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amino acids
-have four groups attached to a central carbon: an amino group (-NH₂), a carboxyl group (-COOH), a hydrogen atom, and an R group -the R group determines chemistry and function
α-amino acids
amino acids in which the amino group and the carboxyl group are bonded to the α-carbon of the carboxylic acid
proteinogenic amino acids
-the 20 α-amino acids encoded by the human genetic code -most are chiral and optically active (except glycine) -all chiral amino acids used in eukaryotes are L-amino acids (except cysteine)
which amino acid is achiral?
glycine
which amino acid has an (R) absolute configuration?
cysteine
amino acid side chains
can be polar or nonpolar, aromatic or nonaromatic, charged or uncharged
nonpolar, nonaromatic amino acids
glycine, alanine, valine, leucine, isoleucine, methionine, proline
aromatic amino acids
tryptophan, phenylalanine, tyrosine
polar amino acids
serine, threonine, asparagine, glutamine, cysteine
negatively charged (acidic) amino acids
aspartate, glutamate
positively charged (basic) amino acids
lysine, arginine, histidine
alanine
Ala, A nonpolar, nonaromatic
arginine
Arg, R positively charged (basic)
asparagine
Asn, N polar
aspartic acid
Asp, D negatively charged (acidic) anion is aspartate
cysteine
Cys, C polar
glutamic acid
Glu, E negatively charged (acidic) anion is glutamate
glutamine
Gln, Q polar
glycine
Gly, G nonpolar, nonaromatic
histidine
His, H positively charged (basic)
isoleucine
Ile, I nonpolar, nonaromatic
leucine
Leu, L nonpolar, nonaromatic
lysine
Lys, K positively charged (basic)
methionine
Met, M nonpolar, nonaromatic
phenylalanine
Phe, F aromatic
proline
Pro, P nonpolar, nonaromatic
serine
Ser, S polar
threonine
Thr, T polar
tryptophan
Trp, W aromatic
tyrosine
Tyr, Y aromatic
valine
Val, V nonpolar, nonaromatic
classifying amino acids as hydrophobic or hydrophilic
-hydrophobic: have long alkyl chains -hydrophilic: are charged
hydrophobic amino acids
alanine, isoleucine, leucine, valine, and phenylalanine
hydrophilic amino acids
histidine, arginine, lysine, glutamate, aspartate, asparagine, glutamine
amphoteric species
-can accept or donate protons -how they react depends on the pH of their environment
pKa
the pH at which half of the species is deprotonated, [HA] = [A⁻]
pKa₁
-the pKa for the carboxyl group -usually around 2
pKa₂
-the pKa for the amino group -usually between 9 and 10
amino acid protonation (pH and pKa)
-if pH < pKa: mostly protonated -if pH > pKa: mostly deprotonated
amino acid protonation (pH)
-at low (acidic) pH: fully protonated -at pH near the pI of the amino acid: neutral zwitterion -at high (alkaline) pH: fully deprotonated
amino acid charge (pH)
-at low (acidic) pH: positively charged -at pH near the pI of the amino acid: as both a positive and a negative charge, but overall is electrically neutral -at high (alkaline) pH: negatively charged
isoelectric point (pI)
the pH at which the molecule is electrically neutral
calculating the pI of amino acids without charged side chains
calculated by averaging the two pKa values
calculating the pI of amino acids with charged side chains
calculated by averaging the two pKa values that correspond to protonation and deprotonation of the zwitterion
isoelectric point of a neutral amino acid
pI = [pKa (NH₃⁺ group) + pKa (COOH group)]/2 ∼6
isoelectric point of a acidic amino acid
pI = [pKa (R group) + pKa (COOH group)]/2 well below 6
isoelectric point of a basic amino acid
pI = [pKa (NH₃⁺ group) + pKa (R group)]/2 well above 6
titration curve of amino acids
-nearly flat at the pKa values of the amino acid -nearly vertical at the pI of the amino acid
peptides and amino acid residues
peptide bond
-a specialized form of an amide bond that forms between the -COO⁻ group of one amino acid and the NH₃⁺ group of another amino acid -forms the functional group -C(O)NH-
peptide bond formation
-a condensation or dehydration reaction (releases one molecule of water) -the nucleophilic amino group of one amino acid attacks the electrophilic carbonyl group of another amino acid, and the hydroxyl group of the carboxylic acid is kicked off
what type of reaction is the formation of a peptide bond?
condensation or dehydration
resonance in a peptide bond
-amide bonds are rigid because of resonance -because amide groups have delocalizable π electrons in the carbonyl and in the lone pair on the amino nitrogen, they can exhibit resonance -the C-N bond in the amide has partial double bond character, and rotation of the protein backbone around its C-N amide bonds is restricted, which makes the protein more rigid
N-terminus
-aka amino terminus -the free amino end of a peptide
C-terminus
-aka carboxy terminus -the free carboxyl end of a peptide
how are peptides conventionally drawn and read?
