acid, a hydrogen and a side chain all at once?
  2. Worked exampleFind why every natural amino acid is L, and find the one that comes out R instead of S.
  3. Common mistakeWhy isn't the L label the same as saying a molecule rotates polarized light to the left?
  4. Going furtherWhat changes about glycine that leaves it the one amino acid with no handedness at all?
Your turneasy1 of 3
A peptide is built from 17 amino acid residues, 4 of which are glycine. How many of its alpha carbons are stereocenters?

5D. Classification of Amino Acid Side Chains

  1. How it worksHow does sorting twenty side chains by charge and polarity predict where each one ends up?
  2. Worked exampleCompare arginine, valine and serine and place each one inside or outside a globular protein.
  3. Worked exampleFind which side chains carry a full charge at pH 7 and which only carry a dipole.
  4. Going furtherWhat changes about the side chain layout of a membrane protein compared with a soluble one?
Your turneasy1 of 3
A protein segment contains 5 lysine, 5 glutamate, 6 serine and 3 valine residues. How many of these side chains carry a full formal charge at pH 7.0?

5D. Zwitterions, Amino Acid pKa Values and the Isoelectric Point

  1. How it worksHow does dragging an amino acid from pH 1 up to pH 13 flip its net charge twice?
  2. Worked exampleFind the isoelectric point of glycine from pKa values of 2.3 and 9.6.
  3. Worked exampleFind the isoelectric point of aspartate from pKa 2.1, 3.9 and 9.8 and show which two you average.
  4. Common mistakeWhy isn't the isoelectric point the average of all three pKa values for an acidic amino acid?
  5. Ties togetherHow does an amino acid's isoelectric point decide where it halts during isoelectric focusing?
Your turneasy1 of 3
An amino acid with no ionizable side chain has an alpha-carboxyl pKa of 2.496 and an alpha-amino pKa of 9.97. What is its isoelectric point?

5D. Strecker and Gabriel Amino Acid Synthesis

  1. How it worksHow does the Strecker synthesis turn an aldehyde, ammonia and cyanide into an amino acid?
  2. How it worksHow does the Gabriel synthesis use phthalimide to deliver a clean primary amine with no overalkylation?
  3. Worked exampleWalk me through making alanine by the Strecker route starting from acetaldehyde.
  4. Common mistakeWhy doesn't either synthesis hand you a single enantiomer of the product?
Your turneasy1 of 3
A straight-chain aldehyde containing 6 carbon atoms is treated with ammonia and potassium cyanide, and the aminonitrile is then hydrolyzed in aqueous acid. How many carbon atoms does the amino acid product contain?

5D. The Peptide Bond and Its Hydrolysis

  1. How it worksHow does a condensation between an amine and a carboxyl group squeeze out a water molecule?
  2. How it worksHow does resonance across the peptide bond flatten six atoms into one rigid plane?
  3. Worked exampleShow why the amide C-N bond is planar and cannot rotate the way an ordinary single bond does.
  4. Going furtherWhat happens to a peptide bond in hot acid, and why is that so slow without an enzyme helping?
Your turneasy1 of 3
A linear peptide contains 19 amino acid residues. How many peptide bonds hold it together, and therefore how many water molecules were released when it was assembled?

5D. Disulfide Bonds, Cysteine and Cystine

  1. How it worksHow do two cysteine thiols get oxidized into a single cystine disulfide bridge?
  2. Worked exampleFind how many distinct disulfide pairings six cysteines in one chain could possibly form.
  3. Common mistakeWhy aren't disulfide bridges treated as part of a protein's secondary structure?
  4. Going furtherWhat changes about disulfide bonds inside the reducing cytoplasm versus outside the cell?
Your turnmedium1 of 3
A single polypeptide chain carries 8 cysteine residues. How many distinct pairs of those cysteines could in principle be bridged by a disulfide bond?

5D. Primary and Secondary Protein Structure

  1. How it worksHow do backbone hydrogen bonds four residues apart wind a chain into an alpha helix?
  2. How it worksHow do backbone hydrogen bonds between separate strands build a pleated beta sheet?
  3. Worked exampleFind why proline snaps an alpha helix and why glycine loosens one.
  4. Common mistakeWhy isn't secondary structure held in place by the side chains rather than the backbone?
Your turneasy1 of 3
An alpha helix contains 31 residues. Using a rise of 1.5 angstroms per residue along the helix axis, how long is the helix?

