The presence of what element differentiates proteins from carbohydrates and lipids?
Nitrogen. Comprises about 16% of molecular weight of protein
What is at the nucleus of an amino acid and what is attached to it? Which form, L or D predominates?
alpha carbon. Carboxylic acid (-COOH) and amine (-NH3) groups are attached. Also attached are a hydrogen and an R group. L form predominates.
Essential Amino Acids
AAs that must be present in the diet: valine, leucine, isoleucine, phenylalanine, tryptophan, threonine, methionine and lysine
AAs are Amphoteric
AAs contain at least two ionizable sites and, depending on the pH the sites can be negative, positive or neutral.
What gives an AA a net positive or negative charge?
In very low pH (acidic): net positive charge. In alkaline solutions (high pH): net negative charge.
Ampholyte or Zwitterion
At physiological pH (7.4) both sites on AA are ionized: COOH easily loses a hydrogen ion & becomes COO- & the NH2 easily gains the hydrogen ion and becomes NH3+.
Isoelectric point (pI)
pH at which AA is neutral: having no net surface charge. Is a function of the R-group. (pI ranges from 3-10)
carboxyl group of one amino acid covalently binds the amino group of the next AA. Molecule of water is formed as a by-product; this is a dehydration synthesis. Energy needed (endergonic) to form the peptide bond while reverse reaction (hydrolysis) is exergonic.
Primary structure of proteins
determined by the type and number of amino acids (amino acid sequence) linked by covalent peptide bonds.
Can the peptide bond rotate?
formed at a specific angle (125 degrees) and is not free to rotate. The alpha C bonds to the alpha amine and alpha carbonyl groups can rotate.
the 2D shape AAs strand takes as AAs interact with adjacent AAs via hydrogen bonds. There are also a small amount of disulfide bonding between the cysteine/methionine amino acids and other interactions (attractive and repulsive) between polar and nonpolar R group.
What are the secondary shapes the result of?
Many of the bonds associated with R groups can rotate & this rotation allows conformational changes that cause the secondary shapes to form. Secondary shapes: alpha helix, beta pleated sheet or random coil. Depend largely on H bonds to maintain these shapes
permits AA sequence to coil, reducing length. This brings carbonyl and amine groups of AAs that are normally 3 to 6 residues apart into close proximity allowing hydrogen bond formation that will maintain the helical form. Protein helix has 1 turn per 3.6 AA.
Beta pleated sheet
occurs due to parallel-antiparallel AA sequences which are close enough to form H-bonds. The R groups may be located between the AA strings or to the outside, depending on the folding of the primary AA sequence.
Hold alpha and beta regions together in proteins. Not truly random, but based on specific AA sequences that fold into specific shapes.
Contrast structural proteins and enzymes in terms of secondary structures
Structural proteins such as collagen or keratin tend to have more pleated sheet and helical regions than would a functional protein like an enzyme.
3D structure that forms as the AAs interact at the R groups causing the AA chain to fold and take its characteristic 3D shape. These interactions are the result of hydrophobic interactions, hydrogen bonds, covalent (disulfide, lysinoleucine) and van der Waals (repulsive) forces.
Refers to a more complex molecule which may include multiple, different protein units (forming dimers, tetramers or oligomers) and non-protein components, such as heme which contains non-organic molecules and metal ions.
Two Generic Protein Shapes
Globular & Fibrous. Globular proteins are compact, tightly folded and coiled chains. The majority of serum proteins are globular. Fibrous proteins such as hair, collagen and fibrin are mostly structural proteins.