4.1 Molecular Structure of Proteins Flashcards
the exact order of amino acids in a protein determines:
the protein’s shape and function
alpha carbon
the central carbon atom of each amino acid
amino group
NH2; a nitrogen atom bonded to two hydrogen atoms, covalently linked to the central carbon atom of an amino acid
carboxyl group
COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group
side chain/R group
a chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid
describe the general structure of an amino acid:
central carbon atom (alpha carbon), connected by covalent bonds to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain or R group
in the environment of a cell (pH: 7.35-7.45), what are the changes to the amino acid?
the amino group gains a proton and becomes NH3+ and the carboxyl group loses a proton and becomes COO-
the four covalent bonds from the alpha carbon are at:
equal angles-the amino acid forms a tetrahedron
what is different from one amino acid to the next?
the R groups
amino acids differ in their:
chemical and physical properties
some R groups have special characteristics that might affect a protein’s structure. these properties strongly influence:
how a polypeptide folds, and hence the 3D shape of the protein
describe hydrophobic amino acids:
do not readily interact with water or form hydrogen bonds.
nonpolar R groups-tend to aggregate with each other
the aggregation of non-polar amino acid R groups is also stabilized by:
weak van der Waals forces in which asymmetries in electron distribution create temporary charges in the interacting molecules, which are then attracted to each other
where are most hydrophobic amino acids located?
in the interior of folded proteins, where they are kept away from water
amino acids with polar R groups have a permanent charge separation, this means that:
one end of the R group is slightly more negatively charged than the other
the R groups of the basic and acidic amino acids are strongly:
polar
at the pH of a cell, the R groups of the basic amino acids tend to:
gain a proton and become positively charged
at the pH of a cell, the R groups of an acidic amino acid tend to:
lose a proton and become negatively charged
because the R groups of basic/acidic amino acids are charged, where are they usually located?
on the outside surface of the folded molecule
charged groups can also form ionic bonds with each other and with other charged molecules in the environment. apply this to the amino acids/proteins:
the ability to bind another molecule of opposite charge is one important way in which proteins can associate with each other or with other macromolecules such as DNA
peptide bond
a covalent bond that links the carbon atom in the carboxyl group of one amino acid to the nitrogen atom in the amino group of another amino acid, a water molecule ends up being released
the peptide bond has some of the characteristics of a:
double bond-ex. peptide bond is shorter than a single bond and is not free to rotate
amino end
the end of a polypeptide that has a free amino group
carboxyl end
the end of a polypeptide chain that has a free carboxyl group
polypeptide
a polymer of amino acids connected by peptide bonds
protein
the key structural and functional molecules that do the work of the cell, providing structural support and catalyzing chemical reactions. the term “protein” of often used as a synonym for “polypeptide”
residue
in the context of protein synthesis, any of the amino acids that is incorporated into a protein
in a polypeptide chain at physiological pH:
the amino and carboxyl ends are in their charged states (NH3+, COO-)
primary structure
the sequence of amino acids in a protein
secondary structure
the structure formed by interactions between stretches of amino acids in a protein
tertiary structure
the overall three-dimensional shape of a protein, formed by interactions between secondary structures
quaternary structure
the structure that results from the interactions of several polypeptide chains
the ability to carry out a function depends on:
the 3D shape of the protein
what is the order of amino acids?
starting at the amino end and proceeding to the carboxyl end
secondary structures result from:
hydrogen bonding in the polypeptide backbone (between the carbonyl group and the amide group) allowing localized regions of the polypeptide chain to fold
alpha helix
one of the two principal types of secondary structure found in proteins
beta sheet
one of the two principal types of secondary structure found in proteins
tertiary structure is determined by:
spatial distribution of hydrophilic and hydrophobic R groups along the molecule, as well as by different chemical bond sand interactions that form between various R groups
denaturation
the unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strand of nucleic acid
chaperone
a protein that helps shield a slow-folding protein until it can attain its proper 3D structure