5D. Tertiary Structure and the Hydrophobic Effect

  1. How it worksHow does water gaining entropy, rather than oil losing energy, drive nonpolar side chains inward?
  2. Common mistakeWhy isn't the hydrophobic effect an attraction between nonpolar groups?
  3. Worked exampleCompare the folding drive from burying one leucine with the drive from a single salt bridge.
  4. Going furtherWhat changes about the greasy core when the protein sits inside a membrane instead of water?
Your turnmedium1 of 3
Moving one leucine side chain from water into a protein's core changes the enthalpy by 0.98 kilojoules per mole and the entropy by plus 72 joules per mole per kelvin. What is the free-energy change at 310 kelvin, in kilojoules per mole?

5D. Quaternary Structure, Folding and Denaturation

  1. How it worksHow does a protein find its one correct fold out of an astronomical number of alternatives?
  2. Worked exampleFind what urea, heat and extreme pH each attack when they denature a protein.
  3. Common mistakeWhy isn't a denatured protein one whose peptide bonds have been cut apart?
  4. Going furtherWhat happens when a denatured protein is allowed to refold slowly instead of all at once?
  5. Ties togetherHow does hemoglobin's four-subunit assembly turn a plain binding curve into a cooperative one?
Your turnhard1 of 3
Each residue of an unfolded chain can take up 7 distinct backbone conformations, independently of the others. Write the number of conformations available to a chain of x residues.

5D. Nonenzymatic Protein Function

  1. How it worksHow does an antibody's variable region mold itself around one antigen and no other?
  2. How it worksHow does myosin walk along actin by cycling through binding, power stroke and release?
  3. Worked exampleCompare a binding protein, a motor protein and an antibody by what each does with its energy.
  4. Going furtherWhat changes about collagen's strength when one glycine in the repeat is swapped for something bulkier?
Your turneasy1 of 3
A collagen alpha chain is built from 267 repeats of the Gly-X-Y triplet. How many residues long is the chain?

5D. Fatty Acids and Triacylglycerols

  1. How it worksHow do three fatty acids esterify onto one glycerol backbone to build a storage fat?
  2. Worked exampleCompare stearic acid with oleic acid and account for the 60 degree gap in their melting points.
  3. Common mistakeWhy isn't a saturated fat one that has soaked up as much water as it can hold?
  4. Going furtherWhat changes about packing when a cis double bond is flipped to trans in the same fatty acid?
Your turneasy1 of 3
45 millimoles of glycerol are fully esterified with fatty acids to give triacylglycerols. How many millimoles of water are released?

5D. Saponification

  1. How it worksHow does hydroxide attack an ester carbonyl and split a triacylglycerol into soap and glycerol?
  2. Worked exampleFind how many moles of NaOH it takes to saponify one mole of a triacylglycerol completely.
  3. Going furtherWhat changes about the product when potassium hydroxide is used instead of sodium hydroxide?
  4. Ties togetherHow does a soap molecule's split personality explain the micelle that carries grease into water?
Your turneasy1 of 3
11 moles of a triacylglycerol are saponified completely with aqueous sodium hydroxide. How many moles of NaOH are consumed?

5D. Phospholipids, Sphingolipids and Waxes

  1. How it worksHow does swapping one fatty acid of a fat for a phosphate head create an amphipathic lipid?
  2. Worked exampleDraw phosphatidylcholine and label the glycerol, the two tails and the charged head group.
  3. Common mistakeWhy isn't a bilayer held together by covalent bonds between neighboring lipids?
  4. Going furtherWhat changes about the backbone when sphingosine takes the place of glycerol?
Your turnmedium1 of 3
A patch of lipid bilayer measures 76 square nanometers. If each phospholipid head group occupies 0.65 square nanometers, how many phospholipid molecules does the patch hold, counting both leaflets?

5D. Steroids, Terpenes and Fat-Soluble Vitamins

  1. How it worksHow does one rigid four-ring skeleton get decorated into cholesterol, testosterone and cortisol?
  2. How it worksHow do five-carbon isoprene units stack up into terpenes of every size?
  3. Worked exampleFind the number of isoprene units in a thirty-carbon molecule and name that terpene class.
  4. Going furtherWhat changes about storage and toxicity when a vitamin dissolves in fat rather than in water?
Your turneasy1 of 3
A terpene is assembled head to tail from 6 isoprene units. How many carbon atoms does it contain?

5D. Monosaccharides and Fischer Projections

  1. How it worksHow does a Fischer projection flatten a three-dimensional sugar onto paper without losing stereochemistry?
  2. Worked exampleDraw D-glucose as a Fischer projection and mark all four of its stereocenters.
  3. Worked exampleFind whether a sugar is D or L by reading nothing but its bottom stereocenter.
  4. Common mistakeWhy isn't a D sugar necessarily one that rotates polarized light to the right?
Your turnmedium1 of 3
An aldose contains 6 carbon atoms in its open-chain form. How many stereoisomers of that aldose exist?

