Chapter 4 Flashcards
what biological macromolecules perform most biochemical functions and catalyze most biochemical reactions?
proteins
what are proteins made of? how linked?
amino acids linked by peptide bonds (aka polypeptides)
what size range are most proteins?
100-1000 amino acids long
what determines the structure of a protein?
the amino acid sequence
what determines the function of a protein?
the structure, determined by the amino acid sequence
what are residues?
amino acids within a polypeptide chain that are linked together
what are amino acids called by themselves?
amino acids (versus residues when they are linked together)
how many common amino acids are there?
20
how do amino acids differ?
by side chain (R group)
how many amino acid side chains are ionizable?
7
what are 3 ways that the side chain can contribute dofferences to an amino acid?
- polarity
- charge
- size
are amino acids chiral or achiral? what does this mean?
they are chiral; means alpha carbon is attached to 4 unique groups
what are the 4 unique groups that the chiral alpha carbon of an amino acid is attached to?
- amino grouo
- carboxyl group
- hydrogen
- side chain
what amino acid is the exception to the chiral rule and why?
glycine has a hydrogen side chain, so its alpha carbon is connected to 2 hydrogens, making it achiral
what are the 2 possible configurations of an amino acid? which one are natural amino acids always in?
L and D; natural amino acids are always in L form
Know the 3 letter and 1 letter names of all 20 amino acids
see flashcards!
what is a special property of aromatic amino acids? name property and the 3 aromatic amino acids
they can absorb and emit radiation
1. phenylalanine
2. tyrosine
3. tryptophan
what is a unique property of cysteine?
in can form disulfide bonds, which helps form tertiary and quarternary protein structures
what is a unique property of proline?
its backbone is fused to its sidechain, makes for kinky polypeptide chains ;)
what is a unique property of glycine?
its alpha carbon is NOT chiral!! (hydrogen is side chain)
give the levels of protein structure from smallest to largest (4)
- primary
- secondary
- tertiary
- quarternary
describe primary protein structure
the amino acid sequence; governs all subsequent structure levels
describe secondary protein structure
3D arrangement of polypeptide backbone into a few common structures
describe tertiary protein structure
folding and arrangement of secondary structures
describe quarternary protein structure
3D arrangement of separate polypeptide chains; the only structure level that involves multiple chains
what kind of reaction forms peptide bonds? give the 2 names
amino-carboxylate condensation aka dehydration synthesis
where does peptide bond formation take place?
in the ribosome
how can peptide bonds be broken? give general process then 2 examples
peptide bond hydrolysis
1. proteases
2. peptidases
what kinds of amino acids are used in acid/base catalysis?
ionizable amino acids
list the 7 ionizable amino acids
- aspartate (aspartic acid)
- glutamate (glutamic acid)
- tyrosine
- cysteine
- histidine
- lysine
- arginine
how many pKas do ALL amino acids have and why?
2; 2 for N terminus and 1 for C terminus
why does the N terminus have a higher pKa than the C terminus?
it has a more basic group than the carboxylic acid end
what is the net charge of an amino acid? what does it depend on?
the overall charge of a molecule; the sum of all charges; depends on pH
what is the isoelectric point?(pI)
the average pH at which a molecule has no net electrical charge
what is the pI governed by?
two pKas that create the neutral species
what does the pI form?
a zwitterion
what is a zwitterion?
electroneutral molecule that contains both positive and negative charges
what are the 3 steps for calculating the net charge of a peptide?
- find the ionizable groups
- determine the charge of each ionizable group at the given pH
- sum charges of all ionizable groups
give the 5 steps for calculating pI?
- find all ionizable groups
- sort pKa’s from lowest to highest
- determine net charges as pH increases (pH=0)
- once the net charge = 0, take pKa above and below current pH
- average the 2 pKas