KA2: Proteins: Protein structure, ligand binding and conformational change: Amino acid sequence determines protein structure

Question 1

what are proteins?

Answer 1

polymers of amino acid monomers

Question 2

What links amino acids together to form polypeptides?

draw the link

Answer 2

peptide bonds

draw peptide bond

Question 3

describe the basic structure of an amino acid

Answer 3

amine group, carboxylic acid group, variable R group

Question 4

how do the R groups of amino acids vary?

Answer 4

*size
*shape
*charge
*hydrogen bonding capacity
*chemical reactivity

Question 5

how are amino acids classed ?

name all the classifications.

Answer 5

according to their R groups

*basic (+charge)
*acidic (-charged)
*polar
*hydrophobic

Question 6

what does the wide range of functions carried out by proteins results from?

Answer 6

the diversity of R groups

Question 7

describe the primary sequence of a protein (mention bonds present)

Answer 7

involves peptide bonds which are covalent

the sequence in which the amino acids are synthesised into the polypeptide

Question 8

what results in regions of secondary structure?

list the types of secondary structure.

Answer 8

Hydrogen bonding along the backbone of the protein strand

*alpha helices
*parallel or anti-parallel beta-pleated sheets
*turns

Question 9

describe alpha helices

Answer 9

it is a spiral with the R groups sticking outwards

Question 10

Describe the beta pleated sheet.

Answer 10

parts of the chain running alongside each other forming a sheet

the R groups sit above and below the sheet

Question 11

what can beta-pleated sheets usually be and what does it mean?

Answer 11

parallel/antiparallel

the chains run in opposite directions from each other

Question 12

sheets are anti-parallel or parallel depending on what?

Answer 12

their N and C termini

Question 13

what are turns?

Answer 13

they serve to reserve the direction of the polypeptide chain

Question 14

what is the role of turns?

Answer 14

-bring together and allow interactions between regular secondary structure elements

Question 15

what do polypeptides fold into?

what is this conformation stabilised by?

Answer 15

tertiary structure

interactions between R groups:

*hydrophobic interactions
*ionic bonds
*london dispersion forces
*hydrogen bonds
*disulfide bridges

Question 16

what are hydrophobic regions?

Answer 16

Hydrophobic amino acids do not “like” to be in contact with water.

They tend to cluster together on the interior of a protein away from the surface.

Question 17

what are ionic bonds?

Answer 17

involves the electrostatic attraction between oppositely charged ions.

Question 18

what are hydrogen bonds?

Answer 18

the electromagnetic attractive interaction between polar molecules, in which hydrogen is bound to a highly electronegative atom, such as nitrogen, oxygen or fluorine.

Question 19

what are ldf’s?

what do they result from?

Answer 19

a temporary attractive force

results when the electrons in two adjacent atoms occupy positions that make the atoms form temporary dipoles.

Question 20

What are disulfide bridges?

How are they produced?

Answer 20

covalent bonds between R groups containing sulfur

the coupling of two thiol (SH) groups.

Question 21

What is a prosthetic group?

give an example

Answer 21

a non-protein unit tightly bound to a protein and necessary for its function

haem group

Question 22

what is the ability of haemoglobin to bind to ixygen dependent upon?

Answer 22

the non-protein haem group

Question 23

Where does the quaternary structure exist?

What does quaternary structure describe?

Answer 23

in proteins with two or more connected polypeptide subunits

the spatial arrangement of the subunits

Question 24

what are two factors that effect R group interactions?

Answer 24

temperature and pH

Question 25

describe how interactions of R groups can be influenced by temperature

Answer 25

increasing temp=> disrupts the interactions that hold the protein in shape

the protein begins to unfold, eventually becoming denatured

Question 26

describe how interactions of R groups can be influenced by pH

Answer 26

The charges on acidic and basic R groups are affected by pH.

pH increases or decreases from the optimum=> normal ionic interactions between charged groups are lost => gradually changes the conformation of the
protein until it becomes denatured.

Question 27

The secondary structure of a protein can be altered more easily than the primary structure.

Explain this in terms of the bonds involved.

Answer 27

bonds in primary are strong and covalent (both OR peptide)

in secondary they are weak and hydrogen (both)

Question 28

The binding region of the engrailed protein contains a high proportion of lysine residues.

Suggest how the presence of these amino acids would assist in the binding of the engrailed protein to DNA.

Answer 28

Positive charges (of lysine) interact/bond with/attracted to the negative charges on DNA