Proteins Flashcards
What is the proteome?
The entire set of proteins expressed by a genome
Why is the proteome larger than the number of genes, particularly in eukaryotes?
Because more than 1 protein can be produced from a single gene as a result of alternative RNA splicing.
—— —— genes are expressed as proteins in a particular cell type
Not all
Non coding RNA genes?
Genes that do not code for proteins. Includes those that are transcribed to produce RNA, tRNA and rRNA 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 condition.
Some factors affecting the set of proteins expressed by a given cell type are?
- The metabolic activity of the cell
- cellular stress
- The response to signalling molecules
- diseased VS healthy cells.
Eukaryotic cells have a…
System of internal membranes, which increase the total area of the membrane.
Because of their size, eukaryotes have a relatively ——— surface area to volume ratio
Small
The plasma membrane of eukaryotic cells is too small an area to carry out…
All the vital functions carried out by membranes.
The ER?
Forms a network of membrane tubules continuous with the nuclear membrane.
The RER?
Ribosomes on its cystolic face
The SER?
Lacks ribosomes
The Golgi apparatus?
Series of flattened membrane discs.
Lysosomes?
Membrane-bound organnelles containing a variety of hydrolyses that digest proteins, lipids, nucleic acids and carbohydrates.
Vesicles?
Transport materials between membrane compartments.
Where are lipids and proteins synthesised?
In the ER
Where specifically are lipids synthesised and inserted?
Synthesised in the SER and inserted into its membrane.
Where does the synthesis of all proteins begin?
Cystolic ribosomes.
What is synthesised in the cystolic ribosomes?
Cystolic proteins and they remain in the cytosine.
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 the RER.
What is a signal sequence?
Short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.
What continues after docking?
Translation continues after docking and the protein is inserted into the membrane of the ER
What happens 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 as proteins move through the Golgi apparatus?
They undergo post-translational modification.
How do molecules move through the Golgi discs?
In 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 the carbohydrates.
What is the major modification?
The addition of carbohydrate groups
Where do vesicles that leave the Golgi apparatus take proteins?
To the plasma membrane and lysosomes.
What do vesicles move along?
Vesicles move along microtubules to other membranes and fuse with them within the cell.
Where are secreted proteins translated and where do they enter?
In ribosomes on the RER and enter its lumen.
Examples of secreted proteins?
Peptide hormones and digestive enzymes.
The secreted proteins move through the Golgi apparatus and are then…
Packages into secretory vesicles. These vesicles move to and fuse with the plasma membrane, releasing proteins out of the cell
Proteolytic cleavage?
Another type of post translational modification.
Why secreted proteins require proteolytic cleavage?
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins.
Examples of secreted proteins that require proteolytic cleavage?
Digestive enzymes
What are proteins?
Polymers of amino acid monomers.
Amino acids are linked by —— —— to form polypeptides
Peptide bonds.
Amino acids have the same basic structure, differing only in?
The R groups present
R groups of amino acids vary in…
Size, shape, charge, hydrogen bonding capacity and chemical reactivity.
Basic amino acids?
Hydrophilic and the key component of their R group is an amine group (+vely charged at pH7)
Acidic amino acids
Hydrophilic and the key component of their R group is a carboxylic acid group (-vely charged at pH7)
Polar amino acids?
Hydrophilic and the key component of their R group are hydrophilic groups such as carobonyl, hydroxyl or amine groups.
Hydrophobic amino acids?
Non polar and the key component of their R group is a hydrocarbon group.
The wide range of functions carried out by proteins results from the…
Diversity of R groups.
Primary structure?
The sequence in which the amino acids are synthesised into the polypeptide.
Secondary structure?
Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure.
Regions of secondary structure?
- Alpha helices
- Parallel or antiparallel beta pleated sheets
- Turns
Tertiary structure?
Polypeptide folds into a tertiary structure.
Tertiary structure is stabilised by?
- Hydrophobic interactions
- Ionic bonds
- LDFs
- Hydrogen bonds
- Disulphide bridges
What are disulphide bridges?
Covalent bonds between R groups containing sulfur.
Quarternary structure?
Exists in proteins with 2+ connected polypeptide subunits.
It describes the spatial arrangement of the subunits
Prosthetic groups?
A non-protein unit tightly bound to a protein and necessary for its function.
The ability of Haemoglobin to bind oxygen is dependant upon the…
Non-protein haem group.
Interactions of the R groups can be influenced by?
Temperature and pH.
What does increasing temperature do to interactions of R groups?
Disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.
Effect of pH on charges of acidic and basic 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 is a ligand?
Substance that can bind to a protein.
What type of R groups allow ligand binding?
R groups not involved in protein folding can allow binding to ligands.
Bonding sites will have — — — — to the ligand
Complementary shape and size
What happens as a ligand binds to a protein binding site?
The conformation of the proteins changes.
What does the change of conformation of a protein cause?
Functional change in the protein.
Allosteric interactions occur between?
spatially distinct sites
Why are allosteric interactions biologically important?
Because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.
Many allosteric proteins consist of…
Multiple subunits.
Cooperativity?
Allosteric proteins with multiple subunits show cooperativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits.
Allosteric enzymes contain a second type of active site called …
An allosteric site.
The bonding and release of oxygen in haemoglobin shows…
Cooperativity.
Changes in binding of oxygen at one subunit alter the affinity of?
The remaining subunits for oxygen.
Effect of a decrease in pH and increase in temperature on binding of oxygen
Lowers affinity of Haemoglobin for oxygen so the binding of oxygen is reduced.
Effect of an increase in pH and decrease in temperature in actively respiring tissue?
Will reduce binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue.
Modulators?
Regulate the activity of the enzyme when they bind to the allosteric site.
Following binding of a modulator, the conformation of the enzyme changes and this…
Alters the affinity of the active site for the substrate.
Positive modulators?
Increase enzymes affinity for the substrate
Negative modulators?
Reduce the enzymes affinity for the substrate.
The addition or removal of phosphate can cause…
Which is a common form of —— ——
Reversible conformational change in proteins.
Post translational modification.
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 brings about…
Conformational changes which can affect a proteins activity.
The activity of many cellular proteins such as — and —— is regulated by phosphorylation.
Enzymes and receptors
Some proteins are activated by phosphorylation while other are ——
Inhibited.
Adding a phosphate group adds…
Negative charges.
Phosphorylation- Ionic interactions in the unphosphorylated protein can be …
Disrupted and new ones created.
The binding of a substrate molecule to one active site of an allosteric enzyme, does what?
increases the affinity of the other active sites for binding of subsequent substrate molecules.
