MCAT Biochem: Amino acids, proteins

Negatively charged, acidic amino acids

1. Aspartic acid (aspartate) 2. Glutamic acid (glutamate) - have -COO- in their side chains

Non-polar, non-aromatic amino acids

1. Glycine 2. Alanine 3. Valine 4. Leucine 5. Isoleucine - all have alkyl side chains 6. Methionine - contains sulfur with a methyl group and is non-polar 7. Proline - cyclic amino acid, has an effect on secondary structure of a protein

Positively charged, basic amino acids

1. Lysine - terminal primary amino group 2. Arginine - three nitrogen atoms, positive charge is delocalized over all three nitrogens 3. Histidine - aromatic ring with two nitrogens (imidazole) - under acidic conditions, both nitrogens are protonated to give positive charge

Protonation and deprotonation

1. pH = 1, very acidic - amino group is fully protonated and positive (-NH3+) - carboxylic acid is fully protonated and neutral (-COOH) - molecule is overall positive 2. Zwitterion at neutral pH - amino group is fully protonated and positive (-NH3+) - acid is fully deprotonated and negative (-COO-) - molecule is overall neutral, exists in water as a salt 3. pH = 9-10, very basic - amino group is fully deprotonated and neutral (-NH2) - acid is fully deprotonated and negative (-COO-) - molecule is overall negative

Glycine

Achiral amino acid since R group is H.

Secondary structure

Local structure of neighboring AAs. Primarily result of hydrogen bonding between AAs. Hydrogen bonds between neighboring residues give structures stability. Two types: 1. Alpha helices 2. Beta pleated sheets

Amphoteric species

Can accept a proton or donate a proton to be acidic or basic. Amino acids have an acidic acid group and a basic amino group. How they react depends on the pH.

Beta pleated sheets

Can be parallel or antiparallel. Peptide chains lie alongside each other to make rows or strands held together by H bonds between chains.

Peptides

Composed of amino acid subunits called residues. Dipeptides have two, tripeptides have three. Oligopeptides have more than 3 but less than 20. Polypeptides have over 20 residues.

Hemoglobin

Consists of four different subunits, which can each bind a molecule of oxygen.

IgG antibody

Contain four distinct subunits.

Amino acids

Contain two functional groups: amino group (-NH2) and carboxyl group (-COOH). Alpha-amino acids have both groups bonded to the same carbon, alpha-carbon. Also have hydrogen and R group. 20 alpha-amino acids are encoded by the human genome. Called proteinogenic amino acids.

Conjugated proteins

Derived part of function from covalently attached prosthetic groups. Include lipoproteins, glycoproteins, and nucleoproteins.

Solute denaturation

Directly interfere with the forces holding a protein together. Disrupt tertiary and quaternary structures by breaking disulfide bridge to reduce cystine. Can overcome hydrogen bonds and side chain interactions in secondary structures. Detergents can solubilize proteins to denature them.

Titration for uncharged amino acids

Each proton is titrated at a distinct step. Titration with NaOH: 1. Low pH, fully protonated and positive 2. Acid group deprotonated first - more acidic, lower pKa value 3. 0.5 equivalents of NaOH - pH = pKa1 4. 1.0 equivalent NaOH - pH= pI 5. Amino group deprotonates second - more basic, higher pKa value 6. 1.5 equivalents NaOH - pH = pKa2 7. 2.0 equivalents NaOH - molecule is fully deprotonated

Peptide bond formation and cleavage

Formation: - condensation/dehydration reaction, results in removal of H2O molecule - electrophilic carbonyl carbon of first AA attacked by nucleophilic amino group of second AA - hydroxyl group of carboxylic acid is removed to form the peptide bond Cleavage: - peptide bond is hydrolyzed by hydrolytic enzymes -trypsin and chymotrypsin in digestion - add a hydrogen atom to the amide nitrogen and -OH to the carbonyl carbon

Aromatic amino acids

Have uncharged aromatic side chains. 1. Tryptophan - largest, double-ring system, contains nitrogen 2. Phenylalanine - has a benzyl side chain 3. Tyrosine - has a phenol group, is relatively polar

Heat denaturation

Heat increases the average kinetic energy, which can increase enough to overcome hydrophobic interactions and cause the protein to unfold.

Hydrophobic vs. hydrophilic

Hydrophobic: - long alkyl side chains - found in protein interiors Hydrophilic: - charged side chains - found on the protein surface

Disulfide bond

Important part of tertiary structure. Bond that forms when two cysteines become oxidized to cystine. Create loops in the protein chain. Formation of the bond requires the loss of two protons and two electrons.

