Proteins

Question 1

State the differences between an organism’s genome and its proteome.

Answer 1

An organisms genome is its complex set of DNA including both protein coding genes and non-coding RNA genes.

The proteome is the entire set of proteins that can be expressed by a genome.

The proteome is much larger than the genome due to alternative RNA splicing depending which RNA segments are treated as introns and which as exons.

Question 2

State the factors which affect the set of proteins expressed by a given cell type.

Answer 2

Factors that affect the set of proteins expressed by a given cell type are the metabolic activity of the cell, cellular stress and response to signalling molecules.

Question 3

What is the benefit of specific marker proteins?

Answer 3

Specific marker proteins in the proteome can be early indicators for conditions such as heart disease or cancer.

Question 4

What is the key structural difference between eukaryotes and prokaryotes?

Answer 4

The key structural difference between eukaryotes and prokaryotes are the presence or absence of intracellular membrane structures.

Question 5

Explain in detail the key structural differences between a eukaryote and a prokaryote.

Answer 5

IN PROKARYOTES, the size of the prokaryote is limited by the amount of metabolic reactions it can carry out in its plasma membrane. Prokaryotes lack intracellular membrane structures in their cytoplasm, therefore many of these functions are carried out by the plasma membrane, placing a limit on the maximum rate of metabolic reactions and therefore its size.

IN EUKARYOTES, its system of internal membranes greatly increase the surface area available for metabolic reactions to be carried out by membranes. Eukaryotes have a relatively small surface area to volume ratio, meaning their plasma membranes have too small an area to carry out their vital functions. The eukaryotes system of internal membranes increase the total area of membrane available for the vital metabolic processes.

Question 6

Describe the structure and function of the endoplasmic reticulum.

Answer 6

The endoplasmic reticulum is a network of membrane tubules continuous with the nuclear membrane. Lipids and proteins are synthesised by the endoplasmic reticulum.

Question 7

Describe the function of vesicles.

Answer 7

Vesicles transport materials between the membrane compartments or to the plasma membrane.

Question 8

Describe the function of lysosomes.

Answer 8

Lysosomes are membrane bound organelles that contain a variety of hydrolyse enzyme.

Question 9

Define ‘Golgi apparatus’

Answer 9

The Golgi apparatus is a series of membrane discs where proteins undergo post transnational modifications.

Question 10

Identify two parts of the cytoplasm.

Answer 10

The cytoplasm has two parts:

The cytosol which is the liquid part of the cytoplasm.

And the ribosomes and the membrane bound organelles which are suspended in the cytosol.

Question 11

How is the synthesis of proteins for cytosol carried out.

Answer 11

The synthesis of proteins for cytosol is carried out entirely by cytosolic ribosomes. Once completed the proteins are released into the cytosol. These proteins include proteins of glycolysis and enzymes that attach amino acids to tRNA.

Question 12

Explain in detail the difference between rough and smooth endoplasmic reticulum.

Answer 12

Note that both the rough and the smooth endoplasmic reticulum are connected.

The rough endoplasmic reticulum has ribosomes attached to the cytosol face of its membranes while the smooth endoplasmic reticulum has none.

The SER carries out the synthesis of lipids by its enzymes. (Oils, phospholipids and steroid hormones.) the phospholipids synthesised are then inserted into the membrane of the SER.

Question 13

Describe in detail the process of synthesising transmembrane proteins.

Answer 13

The synthesis of transmembrane proteins begins at the cytosolic ribosome.

STEP 1 - a polypeptide starts with a short stretch of about 20 amino acids known as a signal sequence. When the signal sequence emerges from a ribosome, a cytosolic particle binds to it and temporarily halts translation.

STEP 2 - the cytosolic particle directs the ribosome to dock with a protein pore in the endoplasmic reticulum thus forming the rough endoplasmic reticulum.

STEP 3 - after docking, the protein pore removes the cytosolic particle and the signal sequence so translation can continue.

NOTE THAT A SIGNAL SEQUENCE is a short stretch of amino acids at the end of a polypeptide that determines the eventual location of a protein in a cell.

