What are proteins and peptides made of, and what is unique about the bond that connects these components?
They are made of amino acids connected by amide linkages (peptide bonds). The bond is rigid due to tautomerism
What are some functions that proteins serve?
Proteins play major structural roles in the body.
They catalyze biochemical reactions (enzymes).
They are involved in contractile structures.
They carry oxygen and carbon dioxide from cells (hemoglobin)
Transport other molecules.
Have unique binding properties.
Analysis of proteins in the blood or urine can be used in diagnostic tests.
Describe the general solubility properties of proteins.
Proteins can be fibrous and insoluble such as collagen, keratin, and elastin.
They can be globular with hydrophobic residues inside and hydrophilic outside.
Fibrous and soluble such as fibrinogen.
Describe what primary, secondary, tertiary, and quaternary structures of proteins are.
Primary - the amino acid sequence.
Secondary - The alpha helices, beta pleated sheets, beta turns, and random coil arrangements that give a protein its 3-D shape
Tertiary - The folding of the secondary structures to make the protein more compact. The protein is folded so that the hydrophobic portions face inwards and the hydrophilic portions face outward.
Quaternary - Proteins containing two or more polypeptide chains(subunits)
What are the commonly occurring modifications of amino acids found in some proteins?
Acetylation - Acetylation of N-terminal residues makes them resistant to degradation.
Carboxylation - Glutamate is acetylated. Deficiency in vitamin K causes hemorrhages.
Hydroxylation - Proline is hydroxylated in collagen to stabilize the fibers. Deficiency in vitamin C prevents hydroxylation in collagen which leads to scurvy
Glycosylation - Many proteins are secreted from cells, for example antibodies acquire oligosaccharide chains on specific arganine residues.
Phosphorylation - A switch to control regulation of cellular processes.
Disulfide linkages - 2 cystine sulfhydryls can react to form a disulfide bond, linking different parts of a polypeptide chain together.
What amino acids are sometimes found to be phosphorylated in proteins?
Serine, threosine, and tyrosine.
Describe alpha helix, beta pleated sheet, and beta turn structures.
Alpha helix - Tightly coiled formation stabilized by hydrogen bonds between imido N-H groups and the carbonyl oxygen of main chains. Right hand helix with 3.6 amino acids per turn found in globular and fibrous proteins. Alpha keratin is main component of hair.
Beta pleated sheet - Hydrogen bonding between neighboring chains. Found in silk fibroin. Anti parallel making strong hydrogen bonds.
Beta turn - Accomplish reversals in direction of peptide chains.
What stabilizes higher order structures in proteins?
Electrostatic attraction of charged residues(salt bridges)
Internal hydrogen bonding
Short range Van Der Waals and London Dispersion Forces between neutral residues (dipole-dipole and polarizability)
Entropy driven hydrophobic effect
What amino acids are likely to carry charges on their side chains at neutral pH?
Negative charge = Apartic acid, glutamic acid
Positive charge = Lysine, arganine, hystidine
Negative charge = Tyrosine, cysteine
What are zinc fingers, kringle domains, and leucine zippers?
Zinc fingers - Zinc ions are complexed into four amino acids causing a loop of about 12 amino acids to protrude.
Kringle domains - Conserved sequences that fold into large loops stabilized by 3 disulfide linkages (important in blood coagulation)
Leucine zippers - Arrangements of leucine along one side of alpha helix regions in two proteins so that the proteins can form dimers leaving basic amino acid regions to bind to DNA.
How can proteins be denatured?
Drastic pH changes
What is the hydrophobic effect?
It is entropy driven. Negative delta G is favored (in Gibbs Free Energy equation). Hydrophobic molecules aggregate to squeeze out water and increase entropy