IB Biology B1.2: Proteins worked solutions

The amine group, the carboxyl group and the hydrogen atom are the same in every amino acid. Only the R group (side chain) differs (C).

A peptide bond joins the carbon of a carboxyl group to the nitrogen of the next amino acid, so it is the C to N bond marked 2 (B). Bond 1 and bond 3 are inside amino acids, and bond 4 is the C=O double bond.

Joining two amino acids is a condensation reaction and releases one water molecule (D). Hydrolysis is the reverse reaction and uses water.

A chain of 25 amino acids has 25-1=24 peptide bonds, and each bond broken uses one water molecule, so 24 (A).

A non-essential amino acid can be made by the body from other amino acids (C). It is still needed, so A is wrong. The word essential refers to the diet, not to plant or animal origin (B, D).

Heat breaks the weak interactions between R groups, so the shape changes and the active site is lost (D). The peptide bonds and the amino acid sequence are not changed (A, B, C).

The helix is held by hydrogen bonds between backbone C=O and N–H groups (A). Disulfide bonds and ionic bonds are between R groups and belong to tertiary structure, and peptide bonds run along the chain.

Hydrophilic R groups are mainly on the surface, where they bond to water, and hydrophobic R groups cluster in the core (C).

Haemoglobin carries a haem prosthetic group, so it is conjugated (B). Insulin and collagen are quaternary but have no prosthetic group, and a single chain without one is not conjugated.

(a) The alpha carbon is drawn at the centre (1) with an amine group, a carboxyl group, a hydrogen atom and an R group each bonded to it (1). (b) The two amino acids are drawn with the carboxyl group of one next to the amine group of the other (1); the dipeptide has a C–N peptide bond with the C=O and N–H kept (1); water is shown as the other product (1); the reaction is named as condensation (1).

(a) Essential amino acids cannot be synthesised by the body (1) and must be obtained from the diet (1). (b) Lysine, because the wheat value of 25 is below the reference of 50 (1); \dfrac{25}{50}\times100=50\% (1). (c) Soya is at or above the reference for all three amino acids shown (62, 26, 13 against 50, 25, 7), so it could be the only source of these (1); the table shows only three of the essential amino acids and says nothing about digestibility or how much is eaten, so adequacy is not proved (1).

(a) 70\,{}^\circC, the temperature with the highest activity (1). (b) Activity falls from 100\% at 40\,{}^\circC to 0\% at 60\,{}^\circC (1), by 75 units between 40 and 50\,{}^\circC but only 25 units between 50 and 60\,{}^\circC (1). (c) Higher temperature makes the molecule vibrate more and breaks the weak interactions between R groups (1); the shape changes, so the active site no longer fits the substrate (1); the protein is denatured, though the peptide bonds and sequence are unchanged (1).

(a) 9-1=8 peptide bonds, each made with one water molecule released, so 8 of each (1); 20^9=5.12\times10^{11} (1). (b) There are twenty types of amino acid (1) and any of them can be placed at any position, in any order (1); chains can also have any length, from a few to thousands, so the number of possible polypeptides is extremely large and each has its own sequence of R groups (1).

(a) Alpha helix (1); between backbone C=O and N–H groups (1). (b) Secondary structure is a regular, local pattern such as the helix or sheet (1) held by hydrogen bonds between backbone groups (1); tertiary structure is the overall three-dimensional fold of one polypeptide (1) held by interactions between R groups (maximum 3).

(a) The order and number of amino acids, held by peptide bonds (1). (b) The charged, hydrophilic R group lies in a core made of hydrophobic groups (1) so it cannot form the hydrophobic interactions that held the fold (1) and may attract water or opposite charges, changing the tertiary structure (1). The shape of the active site changes, so the substrate fits less well and activity falls (1).

(a) Quaternary structure (1); not conjugated, because there is no prosthetic group (1). (b) Both have more than one polypeptide chain, so both have quaternary structure (1); haemoglobin has four chains and four haem prosthetic groups, so it is conjugated (1); insulin has two chains and no prosthetic group, so it is not (1).

(a) Collagen has three polypeptide chains wound into a triple helix (1) and many molecules lie side by side in fibres, so it is strong and resists stretching (1). (b) Insulin is compact with hydrophilic R groups on its surface, so it is soluble and can be carried in the blood (1); collagen is long and rope-like and insoluble in water, which suits a structural role (1).