5D. Epimers, Anomers and Mutarotation

  1. How it worksHow does the ring opening and closing again at the anomeric carbon convert alpha into beta?
  2. Worked exampleFind which carbon makes glucose and galactose epimers and which one makes them only anomers.
  3. Common mistakeWhy isn't an anomer just another word for an epimer?
  4. Going furtherWhat changes about the alpha to beta ratio at equilibrium in a furanose rather than a pyranose?
Your turnhard1 of 3
Alpha-D-glucopyranose has a specific rotation of plus 114 degrees and the beta anomer plus 21 degrees. Write the specific rotation of a mixture in which the beta anomer makes up a fraction x of the total.

5D. Cyclic Hexoses and Haworth Projections

  1. How it worksHow does the C5 hydroxyl attack the C1 aldehyde to close a six-membered pyranose ring?
  2. Worked exampleDraw beta-D-glucose as a Haworth projection and then redraw it in its favored chair.
  3. Going furtherWhat happens to the ring's stability when every bulky group can sit equatorial at the same time?
  4. Ties togetherHow does a sugar closing its own ring reuse exactly the hemiacetal chemistry of a plain aldehyde?
Your turnmedium1 of 3
At equilibrium in water, D-glucose is 60 percent beta-pyranose and 34 percent alpha-pyranose, with everything else open-chain or furanose. What percentage is open-chain or furanose?

5D. Glycosidic Linkages, Disaccharides and Polysaccharides

  1. How it worksHow does an anomeric carbon bond to another sugar's hydroxyl to form a glycosidic linkage?
  2. Worked exampleCompare the alpha-1,4 linkage of starch with the beta-1,4 linkage of cellulose and explain the shape gap.
  3. Worked exampleFind which of lactose, sucrose and maltose fails a reducing sugar test and explain why.
  4. Going furtherWhat changes about the polymer when alpha-1,6 branch points are added to a straight glucose chain?
Your turneasy1 of 3
A linear polysaccharide is built from 294 glucose units joined end to end. How many glycosidic bonds does it contain?

5D. Keto-Enol Tautomerism in Monosaccharides

  1. How it worksHow does an enediol intermediate let a sugar shuffle its carbonyl from C1 over to C2?
  2. Worked exampleWalk me through converting glucose into fructose through an enediol under basic conditions.
  3. Common mistakeWhy isn't fructose exempt from a reducing sugar test when it carries no aldehyde group?
Your turnmedium1 of 3
D-glucose left in dilute base at pH 11 slowly becomes a mixture containing D-fructose and D-mannose. What intermediate makes that possible?

5D. Nucleophilic Addition at the Carbonyl

  1. How it worksHow does a nucleophile attack a carbonyl carbon and shove the π electrons up onto oxygen?
  2. Worked exampleCompare formaldehyde, acetaldehyde and acetone for reactivity toward the same nucleophile.
  3. Common mistakeWhy isn't a ketone as reactive as an aldehyde when the two share the identical carbonyl group?
  4. Going furtherWhat changes about carbonyl reactivity when an electron-withdrawing chlorine sits next door?
Your turnmedium1 of 3
Formaldehyde, acetaldehyde and acetone are each treated with the same concentration of cyanide, and the three rate constants measured are 1636, 288 and 37 per second. Which assignment is right?

5D. Acetals and Hemiacetals

  1. How it worksWalk me through the acid-catalyzed path from an aldehyde to a hemiacetal and on to an acetal.
  2. Worked exampleFind the product when acetaldehyde meets two equivalents of methanol and a trace of acid.
  3. Common mistakeWhy isn't acetal formation irreversible, given how finished the product looks?
  4. Going furtherWhat changes about the equilibrium when water is pulled off as fast as it forms?
  5. Ties togetherHow does the reversibility of acetal formation make it the standard way to protect a ketone?
Your turneasy1 of 3
15 moles of acetaldehyde are converted completely to the dimethyl acetal with methanol and a trace of acid. How many moles of methanol are consumed?