Question 14

What kind of proteins are synthesised entirely by cytosolic ribosomes?

Answer 14

Proteins that are synthesised by cytosolic ribosomes are destined for use in the mitochondria, chloroplasts/interior of the nucleus.

Question 15

Describe the synthesis of polypeptides.

Answer 15

Polypeptides that are destined to be a part of a lysosome enzyme or secreted protein start their synthesis at a cytosolic ribosome and have a signal sequence that takes the ribosome to the rough endoplasmic reticulum.

As they are transported through the protein pore in the RER, they are released directly into the lumen of the RER instead of the membrane.

Question 16

What happens to polypeptides produced in the RER?

Answer 16

Polypeptides that are produced in the RER are transported by vesicles that bind off the RER.

The vesicles move along the mitochondria and then fuse with the Golgi apparatus.

As the polypeptides move through the stacks of discs in the Golgi apparatus, they undergo post-translational modifications. Enzymes modify the polypeptides by catalysing the addition of various sugars in multiple steps to form carbohydrate groups attached to the polypeptide.

The polypeptides, as a result are converted into glycoproteins. Glycoproteins make up most secreted proteins but are also found in the membrane.

Question 17

What is proteolytic cleavage?

Answer 17

Proteolytic cleavage is a type of post-translational modification.

Question 18

What is the major modification carried out in the Golgi apparatus?

Answer 18

The major modification carried out in the Golgi apparatus is the addition of carbohydrate groups.

Question 19

Describe the process in which a protein leaves the Golgi apparatus.

Answer 19

STEP 1 - before a protein leaves the Golgi apparatus, phosphate groups can be added to identify its destination.

STEP 2 - vesicles carrying the protein bind off and line the Golgi apparatus. These vesicles then move along microtubules to other membranes and then fuse with them.

Question 20

What are the 4 possible fates of vesicles?

Answer 20

ONE - vesicles can fuse with the plasma membrane to build the membrane and add transmembrane proteins.

TWO - vesicles can fuse with the plasma membrane to allow a protein to be secreted.

THREE - they can fuse with the membranes of mitochondria, chloroplasts or nuclei to build their outer membranes and add transmembrane proteins.

FOUR - the vesicles can form a lysosome in the cytosol.

Question 21

What is the function of hydrolyses?

Answer 21

Hydrolyses digest proteins, lipids, nucleic acids and carbohydrates. Lysosomes contain a variety of hydrolyses allowing them to digest damaged organelles which in turn allow cells to recycle their component molecules.

Question 22

State examples of secreted proteins

Answer 22

Secreted proteins include peptide hormones and digestive enzymes.

Question 23

Why do proteins require proteolytic cleavage?

Answer 23

Secreted proteins require proteolytic cleavage when they are synthesised as inactive precursors.

Question 24

Give two examples of chemicals that undergo proteolytic cleavage.

Answer 24

INSULIN - which undergoes proteolytic cleavage in the secretory vesicle before being secreted.

PEPSIN - the digestive enzyme undergoes proteolytic cleavage by the acid in the stomach before it becomes active.

Question 25

What are polypeptides?

Answer 25

Polypeptides are polymers of amino acid monomers. The amino sequence determines protein structure.]

Question 26

Describe the structural properties of amino acids.

Answer 26

Amino acids have the same general structure. All amino acids have a central carbon atom which has 4 groups linked to it: an NH2 amine group, a COOH carboxylic acid group, a hydrogen and a variable R group.

Question 27

What are the four classes of amino acids?

Answer 27

The four classes of amino acids are: acidic, basic, polar and hydrophobic. These are defined by its functional R group.

Question 28

Comment on the interactions that R groups share with the cell.

Answer 28

Because R groups also interact with aqueous solutions of the cell, the -COOH groups will become negatively charged (COO-) while the basic NH2 groups will become positively charged. (NH3+) Polar R groups have groups which are slightly charged so they can form hydrogen bonds with other molecules such as water. Hydrophobic R groups carry no charge and therefore do not form any hydrogen bonds with water.