(a) \dfrac{62-31}{62}\times100=50\% (1 for the working, 1 for the value). (b) Rats on Q gained 60-31=29 g less than those on R (1); the ranges do not overlap (25 to 37 and 55 to 65), so the difference is likely to be real (1). (c) Lysine is an essential amino acid and cannot be made by the body, so with half the lysine protein synthesis and growth are limited (1); adding it back removed the shortage and restored growth to about the level of diet P (1). (d) The data support the claim that a shortage of one essential amino acid limits growth (1); but the study used rats for three weeks, changed only lysine and used small groups, so it cannot justify firm advice for people (1).

(a) 60-1=59 peptide bonds, and one water molecule for each, so 59 (1 for both values). (b) pH 7, the highest value (1); \dfrac{9.6-1.2}{9.6}\times100=88\% decrease (1). (c) At pH 2 the R groups gain or lose H^+ so their charges change (1); the interactions holding the shape break, the active site changes and the substrate no longer fits (1). (d) A water molecule adds OH to the carbonyl carbon and H to the nitrogen (1), which breaks the C–N peptide bond and releases two amino acids (1).

(a) -\mathrm{NH_3^+}\rightarrow-\mathrm{NH_2}+\mathrm{H^+}, a balanced change of atoms and charge (1). (b) The side chain loses its positive charge (1), so there is no electrostatic attraction to the negative glutamate side chain and the ionic bond is lost (1). (c) The loss of ionic bonds changes the three-dimensional fold, the tertiary structure (1); the shape of the active site changes, so the substrate no longer fits and activity falls (1). (d) The sequence is unchanged because the covalent peptide bonds are not broken (1); only weak interactions between R groups are lost, so the shape changes but the order of amino acids does not (1). If the pH returns to its earlier value the lysine regains H^+ and the bond can re-form, so a mild change may be reversible, but an extreme change denatures the enzyme for good (1).

(a) \dfrac{40}{200}\times100=20\% and \dfrac{160}{200}\times100=80\% (1 each). (b) The fraction of images with the complex rises from 20\% to 80\%, four times as common (80/20=4), at the higher concentration of T (1), so more T gives more association of P and T under matched classification (1). (c) The images show the outlines in contact, but outline contact does not identify an ionic bond, hydrogen bond or any other bond (1). (d) A protein with two polypeptide chains has quaternary structure (1), and the haem group is a non-protein prosthetic group, so it is conjugated (1).

One mark for each point, maximum 7: the primary structure is the exact sequence of amino acids joined by peptide bonds (1); each position has an R group with particular properties (1); the sequence therefore decides which interactions can form (1); the secondary structure is helices and sheets held by hydrogen bonds between backbone groups (1); the tertiary structure is the fold of the whole chain held by hydrogen bonds, ionic bonds, hydrophobic interactions and disulfide bonds between R groups (1); hydrophobic R groups cluster in the core and hydrophilic ones face the water, so the enzyme is soluble (1); the fold gives an active site of a particular shape that fits only its substrate, so function depends on structure (1); a change in the sequence can change the fold and the active site (1).

(a) The amino acids are joined by peptide bonds (1) and the glucose units by glycosidic bonds (1). (b) Each bond is broken by the addition of a water molecule (1). (c) A chain of 41 amino acids has 41-1=40 peptide bonds, so 40 waters (1); an unbranched chain of 100 glucose units has 100-1=99 glycosidic bonds, so 99 waters (1). (d) The active site of a protease has a shape that fits polypeptides and not starch, so the enzyme is specific (1).

(a) The folded chain brings particular R groups together in the active site (1); their shape and charge fit the substrate and not other molecules, so the enzyme is specific (1). (b) A mutation far from the active site can change an R-group interaction (1) and so the tertiary structure, which alters the shape of the active site (1). (c) High temperature breaks interactions between R groups and changes the shape for good (1); low temperature slows molecules down but does not change the shape, so activity returns on warming (1).

(a) The primary structure, the order of amino acids, is changed first (1). (b) Glutamate has a charged, hydrophilic R group that faces the water (1), while valine is hydrophobic, so the surface patch is attracted to a hydrophobic site on another haemoglobin molecule and the molecules stick together (1). (c) Haem is the prosthetic group, so haemoglobin is a conjugated protein (1). (d) The sticking reduces the solubility of the haemoglobin (1), so long fibres can form in the cell (1).