5D. Imines, Enamines and Cyanohydrins

  1. How it worksHow does a primary amine attack a ketone and then lose water to leave a carbon-nitrogen double bond?
  2. How it worksHow does a secondary amine end up an enamine because it has no second hydrogen left to lose?
  3. Worked exampleFind the product when cyclohexanone reacts with methylamine at pH 5, and explain that pH choice.
  4. Going furtherWhat changes about the product when cyanide adds to the ketone instead of an amine?
Your turnmedium1 of 3
Cyclohexanone is treated with methylamine at pH 5 to give an imine. Why is that pH chosen rather than pH 1 or pH 10?

5D. Hydride Reduction and the Oxidation of Aldehydes

  1. How it worksHow does a hydride reagent deliver a hydrogen with its electrons straight onto a carbonyl carbon?
  2. Worked exampleFind the products when sodium borohydride and then lithium aluminum hydride are used on an ester.
  3. Common mistakeWhy doesn't sodium borohydride reduce a carboxylic acid the way it reduces a ketone?
  4. Going furtherWhat changes about oxidation state climbing from methane to methanol to formaldehyde to formic acid?
Your turnmedium1 of 3
In a one-carbon molecule the single carbon makes four bonds, 3 of them to oxygen and the rest to hydrogen. What is the oxidation state of that carbon?

5D. Enolates, the Acidic Alpha Hydrogen and Keto-Enol Tautomerism

  1. How it worksHow does pulling off an alpha hydrogen leave a carbanion whose charge parks on oxygen?
  2. How it worksHow does a ketone flicker between its keto form and its enol form under acid or base?
  3. Worked exampleFind which alpha position of 2-methylcyclohexanone loses a proton faster and which gives the stabler enolate.
  4. Common mistakeWhy doesn't a stereocenter sitting alpha to a ketone keep its optical purity in base?
Your turneasy1 of 3
The alpha hydrogen next to a ketone carbonyl has a pKa of 21, while an ordinary alkane C-H has a pKa of 51. By what power of ten is the alpha hydrogen the stronger acid?

5D. Aldol Condensation and the Retro-Aldol

  1. How it worksHow does the enolate of one aldehyde attack the carbonyl of another to forge a new carbon-carbon bond?
  2. Worked exampleWalk me through the aldol condensation of two acetaldehyde molecules through to the dehydrated product.
  3. Worked exampleFind the retro-aldol cleavage products of fructose-1,6-bisphosphate and name the two trioses.
  4. Going furtherWhat changes about which enolate forms when a bulky base is used cold instead of heat?
  5. Ties togetherHow does the aldolase step of glycolysis run exactly the retro-aldol you would draw on paper?
Your turneasy1 of 3
An aldol condensation joins two molecules of the same aldehyde, each with 6 carbon atoms, and the product is then dehydrated. How many carbon atoms does the enone contain?

5D. Alcohols: Acidity, Hydrogen Bonding and Oxidation

  1. How it worksHow does oxidizing a primary alcohol take it to an aldehyde and then push on to an acid?
  2. Worked exampleFind the product when 2-propanol meets a chromium oxidant, and explain why it stops where it does.
  3. Common mistakeWhy isn't a tertiary alcohol oxidizable by ordinary chromium reagents?
  4. Going furtherWhat changes about alcohol acidity when three fluorines are hung on the neighboring carbon?
Your turneasy1 of 3
59 millimoles of 2-propanol are treated with a chromium(VI) oxidant in aqueous acid. What is the product, and why does the oxidation stop there?

5D. Substitution, Tosylation and Protection of Alcohols

  1. How it worksHow does making a tosylate turn a terrible leaving group into an excellent one?
  2. How it worksHow does protonating an alcohol let it walk away as neutral water in an SN1 reaction?
  3. Worked exampleFind whether 2-methyl-2-butanol reacts with HBr by SN1 or SN2 and predict the stereochemistry.
  4. Going furtherWhat changes about a molecule's reactivity once a silyl group is parked on its alcohol?
Your turnhard1 of 3
An alcohol is converted to its tosylate, whose conjugate acid has a pKa near minus 3. Why does that make substitution possible?

5D. Carboxylic Acid Acidity and Substituent Effects

  1. How it worksHow does spreading a negative charge across two equivalent oxygens stabilize a carboxylate?
  2. Worked exampleCompare the pKa of acetic, chloroacetic and trichloroacetic acid and account for the trend.
  3. Worked exampleFind which is the stronger acid, 2-chlorobutanoic or 4-chlorobutanoic, and roughly by how much.
  4. Common mistakeWhy isn't inductive withdrawal just as powerful four carbons away as it is one carbon away?
Your turnhard1 of 3
A carboxylic acid has a pKa of 4.47. Write the fraction of it present as the carboxylate anion as a function of the pH, calling the pH x.

