Chapter 4 Flashcards
the common amino acids are known as … because they have a primary … as a substituent of the … atom, the carbon next to the carboxylic acid group
alpha-amino acids; amino group; alpha carbon
… has a secondary amino group as a substituent
proline
at physiological pH (about …), the amino groups are … and the carboxylic acid groups are in their .. (…) form
7.4; protonated; conjugate base; carboxylate
molecules such as amino acids, which bear charged groups of opposite polarity, are known as … ions or …
dipolar; zwitterions
amino acids can be polymerized to form chains. this process can be represented as a … reaction. the resulting CO-NH linkage, an … linkage, is known as a … bond
condensation; amide; peptide
after they are incorporated into a peptide, the individual amino acids (the monomeric units) are referred to as amino acid …
residues
variations in the … and the … of polypeptides are major contributors to the diversity in the shapes and biological function of proteins
length; amino acid sequence
Nonpolar amino acids with H, or alkyl substituents: … … … .. …
glycine alanine valine leucine isoleucine
nonpolar amino acid with thioether side chain:
…
methionine
nonpolar amino acids with aromatic R groups:
… and …
phenylalanine; tryptophan
nonpolar amino acid with cyclic pyrrolidine side group:
proline
uncharged polar side chains: … and … bear hydroxylic R groups … and … have amid bearing side chains … has a phenolic group and is aromatic … has a thiol group that can form a disulfide bond with another one of this type of amino acid through the oxidation of the two thiol groups
serine; threonine;
asparagine; glutamine
tyrosine
cysteine
charged polar side chains: … has a butylammonium side chain … bears a guanidine group … carries an imidazolium moiety … and … are negatively charged above pH 3
lysine
arginine
histidine
aspartic acid; glutamic acid (aspartate and glutamate in ionized state)
… with a pKr of …, readily ionizes within the physiological pH range (only amino acid that does). consequently, both the neutral and cationic forms occur in proteins. in fact, the protonation-deprotonation of this amino acid’s side chains is a feature of numerous enzymatic reaction mechanisms
histidine; 6.04
inclusion of a particular amino acid in one group/another reflects not just the properties of the isolated amino acid, but its behavior when its part of a …
polypeptide
in aqueous solution, the unionized form of glycine is present …
only in vanishingly small quantities
the pH at which a molecule carries no net electric charge is known as its … point
isoelectric (pI)
pI of neutral aas is calculated by averaging the two pKa values for the … and … groups
amino; carboxyl
pI for glutamic and aspartic acids is calculated by averaging the
pKa of the R group and of the carboxyl group
pI for lysine, arginine, and histidine (basic amino acids) is calculated by averaging the
pKa of the amino group and the pKa of the R group
in free amino acids, the pKa values are much …, because the positively charged ammonium group electrostatically stabilizes the COO- group, in effect making it easer for the carboxylic acid group to …
lower; ionize
amino acid residues in polypeptides are named by dropping the suffix, usually …, in the name of the amino acid and replacing it by …
Polypeptide chains are described by starting at the N-terminus and proceeding to the C-terminus. the amino acid at the C-terminus is given the name of its …
-ine; -yl; parent amino acid
with the exception of glycine, all the amino acids recovered from polypeptides are …; that is, they rotate the plane of polarized light (they’re chiral). the direction and angle of rotation can be measured using an instrument known as a polarimeter
optically active
optically active molecules are …
asymmetric
for Fischer projections, the configuration of the groups around an asymmetric center is compared to that of …
glyceraldehyde
L-glyceraldehyde and L-alpha-amino acids are said to have the same …
relative configuration
all amino acids derived from proteins have the … stereochemical configuration
L
Many L-amino acids are …
dextrorotatory
biosynthetic processes almost invariably produce
pure stereoisomers
D-amino acid residues are components of some relatively short bacterial polypeptides. these polypeptides are perhaps most widely distributed as constituents of bacterial cell walls. the presence of the D-amino acids renders bacterial cell walls less susceptible to attach by … (enzymes that hydrolyze peptide bonds) that are produced by other organisms to digest bacteria.
peptidases
Most peptides containing D-amino acids aren’t synthesized through the whole transcription translation process. instead, the D-amino acids are directly joined together by the action of …
specific bacterial enzymes
many drugs are chemically synthesized as …, although only one enantiomer has biological activity
racemic mixtures
one of the drugs synthesized as racemic mixture with no issue is …
however, some drugs have an enantiomer that is biologically harmful, such as …
ibuprofen; thalidomide
there are many other amino acids besides the standard 20 that are components of certain proteins. in almost all cases, these unusual amino acids result from the specific … of an amino acid residue after the … has been synthesized
modification; polypeptide chain
in a few cases, the …of amino acid metabolism have functions beyond their immediate use as precursors or degradation products of the 20 standard amino acids. many amino acids are also synthesized not to be residues of polypeptides but to function independently
intermediates
amino acids and their derivatives often function as … for communication between cells
e.g. glycine, gamma-aminobutyric acid (GABA) and dopamine (tyrosine derivative) are neurotransmitters
histamine is a decarboxylation product of histidine
thyroxine (tyrosine derivative) is an iodine containing thyroid hormone that generally stimulates vertebrate metabolism
intermediates
ubiquitous tripeptide called … plays a role in cellular metabolism (made up of glu-cys-gly in which the gamma-carboxylate group of the glutamate side chain forms an … bond with the amino group of the Cys residue)
oxidation of two of these tripeptides form a dimeric disulfide linked structure called ..
glutathione; isopeptide; glutathione disulfide
glutathione helps inactivate … compounds that could potentially damage cellular structures
oxidative
