Biological Molecules: Proteins (AQA A Level Biology)

Describe how a dipeptide forms from two amino acids. 

Polypeptides are formed from hundreds of amino acids joined together. A polypeptide contains 288 peptide bonds.

Calculate the total number of amino acids in this polypeptide.

Explain your answer. 

State how a functional protein differs from a polypeptide.

There is a general structure that can be applied to all amino acids. Figure 1 below shows the structure of the amino acid valine.

Figure 1

Draw a circle around the part of the molecule that would be identical in all amino acids.

Describe how a polypeptide is formed.

DNA polymerases are a vital group of enzymes. Different variations are found in all living cells. DNA polymerases are responsible for replicating DNA during semi-conservative replication. 

Explain why most cellular enzymes like DNA polymerases are made predominantly from protein.

Some washing powders contain molecules that break down and hydrolyse the peptide bonds between amino acids. The degree to which a protein is broken down can be called the degree of hydrolysis (DH). The DH value is calculated using the equation

Washing powder was applied to a molecule of protein. The DH value after exposure to the washing powder was 28 and a total of 140 peptide bonds were hydrolysed. Calculate the number of amino acids in the protein.

Suggest why it is beneficial for washing powders to contain molecules with the ability to break down proteins.

Collagen protein molecules have a quaternary structure and are vital in providing structural support in a wide variety of organisms. There are different types of collagen but all types share the same basic features. 

One of the polypeptide chains that forms a molecule of collagen contains 1049 peptide bonds.

Assuming that all the chains in collagen are identical in length, calculate the number of amino acids that would be found in a single molecule of collagen.

Explain your answer. 

Explain why collagen is described as having a quaternary structure rather than a tertiary structure. 

Scientists wanted to test for the presence of protein while developing a new meal replacement shake.

Describe the test that they should use and state what a positive test result would look like.

Compare the chemical elements found in proteins and carbohydrates.

Explain how a polypeptide's tertiary structure is determined by bonds between amino acids. 

Haemoglobin and collagen are both two important proteins found in the human body.

Complete Table 1 below to accurately describe their properties.

Table 1 

Describe the function of haemoglobin and collagen. Explain how their structure is related to their function.

Haemoglobin is made of alpha and beta polypeptides. Each alpha polypeptide has 141 amino acids and each beta polypeptide has 146 amino acids.

Calculate the total number of peptide bonds present in one alpha polypeptide and one beta polypeptide.

Figure 1 below shows a single amino acid. Draw out the mechanism by which two amino acids form a dipeptide.

Figure 1

A lab technician investigating the amino acid composition of new food supplement decided to use paper chromatography to separate out and identify the different amino acids present.

The technician placed a concentrated drop of the food supplement mixture on the origin line. She then placed concentrated drops of known amino acids at other points along the origin line. The paper was placed in a tank containing solvent for 2.5 hours. When the solvent reached the top of the paper, she marked the solvent front using a pencil. The paper was then sprayed with ninhydrin and heated in a 100^oC oven. The chromatogram results can be seen in Figure 2 below.

Figure 2

State which amino acids are not present in the food supplement. Explain your answer.

The R_f value of amino acid C was 0.2. Using the equation below, calculate the distance in mm that the amino acid moved from the origin line. 

The influenza A virus remains a prevalent human pathogen partly because of its ability to evade human antibodies. The antibodies produced by humans in response to influenza are specific to the influenza attachment protein hemagglutinin (HA).

Explain how changes in the influenza HA gene segment would prevent human antibodies from binding.

Figure 1 shows the molecular structure of the amino acid isoleucine.

Figure 1

Draw a circle around the central carbon atom (∝-carbon) in Figure 1.

Draw the structure of the dipeptide formed from two molecules of isoleucine. Name and label the bond that forms between the two molecules and any by-products formed.

Mixtures of amino acids can be separated by two-way thin-layer chromatography. In this technique, the mixture is placed on a thin layer of inert, solid material spread over a flat aluminium plate and run with Solvent A until the solvent reaches the top of the plate. The plate is then dried, turned 90° and run with Solvent B. The plate is then re-dried and developed with ninhydrin spray to expose the individual amino acids.

Explain why different solvents have to be used in each stage of this technique.

Table 1 sets out the R_f values of a mixture of selected amino acids using two separate solvents in thin-layer chromatography.  Abbreviations have been used for the amino acid names.  

Table 1

Explain why R_f values do not have units.

Using the information from Table 1, identify two pairs of amino acids that would not be separated by two-way thin layer chromatography.  Justify your selections

State and explain the factors that affect the R_f value when separating amino acids out by thin-layer chromatography.  Assume the same solvent, layer thickness, layer medium, temperature and depth of solvent are being used.

Explain how the secondary structure of a protein contributes to its overall 3-D shape.

Collagen is the most abundant protein in the human body, and is an important element in connective tissue such as skin, bones, teeth and tendons. Collagen contains repeating triplets of the amino acids glycine, proline and hydroxyproline, resulting in a tightly-coiled helix. Glycine is the simplest amino acid, with a single hydrogen atom as its R group, whereas proline and hydroxyproline have large organic R groups.  

Suggest and explain a role for glycine as part of the repeating structure.

The gene coding for a bacterial protein contains 579 base pairs of DNA.  Bacteriologists have measured that 5.6 molecules of the protein can be synthesised per minute per ribosome. Calculate the rate of translation and express your answer, to the nearest whole number, in amino acids s^-1.

Identify the types of interaction labelled A, B, C and D in Figure 1.

A molecule of haemoglobin contains four prosthetic groups containing iron. Define the term ‘prosthetic group’. 

Describe the quaternary structure of haemoglobin and explain how its structure relates to its function in mammals.

A 70 kg athlete, when at rest, uses oxygen at a rate of 16 cm³ kg^-1 min^-1.  Haemoglobin binds to oxygen at 1.34 cm³  g^-1.

Calculate the mass of haemoglobin in grammes per 100 cm³ of athlete’s blood. Assume that the athlete's total blood volume is 5 dm³ and that their blood circulates the body once a minute on average whilst at rest.

The amino acid sequence of haemoglobin chains has been determined in many species. Llamas and high-soaring migratory birds have an 18 % difference in their amino acid sequence compared to that of humans. 

Suggest and explain the differences between llama haemoglobin and human haemoglobin structure.

Describe a biochemical test to prove that a solution contains protein and outline a positive result.   

The molecular structure of the amino acid tryptophan is shown in Figure 1.

Figure 1

Draw a circle on Figure 1 to highlight the R group of tryptophan.

Figure 2 shows the structure of a different amino acid, cysteine. 

Figure 2

Identify and explain the component of cysteine’s structure that plays an important role in a protein’s tertiary structure.  

Draw out the structure of the bond that forms between a molecule of tryptophan and a molecule of cysteine.