1.2 Proteins Flashcards
what is the genome
all of the genetic material in a cell including DNA and RNA
what is the proteome
the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time
why is the proteome larger than the genome
more than one protein can be produced from a single gene as a result of alternative splicing
what are genes which do not code for proteins 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 sets of proteins expressed over a given cell type…
can vary over time and under different conditions
which factors affect the set of proteins expressed by a given cell type
metabolic activity rate of the cell cellular stress the response to signalling molecules diseased versus healthy cells
what does eukaryotic cells having a system of internal membranes result in
increase in total area of membrane
because of their size, eukaryotes have a…
small surface area to volume ratio
what does eukaryotes having a small surface area to volume ratio mean
the plasma membrane of eukaryotic cells is too small an area to carry out all the vital functions carried out by membranes
what does the endoplasmic reticulum form
network of membrane tubules continuous with the nuclear membrane
what is the endoplasmic reticulum
a network of membranes found throughout the cell and connected to the nucleus
the membranes are slightly different from cell to cell and a cell’s function determines the size and structure of the ER
what are the different types of ER
rough ER
smooth ER
what is the difference between the rough ER and the smooth ER
they have the same types of membranes but different shapes
rough ER looks like sheets or disks of bumpy membranes while smooth ER looks more like tubes
rough ER is called rough because it has ribosomes attached to its cytosilic face
what is the function of the ER
it is mainly responsible for the transportation of proteins and other organelles, which includes lysosomes, Golgi apparatus, plasma membrane etc
they provide the increased surface area for cellular reactions
they help in the formation of the skeletal framework
they play a vital role in the synthesis of proteins, lipids, glycogen and other steroids like cholesterol, progesterone, testosterone, etc
what is the Golgi apparatus
a series of flattened membrane discs found in most cells
what is the function of the Golgi apparatus
to process and bundle macromolecules like proteins and lipids as they are synthesised within the cell
it is sometimes compared to a post office inside the cell since one major function is to modify, sort, and package proteins to be secreted
which cells contain more sets of Golgi apparatus than other cells
specialised secretory cells
what is the Golgi apparatus made up of
sacs called cisternae
usually 5 to 8 cisternae are present in one Golgi apparatus, but 60 has been observed by scientists
what do the bundles of sacs in Golgi apparatus have
five distinct and functional regions, and each region has different enzymes to help it modify the contents, depending on where they are to end up
why is the Golgi apparatus important
transports lipids throughout the cell and the creation of lysosomes
what are lysosomes
membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids, and carbohydrates
what is the importance of lysosomes
lysosomes are important in different aspects of organisms which include: intra-cellular digestion cell renovation apoptosis prevent the entry of harmful agents into the cell fertilisation kill infection health disorders
what are vesicles
transport material between membrane compartments
what are membranes composed of
a phospholipid bilayer with proteins and is represented by the fluid mosaic model
where are lipids synthesised
in the SER and inserted into its membrane
where does the synthesis of all protein begin
in cytosolic ribosomes
where is the synthesis of cytosolic proteins completed
in cytosolic ribosomes and the proteins remain in the cytosol
how does the synthesis of all proteins begin
by transcription of the gene encoding that protein and translation of the mRNA (after splicing if necessary) on free ribosomes within the cytoplasm
where are proteins located
some are intracellular (remain inside the cell)
other are located in/on the membrane
others still are secreted extracellularly
what is a signal sequence
a short stretch of amino acids at one end of the polypeptide that determines the eventual location of that protein in a cell
what is the signal peptide that sends a protein into the endoplasmic reticulum during translation
a series of hydrophobic amino acids, usually found near the beginning of the proteins
what does a signal sequence do
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 stage 1 of synthesis membrane components by RER
proteins are synthesised by ribosomes in the cytoplasm
what is stage 2 of synthesis membrane components by RER
a signal protein (signal recognition particle) from the membrane binds to the ribosome and stops translation
what is stage 3 of synthesis membrane components by RER
