Chapter 4 Flashcards by Gail I

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

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… has a secondary amino group as a substituent

proline

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at physiological pH (about …), the amino groups are … and the carboxylic acid groups are in their .. (…) form

7.4; protonated; conjugate base; carboxylate

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molecules such as amino acids, which bear charged groups of opposite polarity, are known as … ions or …

dipolar; zwitterions

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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

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after they are incorporated into a peptide, the individual amino acids (the monomeric units) are referred to as amino acid …

residues

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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

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Nonpolar amino acids with H, or alkyl substituents: 
… 
… 
… 
.. 
…

glycine
alanine
valine
leucine
isoleucine

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nonpolar amino acid with thioether side chain:

…

methionine

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nonpolar amino acids with aromatic R groups:

… and …

phenylalanine; tryptophan

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nonpolar amino acid with cyclic pyrrolidine side group:

proline

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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

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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)

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… 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

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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

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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

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