Task Answers

Topic 1, Key Area 2

Task 14

  1. The proteome is the entire set of proteins within a cell.

  2. Genome is fixed; proteome is dynamic and changes between cells and at different times throughout development

  3. Mass spectrometry allows identification of individual proteins. The process involves shooting charged protein molecules, or fragments of them, through a vacuum tube and measuring the time it takes for the molecules to travel a fixed distance. The time to travel is directly proportional to their mass

  4. Studying the proteome helps scientists develop revolutionary drugs, with fewer side effects; it helps us understand the intricacies of many organisms; it may help us understanding bacterial resistance to antibiotics.

Task 15

Reflect back to your Higher/Higher Human Biology course. Engage in a quick Retrieval Practice by producing a Brain Dump that reflects your understanding of the following image.

Some submitted responses are shown below.


SQA Past Paper Question 5

Answer: Proteome

This solution does not emanate from the SQA.

Task 16

Using information you have gained so far, state the function of the following organelles:

  1. Endoplasmic reticulum

  2. Golgi apparatus

The endoplasmic reticulum is responsible for the synthesis and modification of proteins.

The Golgi apparatus is responsible for the modification of translated proteins.

Task 17

Use this space to sketch a labelled diagram of a eukaryotic cell, featuring previously-known organelles together with your new understanding of intracellular membranes.

Task 18

Include a quick sketch to show the structure of cell membranes.

2 possible answers are included below:

Task 19

Use this space to sketch the RER and the SER.

Task 20

Use this space to draw a flowchart outlining where materials required for membrane formation are synthesised.

Task 21

Catriona had been reading about this during her Home Learning session through the week and stumbled across the diagram below. She put an explanation of what she thought was going on. Read Catriona's explanation of the diagram. Do you agree or disagree with her statement and, if you disagree, can you suggest a suitable alternative.

All proteins are synthesised in the cytosol. The mRNA encodes the protein (shown in the blue) and the protein can stay in the cytosol. Sometimes a protein is made on ribosomes that become attached to the endoplasmic reticulum. These proteins (green) then enter the ER after translation.

Answer:

All proteins BEGIN their translation on cytosolic ribosomes. The mRNA (blue) encodes the protein (green) and, if the mRNA does not encode a signal sequence, it will complete its full translation on cytosolic ribosomes and become a cytosolic protein.

Sometime a mRNA will encode a signal sequence (red) and this signal sequence causes the cytosolic ribosome to dock with the ER, forming the RER. At this point, translation will continue and the translated protein will enter the membrane of the ER.

Task 22

Having watched the video about vesicular transport of proteins between the ER and Golgi and subsequent modification within the Golgi apparatus, rearrange the following statements into the correct order.

Task 23

In Task box 23, carry out your own brief research into one protein that undergoes proteolytic cleavage as a post-translational modification.

Suggested research: Insulin

Insulin is a hormone that functions in the regulation of blood glucose concentration. Initially, the mRNA transcript for the protein engages with cytosolic ribosomes that detect the signal sequence on the "preproinsulin" structure. Since insulin requires secretion from the cell, it enters the secretory pathway and the ribosome docks on the ER, where translation continues. The signal sequence is removed in the ER, forming "proinsulin" and disulfide bonds form between sections of the protein. Proinsulin consists of an A and B chain, linked via a C-peptide. Along the secretory pathway, within secretory vesicles, proinsulin is converted to insulin by the action of two proteases. This acts to remove the c-peptide - the A and B chains remain attached by disulphide bridges. Mature insulin now has high affinity for its membrane receptor (proinsulin lacks affinity for the receptor) and is thus considered active.

Task 24

Sketch the basic structure of an amino acid in your notes.

Task 25

You must be able to recognise the chemical structure of a peptide bond from a diagram. Draw 3 amino acids joined via a peptide bond.

Task 26

You must be able to classify amino acids according to the R group present. You will NOT need to know the names and structures of individual amino acids for the exam. In the space below, name and draw an example of:

  1. A hydrophobic/non-polar amino acid

  2. A polar amino acid

  3. A basic/positively-charged amino acid

  4. An acidic/negatively-charged amino acid

Task 27

As an added level of challenge, now draw a short polypeptide consisting of a hydrophobic, polar, basic and acidic amino acid. This should include 3 peptide bonds.

Task 28

As an added level of challenge, now draw a short polypeptide consisting of a hydrophobic, polar, basic and acidic amino acid. This should include 3 peptide bonds.

Task 29

In this space, include a diagram of 2 polypeptide chains of 3 amino acids long in a manner that would allow a beta sheet to form.

Task 30

Consider the image of the folded protein below. Can you identify the tertiary interactions (A-E) that have formed between R groups in this protein?

A = Hydrophobic interaction

B = Peptide bonds (not a tertiary interaction)

C = Disulphide bridge

D = Ionic bond

E = Hydrogen bond

Task 31

Carry out a quick piece of research to find a protein (other than haemoglobin) that has quaternary structure. Include a sketch of this protein structure (or an image from a good source, such as Protein Data Bank) detailing how many subunits are present in the quaternary structure of the protein.


