Advanced Higher Biology Unit 1-Key Area 2: Proteins

What is the proteome?

The entire set of proteins expressed by a genome

Why is the proteome larger than the genome?

More than one protein can be produced from a single gene as a result of alternative RNA splicing

Are all genes expressed as proteins?

No

What are genes that don't code for proteins called?

They are called non coding RNA. They include those that are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes

What can happen to the set of proteins expressed by a given cell type?

They can vary under different conditions

What are some factors affecting the set of proteins expressed?

The metabolic activity of the cell, cellular stress, the response to signalling molecules and diseased versus healthy cells

What do eukaryotic cells have?

A system of internal membranes which increase the total surface area of the cell

What is the advantage of the internal system of membranes?

Because of their size, eukaryotes have a relatively small surface area to volume ratio. The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions of the cell

Diagram of a cell showing the ER, vesicle, lysosome and golgi apparatus

What is the endoplasmic reticulum?

It forms a network of membrane tubules continuous with the nuclear membrane

What are the two types of ER?

Smooth and rough

What is the golgi apparatus?

A series of flattened membrane discs

What are lysosomes?

Membrane-bound organelles containing a variety of hydrolysed enzymes that digest proteins, lipids and fats

What are vesicles?

Things that transport materials between membrane compartments

Where are lipids and proteins synthesised?

In the ER

What is the difference between rough ER and smooth ER

Rough ER (RER) has ribosomes on its cytosolic face whereas smooth ER (SER) lacks ribosomes

Where are lipids synthesised?

The smooth ER and they are then inserted into its membrane

Where does the synthesis of all proteins begin?

The cytosolic ribosomes

Where is the synthesis of cytosolic proteins completed?

In the cytosolic ribosomes. The proteins then stay in the cytosol

What do transmembrane proteins do?

Carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER forming RER. Translation continues after docking and the protein is inserted into the membrane of the ER

What is a signal sequence?

A short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell

What happens to the proteins when they are in the ER?

They are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus

What do molecules use to move through the Golgi discs?

Vesicles that bud off from one disc and fuse to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form carbohydrates

What happens to proteins as they move through the Golgi apparatus?

They undergo post-translational modification

What is a major modification?

The addition of carbohydrate groups to proteins

Where do vesicles that leave the Golgi apparatus take proteins?

The plasma membrane and lysosomes

What do vesicles do with microtubules?

Move along them and fuse with them within the cell

What happens to secreted proteins?

They are translated in ribosomes on the RER and enter its lumen

What are some examples of secreted proteins?

Peptide hormones and digestive enzymes

What is the secretory pathway? (simplified)

Rough ER -> Golgi -> secretory vesicles -> cell exterior

What is the secretory pathway (detailed)

Proteins move through the Golgi apparatus and are then packed into secretory vesicles
These vesicles then move to and fuse with the plasma membrane, releasing proteins out of the cell
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins

What is proteolytic cleavage?

Another type of post translational modification

What is one example of secreted proteins that require proteolytic cleavage to become active?

Digestive enzymes

What are proteins?

Polymers of amino acid molecules

How are amino acids linked?

By peptide bonds to form polypeptides

How does the structure of amino acids differ?

Only in the R group present

How can R groups of amino acids vary?

In size, shape, charge, hydrogen bonding capacity and chemical reactivity

What is the basic structure of an amino acid?

How can the different types of amino acids be classified?

According to their R groups

What are the different groups of amino acids?

· Basic (positively charged)
· Acidic (negatively charged)
· Polar
· Hydrophobic

What does the wide range of functions carried out by proteins result from?

The diversity of R groups

What is the primary structure of a protein determined by?

The sequence in which amino acids are synthesised into the polypeptide

How is the secondary structure of a protein determined?

Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure. The hydrogen bonding occurs between the N-H and C=O sections of an amino acid molecule. The different types of secondary structure are alpha helices, parallel or antiparallel beta sheets and turns.

How is the tertiary structure determined?

The polypeptide folds into a tertiary structure. This confirmation is stabled by interactions between R groups. These interactions include:
· Hydrophobic interactions
· Ionic bonds
· London dispersion force
· Hydrogen bonding
· Disulfide bridges

What are hydrophobic interactions?

Interactions between two non-polar molecules

What are ionic bonds?

Interactions between positive and negative groups on the amino acids

What are london dispersion forces?

Weak forces of attraction between covalently bonded molecules

What is hydrogen bonding?

Intermolecular forces that occur when hydrogen atoms are bonded to highly electronegative elements like nitrogen or oxygen

What are disulfide bridges?

Covalent bonds between R groups containing sulfur

When does quaternary structure exist?

In proteins with two or more connected polypeptide subunits. Quaternary structure describes the spatial arrangement of the subunits

What is a prosthetic group?

A non-protein unit tightly bound to a protein and necessary for its function

What is an example of a protein with a prosthetic group?

Haemoglobin. The ability of haemoglobin to bind to oxygen is dependent upon the non-protein haem (iron) group

What can interactions between R groups be influenced by?

Temperature and pH

How does increasing temperature affect protein shape?

It disrupts the interactions that hold the protein in shape. The protein begins to unfold and eventually becomes denatured

How does pH affect protein shape?

It affects the charges on acidic and basic R groups. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changed the conformation of the protein until it becomes denatured

What is the name of a substance that binds to a protein?

A ligand

What are involved in ligand binding?

R groups not involved in protein folding

What will binding sites have?

Complementary shape and chemistry to the ligand

What happens when a ligand binds to a protein binding site?

The conformation of the protein changes. This change in conformation causes a functional change in the protein

What are allosteric interactions?

Interactions that occur between spatially distant sites. The binding site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules

What is the biological importance of allosteric interactions?

The activity of allosteric enzymes can vary greatly with small changes in substrate concentration

What do many allosteric proteins consist of?

Multiple subunits (they have a quaternary structure)

What do allosteric proteins with multiple subunits show?

Cooperativity in binding in which changing in binding at one subunit alter the affinity of the remaining subunits

What do allosteric enzymes contain?

A second type of site called an allosteric site

What is an allosteric site?

A site on the enzyme other than the active site

What do modulators do?

They regulate the activity of an enzyme when they bind to the allosteric site

What occurs after binding of a modulator?

The conformation of the enzyme changes and this alters the affinity of the active site for the substrate

What do positive modulators do?

Increase the enzyme's affinity for the substrate

What do negative modulators do?

Reduce the enzyme's affinity for the substrate

What shows an example of cooperativity?

The binding and relays of oxygen in haemoglobin. Changes in binding of oxygen at one subunit alters the affinity for the remaining subunits of oxygen

What can influence the binding of oxygen?

Temperature and pH

How does a decrease in pH or an increase in temperature affect haemoglobin?

It lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue

What is the effect of the addition or removal of a phosphate on a protein?

It causes a reversible conformational change in the protein

What is the addition or removal of phosphates?

A common form of post translational modification

What do protein kinases do?

Catalyse the transfer of a phosphate group to other proteins. The terminal phosphate of ATP is transferred to specific R groups

What do protein phosphatases do?

Catalyse the reverse reaction (the removal of phosphate groups)

What does phosphorylation do?

Brings about a conformational change which can affect a protein's activity

What is the activity of cellular proteins like enzymes regulated by?

Phosphorylation

What two effects can phosphorylation have on a protein?

Some proteins are activated while others are inhibited

What does adding a new phosphate group do?

Adds a negative charge. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created