Advanced Higher Biology 1.2

What is a common form of post-translational modification

Addition or removal of a phosphate

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

What is the function of genes NOT expressed as proteins in a particular cell type

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

The set of proteins expressed by a given cell type can vary over time and under different conditions. What factors affect this?

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

Eukaryotic cells have a system of internal membranes, why?

They increase the total area of membrane

Why is the plasma membrane of eukaryotic cells is too small an area to carry out all the vital functions carried out by membranes?

Because of their size, eukaryotes have a relatively small surface area to volume ratio.

The endoplasmic reticulum (ER)

forms a network of membrane tubules continuous with the nuclear membrane

The Golgi apparatus

A series of flattened membrane discs

Lysosomes

Membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates

Vesicles

Transport materials between membrane compartments

Rough ER (RER)

Has ribosomes on its cytosolic face

smooth ER (SER)

L acks ribosomes. Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane

Where does the synthesis of all proteins begin?

In the cytosolic ribosomes. The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol.

Transmembrane proteins carry a signal sequence, what does this sequence do?

It halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER.

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.

How are proteins transported in the ER?

Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus

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

They undergo post-translational modification

Molecules move through the Golgi discs in vesicles that ...........

..............bud off from one disc and fuse to the next one in the stack

What is a major modification?

The addition of carbohydrate groups

What do vesicles that leave the Golgi apparatus do?

They take proteins to the plasma membrane and lysosomes

How do vesicles move to other membranes and fuse with them within the cell?

along microtubules

What happens to secreted proteins?

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

Name examples of secreted proteins

Peptide hormones and digestive enzymes

Where are the proteins packaged into secretory vesicles?

In the Golgi apparatus

How are the proteins released out of the cell?

These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell

How are many secreted proteins synthesised?

As inactive precursors and require proteolytic cleavage to produce active proteins

What is required to produce an active protein from an inactive precursor?

Proteolytic cleavage

What is proteolytic cleavage?

Another type of posttranslational modification.

Give an example of a a group of proteins that requires proteolytic cleavage to become active

Digestive Enzymes

What determines protein structure?

Amino Acid Sequence

Name the monomers that make up the protein polymer

Amino Acids

What bond links amino acids in a polypeptide?

Peptide Bond

What differs between amino acids?

The R Group

How do R groups differ?

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

Basic Amino Acids

Have amino groups in their side chains that are generally positive in charge

Acidic Amino Acids

have side chains with a carboxylate group and are generally negatively charged

Polar Amino Acids

The end of the R group contains atoms that are far apart in electronegativity eg -OH

Hydrophobic Amino Acids

The end of the 'R' group contains atoms which are not far apart electronegatively e.g. CH3 They do not form Hydrogen bonds with water

What accounts for the wide range of functions carried out by proteins?

The diversity of R groups

The primary structure of a protein is....

The sequence in which the amino acids are synthesised into the polypeptide

What bond is present in primary protein structure?

Peptide bond

Secondary Protein Structure....

alpha helices, parallel or antiparallel beta-pleated sheets, or turns

What bonds form in secondary protein formation?

Hydrogen bonds

What happens during tertiary protein structure?

This conformation is stabilised by interactions between R groups

What type of bonds exist in tertiary protein structures?

hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges

What are disulphide bridges/bonds?

Covalent bonds between R groups containing sulfur.

What happens during quaternary protein structure?

Proteins with two or more connected polypeptide subunits and 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 the ability of haemoglobin to bind oxygen dependent upon?

The non-protein haem group.

What can interactions of the R groups be influenced by?

Temperature and pH

What does increasing temperature do to protein structure?

It disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured

What is affected by pH in proteins?

The charges on acidic and basic R groups

What happens to protein structure as pH increases or decreases from the optimum?

The normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured.

What is a ligand?

A substance that can bind to a protein

What can allow binding to ligands?

R groups not involved in protein folding

What will binding sites have?

Complementary shape and chemistry to the ligand

As the ligand binds to the protein-binding site, what happens to the protein?

The conformation of the protein changes

What does a change in protein conformation cause?

A functional change in the protein

Where does allosteric interactions occur?

Allosteric interactions occur between spatially distinct sites

What does the binding of a substrate molecules to one active site of an allosteric enzyme cause?

It increases the affinity of the other active sites for binding of subsequent substrate molecules.

What is the biological significance of allosteric enzymes?

This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.

What do many allosteric proteins consist of?

Multiple subunits (have quaternary structure)

What do many allosteric enzymes with multiple subunits show?

Co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits

What do many allosteric enzymes contain?

A second type of site, called an allosteric site

What regulates the activity of the enzyme when they bind to the allosteric site?

Modulators

What occurs following the 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 co-operativity in haemoglobin?

The binding and release of oxygen in haemoglobin shows co-operativity

What does changes in binding of oxygen at one subunit do to the remaining subunits?

It alters the affinity of the remaining subunits for oxygen

Describe the influence and physiological importance of temperature and pH on the binding of oxygen

A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.

What will reduce the binding of oxygen to haemoglobin

Reduced pH and increased temperature in actively respiring tissue

What does reduced pH and increased temperature in actively respiring tissue cause?

promoting increased oxygen delivery to tissue

What does the addition or removal of phosphate cause?

Reversible conformational change in proteins

What do protein kinases catalyse?

The transfer of a phosphate group to other proteins

What do protein phosphatases do?

Catalyse the reverse reaction

What does phosphorylation do?

Brings about conformational changes, which can affect a protein's activity

What are some proteins activated or inhibited by?

Phosphorylation

What does adding a phosphate add?

Adds negative charges.