4.1 Molecular Structure of Proteins

Question 1

the exact order of amino acids in a protein determines:

Answer 1

the protein’s shape and function

Question 2

alpha carbon

Answer 2

the central carbon atom of each amino acid

Question 3

amino group

Answer 3

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

Question 4

carboxyl group

Answer 4

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

Question 5

side chain/R group

Answer 5

a chemical group attached to the central carbon atom of an amino acid, whose structure and composition determine the identity of the amino acid

Question 6

describe the general structure of an amino acid:

Answer 6

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

Question 7

in the environment of a cell (pH: 7.35-7.45), what are the changes to the amino acid?

Answer 7

the amino group gains a proton and becomes NH3+ and the carboxyl group loses a proton and becomes COO-

Question 8

the four covalent bonds from the alpha carbon are at:

Answer 8

equal angles-the amino acid forms a tetrahedron

Question 9

what is different from one amino acid to the next?

Answer 9

the R groups

Question 10

amino acids differ in their:

Answer 10

chemical and physical properties

Question 11

some R groups have special characteristics that might affect a protein’s structure. these properties strongly influence:

Answer 11

how a polypeptide folds, and hence the 3D shape of the protein

Question 12

describe hydrophobic amino acids:

Answer 12

do not readily interact with water or form hydrogen bonds.

nonpolar R groups-tend to aggregate with each other

Question 13

the aggregation of non-polar amino acid R groups is also stabilized by:

Answer 13

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

Question 14

where are most hydrophobic amino acids located?

Answer 14

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

Question 15

amino acids with polar R groups have a permanent charge separation, this means that:

Answer 15

one end of the R group is slightly more negatively charged than the other

Question 16

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

Answer 16

polar

Question 17

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

Answer 17

gain a proton and become positively charged

Question 18

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

Answer 18

lose a proton and become negatively charged

Question 19

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

Answer 19

on the outside surface of the folded molecule

Question 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:

Answer 20

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

Question 21

peptide bond

Answer 21

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

Question 22

the peptide bond has some of the characteristics of a:

Answer 22

double bond-ex. peptide bond is shorter than a single bond and is not free to rotate

Question 23

amino end

Answer 23

the end of a polypeptide that has a free amino group

Question 24

carboxyl end

Answer 24

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

Question 25

polypeptide

Answer 25

a polymer of amino acids connected by peptide bonds

Question 26

protein

Answer 26

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”

Question 27

residue

Answer 27

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

Question 28

in a polypeptide chain at physiological pH:

Answer 28

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

Question 29

primary structure

Answer 29

the sequence of amino acids in a protein

Question 30

secondary structure

Answer 30

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

Question 31

tertiary structure

Answer 31

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

Question 32

quaternary structure

Answer 32

the structure that results from the interactions of several polypeptide chains

Question 33

the ability to carry out a function depends on:

Answer 33

the 3D shape of the protein

Question 34

what is the order of amino acids?

Answer 34

starting at the amino end and proceeding to the carboxyl end

Question 35

secondary structures result from:

Answer 35

hydrogen bonding in the polypeptide backbone (between the carbonyl group and the amide group) allowing localized regions of the polypeptide chain to fold

Question 36

alpha helix

Answer 36

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

Question 37

beta sheet

Answer 37

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

Question 38

tertiary structure is determined by:

Answer 38

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

Question 39

denaturation

Answer 39

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

Question 40

chaperone

Answer 40

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