module 3 Flashcards
what are amino acids? what are proteins?
-building blocks of proteins
-proteins are linear polymers of amino acids
-all proteins are produced from 20 standard amino acids
-all living organisms use the same pool of amino acids to build their proteins
twenty building blocks enables great diversity of sequences. for example?
-a peptide of three residues could be produced 8000 ways
-a protein of 100 residues has 1.3x10 ^130 possible sequences
what are the distinct advantages of creating biomolecules as polymers of smaller, simpler building blocks
-simplicity of chemistry: one type of reaction for polymerization, a second type of reaction for degradation
-recycling: biomolecules can be digested back to component building blocks which are reusable for production of other biomolecules
-diversity: the vast number of molecules of varying lengths and sequences
what are the commons features of amino acids?
-the 20 amino acids differ in their side chain (R) groups
-the side chains define the unique characteristics of each amino acid
what are the chirality of amino acids?
-for all amino acids except glycine, the alpha carbon is bonded to four different groups, this creates a chiral center
-the four different groups occupy unique spatial arrangements giving different stereoisomers labelled as the L and D isomers
-biologically proteins are made almost exclusively from L amino acids
the text groups the amino acids based on the properties of their side chains. These groups include:
-non-polar aliphatic
-aromatic
-polar, uncharged
-polar, positively charged
-polar, negatively charged
is there only 1 way to sub-divide the amino acid?
-these groupings are man-made and there are many other equally valid ways to group amino acids
-it is more important to be able to “compare and contrast” all the amino acids rather assign them to specific groups
what are the nonpolar, aliphatic amino acids?
mainly hydrocarbon side chains
-residues with non-polar chains are often buried in the core of a protein
-proline often found at polypeptide turns, usually in combination with glycine
-glycine is the smallest amino acid and is the only one which is not chiral
-methionine is one of two amino acids with a sulfur group within its side chain
what are the aromatics amino acid?
-histidine can also be considered as an aromatic
-tyrosine
-tryptophan
-phenylalanine
what is tyrosine?
can be post-translation modified through phosphorylation
-phosphorylation is a mechanism to regulate protein function
-other amino acids with hydroxyl groups (serine and threonine) also can be phosphorylated
what is tryptophan?
-a precursor of serotonin, became popular supplement in the 1980s
-a disease-outbreak among users lead to its ban by the FDA
-largest
what are the three amino acids with hydroxyl groups on side chains?
-tyrosine
-serine
-threonine
where are non-polar (hydrophobic) amino acids most commonly found?
-buried within the core of protein
why is glycine special?
-only amino acid that does not have a chiral alpha carbon
what are the polar, uncharged amino acids?
-cysteine (Cys, C)
-Asparagine (Asn, N)
-Glutamine (Gln, Q)
-Serine (ser, S)
-threonine (Thr, T)
what can serine and threonine undergo?
-phosphorylation of their hydroxyl
-what can two cysteines form?
-a covalent linkage called a disulfide bond
-disulfide bonds are important covalent linkages for stabilization of some protein structure
what are disulfide bonds?
-form through the oxidation of the sulfhydryl groups of two cysteine residues to form a covalent linkage
-stabilize protein structures
-cysteine residues forming a disulfide bond must be in close proximity in space within the protein structure
-can be intra or inter molecular
what are the positively charged amino acids?
-Lysine (Lys, K)
-Arginine (Arg, R)
-Histidine (His, H)
what are Histidine?
-histidine’s imidazole group has a pKa near physiological pH such that a fraction of cellular histidines with be +1 and the rest will carry a net charge of 0
-in any enzymatic reactions His serves as a proton acceptor/donor
why are Lys and Arg similar?
-always carry a +1 net charge at physiological pH
what are the negatively charged amino acids?
-aspartate (Asp, D)
-glutamate (Glu, E)
-aka aspartic acid and glutamic acid
-carry a net charge of -1 at physiological pH
-glutamate s responsible for one of the five basic tastes (umami): used as a flavor enhancer (monosodium glutamate MSG)
what are the post-translational modification of amino acids? (phosphorylation)
-phosphorylation is a central example of post translational modification
-phosphoryl groups are added by kinases to specific, hydroxyl-group containing amino acids (Tyr, Ser and thr)
-are often reversible
what are diprotic?
-every amino acid has at least two groups that accept and donate protons (diprotic)
-all amino acids have the alpha carbon carboxyl group and amino groups
-have two buffering regions
what are triprotic?
-triprotic amino acids have ionizable groups in their side chains (Lys, Arg, His, Asp, Glu, Cys and Tyr)
-have three buffering regions
what are the ionizable groups in the amino acids?
-carboxyl groups
-amino group
-side chains of the triprotic amino acids
what does each ionizable group have?
-has a specific pKa
-this is the pH at which that group changes its protonation state
when are amino acids protonated and unprotonated?
-when pH is below the pKa, the protonated form predominates (HA)
-when pH is above the pKa, the unprotonated form predominated (A-)
what is the pKa of carboxyl and amino groups?
-all amino acids have both carboxyl (pKa=2.0) and an amino group (pKa=10.0)
-at pH 7.4, these groups will be in the COO- and NH3- forms
what is a zwitterion?
-the dipolar ion of an amino acid
what is the isoelectric point of an amino acid?
-pl
-the pH at which the net charge on the molecule is equal to zero
-is the average of the pKas on either side of where the net charge is equal to zero
