Questions on protein structure and function

Question 1

Describe the four levels of protein structure, naming in each case the type of bond that holds that level together.

Accepted Answer

B1 primary structure is the sequence of amino acids in the polypeptide, held by peptide bonds B1 secondary structure is the regular coiling into an α-helix or pleating into a β-pleated sheet, held by hydrogen bonds between groups in the backbone B1 tertiary structure is the overall three-dimensional fold of one polypeptide, held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions between side chains B1 quaternary structure is the arrangement of two or more polypeptides, together with any prosthetic groups, in the finished protein, held by the same interactions as the tertiary level acting between the chains

Question 2

Compare the structure of haemoglobin with the structure of collagen, and relate the difference in each case to what the protein does.

Accepted Answer

B1 haemoglobin is globular and compact, whereas collagen is fibrous and forms long strands B1 haemoglobin has an irregular amino acid sequence, whereas collagen has a repetitive one in which about every third amino acid is glycine B1 haemoglobin carries hydrophilic side chains on the outside so it is soluble and can be transported in solution, whereas collagen is insoluble, which suits it to a structural role B1 haemoglobin is four polypeptides each holding one haem prosthetic group that binds one oxygen molecule, whereas collagen is three chains wound round each other and cross-linked, giving strength in tension

Question 3

Describe how extreme pH denatures a protein, referring to the charge on side chains and to the bonds affected.

Accepted Answer

B1 extreme pH adds or removes hydrogen ions from the side chains of a protein's amino acids, changing the charge some of them carry B1 that change in charge disrupts the ionic bonds that normally form between oppositely charged side chains in the tertiary structure B1 hydrogen bonds within the folded protein can also be disrupted as the pattern of charge and polarity around them changes B1 the tertiary structure unfolds and the protein loses its specific shape and function, while the covalent peptide bonds of the primary structure remain intact

Question 4

A protein folds into a compact shape with all of its charged and polar side chains on the outside and all of its non-polar side chains buried inside. Suggest what this arrangement indicates about the protein's solubility, and suggest whether it is more likely to be a structural protein or one that is transported in blood.

Accepted Answer

B1 hydrophilic, charged or polar side chains on the outside interact with water molecules, so the protein is likely to be soluble B1 hydrophobic, non-polar side chains buried in the interior are shielded from water, which is what compact globular folding achieves B1 this compact, soluble arrangement is characteristic of a globular protein rather than a fibrous one, so it is more likely to be a protein that must dissolve and be carried in blood, such as an enzyme or a transport protein B1 a structural fibrous protein such as collagen or keratin is by contrast insoluble and does not need this arrangement, since it is not required to dissolve in a body fluid

Question 5

Explain why a prosthetic group such as the haem group of haemoglobin is essential to the protein's function even though it is not made of amino acids.

Accepted Answer

B1 a prosthetic group is a non-protein component that is permanently associated with a protein and is required for it to function B1 the haem group of haemoglobin is not built from amino acids, so it is not part of the polypeptide's own primary, secondary or tertiary structure, though it is held within the folded protein by non-covalent interactions B1 each haem group contains one iron(II) ion, and it is that ion which actually binds one molecule of oxygen, a job none of haemoglobin's amino acid side chains can do alone B1 a haemoglobin molecule that had folded correctly but lacked its four haem groups would be unable to transport oxygen

Question 6

A polypeptide is made from 150 amino acids, each of average relative molecular mass 110 as a free amino acid. Taking the relative molecular mass of water as 18, calculate the number of peptide bonds formed, and calculate the relative molecular mass of the finished polypeptide.

Accepted Answer

M1 number of peptide bonds = 150 − 1 = 149, since bonds form between amino acids rather than on each one M1 total mass of the 150 free amino acids before joining = 150 × 110 = 16 500 M1 total mass of water lost = 149 × 18 = 2682, one water molecule released per peptide bond formed A1 mass of the polypeptide = 16 500 − 2682 = 13 818

Question 7

While one molecule of a polypeptide was being assembled, water of total relative mass 3582 was released. Taking the relative molecular mass of water as 18, calculate the number of amino acids in that polypeptide.

Accepted Answer

M1 number of water molecules released = 3582 divided by 18 M1 = 199 molecules of water, which is also the number of peptide bonds formed A1 200 amino acids, because n amino acids give n − 1 peptide bonds

Question 8

A patient's body temperature rises to 43 °C and several of her proteins stop working. Explain what has happened to those proteins, referring to the bonds involved.

Accepted Answer

B1 the heat breaks the hydrogen bonds and ionic bonds holding the tertiary structure together B1 the chain unfolds, so the specific three-dimensional shape is lost and with it the function, which is denaturation B1 peptide bonds are covalent and survive, so the primary structure is unchanged

Question 9

A protein taken from a bacterium living in a hot spring contains far more cysteine than the equivalent human protein does. Suggest why this helps the bacterial protein keep its shape at high temperature.

Accepted Answer

B1 two cysteine side chains anywhere in the chain can bond to each other, forming a disulfide bridge B1 a disulfide bridge is covalent and therefore much stronger than the hydrogen and ionic bonds that also hold the tertiary structure B1 heat that breaks those weaker bonds does not break the disulfide bridges, so the fold is held at a temperature that would denature the human protein

Question 10

State the biuret test for protein: state the two reagents added, in order, and state the colour change that shows a positive result.

Accepted Answer

B1 sodium hydroxide solution is added first B1 a few drops of copper(II) sulfate solution are then added B1 a colour change from blue to purple shows a positive result, meaning peptide bonds are present

Question 11

Explain why a solution of free amino acids gives a negative biuret test, whereas a solution of the polypeptide those same amino acids came from gives a positive one.

Accepted Answer

B1 the biuret reagent detects the peptide bond itself, turning purple in its presence, rather than reacting with amino acids as separate molecules B1 free amino acids in solution are not joined by peptide bonds, so none are present for the reagent to detect, and the solution stays blue B1 the polypeptide contains many peptide bonds joining its amino acids together, so the reagent gives a positive, purple result

Question 12

Compare primary structure with secondary structure, referring to what is arranged at each level and to the bond holding it.

Accepted Answer

B1 primary structure is the sequence of amino acids in the polypeptide chain, held together by covalent peptide bonds, whereas secondary structure is the coiling or pleating of that chain into an α-helix or a β-pleated sheet B1 secondary structure is held by hydrogen bonds between groups in the backbone, rather than by the peptide bonds that hold primary structure B1 secondary structure could not exist without primary structure to fold, since it is the same backbone, already joined by peptide bonds, arranged into a specific pattern

Question 13

An enzyme is a single polypeptide chain folded into an active shape. Explain why this enzyme has no quaternary structure, using the definition of quaternary structure in your answer.

Accepted Answer

B1 quaternary structure is the arrangement of two or more polypeptide chains, together with any prosthetic groups, in a functioning protein B1 this enzyme is described as a single polypeptide chain, so only one chain is present, and quaternary structure by definition requires more than one B1 the enzyme's function therefore depends on its primary, secondary and tertiary structure alone, without any interaction between separate chains

Question 14

State the three groups that every amino acid carries on its central carbon, and state what varies between the twenty amino acids.

Accepted Answer

B1 an amine group, a carboxyl group and a hydrogen atom, all attached to the same central carbon B1 they differ only in the R group, also accepted as the side chain

Question 15

Name the bond formed when two amino acids are joined together, and name the molecule released as it forms.

Accepted Answer

A1 a peptide bond, formed between the amine group of one amino acid and the carboxyl group of the next A1 water is the molecule released, the reaction being a condensation