Question 29

How are amino acids linked?

Answer 29

Amino acids are linked during translation at the ribosome. An enzyme causes a condensation reaction between two adjacent amino acids. A water molecule is removed by joining an OH from a COOH to a hydrogen to form another amino acid.

Question 30

Draw the structure of an amino acid.

Answer 30

Refer to notebook for diagram

Question 31

Where are the NH2 and COOH groups located on a polypeptide?

Answer 31

The polypeptide chain has an NH2 group at the N-terminus and a COOH at the C-terminus.

Question 32

Draw a polar and a hydrophobic amino R group.

Answer 32

Refer to the notebook for diagrams

Question 33

Explain what is meant by primary structure.

Answer 33

The primary structure is the sequence in which the amino acids are synthesised into the polypeptide. This amino acid sequence determines protein structure and hence the function of the protein.

Question 34

Explain what is meant by secondary structure.

Answer 34

Secondary structure is stabilised by hydrogen bonds along the back bone of the polypeptide strand. These hydrogen bonds exist between different peptide bonds.

Question 35

Describe the three types of secondary structure.

Answer 35

α-helix is a spiral with the R groups sticking outwards. The β-pleated sheet has parts of the polypeptide chain running alongside each other to form a corrugated sheet with the R groups sitting above and below. The β-pleated sheets are usually anti-parallel but they can also be parallel The polypeptide chain can also form turns where the chain folds back on itself.

Question 36

Describe what is meant by tertiary structure.

Answer 36

The tertiary structure is known as the final folded shape of the polypeptide. The tertiary structure is a 3-dimensional conformation containing regions of secondary structure stabilised by interactions between R groups. As folding of secondary level brings R groups closer, this allows them to connect.

Question 37

Describe the different possible interactions between R groups.

Answer 37

HYDROPHOBIC INTERACTIONS - as the polypeptide folds, the hydrophobic R groups are repelled by water and therefore end up on the inside of the polypeptide. IONIC BONDS - COOH and NH2 ionise to become COO- and NH3+, these groups are strongly charged therefore repel each other. LONDON DISPERSION FORCES - these are very weak forces of attraction between clouds of atoms. HYDROGEN BONDS - strong attraction between molecules containing OH or NH DISULPHIDE BRIDGES - covalent bonds form between sulphur containing R groups.

Question 38

In what way can these interactions be affected?

Answer 38

These interactions can be affected by temperature and pH! A higher temperature would cause the structure to be come destabilised leading the proteins to becoming denatured. A higher temperature would also cause the polypeptide to shake due to kinetic energy breaking weaker ionic bods and LDFs and hydrogen bonds. Changes in pH causes a change in the charge they carry as it affects the ionisation of acidic and basic groups. This causes the protein to unfold as they can no longer bond correctly. As pH increases or decreases from the optimum, the ionic interactions are lost which eventually causes the protein to denature.

Question 39

Explain what is meant by quaternary structure?

Answer 39

Quaternary structure is where two or more polypeptide chains interact to form a protein. Quaternary structures are stabilised by hydrogen bonds and disulphide bridges etc.

Question 40

Describe the purpose of prosthetic groups.

Answer 40

Prosthetic groups are non-protein groups that are tightly bound to a polypeptide unit and are essential to the proteins function.

Question 42

Define a ‘ligand’

Answer 42

A ligand is the term used to describe any substance that binds to a protein. When a ligand binds, the shape of the protein changes slightly. (Conformational change.)

Question 43

How does ligand binding occur?

Answer 43

Ligand binding occurs when a protein folds. R groups not involved in the proteins function may be exposed to the outer surface of the protein which produces ligand binding sites on the surface of the protein. These binding sites have a complementary shape and chemistry to the ligand. The R groups match with the ligands charged, polar and non-polar areas allowing them to interact and bind.

Question 44

Why is ligand binding important?

Answer 44

Ligand binding pulls the polypeptide structure toward the ligand causing a conformational change in shape. This conformational change causes a functional change in the protein and is used to regulate the activity of proteins.

