Proteonomics Flashcards
What is a genome?
The genome is all of the hereditary information encoded in DNA
What is the proteome
the proteome is the entire set of proteins expressed by a genome
The proteome is larger than the number of genes, particularly in eukaryotes, because of?
Alternative RNA splicing (one gene many proteins)
Factors affecting the set of proteins expressed by a given cell type?
metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells
What are genes not coding for a protein called? examples?
non-coding RNA genes
tRNA, rRNA and RNA
Why do eukaryotic cells have a system of internal membranes?
to increase total area of membranes and provides a larger surface area for vital functions to take place
Describe the ER
forms a network of membrane tubules continuous with the
nuclear membrane
Describe the Golgi apparatus
series of flattened membrane discs
Describe lysosomes and their function
membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
Role of vesicles?
transport materials between membrane compartments
What is synthesised in the ER?
Lipids and proteins
Synthesis of lipids?
synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
Where does the synthesis of all proteins start?
cytosolic ribosomes
Pathway of synthesis for cytosolic proteins?
Completed in the cytosolic ribosome and remain in the cytosol
Examples of cytosolic proteins?
Nucleus, mitochondria and chloroplasts
Pathway of synthesis for transmembrane protein
Cytosolic ribosome
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
How do proteins travel 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 from the Golgi Apparatus?
they undergo post-translational modification
What are examples of post-translational modifications
addition of carbohydrate groups is the major modification
phosphorylation and a disulphide bond
Vesicles that leave the Golgi apparatus take proteins where?
plasma membrane and lysosomes
How do vesicles travel along a cell?
move along microtubules to other membranes and fuse with them within the cell
Pathway of secreted proteins
Secreted proteins are translated in ribosomes on the RER and enter its lumen
The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
Many secreted proteins are synthesised as inactive precursors and require what to produce active proteins?
proteolytic cleavage
Examples of secreted proteins?
insulin and trypsin
Amino acids are linked by?
peptide bonds to form polypeptides
What four R groups are present on amino acids
basic (positively charged); acidic (negatively charged); polar; hydrophobic
Diversity of R groups lead to
The wide range of functions carried out by proteins
What is primary structure?
the sequence in which the amino acids are synthesised into the polypeptide
What is secondary structure and examples?
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 structure?
folded polypeptide
How is tertiary structure stabilised?
R group interactions like hydrophobic interactions;
ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges
What is quaternary structure?
proteins with two or more connected polypeptide subunits
What is a prosthetic group?
non-protein unit tightly bound to a protein and necessary for its function
How can pH and temperature influence R groups?
Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured.
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 can bind to a ligand?
R groups not involved in protein folding
Describe binding site for a ligand?
complementary shape and chemistry to the ligand
What happens when a ligand binds?
conformation of the protein changes which causes a functional change in the protein
Allosteric interactions occur?
between spatially distinct sites
Structure of many allosteric proteins?
consist of multiple subunits (have quaternary structure)
Allosteric proteins with multiple subunits show co-operativity in binding which means?
changes in binding at one subunit alter the affinity of the remaining subunits
Allosteric enzymes contain a second type of site called?
an allosteric site
Function of modulators?
Modulators regulate the activity of the enzyme when they bind to the allosteric site
What happens when a modulator binds?
conformation of the enzyme changes and this alters
the affinity of the active site for the substrate. Negative modulators reduce the enzyme’s affinity for the substrate and positive modulators increase the enzyme’s affinity for the substrate.
Example of protein that shows co-operativity?
haemoglobin
Describe structure of haemoglobin?
demonstrates quaternary structure in that is made up of four polypeptide subunits, each of which contain a haem group capable of binding a molecule of oxygen
What are the two main factors that affect haemoglobin’s ability to bind to oxygen
temperature - as temperature increases, affinity for oxygen decreases, curve shifts right
pH - as pH decreases, affinity for oxygen decreases, curve shifts right
The addition and removal of phosphate can cause?
reversible conformational change in proteins
Function of kinases?
catalyse the transfer of a phosphate group to other proteins
the terminal phosphate of ATP is transferred to?
specific R groups
Function of phosphotase
catalyses dephosphorylation
What does adding a phosphate group do to amino acids?
adds negative charge
How to regulate the activity of many cellular proteins, such as enzymes and receptors
Phosphorylation brings about conformational changes, which can affect a protein’s activity
What 2 outcomes can happen by phosphorylation of a protein?
Some proteins are activated by phosphorylation while others are inhibited
