1.2 Proteins Flashcards
What is the proteome?
The proteome is the entire set of proteins expressed by the genome.
Why is the proteome larger than the number of genes?
The proteome is larger then the number of genes, particularly in eukaryotes, because more than one protein can be produced from a single gene as a result of alternative RNA splicing.
Are all genes expressed as proteins?
Not all genes are expressed as proteins in a particular cell type.
Genes that do not code for proteins
Genes that do not code for proteins 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.
Can the set of proteins expressed vary?
The set of proteins expressed by a given cell type can vary over time and under different conditions.
What factors effect the set of proteins produced by a given cell type?
- The metabolic activity of the cell
- Cellular stress
- The response to signalling molecules
- Diseased versus healthy cells
Why do eukaryotic cells have a system of internal membranes?
Eukaryotic cells have a system of internal membranes, which increases the total area of membrane.
Why do eukaryotes have a small surface area to volume ratio and what does this mean for them?
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 carried out by membranes.
What does the ER do?
The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane.
What is the Golgi apparatus?
The Golgi apparatus is a series of flattened membrane discs.
What are lysosomes?
Lysosomes are membrane bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates.
What do vesicles do?
Vesicles transport materials between membrane compartments.
Where are lipids and proteins synthesised?
Lipids and proteins are synthesised in the ER.
What is the difference between the RER and the SER?
Rough ER (RER) has ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes.
Where are lipids synthesised?
Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane.
Where does the synthesis of all proteins begin?
The synthesis of all proteins begins in cytosolic ribosomes.
Where are cytosolic proteins synthesised?
The synthesis of cytosolic proteins is completed in cytosolic ribosomes, and these proteins remain in the cytosol.
Transmembrane proteins
Transmembrane proteins 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 signal sequence is 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 once proteins are in the ER?
Once proteins are in the ER, the 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?
As proteins move through the Golgi apparatus they undergo post-translational modification.
How to proteins move through the Golgi apparatus?
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 the major post-translational modification and how does it work?
The addition of carbohydrate groups is the major modification.
Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.
What happens to vesicles that leave the Golgi apparatus?
Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes.
How to vesicles move?
Vesicles move along microtubules to other membranes and fuse with them within the cell.
Secreted proteins
Secreted proteins are translated on ribosomes in the RER and enter its lumen.
The proteins move through the Golgi apparatus and are the packaged into secretory vesicles.
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell.
Give two examples of secreted proteins
- Peptide hormones
2. Digestive enzymes
Why is proteolytic cleavage required?
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins.
What is proteolytic cleavage?
Proteolytic cleavage is another type of post-translational modification.
Give an example of proteins that require proteolytic cleavage
Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.
What does amino acid sequence determine?
Amino acid sequence determines protein structure.
Proteins are polymers of amino acid monomers.
What forms polypeptides?
Amino acids are linked by peptide bonds to form polypeptides.
How do amino acids differ from each other?
Amino acids have the same basic structure, differing only in the R group present.
How do R groups of amino acids vary?
R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.
How can amino acids be classified?
Amino acids are classified according to their R groups: basic (positively charged), acidic (negatively charged), polar, or hydrophobic (non-polar).
Basic (positively charged) amino acids
Their R groups will be positively charged (contain a +).
Acidic (negatively charged amino acids
Their R groups will be negatively charged (contain a -).
Polar amino acids
Their R groups will contain CO, OH or NH.
Hydrophobic (non-polar) amino acids
Their R groups will contain H and C (and can have N or S).
Why do proteins have a wide range of functions?
The wide range of functions carried out by proteins results from the diversity of R groups.
Primary protein structure
The primary structure is the sequence in which the amino acids are synthesised into the polypeptide.
Secondary protein structure
Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure - alpha helices, parallel or anti-parallel beta-pleated sheets, or turns.
Tertiary protein structure
The polypeptide folds into a tertiary structure.
What stabilises the folded polypeptide?
This conformation is stabilised by interactions between R groups: Hydrophobic interactions Ionic bonds London dispersion forces Hydrogen bonds Disulphide bridges
What are disulphide bridges?
Disulphide bridges are covalent bonds between R groups containing sulphur.
Quaternary protein structure
Quaternary structure exists in proteins with two or more connected polypeptide subunits.
It describes the spatial arrangement of the subunits.
What is a prosthetic group?
A prosthetic group is a non-protein unit tightly bound to a protein and necessary for its function.
Give an example of a prosthetic group
The ability of haemoglobin to bind to oxygen is dependent upon the non-protein haem group.
What can influence interactions between R groups?
Interactions of the R groups can be influenced by temperature and pH.
How does increasing the temperature affect interactions between R groups?
Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.
What affects the charges on R groups?
The charges on acidic and basic R groups are affected by pH.
How do changes in pH influence interactions between R groups?
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 does ligand binding affect?
Ligand binding changes the conformation of a protein.
What is a ligand?
A ligand is a substance that can bind to a protein.
What do R groups not involved in protein folding do?
R groups not involved in protein folding can allow binding to ligands.
How does ligand binding work?
Binding sites will have complementary shape and chemistry to the ligand.
As a ligand binds to the protein-binding site the conformation of the protein changes.
This change in conformation causes a functional change in the protein.
What are allosteric interactions?
Allosteric interactions occur between spatially distinct sites.
What structure do many allosteric proteins have?
Many allosteric proteins consist of multiple subunits (have a quaternary structure).
Co-operativity in allosteric proteins
Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits.
The binding of a substrate molecule to one active site of a allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules.
Why is co-operativity in allosteric proteins important?
This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.
What site (other than the active site) do allosteric enzymes contain?
Allosteric enzymes contain a second type of site, called an allosteric site.
What do modulators do?
Modulators regulate the activity of the enzyme when they bind to the allosteric site.
What happens after a modulator binds?
Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate.
Positive and negative modulators
Positive modulators increase the enzyme’s affinity for the substrate, whereas negative modulators reduce the enzyme’s affinity.
Co-operativity in haemoglobin
The binding and release of oxygen in haemoglobin shows co-operativity.
Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen.
What is the effect and physiological importance of pH and temperature on the binding of oxygen?
A decrease in pH or an increase in temperature lower 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.
Reversible binding of phosphate
The addition or removal of phosphate can cause reversible conformational change in proteins.
This is a common form of post-translational modification.
What do protein kinases and phosphatases do?
Protein kinases catalyse the transfer of a phosphate group to other proteins.
The terminal phosphate of ATP is transferred to specific R groups.
Protein phosphatases catalyse the reverse reaction.
Phosphorylation
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.
What effect does adding a phosphate group have?
Adding a phosphate group adds negative charges.
Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.
