1.3 Biological Molecules: Proteins

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.  The solvents used are isopropanol and methanol, in that order. Justify your selections

Describe 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 main aspects of the tertiary structure labelled A, B, C and D in Figure 1 and deduce what all four aspects have in common.

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 male 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 his total blood volume is 5 dm³ and that his blood circulates his 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.   

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 all the chains that form collagen are identical in length, how many
amino acids 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 and contrast the different chemical elements found in proteins and
carbohydrates.

Explain how a polypeptides’ tertiary structure is determined by bonds between amino
acids. 

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

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 work out 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). Changes
in the influenza HA gene segment prevents human antibodies from binding. Explain how.