Proteins

Question 1

What is a proteome?

Answer 1

All of the proteins expressed by the genome

Question 2

The phrase “one gene - many proteins” is often used to describe proteomics in eukaryotic cells. What does this mean and why does it happen?

Answer 2

A single gene can produce multiple proteins. Usually due to alternative RNA splicing. (inconsistent assembly-many translations-finished product)

Question 3

Why is this likely to happen in eukaryotes more than in prokaryotes?

Answer 3

Prokaryotes are unable to carry out splicing

Question 4

What name do we give to genes that do not code for proteins? What are the 3 products of these genes?

Answer 4

Non-coding RNA genes. tRNA, rRNA & other RNA molecules.

Question 5

If the proteome of a certain cell is determined today and then that cell is analysed to produce a proteome tomorrow these are likely to be different. Explain why and give 4 factors that will affect what proteins are produced.

Answer 5

A cell’s proteome differs depending on when it’s assessed. Cell’s metabolic activity; cellular stress; response to signalling molecules; diseased vs. healthy cells.

Question 6

What is a transmembrane protein?

Answer 6

A protein which spans the cell membrane (transporters, receptors, enzymes, etc)

Question 7

What types of molecules are synthesised in the endoplasmic reticulum?

Answer 7

Lipids

Question 8

What are the differences between the rough ER and the smooth ER?

Answer 8

RER is covered in ribosomes & stores proteins. SER lacks ribosomes & stores lipids and proteins.

Question 9

Describe how and why a ribosome attaches to the ER instead of completing translation in the cytosol.

Answer 9

A signal sequence is present and directs the ribosome to dock with the ER.

Question 10

What is a “signal sequence” and what is the importance of “signal sequences”?

Answer 10

A signal sequence is a short peptide present at the N-terminus of the majority of newly synthesised proteins that are destined towards the secretory pathway.

Question 11

How are proteins modified in the Golgi apparatus and why does this happen?

Answer 11

Enzymes catalyse the addition of sugars to form carbohydrates

Question 12

What are vesicles and how are they important in the processing and delivery of proteins in the cell?

Answer 12

Vesicles bud off from the Golgi from one disc and fuse to the next, these are what allows molecules to travel across the Golgi apparatus. Vesicles are Lysosomes which are membrane bound organelles found in the cytosol. They contain digestive enzymes and are involved in degradation reactions.

Question 13

What is the function of microtubules in the movement of proteins between membranes?

Answer 13

They allow vesicles to move to other membranes and fuse them within the cell

Question 14

In what ways do the production of secretory proteins differ from the production of transmembrane proteins?

Answer 14

Proteins for secretion are inserted directly into the lumen of the Golgi apparatus.

Question 15

What are 2 types of post-translational modifications?

Answer 15

Addition of chemical groups (i.e. carbohydrates) & the proteolytic cleavage of the polypeptide

Question 16

How is pepsin produced from its precursor pepsinogen?

Answer 16

Pepsin’s proenzyme, pepsinogen, is released by the chief cells in the stomach wall, and upon mixing with the hydrochloric acid of the gastric juice, pepsinogen activates to become pepsin (undergoes proteolysis)

Question 17

What is the general structure of an amino acid?

Answer 17

Amino group - carbon with side chain - carboxyl group

Question 18

What are the four types of amino acids and the key component of the R group in each type? Indicate which groups are hydrophilic and which are hydrophobic

Answer 18

Basic (positively charged - hydrophilic); Acidic (negatively charged - hydrophilic); polar (OH group - hydrophilic); hydrophobic (hydrocarbon - hydrophobic),

Question 19

What are 5 features of R groups which vary?

Answer 19

Size, shape, charge, hydrogen bonding capacity, chemical reactivity

Question 20

What is the reaction which takes place to link amino acids and draw such a reaction between two amino acids? Label the peptide bond.

Answer 20

Condensation reaction, the -OH from one amino acid bonds to the -H from the NH2 group on the other amino acid. The two amino acids bond together and water(H2O) is produced.

Question 21

What is meant by the primary structure of a protein? Draw a chain of three amino acids (use R for side chains) labelling the peptide bonds, N-terminus and C-terminus.