5D. Decarboxylation and Reduction of Carboxylic Acids

  1. How it worksHow does a six-membered cyclic transition state let a beta-keto acid shed CO2 with no reagent?
  2. Worked exampleFind the product when 3-oxobutanoic acid is heated, and trace the enol that appears first.
  3. Common mistakeWhy doesn't an ordinary carboxylic acid decarboxylate when a beta-keto acid does it so readily?
  4. Ties togetherHow does the decarboxylation drawn on paper show up twice per turn of the citric acid cycle?
Your turneasy1 of 3
A beta-keto acid with 8 carbon atoms is warmed gently until it stops bubbling. How many carbon atoms does the ketone product contain?

5D. Nucleophilic Acyl Substitution

  1. How it worksWalk me through the addition-elimination arrow pushing that swaps one group on a carbonyl for another.
  2. Worked exampleFind the product when acetyl chloride meets methanol, and draw every arrow along the way.
  3. Common mistakeWhy isn't acyl substitution a one-step backside attack at the carbonyl carbon?
  4. Going furtherWhat changes about the outcome when the tetrahedral intermediate has no good leaving group to expel?
Your turnhard1 of 3
A nucleophile reacts with an acid chloride at 14 degrees Celsius and replaces the chloride. Why is that not a one-step backside attack at the carbonyl carbon?

5D. Relative Reactivity of the Acid Derivatives

  1. How it worksHow does the stability of the leaving group set the whole ladder from acid chloride down to amide?
  2. Worked exampleCompare an anhydride, an ester and an amide toward one nucleophile and rank all three.
  3. Going furtherWhat changes about an amide's reactivity when it is trapped in a strained beta-lactam ring?
  4. Common mistakeWhy isn't steric bulk the main reason an amide reacts more slowly than an acid chloride?
Your turnmedium1 of 3
An anhydride, an ester and an amide are each treated with the same nucleophile, and the three relative rates measured are 15446, 137 and 9. Which assignment is right?

5D. Hydrolysis of Amides and Transesterification

  1. How it worksHow does acid catalysis make an amide carbonyl electrophilic enough for water to attack?
  2. Worked exampleWalk me through turning methyl benzoate into ethyl benzoate with ethanol and acid.
  3. Going furtherWhat changes about a transesterification equilibrium when you flood it with the new alcohol?
Your turnhard1 of 3
Transesterifying methyl benzoate with ethanol has an equilibrium constant of 1. Starting from 1 mole of methyl benzoate and 15 moles of ethanol in a fixed volume, what fraction of the ester ends up as ethyl benzoate?

5D. Phenols and Biological Two-Electron Redox Centers

  1. How it worksHow does the ring soak up a phenoxide's negative charge across four positions at once?
  2. How it worksHow does a hydroquinone hand off two electrons and two protons to become a quinone?
  3. Worked exampleCompare the pKa of phenol, para-nitrophenol and para-methylphenol and explain the ordering.
  4. Ties togetherHow does the quinone redox cycle let ubiquinone ferry electrons inside a mitochondrial membrane?
Your turneasy1 of 3
Phenol has a pKa of 10.2 and cyclohexanol a pKa of 16.68. By what power of ten is phenol the stronger acid?

5D. Aromaticity and Hückel's Rule

  1. How it worksHow do a flat ring, an unbroken p orbital loop and 4n plus 2 electrons together make a ring aromatic?
  2. Worked exampleFind which of cyclobutadiene, benzene and cyclooctatetraene is aromatic, antiaromatic or neither.
  3. Common mistakeWhy isn't every flat ring with alternating double bonds aromatic?
  4. Going furtherWhat changes when a ring picks up two electrons and jumps from antiaromatic to aromatic?
Your turneasy1 of 3
Huckel's rule says an aromatic ring holds 4n plus 2 π electrons. How many π electrons does that give for n equal to 4?

5D. Polycyclic and Heterocyclic Aromatic Compounds

  1. How it worksHow does pyridine keep its lone pair outside the ring while pyrrole commits its own pair inside?
  2. Worked exampleCompare the basicity of pyridine, pyrrole and imidazole and explain each from orbital placement.
  3. Going furtherWhat changes about the electron count when two aromatic rings fuse, as in naphthalene or a purine?
  4. Ties togetherHow do the aromatic rings of the nucleobases explain the base stacking that steadies a double helix?
Your turneasy1 of 3
A linear polycyclic aromatic hydrocarbon is built from 4 fused six-membered rings sharing edges, as benzene, naphthalene and anthracene are. How many π electrons does it hold?

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