-drawn with the N-terminus on the left and the C-terminus on the right -read from N-terminus to C-terminus (left to right)
peptide bond hydrolysis
-catalyzed by hydrolytic enzymes such as trypsin and chymotrypsin, which: •are specific, in that they only cleave at specific points in the peptide chain •break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon
hydrolytic enzymes
trypsin & chymotrypsin
what type of reaction is the breaking of a peptide bond?
hydrolysis
chymotrypsin
cleaves at the carboxyl end of phenylalanine, tryptophan, and tyrosine (aromatics)
trypsin
cleaves at the carboxyl end of arginine and lysine
proteins
polypeptides that range from just a few amino acids in length up to thousands
four levels of protein structure
-primary: amino acid sequence (peptide bonds) -secondary: amino acid structure (α-helices, β-pleated sheets, hydrogen bonds) -tertiary: 3D shape (hydrophobic interactions, salt bridges, hydrogen bonds, disulfide bonds) -quaternary: interaction between subunits
stabilizing bonds in each level of protein structure
-primary: peptide (amide) -secondary: hydrogen -tertiary: van der Waals, hydrogen, ionic, covalent -quaternary: van der Waals, hydrogen, ionic, covalent
primary structure
-the linear sequence of amino acids in a peptide -stabilized by peptide bonds
secondary structure
-the local structure of neighboring amino acids -stabilized by hydrogen bonding between amino groups and nonadjacent carboxyl groups -key features: α-helices, β-pleated sheets
α-helices
-a rodlike structure in which the peptide chain coils clockwise around a central axis -stabilized by intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom four residues down the chain -the side chains point away from the helix core
example of a protein with α-helices
keratin (a fibrous structural protein found in human skin, hair, and fingernails)
β-pleated sheets
-a parallel or antiparallel structure in which the peptide chains lie alongside one another, forming rows or strands -held together by intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain -assume a pleated, or rippled, shape to accommodate as many hydrogen bonds as possible -the R groups point above and below the plane
example of a protein with β-pleated sheets
fibroin (the primary protein component of silk fibers)
proline and secondary protein structure
-can interrupt secondary structure because of its rigid cyclic structure -introduces a kink in the peptide chain when it is found in the middle of an α-helix
tertiary structure
-the three-dimensional shape of a single polypeptide chain -mostly determined by hydrophilic and hydrophobic interactions between R groups of amino acids -stabilized by hydrophobic interactions, acid-base interactions (salt bridges), hydrogen bonding, and disulfide bonds -stabilizing bonds: van der Waals, hydrogen, ionic, covalent
salt bridges
created as a result of acid-base interactions between amino acids with charged R groups
disulfide bonds
-the bonds that form when two cysteine molecules become oxidized to form cystine -create loops in the protein chain and determine how wavy or curly human hair is -formation requires the loss of two protons and two electrons (oxidation)
fibrous proteins
-have structures that resemble sheets or long strands -ex: collagen
globular proteins
-tend to be spherical -ex: myoglobin
protein folding and entropy
-by moving hydrophobic residues away from water molecules and hydrophilic residues toward water molecules, a protein achieves maximum stability -this is an energetically favorable (∆S > 0) and spontaneous (∆G < 0) process
quaternary structure
-the interaction between peptides in proteins that contain multiple subunits -only exist for proteins that contain more than one polypeptide chain -stabilizing bonds: van der Waals, hydrogen, ionic, covalent
roles of the quaternary structure
-can be more stable, by further reducing the surface area of the protein complex -can reduce the amount of DNA needed to encode the protein complex -can bring catalytic sites close together, allowing intermediates from one reaction to be directly shuttled to a second reaction -can induce cooperativity, or allosteric effects
cooperativity
-aka allosteric effects -one protein subunit can undergo conformational or structural changes, which either enhance or reduce the activity of the other subunits
conjugated proteins
proteins with covalently attached molecules
prosthetic group
-molecules that are covalently attached to a conjugated protein -have major roles in determining the function of their respective proteins -ex: metal ion, vitamin, lipid, carbohydrate, nucleic acid
denaturation
-loss of three-dimensional protein structure, caused by heat or increasing solute concentration -causes a loss of protein function
denaturation (heat)
-when the temperature of a protein increases, the average kinetic energy increases -when the temperature gets high enough, the extra energy can be enough to overcome the hydrophobic interactions that hold a protein together, causing the protein to unfold -ex: cooking egg whites
denaturation (solutes)
-solutes denature proteins by directly interfering with the forces that hold the protein together -can disrupt tertiary and quaternary structures by breaking disulfide bridges, reducing cystine back to two cysteine residues -can overcome the hydrogen bonds and other side chain interactions that hold α-helices and β-pleated sheets intact -detergents such as SDS can solubilize proteins, resulting in a hydrophobic core that promotes denaturation of the protein -ex: urea
enzymes
biological catalysts that are unchanged by the reactions they catalyze and are reusable
catalysts
-lower the activation energy necessary for biological reactions -do not alter the free energy (∆G) or enthalpy (∆H) change that accompanies the reaction nor the final equilibrium position; rather, they change the rate (kinetics) at which equilibrium is reached
key features of enzymes
-lower the activation energy -increase the rate of the reaction -do not alter the equilibrium constant -are not changed or consumed in the reaction (appear in both the reactants and products) -are pH- and temperature-sensitive, with optimal activity at specific pH ranges and temperatures
do not affect the overall ∆G of the reaction -are specific for a particular reaction or class of reactions
enzyme specificity
each enzyme catalyzes a single reaction or type of reaction with high specificity
oxidoreductases
-catalyze oxidation-reduction reactions that involve the transfer of electrons -reductant: the electron donor; ex: dehydrogenase, reductase -oxidant: the electron acceptor; ex: oxidase
Examples of oxidoreductases
dehydrogenase, reductase
transferases
-move a functional group from one molecule to another molecule -ex: aminotransferase, kinases
kinases
catalyze the transfer of a phosphate group, generally from ATP, to another molecule
hydrolases
-catalyze cleavage with the addition of water -ex: phosphatase, peptidases, nucleases, lipases
lyases
-catalyze cleavage without the addition of water and without the transfer of electrons -the reverse reaction (synthesis) is often more important biologically -ex: synthases
isomerases
catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers
ligases
responsible for joining two large biomolecules, often of the same type
mnemonic for major enzyme classifications
LI'L HOT: Ligase, Isomerase, Lyase, Hydrolase, Oxidoreductase, Transferase
endergonic reaction
require energy, ∆G > 0
exergonic reaction
release energy, ∆G < 0
Note 
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