Question 45

What does the term allosteric refer to?

Answer 45

Allosteric means other shape, referring to proteins that have interactions between spatially distinct sites on the same protein. Allosteric enzymes have a second type of site called an allosteric site.

Question 46

What are modulators and what do they do?

Answer 46

Modulators regulate the activity of enzymes when they bind to the allosteric site. When a modulator binds, the conformational of the enzyme changes and alters the affinity of the active site for its substrate. POSITIVE modulators increase the enzymes affinity which therefore increases enzyme activity. NEGATIVE modulators decrease the enzymes affinity which therefore decreases enzyme activity.

Question 47

Define ‘cooperativity’

Answer 47

Cooperativity is the increase of affinity of another subunit due to the binding of a ligand to one subunit of a protein. The binding of a substrate molecule to one active site increases the affinity of the other active sites for binding.

Question 48

Why is cooperativity important?

Answer 48

Cooperativity is of biological importance as the activity of allosteric enzymes can vary very greatly with small changes in substrate concentration.

Question 49

What happens when there is a lack of cooperativity?

Answer 49

Without cooperativity the oxygen concentration in the tissue is increased however the oxygen concentration curve is S-shaped, meaning haemoglobin holds more oxygen in high oxygen surroundings and lower in low oxygen surroundings.

Question 50

Comment on the structure of haemoglobin.

Answer 50

Haemoglobin has four polypeptide subunits with an oxygen binding site. When oxygen binds to the subunit, it changes its conformation and the conformation of other subunits increasing their affinity for oxygen. Oxygen affinity increases further as more and more oxygen binds to the haemoglobin which maximises oxygen in areas where oxygen levels are high. Conversely, the release of oxygen decreases its affinity with other subunits, maximising the release of oxygen where it is needed.

Question 51

What factors affect oxygen binding in haemoglobin?

Answer 51

The binding of oxygen to haemoglobin is affected by temperature and pH. These effects have a physiological importance. Hard working tissues generate heat and they also produce carbon dioxide, which reacts with water to form carbonic acid. This increase in temperature and decrease in pH causes haemoglobin to have a lower affinity with oxygen so O2 binding is reduced promoting decreased oxygen delivery to tissues.

Question 52

Summarise what happens to oxygen binding with haemoglobin when there is a high temperature.

Answer 52

HIGH TEMPERATURE -> tissues release CO2 -> CO2 reacts with H2O -> carbonic acid formed LOW PH! -> oxygen affinity to haemoglobin lowered ->increased oxygen delivery to tissues.

Question 53

How are a large subset of inactive proteins activated?

Answer 53

Inactive proteins are activated through post-translational modifications. The most common form of activation is the reversible addition of a phosphate onto the -OH group of particular R groups. The addition or removal of a phosphate is used to cause reversible conformational changes in the protein, regulating the activity of many cellular proteins. Adding a phosphate group adds NEGATIVE charges. Adding a phosphate can both activate and deactivate proteins !!

Question 54

What is the role of protein kinases and phosphatases?

Answer 54

KINASES - catalyse phosphorylation which transfers a phosphate group from ATP to other proteins. Add Phosphates On (KAPO) PHOSPHATASES - catalyse de-phosphorylation which removes a phosphate group. Encourage Phosphates Away (PEPA)

Question 55

How are inactive proteins kinases activated?

Answer 55

Most protein kinases are de-phosphorylated and inactive. They are activated by phosphorylation by another kinase. This reversibility it’s important in ligand transduction cascades where kinases activate other downstream kinases to amplify a signal.

Question 56

What two enzymes are crucial in the control of the cell cycle?

Answer 56

Kinases and phosphatases are crucial in the control of the cell cycle.

Question 57

What are ATPases?

Answer 57

ATPases are a group of transmembrane proteins that hydrolyse ATP and use phosphate to phosphorylate themselves rather than their substrate. When the phosphate binds, their conformation and subsequent function changes which also moves substances across the membrane. All transmembrane ATPases are involved in active transport of ions across the membrane and the sodium potassium pump is an example of this enzyme.