Proteins, Amino Acid Structure

Proteins Amino Acid Structure: The alpha carbon is considered a chiral carbon (glycine is the only amino acid that is not carbon because there are two hydrogen atoms coming off of the alpha carbon) Fischer projections helps show the structure of the amino acid (amino group is typically on the left and is known as an L amino acid, which is the only form found in the human body) ɑ Amino Acid Synthesis: Two main ways to synthesize amino acids: 1. Gabriel Synthesis begins with a molecule of N-phthalimido malonic ester (“Thad”), where base and an alkyl halide is added, followed by acid, and then heat in order to generate an amino acid 2. Strecker Synthesis is considered more “elegant” since it is much more simple Remember, an imine is when the carbonyl oxygen is replaced by NH (shown below) Classification of Amino Acids: Hydrophobic Amino Acids Alkyl Groups: Glycine, Leucine, Valine, Isoleucine, Alanine, Methionine, and Proline Aromatic Groups: Tryptophan and Phenylalanine (might smell good too lol) Hydrophilic Amino Acids Neutral Groups: Serine, Threonine, Asparagine, Cysteine, Glutamine, and Tyrosine Basic Groups: Histidine, Lysine, and Arginine Acidic Groups: Glutamic acid and Aspartic acid Four Levels of Protein Structure: Remember, hydrophobic packing, disulfide bridges, and van der waals are part of tertiary structure Disulfide bridges typically form on the outside of a protein (no antioxidants are found) whereas disulfide bridges are not typically found inside the protein because antioxidants are present here Same stuff involved in tertiary structure have to do with quaternary but involved multiple subunits Conformational Stability: Protein Folding & Denaturation: Conformation refers to the proteins folded 3D structure (active) Denatured refers to proteins have have become unfolded (inactive) Solvation shell is a term referring to layer of water (can be any liquid really) over the protein’s exterior (therefore would be more stable to have polar amino acids on the outside of the protein) Denaturation can occur through a couple different routes: 1. Temperature disrupts secondary, tertiary, and quaternary structure of the protein (increase energy enough to overcome hydrogen bonds) 2. pH changes will alter ionic bonding, disrupting tertiary and quaternary structure 3. Chemicals often disrupt hydrogen bonding within the protein, disrupting secondary, all the way up to quaternary structure 4. Enzymes break the individual covalent bonds between one another, disruption primary, secondary, tertiary, and quaternary structures Non-enzymatic Protein Function: Proteins are in one of two main classes Enzymes which catalyze reactions that help to sustain life (accelerate rate and specificity of the reaction, such as with DNA Polymerase) - If the protein ends with -ase then it is likely an enzyme Non-enzymes are proteins that have the capacity to bind, but not necessarily catalyze reactions Some examples are receptors, ion channels, transport proteins (binds molecules in order to transport them, and need high affinity at high concentrations and low affinity at low concentrations → such as Hb), motor proteins (crucial for cellular motility, such as myosin which is involved in muscle contraction and kinesin/dynein), and antibodies (protein components that mark foreign antigens for destruction by some other cell → antigen is the antibody’s particular ligand with a HIGH affinity) Extra Notes: Remember, proteins made in the RER are typically exported while those made by free floating ribosomes in the cytoplasm tend to stay within the cell Proteins that enter the golgi undergo several modifications in order to specify their final destination (such as glycosylation) Humans (80S, 40S and 60S) and bacteria (70S, 50S and 30S) have different ribosomes ( Missense mutations cause the replacement of a single nucleotide, coding for a different amino acid Nonsense mutations cause the replacement of a single nucleotide, generating an early stop codon