Suggested answer (although there are many!):

Coronaviruses are described as a peplomer - this is a glycoprotein spike on a viral capsid. In some tested variants, the spike is formed from 2 domains (S1 and S2) which interact via a network of hydrophobic interactions between aromatic (ring-based, e.g. histidine) side chains. The spike binds to receptors on target cells and the quaternary structure of S1 and S2 is crucial for this. The quaternary structure of these spike proteins of Coronavirus are instrumental in its ability to infect cells.

Task 32

Explain why changes in temperature or pH can disrupt a protein structure. Be specific to the type of bonds influenced in each case.


Changes in temperature affect the stability of all bonds. As temperatures increase, intramolecular bonds will break and the tertiary structure of the protein will unravel. As pH changes occur, ionic bonds will be primarily affected, with ionisation states altering. The tertiary structure will begin to unravel.

Task 33

Draw a diagram of a ligand bound to a protein, indicating possible bonding between R groups on the protein and molecules on the ligand.

The image above shows the kind of thing published from structural crystallographers who study the structures of proteins. Often, they co-crystallise ligands and proteins together to understand key interactions and amino acids that are important in reactions. In this image, the ligand is shown (mainly) as purple and the protein in green. K = lysine (basic amino acid) involved in an ionic bond with the ligand; F = phenylalanine involved in a hydrophobic interactions with the ligand.


To the left is an (equally ;) good representation of a ligand interacting at a protein site - hydrogen and ionic bonds are playing a part here!

Task 34

Watch the following video and state what is meant by "allosteric enzyme".


Suggested answer: Many enzyme-catalysed reactions in a cell involve allosteric proteins. Regulation of some biochemical reactions involve allosteric proteins, whereby the product of the reaction interacts at an allosteric site of a key enzyme involved at an early stage of the pathway. The product engaged with the allosteric site, causing a conformational change in the enzyme; this prevents the substrate from engaging in the active site and no further reaction is possible. This is often called feedback inhibition - we encountered this during our Higher studies in Biology/Human Biology of phosphofructokinase in Glycolysis.

Task 35

Aspartate transcarbamoylase is an allosteric enzyme of biological importance. Using bioinformatic tools and other online sources, find out about this enzyme. Click the pink button below to access Expasy. In "Query all databases", type: "aspartate transcarbamoylase". Click on the UniProt hits and then select the top Human hit (as shown below: P27708 CAD protein).


ATC is present within the nucleus of the cell, where it is involved in pyrimidine (thymine and cytosine) biosynthesis. It is allosterically regulated by pyrimidines, which bind to a secondary site on the enzyme when in high concentration to modulate the activity. The protein The protein is also regulated by phosphorylation, catalysed by MAP kinases prior to the S phase of the cell cycle when demand for pyrimidine nucleotides is greatest. This protein contains prosthetic groups, including zinc and magnesium. Mutation of this protein is associated with a condition called epileptic encephalopathy in early childhood.

Task 36

Watch the following clip from the Wellcome Trust to answer the following questions:

1. Explain what is meant by "cooperativity".

2. Describe and sketch the "Oxygen Dissociation Curve".

3. State one condition that affects haemoglobin's affinity for oxygen.


Cooperativity means that binding of a ligand at one subunit of a quaternary protein increases the affinity of remaining subunits for the ligand. This is because binding of the ligand at one subunit causes a conformational change in the protein that makes it easier for the ligand to bind to other subunits.

Haemoglobin's affinity for oxygen is affected by temperature and pH: as temperature increases and pH decreases, resulting from increased respiratory activity in tissues and cells, haemoglobin's affinity for oxygen decreases and more oxygen can be delivered to cells. Another way of saying this is that the oxyhaemoglobin concentration in the bloodstream decreases.

Task 37

Sketch the haemoglobin dissociation curve under changing temperature and pH levels. Explain the physiological importance of temperature and pH on the binding of oxygen.

Task 38

In your notes, sketch a phosphate group.

Can you think what R groups are likely to be targeted for phosphorylation?

Suggested answer: Phosphate group shown in image below and likely targets are those R groups with a hydroxyl group.

Task 39

Include the structures of amino acids with R groups that are susceptible to phosphorylation by kinases.

Suggested answers: See diagram above for task 38: R groups with a free hydroxyl group, including serine, threonine and tyrosine.


Task 40

Include a diagram in your notes to show the reversible nature of protein phosphorylation.

Task 41

Using the image and link below (Crash Course: Muscle Cells), explain how phosphorylation facilitates muscle contraction.


Suggested answers: The head of myosin molecules act as an ATPase to hydrolysis ATP (stage 4 --> 1 in the diagram), releasing a phosphate and ADP. The myosin head becomes phosphorylated, which causes a conformational change (stage 1--> 2 in the diagram). In this new "extended position" (like a "spring ready for action"), the phosphorylated myosin head attaches to actin filaments and pulls (stage 2 in the diagram). This shrinks the whole sarcomere (unit of muscle tissue). With the energy having been spent, myosin is dephosphorylated and a new ATP molecule binds (see stage 3 in the diagram). This results in conformational change and the cycle continues (stage 4 in diagram).