1. Amino Acids, Peptides, Proteins
1.1. Proteinogenic Amino Acids
● AAs: amino, CA groups
○ In some AAs, amino and CA groups aren’t bonded to same C (e.g., GABA)
○ Proteinogenic AAs: 20 α-AAs encoded by codons in humans
○ Essential AAs: can’t be biosynthesized to meet demand
■ “Very Heavy MILK WTF”: Val, His, Met, Iso, Leu, Lys, Trp, Thr, Phe
○ Nonessential AAs: can be biosynthesized to meet demand
■ “DEANS”: Asp, Glu, Ala, Asn, Ser
● Stereochemistry: all AAs are chiral, (S), ʟ-isomers
○ Except Gly, which is achiral b/c its side chain is H
○ Except Cys, which is (R) b/c ⦚–CH2SH > ⦚–COOH in priority order
● Hydrophobicity
○ Hydrophobic: nonpolar, hydrocarbon side chains (Ala, Val, Leu, Iso, Phe)
○ Hydrophilic: polar/charged AAs (Ser, Thr, Gln, Asn, Glu, Asp, Lys, Arg, His)
● Side-chain structure
○ Nonpolar, nonaromatic
■ Glycine (Gly, G) ⦚–H
■ Alanine (Ala, A) ⦚–Me
■ Valine (Val, V) ⦚–iPr
■ Leucine (Leu, L) ⦚–CH2–iPr
■ Isoleucine (Iso, I) ⦚–CHMeEt
■ Methionine (Met, M) ⦚–CH2–CH2–SMe
● SMe and not SH, so nonpolar
■ Proline (Pro, P) ⦚–[pyrrolidine] (NH adj. to branch)
● Rigid ring, affects 2° structure
○ Aromatic
■ Tyrosine (Tyr, Y) ⦚–CH2–PhOH (para)
● Somewhat polar
■ Phenylalanine (Phe, F) ⦚–CH2Ph
■ Tryptophan (Trp, W) ⦚–CH2–[indole] (double bond of 5-membered
ring adj. to branch)
○ Polar
■ Serine (Ser, S) ⦚–CH2OH
● Hydroxyl is highly polar, H-bonding
■ Threonine (Thr, T) ⦚–CH(Me)OH
● Hydroxyl is less polar than in Ser (due to Me), H-bonding
■ Cysteine (Cys, C) ⦚–CH2SH
● Thiol is less polar than hydroxyls in Ser/Thr (S is less EN than O)
● Thiol can be oxidized
■ Asparagine (Asn, N) ⦚–CH2–CONH2
● Amide can’t be deprotonated
■ Glutamine (Gln, Q) ⦚–CH2–CH2–CONH2
● Amide can’t be deprotonated
○ Acidic, (–) charged
■ Aspartate (Asp, D) ⦚–CH2–COO–
● CA is acidic
■ Glutamate (Glu, E) ⦚–CH2–CH2–COO–
● CA is less acidic than in Asp (extra alkyl is EDG)
○ Basic, (+) charged
, ■ Lysine (Lys, K) ⦚–CH2–CH2–CH2–CH2NH3+
■ Arginine (Arg, R) ⦚–CH2–CH2–CH2–NH–C(NH2)2+
● Protonating imine delocalizes (+) throughout all 3 N’s
■ Histidine (His, H) ⦚–CH2–[imidazole]+ (NH, double bond adj. to
branch)
● Only imine is protonated at physiological pH (results in resonance)
1.2. Amino Acid Acid–Base
● Amphoteric: basic amino, acidic CA groups
○ Protonated in acidic soln. (low pH), deprotonated in basic soln. (high pH)
■ pH < pKa: most is protonated
■ pH = pKa: half of molecules are deprotonated, [HA] = [A–]
■ pH > pKa: most is deprotonated
○ (+)-charged in acidic soln.: ⦚–NH3+, ⦚–COOH
■ pKa of CA group ≈ 2
○ Zwitterion in neutral soln.: ⦚–NH3+, ⦚–COO–
■ (+)/(–), but electrically neutral
○ (–)-charged in basic soln.: ⦚–NH2, ⦚–COO–
■ pKa of amino group ≈ 9–10
● Titration
○ ⦚–COOH is more acidic than ⦚–NH3+
○ Add 0.5 equiv. base to acidic AA: buffer (pH = pKa, 1), flat curve
○ Add 1 equiv. base to acidic AA: all AAs are zwitterions, isoelectric point reached
■ pIacidic R = ½ (pKa, COOH + pKa, R) ≪ 6
