Chapter 2 - Proteins Flashcards
Proteins are
Linear polymers built of amino acids which are linked end to end
Secondary structures
Three dimensional structure formed by hydrogen bonds between amino acids near one another
Amino acids are
The building blocks of proteins
Almost all amino acids are chiral
L amino acid
Became more dominant in solution due to its solubility
Amino acids in solution at neutral pH exist as
Diplomat ions or zwitterions where the amine group is protonated and the carbonyl group is deprotonated
Amino acid R groups can be characterized as
Hydrophobic amino acids with no polar groups
Polar amino acids with neutral R groups
Positively charged (basic)
Negatively charged (acidic)
The formation of a dipeptide from two amino acids is accompanied by
A loss of water molecule
Peptides are kinetically stable becaus
The rate of hydrolysis is extremely slow
The amino acid sequence is
The link between the genetic message in DNA and the three-dimensional structure that performs a proteins biological function
The molecular weight of an amino acid
110g/mol
Disulfide bonds are formed by
The oxidation of a pair of cysteine residues
Polypeptides are flexible yet constricted
Resonance causes the peptides to be rigid and planar because it makes it less reactive and more stable. Due to the partial double bond character
Why are almost all peptides trans?
Due to steric clashes between R groups. Proline is usually cis.
Freedom of rotations
Allows proteins me to fold in different ways.
Psi angle
Bond between the C and O
Phi angle
Bond between the C and N
Ramachandran plot
Shows favored confirmations of the proteins
Two types of secondary structures
Alpha helix
Beta sheets
Alpha helices
Rodlike structure, stabilized by hydrogen bonds between the NH and C groups.
Rise of amino acid - 1.5A
Residues per turn - 5.6A
In the alpha helix
The CO group of each amino acid forms a hydrogen bond with the NH that is situated 4 residues ahead of the sequence
Not good for alpha helices
Proline, valine, threonine, isoleucine, serine, aspartame, asparagine and glycine
Beta sheet
Fully extended. The distance between adjacent amino acid is 3.5A
Antiparallel confirmation
Stronger that parallel due to hydrogen bond allignment
Omega loop
The CO residue i of the polypeptide chain is hydrogen bonded to the NH group of the residue i + 3 to stabilize the turn
Alpha keratin
Have covalent disulfide bonds that hold the, together and make them very rigid
Structure of proteins
3 dimensional structure
Fulfills biological conformation (native fold)
Cost of conformational entropy
Motifs
Certain combination of secondary structures
Protein folding
Is driven by the strong tendency of hydrophobic residues trying to be excluded from water.
Tertiary structure
The interior consists of almost entirely no polar residues such as leucine, valine, methionine and phenylalanine. Polar charged chains are on the surface
Two major classes of tertiary structures
Fibrous proteins
Globular proteins
Quaternary structures
Each polypeptide is called a subunit. Refers to the spatial arrangement of subunits and the nature of their interactions
Ribonuclease
Is a single polypeptide that has 124 amino acid residues cross linked by four disulfide bonds
Protein stability
Depends on its three dimensional structure
Integrity - denaturation
Urea and mercaptoethanol
Disrupt the noncovalent bonds. They replace water as the molecule solvating the proteins and disrupt the van der Waals
Scientist Annfisten
Made the critical observation that the denatured ribonuclease, freed of urea and mercapto by dialysis, slowly regained enzymatic activity
