Flashcards
Lecture Five - The common amino acids, peptide bond and the primary structure of proteins
Cards in this deck (14)
- 1Concepts to understand-AA structure: Amino group — Side chain — Carboxyl group
-AA are zwitterions
-Recognize the standard 20 amino acids (AA) and their properties
-Stereoisomers of the same AA have different functionality
-Isoelectric point, Inductive effect
-AA form a linear polymer (protein) through the dehydration reaction and formation of the peptide bonds.
-Proteins are synthesized from N to C terminus - 2—
- 3At physiological pH amino acids are ___zwitterions
- 4Aromatic R groups *Tyrosine is polar but still slighty ___ -UV peak at 280 nm is a signature of a ___ (F,Y,W are likely to be present)hydrophobic
protein - 5Sulfur-containing R-groups = Cysteine & Methionine Cysteine forms ___ (covalent bonds) that stabilize protein structure.disulfide bridges (S-S)
- 6Chirality, Stereoisomers and Function Assume 2D universe and 2 types of molecules in it: L and D. L and D have four different groups: L and D cannot be ___ in 2D. L and D are ___ images By analogy in our 3D universe, it takes four (3D+1) independent group to get two mirror molecules Such non-superimposable molecules are called ____superimposed
mirror
enantiomers
- 72^n = total possible configurations ___ = only non-chiral amino acid and is therefore not optically active L or D amino acids are found in life? -Can have R or S configurationsGlycine
L-amino acids - 8There are more than 200 amino acids in living organisms!? There are 23 proteogenic AA: 20 '____' (we covered so far) directly encoded by DNA Selenocysteine, pyrrolysine, N-Formylmethionine use special translation mechanism Non-proteogenic AA's that are formed after translation, including: -AA as-is, or as a part of a protein or smaller polypeptide -Drugs -Role: intermediates in bioreactions, components of bacterial cells, neurotransmitters, toxins, ...standard
- 9Ionization of AA Isoelectric point is pH at which net charge = ____ Variation in pKa values among AA'szero
- 10Inductive effect: pulling of electron density from the affected atom(s) Explains ___ in pKa values among AA's
- 11Protein is a linear ___ of amino acids Peptide bond is formed during translation, ___ reaction Each amino acid has a three (e.g., Ala) or one letter (e.g., A) name You may have your namesake polypeptide.polymer
dehydration - 12Proteins are synthesized and read left-right, _ to _ terminus This condensation reaction is not favorable in water (reverse is) • Cell machinery (ribosomes) uses GTP as an energy sourceN to C terminus
- 13When a peptide bond forms between two AAs, pKa values for amino and carboxyl groups become ___. pKa of the side chain remains ____ for protein folding and enzyme activity. • Similar to AA, pKa varies depending on the neighboring groups.irrelevant
important - 14Linear sequence of AAs is called ___ protein structure Secondary, Tertiary, and Quaternary structure will be discussed later Primary sequence defines higher-order structures and protein ____ Di- , tri-, oligo-, polypeptide, depending on the number of AAsprimary
function