■ pIneutral R = ½ (pKa, COOH + pKa, +NH3) ≈ 6
■ pIbasic R = ½ (pKa, R + pKa, +NH3) ≫ 6
○ Add 1.5 equiv. base to acidic AA: buffer (pH = pKa, 2), flat curve
1.3. Peptide Bond Formation, Hydrolysis
● Peptides: multiple AAs/residues
○ Di/tripeptide: 2, 3 AAs
○ Oligopeptides: ≤ 20 AAs
○ Polypeptides: > 20 AAs
● Formation: ⦚–COO– + +H3N–⦚ ⇌ ⦚–CONH–⦚+ H2O
○ Condensation/dehydration, acyl substitution
○ Partial double-bond character in C–N bond: delocalized π e– in carbonyl, amino
N:
■ [⦚–(O=)C(–NH)–⦚] ↔ [⦚–(–O–)C(=N+H)–⦚]
■ Restricts rotation, rigid backbone
■ Other σ bonds are free to rotate
○ N-terminus (free amino end), C-terminus (free CA end)
■ Proteins are synthesized N to C
● Hydrolysis: reverse rxn., consumes water
○ Hydrolytic enzymes are AA-/terminus-specific
1.4. Primary, Secondary Structure
● 1° structure: AA sequence, from N- to C-terminus
○ Covalent peptide bonds between adjacent AAs
○ Protein sequencing
● 2° structure: backbone interactions
○ H-bonding between backbone groups (carbonyl O, amide H)
, ○ α helix: clockwise spiral
■ H-bonding 4 residues apart
■ Side chains point out from the helix
■ Pro: starts of α helices (rigid)
■ Gly: turns in α helices (conformationally flexible)
○ β-pleated sheet: rippled sheet
■ Anti/parallel H-bonding peptide chains
■ Pro: turns in β-pleated sheets
1.5. Tertiary, Quaternary Structure
● Fibrous (sheets/long strands), globular (spherical) proteins
● 3° structure: side-chain interactions
○ Hydrophobic/philic interactions between side chains
■ Hydrophobic AAs inward, hydrophilic AAs outward
● Hydrophobic AAs outside: ΔH > 0 (break H bonds w/in water), ΔS <
0 (no solvation layer) → ΔG > 0 (nonspontaneous)
● Hydrophobic AAs inside: ΔS > 0 (solvation layer, more
configurations for water) → ΔG < 0 (spontaneous)
○ Salt bridges: acid–base rxns., ionic bonds
○ Disulfide bonds: S–S, forms loops in peptide chain
■ Cys + Cys → cystine + 2 H+ + 2 e– (oxidation)
○ Molten globule: 3° structure formed
○ Denaturation: loss of 3° structure
● 4° structure: multiple subunits
○ Subunits: smaller globular proteins
○ Allostery: conformational/structural change in 1 subunit can change other
subunits’ activity
○ Reduce protein SA, reduce amt. DNA needed to encode protein, bring catalytic
sites closer
○ Conjugated proteins: prosthetic groups (organic molecules, metal ions, etc.)
covalently bonded to protein
■ Lipoproteins (lipids), glycoproteins (carbs), nucleoproteins (NAs)
1.6. Denaturation
● Temperature ↑ = average KE ↑ can overcome hydrophobic interactions
● Solutes can break disulfide bridges (reduction), overcome H bonds
● Detergents can disrupt noncovalent bonds, solubilize proteins
2. Enzymes
2.1. Biological Catalysis
● Catalysts
○ Change kinetics: Ea ↓, easier to form/more stable TS‡, rxn. rate ↑
○ Thermodynamics of rxn. (ΔHrxn, Keq, ΔG) stay the same
■ However, Ea ↓ means optimal temp may be lower (less energy needed to
reach Ea)
○ Not consumed in rxn.
