2.2.9 proteins 2: protein structure & bonding

Question 1

primary structure

Answer 1

sequence of amino acids found in molecule

Question 2

secondary structure

Answer 2

• coiling/folding of amino acid chain (often due to h bond formation between different parts of chain)
• main form: alpha helix or beta pleated sheet

Question 3

tertiary structure

Answer 3

• overall 3-dimensional shape of a protein molecule
• due to interactions eg. h bonding, disulphide bridges, ionic bonds & hydrophobic interactions

Question 4

quaternary structure

Answer 4

protein structure where protein consists of 1+ polypeptide chain

Question 5

what does the order of amino acids in the primary structure determine

Answer 5

shape of protein molecule (through 2nd, 3rd, 4th structure)

Question 6

what’s the alpha helix held by in the secondary structure (& between what)

Answer 6

• hydrogen bonds
• between -NH group of 1 amino acid & -CO group of another 4 places ahead in chain

Question 7

what holds the beta pleated sheet together

Answer 7

• hydrogen bonds
• between the -NH group of 1 amino acid & -CO group of another further down strand

Question 8

how are the alpha helix/beta pleated sheet made stable structures at optimal temp. & pH

Answer 8

due to the amount of hydrogen bonds formed

Question 9

how is the precise shape of the tertiary structure held together

Answer 9

bonds between amino acids (which lie close to each other)

Question 10

what may the tertiary structure adopt

Answer 10

• supercoiled shape (fibrous proteins)
  OR
• spherical shape (globular proteins)

Question 11

what bond primarily holds the secondary structure

Answer 11

hydrogen bonds

Question 12

what do hydrogen bonds form between

Answer 12

hydrogen atoms with slight positive charge & other atoms with slight negative charge

Question 13

in amino acids, where do the h bonds form

Answer 13

form in hydroxyl, carboxyl & amino groups

Question 14

• where can ionic bonds form?
• what do these ionise into?

Answer 14

• between carboxyl & amino groups that are part of R groups
• ionise into NH3+ & COO- = strongly attracted to each other

Question 15

what does the R group of the amino acids cysteine contain

Answer 15

sulfur

Question 16

where are disulfide bridges formed

Answer 16

between R groups of 2 cysteines

Question 17

what are disulfide bridges

Answer 17

strong covalent bonds

Question 18

where are the hydrophobic parts of the R groups found

Answer 18

usually associate together in centre of polypeptide

Question 19

where are the hydrophilic parts of the R group found

Answer 19

edge of polypeptide - close to water

Question 20

what causes twisting of the amino acids chain

Answer 20

hydrophobic & hydrophilic interactions

Question 21

what does this twisting of the amino acids chain cause

Answer 21

changes shape of protein