Amino Acids Flashcards
Primary Structure
Amino Acid Sequence
Central Dogma
DNA to mRNA to Protein
Enantiomers
Chirality isomers, D and L
Chirality of Mammalian Amino Acids
L-configuration
Alipathic Amino Acids
Gly, Ala, Val Leu, Ile, Met, Pro
Special Group on Proline
Imino
Aromatic Amino Acids
Phe, Tyr, Trp
Uncharged Polar Amino Acids
Ser, Thr, Asn, Gln, Cys
Charged Polar Amino Acids
Lys, Arg, His, Asp, Glu
pH with 50% protonation of an amino acid
pKa
Henderson-Hasselbach Equation
pH = pKa + log(A/HA)
pH where an amino acids has net charge of zero
Isoelectric point
Region where the pH does not respond to large additions of H or OH
Buffering
Leading Amino Acid at N-terminus
Met
Covalent bonds formed by the oxidation of cysteine
Disulfide linkage
5’ End
N-Terminus
3’ End
C-Terminus
Orientation of Amide Bond
Planar due to resonance, Trans due to steric interference
Phi Bond
N to Alpha-C
Psi Bond
Alpha-C to Carbonyl
Amide Bond
Carbonyl to N
Driving force for protein folding
Hydrophobic Interactions
Reason proteins have very few structures with low Gibbs free energy and usually only one native structure (Exponential Descent Down the Funnel)
Cooperativty
Length of Turns in Alpha Helix
3.6 Residues, 5.4 A
Order of H-bonds from 5’ to 3’
C=O to H-N, Parallel to Helical Axis
Polarity of Alpha Helix
Amphipathic
Beta Pleated Sheet Orientation
Parallel 5’ to 3’ same direction
Antiparallel alternating 5’ to 3’ and 3’ to 5’
Mixed combination of parallel and antiparallel
Amino acids for hairpin turns
Type I use Proline
Type II use Glycine
Amino acid used for end of alpha helices and beta sheets
Proline
Tertiary Structure
Domains due to R group interactions
Quaternary Structure
Subunits interacting together
Metamorphic Proteins
Multiple stable structures for a single protein
Alpha-Keratin Structure
Two right handed alpha-helices who form a left handed alpha coiled coil.
Alpha-Keratin Coil Bonding
Both non-covalent and covalent disulfide bonds
Collagen Structure
Three left-handed helices called alpha-chain with -Gly-X-Y- sequences where X is proline and Y is often either hydroxyproline or hydroxylysine
Collagen Abundance
20-25% of total body protein
Importance of Ascorbate and disease caused by its deficiency
Required by enzymes for the formation of hydroxyproline and hydroxylysine.
Scurvy which is marked by weakness of collagen in body (i.e. bleeding gums)
Synthesis of Collagen
Left handed helices have residues hydroxylated and begin forming the right handed super helix in the ER
Procollagen shuttled out of cell
Tropocollagen formed by terminating excess N and C terminal peptides allowing the tropocollagen super helices to self-assemble
Structure of Elastin
Connective tissue protein with rubber properties in lungs, arterial walls, and elastic ligaments. Mainly nonpolar amino acids and proline and lysine
Synthesis of Elastin
Tropoelastin released into ECM where it interacts with glycoprotein microfibrils
Some lysyls will be converted to allysine which cross-link lysine to form the matrix of elastin
Degradation of Elastin and Pathology
Alpha-Antitrypsin (alpha-AT) inhibits elastase which degrades elastin.
Genetic deficiency in alpha-AT due to S and Z alleles
Cigarette smoke oxidizes a Met residue which causes alpha-AT not be able to bind to elastin