○ Sensitive to pH, temp
● Major classifications: “LIL HOT”
, ○ Ligases: additions/syntheses between large, similar molecules
■ Require ATP
■ e.g., DNA ligase
○ Isomerases: rearrange bonds w/in molecule
■ Constitutional isomers, stereoisomers
■ e.g., phosphoglucose isomerase, TPI, aconitase
○ Lyases: 1 molecule ⇌ 2 molecules
■ No hydrolysis, no redox
■ e.g., synthases
○ Hydrolases: hydrolysis
■ e.g., phosphatase, lipases, peptidases, nucleases
○ Oxidoreductases: redox
■ Has e–-carrier cofactors, like NAD+
■ Reductants (e– donors), oxidants (e– acceptors)
■ e.g., dehydrogenases, reductases, oxidases
○ Transferases: move functional groups between molecules
■ Kinases: transfer Pi
2.2. Mechanisms
● Provide favorable microenvironments (pH, charge), stabilize TS‡, bring reactive groups
closer together
● Enzyme–substrate binding
○ Substrate binds to active site, forms enzyme–substrate complex
■ H bonding, ionic interactions, transient covalent bonds stabilize binding
○ Lock-and-key theory: no conformational changes
○ Induced-fit model (more accepted): active site changes conformation to
complement substrate
● Cofactors/coenzymes: nonprotein molecules needed for effective activity
○ Cofactors (inorganic/metal): minerals, etc.
○ Coenzymes (organic): vitamins, vitamin derivatives
■ Water-soluble vitamins: easily excreted, must be replenished regularly
● B vitamins ("The RhiNo Paid Pill Boy For Coke")
○ B1: thiamine (TPP)
○ B2: riboflavin (FAD, FMN)
○ B3: niacin (NAD)
○ B5: pantothenate (CoA)
○ B6: pyridoxine
○ B7: biotin
○ B9: folate
○ B12: cobalamin
● C: ascorbate
■ Fat-soluble vitamins: regulated by partition coefficients (non/polar
solubilities)
● A: β-carotene, retinol/al/oic acid
● D: cholecalciferol, etc.
● E: tocopherols, tocotrienols
● K: phylloquinone, menaquinones
○ Apoenzymes (w/o cofactors), holoenzymes (w/ cofactors)
○ Prosthetic groups (tightly bound), cosubstrates (loosely bound)
1.1. Proteinogenic Amino Acids
● AAs: amino, CA groups
○ In some AAs, amino and CA groups aren’t bonded to same C (e.g., GABA)
○ Proteinogenic AAs: 20 α-AAs encoded by codons in humans
○ Essential AAs: can’t be biosynthesized to meet demand
■ “Very Heavy MILK WTF”: Val, His, Met, Iso, Leu, Lys, Trp, Thr, Phe
○ Nonessential AAs: can be biosynthesized to meet demand
■ “DEANS”: Asp, Glu, Ala, Asn, Ser
● Stereochemistry: all AAs are chiral, (S), ʟ-isomers
○ Except Gly, which is achiral b/c its side chain is H
○ Except Cys, which is (R) b/c ⦚–CH2SH > ⦚–COOH in priority order
● Hydrophobicity
○ Hydrophobic: nonpolar, hydrocarbon side chains (Ala, Val, Leu, Iso, Phe)
○ Hydrophilic: polar/charged AAs (Ser, Thr, Gln, Asn, Glu, Asp, Lys, Arg, His)
● Side-chain structure
○ Nonpolar, nonaromatic
■ Glycine (Gly, G) ⦚–H
■ Alanine (Ala, A) ⦚–Me
■ Valine (Val, V) ⦚–iPr
■ Leucine (Leu, L) ⦚–CH2–iPr
■ Isoleucine (Iso, I) ⦚–CHMeEt
■ Methionine (Met, M) ⦚–CH2–CH2–SMe
● SMe and not SH, so nonpolar
■ Proline (Pro, P) ⦚–[pyrrolidine] (NH adj. to branch)
● Rigid ring, affects 2° structure
○ Aromatic
■ Tyrosine (Tyr, Y) ⦚–CH2–PhOH (para)
● Somewhat polar
■ Phenylalanine (Phe, F) ⦚–CH2Ph
■ Tryptophan (Trp, W) ⦚–CH2–[indole] (double bond of 5-membered
ring adj. to branch)
○ Polar
■ Serine (Ser, S) ⦚–CH2OH
● Hydroxyl is highly polar, H-bonding
■ Threonine (Thr, T) ⦚–CH(Me)OH
● Hydroxyl is less polar than in Ser (due to Me), H-bonding
■ Cysteine (Cys, C) ⦚–CH2SH
● Thiol is less polar than hydroxyls in Ser/Thr (S is less EN than O)
● Thiol can be oxidized
■ Asparagine (Asn, N) ⦚–CH2–CONH2
● Amide can’t be deprotonated
■ Glutamine (Gln, Q) ⦚–CH2–CH2–CONH2