Proline structure

Introduces a kink in the peptide chain when in the middle of an a-helix. Rarely found in the middle of pleated sheets. Found frequently as the first residue at the start of an a-helix or in the turns between pleated sheets.

Peptide bonds

Join together the residues in peptides. Specialized amide bond that forms between the COO- group of one AA and the NH3+ group of another. Forms the functional group -C(O)NH-. Has partial double bond character due to resonance. Rotation is restricted around the C-N amide bond. Free amino end is N-terminus (left), free carboxyl end is C-terminus (right).

Cysteine

L-amino acid, chiral. Has absolute (R) configuration since the CH2SH group has priority over the -COOH.

Primary structure

Linear arrangement of amino acids coded in an organism's DNA. Sequence of AA listed from N-terminus to C-terminus. Stabilised by the formation of covalent peptide bonds between adjacent AAs. Encodes all info for higher level folding and structure. Can be determined by lab sequencing using the DNA of that protein.

Quaternary structure

Only exist for proteins with more than one polypeptide chain. Aggregate of smaller globular peptides - subunits - and is the functional form of the protein. Lend stability by reducing surface area, reduce amount of DNA needed for the complex, can bring catalytic sites close together, and can induce cooperativity/allosteric effects.

Prosthetic groups

Organic or inorganic molecules that couple to certain proteins to help them function. Includes vitamins, metal ions, etc.

Isoelectric point (pI)

Point at which molecules in a solution are electrically neutral. Amino acids exist as zwitterions at the pI. Where pKa1 is the pKa of the -COOH group and pKa2 is the pKa of the -NH2 group.

Proteins

Polypeptides that vary in length of amino acids. Serve functions such as enzymes, hormones, membrane pores, receptors, and cell structure. Four levels of protein structure: 1. Primary 2. Secondary 3. Tertiary 4. Quaternary

Heme

Prosthetic group in hemoglobin and myoglobin. Contains an iron atom at its core and binds to and carries oxygen. Without it, hemoglobin is inactive.

Denaturation

Protein loses its three-dimensional structure. May be reversible, more often not.

Side chain

R group of an amino acid. Specific to each amino acid. Determines their specific properties and functions.

Alpha helix

Rodlike structure involving peptide chains coiling clockwise around a central axis. Stabilized by H bond between a carbonyl oxygen and amide hydrogen 4 residues away. Important for structure of keratin in hair, skin, and nails.

Polar amino acids

Side chains that are polar but not aromatic. 1. Serine 2. Threonine - have -OH groups in their side chains, highly polar, make hydrogen bonds 3. Asparagine 4. Glutamine - amine side chains, but do not become 5. Cysteine - has a thiol group (-SH), prone to oxidation due to weaker bond

Solvation layer

Solvent molecules surround the solute molecules in order to solvate them. Water molecules in aqueous solution form H bonds with solute to dissolve it.

Fibrous protein

Structures that resemble sheets or long stands. Includes collagen.

Globular protein

Tend to be spherical in shape and structure. Includes myoglobin.

Ionizable groups

Tend to gain protons in acid and lose protons in base. At low pH, ionizable groups are protonated. At high pH, ionizable groups are deprotonated.

Chirality

The a-carbon of an amino acid is chiral since it has four different groups attached. All are L-amino acids (amino group on left), with absolute (S) configuration for almost all.

Titration for charged amino acids

The proton from the R group is also lost during titration. For acidic - the second proton is lost from the side chain carboxyl, pKa is between 2 and neutral pH. For basic - loses a third proton after the amino group from its amino side chain, pKa is slightly higher than the amino group.

Tertiary structure

Three-dimensional structure of a protein determined by hydrophilic and hydrophobic interactions between R groups. Hydrophobic groups move into the interior of the chain, with hydrophilic groups on the outside which can then interact and stabilize the protein.

pKa

pH at which, on average, half of the molecules are deprotonated and half are protonated. If pH < pKa, a majority will be protonated. If pH > pKa, a majority will be deprotonated. All amino acids have two: 1. pKa1 - pKa for the carboxyl group - around 2 2. pKa2 - pKa for the amino group - between 9-10 Some have a third: 3. pKa3 - pKa for the ionizable side chain

pI for acidic amino acids

pI <<< 6

pI for basic amino acids

pI >>> 6