Proteins (CIE AS Biology)

Proteins are a vital class of macromolecule that are composed of amino acids. Two such amino acids are represented in the diagram in Fig. 1.

[3]

Fig. 1

[2]

Proteins can have various different levels in terms of their structure.

Describe the secondary structure of a protein.

Fig. 2 shows the structure of the enzyme lysozyme.

Fig. 2

With reference to Fig. 2, identify the levels of protein structure visible in the diagram.

People suffering from anaemia are generally lacking in dietary iron. It is recommended that they consume more red meat and green leafy vegetables to increase the iron levels in their blood.

Explain why one of the symptoms of anaemia would be fatigue.

At high altitudes, the partial pressure of oxygen in the air is substantially lower than at sea level. This means that the partial pressure of oxygen in the bloodstream is also much lower at high altitudes compared to at sea level. The partial pressure of oxygen at sea level is about 14.0 kPa, while at 10 000 metres above sea level it is about 4.0 kPa. Table 1 shows the percentage saturation of haemoglobin at different partial pressures of oxygen.

Table 1

With reference to Table 1, calculate the percentage decrease in the percentage saturation of haemoglobin as you travel from sea level to 10 000 metres above sea level.

Show your working.

Compare the different chemical elements found in proteins and carbohydrates.

Enzymes called proteases are able to break proteins down and they are often added to biological washing powders to remove protein-based stains from clothes.

Explain how these enzymes are able to break proteins down.

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 form a molecule of collagen contains 1034 peptide bonds.

Calculate the number of amino acids that would be found in a single molecule of collagen if all the chains are identical in length. Explain your answer.

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

Haemoglobin and collagen are both two important proteins found in the human body. Table 1 lists some of the properties of these proteins.

State the properties of each protein by completing Table 1.

Table 1

Discuss how the structure of a collagen molecule relates to its function in living organisms.

Ustilago maydis is a fungal pathogen affecting maize. They secrete toxins, known as killer toxins, with the best-characterised one being the KP6 toxin. This particular toxin consists of two small polypeptides that are not linked by covalent bonds. Fig. 1 shows the ribbon structure of one of these polypeptides of the KP6 toxin.

Fig. 1

Describe what is shown by the part of the polypeptide labelled A.

Certain enzymes, such as dipeptidase, are involved with protein digestion in the body. Fig. 2 shows a diagram of a dipeptide that can be broken down by dipeptidase.

Fig. 2

Describe how dipeptidase will break down this dipeptide by indicating the peptide bond on Fig. 2 and drawing the amino acid products that will form.

Proteins are very sensitive to changes in the pH of their surroundings as it may affect their tertiary and quaternary structure.

Explain why a decrease in pH could change the structure of a protein.

State how a polypeptide is formed from amino acids.

DNA polymerases are a vital group of enzymes with different variations found in all living cells. These enzymes are involved in replicating DNA during semi-conservative replication.

Explain why most cellular enzymes, such as 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 following 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 a reason why it is beneficial for washing powder to contain molecules with the ability to break down proteins.

Fig. 1 shows the structure of myoglobin, an oxygen transporting protein found in muscles. Myoglobin is responsible for receiving oxygen from the blood and transporting it to the mitochondria of muscle cells in order for cellular respiration to occur. Oxygen molecules will bind to group X indicated on the diagram.

Fig. 1

Compare the structure of myoglobin, shown in Fig. 1, with haemoglobin.

Fig. 2 shows the oxygen dissociation curves for myoglobin and haemoglobin.

Fig. 2

Explain the difference in the dissociation curves in Fig. 2.

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(ii)

Estimate the percentage saturation of myoglobin if the partial pressure of oxygen is 20 mmHg.

[1]

Explain how the tertiary and quaternary levels of protein structure enable haemoglobin to perform its role in the transport of oxygen.

Albumin is a protein found in the plasma of the blood. 

The gene that codes for human albumin is 16 961 DNA bases long. The protein is made up of 585 amino acids. 

Calculate the ratio of non-coding to coding DNA in the albumin gene.

Fig. 1 shows the molecular structure of human albumin.

Fig. 1

Identify one example of secondary structure visible in Fig. 1.

[1]

Describe the bond(s) found in the example identified in part (i).

[2]

Egg whites are mostly made of albumin.

When the albumin in egg white is denatured it changes the white of the egg from a colourless liquid to a white solid.

A student wanted to investigate how temperature affects the denaturing of albumin. 

Outline a method that the student could use to carry out this investigation. 

When the albumin in the egg white is not denatured it is soluble in water, however, when it denatures it becomes insoluble. This is due to the same mechanism that causes the colour change. 

Explain how the albumin protein can have different properties before and after denaturing. 

A theoretical polypeptide chain is 26 amino acids long. 

Calculate the number of different possible combinations of amino acids that could exist within this chain. 

Give your answer in standard form. 

In some rare circumstances some organisms have been found to contain unusual amino acids that are not shared with the majority of other organisms. 

Selenocysteine is one of them, and is shown in Fig. 1 below.

Fig. 1

Using the information in Fig. 1, state what makes selenocysteine so unusual. 

Use the information in Fig. 1 to draw the formation of a dipeptide from two molecules of selenocysteine.

Some amino acids exist that have been artificially synthesises in a laboratory. These amino acids have never occurred in the proteins of living organisms. 

Describe the features that must exist in these synthetic molecules in order for them to be classified as amino acids. 

Insulin is a protein that is produced naturally by most individuals. Patients with insulin-dependent diabetes, however, cannot produce insulin and rely on injecting insulin to replace the protein that they cannot produce for themselves. 

Suggest why the insulin must be injected into the blood instead of being taken orally. 

Many years ago insulin used to be taken from cows and pigs to treat people with diabetes. 

Using your knowledge of protein structure, suggest why pig and cow insulin was less effective at regulating blood glucose levels than human insulin. 

Another example of a protein found in humans is fetal haemoglobin, the structure of which is shown in Fig. 1 below. Fetal haemoglobin is the main type of haemoglobin found in a fetus up until birth. Fetal haemoglobin has a higher affinity for oxygen than adult haemoglobin.

Fig. 1

Using the information in Fig. 1 and your knowledge of the structure of haemoglobin, contrast the structure of fetal haemoglobin with that of adult haemoglobin.

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(ii)

Suggest the impact of the difference in structure identified in part (i).

[1]

Fig. 2 below shows part of a haemoglobin molecule. 

Fig. 2

Identify the part of the haemoglobin molecule shown in Fig. 2.

[1]

Explain how the part identified at (i) facilitates the role of haemoglobin.

[2]

Haemoglobin is a protein whose function depends on a prosthetic group.

Define the term prosthetic group and describe the components that make up the prosthetic group of haemoglobin. 

Outline the mode of operation of the prosthetic group within a haemoglobin molecule.

An individual red blood cell is thought to contain 280 million haemoglobin molecules.

Calculate how many oxygen molecules are bound within a single red blood cell when the cell is 7% saturated with oxygen. 

State your answer to 2 significant figures. 

Explain why a prosthetic group is needed in a haemoglobin molecule.