● Amide can’t be deprotonated
○ Acidic, (–) charged
■ Aspartate (Asp, D) ⦚–CH2–COO–
● CA is acidic
■ Glutamate (Glu, E) ⦚–CH2–CH2–COO–
● CA is less acidic than in Asp (extra alkyl is EDG)
○ Basic, (+) charged
, ■ Lysine (Lys, K) ⦚–CH2–CH2–CH2–CH2NH3+
■ Arginine (Arg, R) ⦚–CH2–CH2–CH2–NH–C(NH2)2+
● Protonating imine delocalizes (+) throughout all 3 N’s
■ Histidine (His, H) ⦚–CH2–[imidazole]+ (NH, double bond adj. to
branch)
● Only imine is protonated at physiological pH (results in resonance)
1.2. Amino Acid Acid–Base
● Amphoteric: basic amino, acidic CA groups
○ Protonated in acidic soln. (low pH), deprotonated in basic soln. (high pH)
■ pH < pKa: most is protonated
■ pH = pKa: half of molecules are deprotonated, [HA] = [A–]
■ pH > pKa: most is deprotonated
○ (+)-charged in acidic soln.: ⦚–NH3+, ⦚–COOH
■ pKa of CA group ≈ 2
○ Zwitterion in neutral soln.: ⦚–NH3+, ⦚–COO–
■ (+)/(–), but electrically neutral
○ (–)-charged in basic soln.: ⦚–NH2, ⦚–COO–
■ pKa of amino group ≈ 9–10
● Titration
○ ⦚–COOH is more acidic than ⦚–NH3+
○ Add 0.5 equiv. base to acidic AA: buffer (pH = pKa, 1), flat curve
○ Add 1 equiv. base to acidic AA: all AAs are zwitterions, isoelectric point reached
■ pIacidic R = ½ (pKa, COOH + pKa, R) ≪ 6
■ pIneutral R = ½ (pKa, COOH + pKa, +NH3) ≈ 6
■ pIbasic R = ½ (pKa, R + pKa, +NH3) ≫ 6
○ Add 1.5 equiv. base to acidic AA: buffer (pH = pKa, 2), flat curve
1.3. Peptide Bond Formation, Hydrolysis
● Peptides: multiple AAs/residues
○ Di/tripeptide: 2, 3 AAs
○ Oligopeptides: ≤ 20 AAs
○ Polypeptides: > 20 AAs
● Formation: ⦚–COO– + +H3N–⦚ ⇌ ⦚–CONH–⦚+ H2O
○ Condensation/dehydration, acyl substitution
○ Partial double-bond character in C–N bond: delocalized π e– in carbonyl, amino
N:
■ [⦚–(O=)C(–NH)–⦚] ↔ [⦚–(–O–)C(=N+H)–⦚]
■ Restricts rotation, rigid backbone
■ Other σ bonds are free to rotate
○ N-terminus (free amino end), C-terminus (free CA end)
■ Proteins are synthesized N to C
● Hydrolysis: reverse rxn., consumes water
○ Hydrolytic enzymes are AA-/terminus-specific
1.4. Primary, Secondary Structure
● 1° structure: AA sequence, from N- to C-terminus
○ Covalent peptide bonds between adjacent AAs
○ Protein sequencing
● 2° structure: backbone interactions
○ H-bonding between backbone groups (carbonyl O, amide H)
, ○ α helix: clockwise spiral
■ H-bonding 4 residues apart
■ Side chains point out from the helix
■ Pro: starts of α helices (rigid)
■ Gly: turns in α helices (conformationally flexible)
○ β-pleated sheet: rippled sheet
■ Anti/parallel H-bonding peptide chains
■ Pro: turns in β-pleated sheets
1.5. Tertiary, Quaternary Structure
● Fibrous (sheets/long strands), globular (spherical) proteins
● 3° structure: side-chain interactions
○ Hydrophobic/philic interactions between side chains
■ Hydrophobic AAs inward, hydrophilic AAs outward
● Hydrophobic AAs outside: ΔH > 0 (break H bonds w/in water), ΔS <
0 (no solvation layer) → ΔG > 0 (nonspontaneous)
● Hydrophobic AAs inside: ΔS > 0 (solvation layer, more
configurations for water) → ΔG < 0 (spontaneous)
○ Salt bridges: acid–base rxns., ionic bonds
○ Disulfide bonds: S–S, forms loops in peptide chain
■ Cys + Cys → cystine + 2 H+ + 2 e– (oxidation)
○ Molten globule: 3° structure formed
○ Denaturation: loss of 3° structure
● 4° structure: multiple subunits
○ Subunits: smaller globular proteins
○ Allostery: conformational/structural change in 1 subunit can change other
subunits’ activity
○ Reduce protein SA, reduce amt. DNA needed to encode protein, bring catalytic
sites closer
○ Conjugated proteins: prosthetic groups (organic molecules, metal ions, etc.)
