1.2 : the proteome Flashcards
golgi apparatus
a series of flattened membrane discs that are connected to allow molecules to move
lysosomes
organelle which contain hydrolases to digest protiens, lipids and nucleic acids
vesicles
transport material between membranes along microtubules
what is the proteome
the entire set of proteins expressed by the genome.
endoplasmic reticulum
network of membrane tubules
rough endoplasmic reticulum
ER with ribosomes of ins cytosolic face.
smooth endoplasmic reticulum
lack ribosomes
what does a eukaryotes small size affect
will have a smaller surface area to volume ratio meaning the plasma membrane is too small to carry out its function so they must have a system of internal membranes which increases area
why is the proteome larger
more than one protien can be expresses due to alternate RNA splicing and post translational modification
factors affecting protein expression
metabolic rate, cellular stress, disease, response to signalling molecules
cytosolic protiens
synthesis begins in the cytosolic ribosomes and the synthesis is then also completed there and the proteins will remain in the cytosol
what are phospholipids and how are they synthesized
they are a lipid that forms the main component of cell membrane and they are synthesized in the SER and inserted into membrane
joining amino acids
through a condensation reaction, and a water molecule is made by taking OH from COOH of 1 amino acid and then the H from NH2 to form a peptide bond
classes of amino acids
acidic (- charge) = R group with COOH
basic (+ charge) = R group with NH2
polar (slight charge, hydrophilic) = with OH group
hydrophobic (no charge) = with hydrocarbon
why does R group detrmine amino acid strcuture
in an aqueous solution, NH2 will gain a hydrogen whereas COOH will loose a hydrogen meaning because of this neutral charge it is up to R group to determine structure and function
what do R groups vary by
size, shape, charge, hydrogen bonding capacity, chemical reactivity
what are the 4 groups bonded in amino acids
amine = NH2
acid = COOH
hydrogen atom
variable R group
polypeptide structure
a polymer of amino acids
why are R groups important
they determine protein structure and allows ligan to bind which determines location within the cell
primary structure
a poly peptide, the sequence in which amino acids are synthesized , this determines proteins functions
secondary structure
when polypeptide is folded into alpha helix, beta pleated sheet or a turn.
hydrogen bonds hold these structures together
what are the interactions for a tertiary structure
hydrophobic, ionic bonds, LDFs, hydrogen bonds, disulphide bridges
what is a disulphide bridge
covalent bonds between R groups containing sulfur
quaternary structure
exist in proteins with 2 or more subunits e.g collagen, hemoglobin
what is a prosthetic group
a non protein unit that is tightly bound to a protein and is necessary for its function
what is proteolytic cleavage
this is a type of post translational modification that allows proteins to become active forms which will break the peptide bonds.
what is a signal sequence
this is a short stretch of amino acids at one end of a polypeptide that determines the eventual location of the protein
how are transmembrane protiens made
the synthesis begins in the cytosolic ribosomes, the transmembrane protiens made carry a signal that halts translation which directs the ribosomes synthesizing the protien to dock with the ER. translation continues after docking and protien is insterted into the membrane
how does the movement of protiens occur
translation continues and the protien is inserted into the ER membrane it is then transported by vesicles which bud off from ER and fuse with Golgi apparatus and undergo PTM
post translational modification process
this occurs when moving through the Golgi apparatus, enzymes will catalase the addition of carbohydrates to form glycoproteins which is the main modification, those vesicles which then leave the Golgi apparatus take the transmembrane protiens to plasma membrane and lysosomes and fuse them within the cell
the secretory pathway
the protiens for secretion are then translated in ribosomes on the RER then enter its lumen, the protiens then move through the Golgi apparatus and are packaged into secretory vesicles they then move and fuse with plasma membrane and are released out of the cell many as inactive precursors
what can influence R group interactions
tempreture and pH
what does increasing tempreture do to R group interactions
raising the tempreture disrupts the interactions that hold the protiens shape which ultimately causes the protiens to denature
how does pH affect R group interactions
pH only affects R groups that are acidic and basic, the normal ionic interactions become disrupted and charges are lost which gradually changes conformation and eventually denatures the enzyme
what is haemoglobin
iron containing oxygen transporting protien present in red blood cells
how to vesicles move
vesicles move along microtubules to other membranes
what are inactive precursors
inactive precursors are inactive versions of protiens that require protealytic cleavage to become active
tertiary structure
usually the final form, the poly peptide fold into a 3D shape and has conformation stabilised by R groups
what is a ligand
a substance that can bind to a protien R group that is not involved with protien folding
what does ligand binding change
ligand binding to a protein changes it conformation, this change in conformation changes the proteins function
what is allosteric
interactions which occur in spatially distinct sites
what does the binding of a substrate to an allosteric enzymes do
increases the affinity for all other active sites
why do allosteric enzymes increase biological importance
because of the increase in affinity, this means that the activity of allosteric enzymes can change greatly with a small change
what do allosteric protiens with many subunits show
cooperativity
what is cooperativity
the binding at one subunit alters the affinity of the remaining subunits
the second site in allosteris enzymes is
allosteric site
what is the allosteric site
a separate site where modulators bind to regulate the enzyme activity
what does the binding of a modulator do
changes the conformation and alters the affinity of the active site for the substrate
positive modulators
increase affinity (activation)
negative modulators
decrease affinity (inhibition)
what is cooperativity
changes of binding at one subunit alter the affinity at others
what shows cooperativity
oxygen and haemoglobin
what is the binding of oxygen affected by
increase in tempreture and decrease in pH
effect of pH on binding of oxygen
decrease in pH decreases the affinity for oxygen (moves to the right)
increase in pH increases affinity (moves to left )
effect of temperature on binding of oxygen
decrease in temperature increases affinity for oxygen ( shifts to left )
increase in temperature decreases affinity ( shifts to right)
addition or removal of a phosphate
a post translational method, the addition or removal of a phosphate causes conformational changes
what are protien kinase
catalyses the transfer of phosphate group to other protiens. it is the terminal phosphate of ATP that is transferred to a specific R group
protien phosphatase
catalyses the reverse reaction of phosphorylation
what can phosporylation affect
brings about conformational change that effects protien activity, it regulates cellular protiens
what does adding a phosphate do
adds a negative charge
what happens to unphosphorylysed protiens
there ionic interactions can be disrupted and new can be created