Answer 21

The primary structure is the sequence of amino acids in a protein. Chains of amino acids are written from the amino terminus (N-terminus) to the carboxyl terminus (C-terminus).

Question 22

What is meant by the secondary structure of protein structure? Name the type of bonds which form and the two types of secondary structure which can result.

Answer 22

There are 2 types of secondary structure α-helix and β–sheet.
α-helix - The helix is right handed with 4 residues (amino acids) per turn. Hydrogen bonds between oxygen (the C=O group) and hydrogen (N-H group) stabilise the helix.
β–sheet - Polypeptide chains are linked together in a side by side formation with hydrogen bonds. β-sheets can be parallel or antiparallel.

Question 23

What is the difference between a parallel and an anti-parallel β sheet?

Answer 23

Helices that are parallel run in the same direction. Helices that are anti-parallel run in opposite directions.

Question 24

What is meant by the term ‘tertiary’ structure of a protein? Name the five types of interaction which can be seen here.

Answer 24

The tertiary structure is all about the interactions between the R groups. These interactions are; hydrophobic interactions, ionic bonds, hydrogen bonds, LDFs, disulfide bridges.

Question 25

What are disulphide bridges? Which amino acid is involved?

Answer 25

Disulfide bridges are strong covalent bonds that form between the -SH groups that are found in different parts of the polypeptide chain. Cysteine.

Question 26

What is the quaternary structure of proteins?

Answer 26

Some proteins are made up of 2 or more polypeptide subunits. Quaternary structure describes the spatial arrangement of the subunits.

Question 27

What is a prosthetic group?

Answer 27

Non-protein groups which are associated with proteins.

Question 28

What is the prosthetic group in haemoglobin? What is its function?

Answer 28

Haeme, allows oxygen to bind to haemoglobin

Question 29

What 2 factors can influence the interactions of R groups and how?

Answer 29

Temperature and pH

Question 30

What is the isoelectric point of a protein?

Answer 30

The pH at which a particular molecule carries no net electrical charge.

Question 31

How can isoelectric point be determined?

Answer 31

Casein (for example) is a soluble protein that becomes insoluble at its isoelectric point. At the isoelectric point, it will precipitate out of solution and can be identified.

Question 32

How does the concept of induced fit lower activation energy?

Answer 32

The binding of the substrate (ligand) temporarily causes the protein to change so the fit is perfect. The chemical environment produced lowers the activation energy needed for the reaction.

Question 33

How does conformational change aid product release from an enzyme?

Answer 33

Once the induced fit reaction takes place the products are released from the active site and the protein reverts to its original conformation.

Question 34

What is a modulator and where on an enzyme does it bind?

Answer 34

Allosteric modulators are ligands that bind to an area of the protein that is not the active site, leading to a conformational change in the protein.

Question 35

What are enzymes controlled by modulators known as?

Answer 35

Allosteric enzymes

Question 36

What is the difference between positive and negative modulators?

Answer 36

A negative modulator is when the binding ligand acts as an inhibitor. A positive modulator is when the binding ligand acts as an activator.

Question 37

By which process can negative modulators prevent overproduction of a substance? Describe the mechanism by which this process works.

Answer 37

End product inhibition/feedback inhibition. When the final product of a cascade of enzyme reactions interacts with an allosteric site of the first enzyme in the cascade to inhibit it and thus the production of the end product.

Question 38

What is the idea of cooperativity with regard to the binding of ligands to proteins with quaternary structure?

Answer 38

Some proteins with quaternary structure show cooperativity in which changes in binding at one subunit alters the affinity of the remaining subunits.

Question 39

What is a protein kinase?

Answer 39

Protein Kinase enzymes phosphorylate other proteins.

Question 40

How does the addition of a phosphate group result in a change in protein conformation?

Answer 40

The terminal phosphate of ATP is transferred to specific R groups. Phosphorylation brings about conformational changes, which can affect a protein’s activity. The activity of many cellular proteins, such as enzymes and receptors, is regulated in this way. Some proteins are activated by phosphorylation while others are inhibited. Adding a phosphate group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created

Question 41

What is the role of protein phosphatases?

Answer 41

Protein phosphatases catalyse the reverse reaction - will cause dephosphorylation.