4.1 Molecular Structure of Proteins Flashcards Preview

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Flashcards in 4.1 Molecular Structure of Proteins Deck (40)
1

the exact order of amino acids in a protein determines:

the protein's shape and function

2

alpha carbon

the central carbon atom of each amino acid

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amino group

NH2; a nitrogen atom bonded to two hydrogen atoms, covalently linked to the central carbon atom of an amino acid

4

carboxyl group

COOH; a carbon atom with a double bond to oxygen and a single bond to a hydroxyl group

5

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

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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

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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-

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the four covalent bonds from the alpha carbon are at:

equal angles-the amino acid forms a tetrahedron

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what is different from one amino acid to the next?

the R groups

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amino acids differ in their:

chemical and physical properties

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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

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describe hydrophobic amino acids:

do not readily interact with water or form hydrogen bonds.
nonpolar R groups-tend to aggregate with each other

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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

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where are most hydrophobic amino acids located?

in the interior of folded proteins, where they are kept away from water

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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

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the R groups of the basic and acidic amino acids are strongly:

polar

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at the pH of a cell, the R groups of the basic amino acids tend to:

gain a proton and become positively charged

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at the pH of a cell, the R groups of an acidic amino acid tend to:

lose a proton and become negatively charged

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because the R groups of basic/acidic amino acids are charged, where are they usually located?

on the outside surface of the folded molecule

20

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

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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

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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

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amino end

the end of a polypeptide that has a free amino group

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carboxyl end

the end of a polypeptide chain that has a free carboxyl group

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polypeptide

a polymer of amino acids connected by peptide bonds

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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"

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residue

in the context of protein synthesis, any of the amino acids that is incorporated into a protein

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in a polypeptide chain at physiological pH:

the amino and carboxyl ends are in their charged states (NH3+, COO-)

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primary structure

the sequence of amino acids in a protein

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secondary structure

the structure formed by interactions between stretches of amino acids in a protein

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tertiary structure

the overall three-dimensional shape of a protein, formed by interactions between secondary structures

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quaternary structure

the structure that results from the interactions of several polypeptide chains

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the ability to carry out a function depends on:

the 3D shape of the protein

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what is the order of amino acids?

starting at the amino end and proceeding to the carboxyl end

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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

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alpha helix

one of the two principal types of secondary structure found in proteins

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beta sheet

one of the two principal types of secondary structure found in proteins

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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

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denaturation

the unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strand of nucleic acid

40

chaperone

a protein that helps shield a slow-folding protein until it can attain its proper 3D structure