covalently bonded to protein
■ Lipoproteins (lipids), glycoproteins (carbs), nucleoproteins (NAs)
1.6. Denaturation
● Temperature ↑ = average KE ↑ can overcome hydrophobic interactions
● Solutes can break disulfide bridges (reduction), overcome H bonds
● Detergents can disrupt noncovalent bonds, solubilize proteins
2. Enzymes
2.1. Biological Catalysis
● Catalysts
○ Change kinetics: Ea ↓, easier to form/more stable TS‡, rxn. rate ↑
○ Thermodynamics of rxn. (ΔHrxn, Keq, ΔG) stay the same
■ However, Ea ↓ means optimal temp may be lower (less energy needed to
reach Ea)
○ Not consumed in rxn.
○ Sensitive to pH, temp
● Major classifications: “LIL HOT”
, ○ Ligases: additions/syntheses between large, similar molecules
■ Require ATP
■ e.g., DNA ligase
○ Isomerases: rearrange bonds w/in molecule
■ Constitutional isomers, stereoisomers
■ e.g., phosphoglucose isomerase, TPI, aconitase
○ Lyases: 1 molecule ⇌ 2 molecules
■ No hydrolysis, no redox
■ e.g., synthases
○ Hydrolases: hydrolysis
■ e.g., phosphatase, lipases, peptidases, nucleases
○ Oxidoreductases: redox
■ Has e–-carrier cofactors, like NAD+
■ Reductants (e– donors), oxidants (e– acceptors)
■ e.g., dehydrogenases, reductases, oxidases
○ Transferases: move functional groups between molecules
■ Kinases: transfer Pi
2.2. Mechanisms
● Provide favorable microenvironments (pH, charge), stabilize TS‡, bring reactive groups
closer together
● Enzyme–substrate binding
○ Substrate binds to active site, forms enzyme–substrate complex
■ H bonding, ionic interactions, transient covalent bonds stabilize binding
○ Lock-and-key theory: no conformational changes
○ Induced-fit model (more accepted): active site changes conformation to
complement substrate
● Cofactors/coenzymes: nonprotein molecules needed for effective activity
○ Cofactors (inorganic/metal): minerals, etc.
○ Coenzymes (organic): vitamins, vitamin derivatives
■ Water-soluble vitamins: easily excreted, must be replenished regularly
● B vitamins ("The RhiNo Paid Pill Boy For Coke")
○ B1: thiamine (TPP)
○ B2: riboflavin (FAD, FMN)
○ B3: niacin (NAD)
○ B5: pantothenate (CoA)
○ B6: pyridoxine
○ B7: biotin
○ B9: folate
○ B12: cobalamin
● C: ascorbate
■ Fat-soluble vitamins: regulated by partition coefficients (non/polar
solubilities)
● A: β-carotene, retinol/al/oic acid
● D: cholecalciferol, etc.
● E: tocopherols, tocotrienols
● K: phylloquinone, menaquinones
○ Apoenzymes (w/o cofactors), holoenzymes (w/ cofactors)
○ Prosthetic groups (tightly bound), cosubstrates (loosely bound)