the SRP (signal recognition particle) binds to a receptor which then directs the ribosome to attach to the endoplasmic reticulum forming the RER
what is stage 4 a) of synthesis membrane components by RER
translation restarts and the protein is now inserted into membrane of the ER
what is stage 4 b) of synthesis membrane components by RER
once translation finished, the ribosome detaches
what happens once the proteins are in the RER
they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
as proteins 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 on the stack
enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates
the addition of carbohydrate groups is the major modification
vesicles move…
along microtubules to other membranes and fuse them within the cell
where are secreted proteins translated
in ribosomes on the RER and enter its lumen
examples of secreted proteins
peptide hormones
digestive enzymes
what happens when the proteins are in the Golgi apparatus
they 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
what are many secreted proteins synthesised as
inactive precursors and require proteolytic cleavage to produce active proteins
what is proteolytic cleavage
another type of post-translational modification
example of secreted proteins
digestive enzymes that requires proteolytic cleavage to become active
another is insulin
proteins are polymers of…
amino acid monomers
what are enzymes linked by
peptide bonds to form polypeptides
amino acids have the same basic structure, differing only in the…
R group present
what can R groups vary in
size shape charge hydrogen bonding capacity chemical reactivity
amino acids are classified according to their R groups
what are they
basic (positively charges)
acidic (negatively charged
polar (hydrophilic)
hydrophobic (non-polar)
what does the diversity of amino acid R groups result in
wide range of functions carried out by proteins
what is the primary structure
the sequence in which the amino acids are synthesised into the polypeptide
what is the secondary structure
hydrogen bonding along the backbone of the protein strand results in regions of secondary structure
these structures are:
alpha helices
parallel or antiparallel beta pleated sheets
turns
what is the tertiary structure
the polypeptide folds into a tertiary structure
this conformation is stabilised by interactions between R groups such as:
hydrophobic interactions
ionic bonds
london dispersion forces
hydrogen bonds
disulfide bridges - covalent bonds between R groups containing sulfur
what are disulfide bridges
covalent bonds between R groups containing sulfur
what is the quaternary structure
quaternary structure exists in proteins with two or more connected polypeptide subunits
it describes the spatial arrangement of the subunits
what are prosthetic groups
a non-protein unit tightly bound to a protein and necessary for its function e.g. heamoglobin
what is heamoglobin
iron-containing oxygen transporting protein present in the red blood cells of almost all vertebrates
what is the ability of heamoglobin to bind to oxygen depend on
the non-protein heam group
what can the interactions of the R group be influenced by
temperature and pH
what does increasing temperature do
disrupts the interactions that hold the protein in shape
the protein begins to unfold, eventually becoming denatured
how are the charges on acidic and basic R groups affected by pH
as the 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 subunit substance that can bind to a protein
R groups not involved in protein folding….
can allow binding to ligands
binding sites will have complimentary shape and chemistry to the ligand
what happens when a ligand binds to a protein-binding site
changes the conformation of the protein
what does allosteric mean
interactions which occur between spatially distinct sites
what is the process of co-operation
the binding of a substrate molecule to one active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules
this is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration
what do allosteric enzymes consist of
multiple subunits which means they have a quaternary structure
what do allosteric proteins with multiple subunits show
co-operativity in binding
what does co-operativity in binding mean
changes in binding at one subunit alter the affinity of the remaining subunits
what is the second type of site in allosteric enzymes called
allosteric site
what does a modulator do
regulate the activity of the enzyme when they bind to the allosteric site
what happens when a modulator binds
the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
what is a positive modulator
increases the enzyme’s affinity for the substrate
what is a negative modulator
reduces the enzyme’s affinity for the substrate
what does the binding and release of oxygen in haemoglobin show
co-operativity
what alters the affinity of the remaining subunits for oxygen
changes in binding of oxygen at one subunit
what is the binding of oxygen to haemoglobin affected by
pH and temperature
what is the effect of decreasing pH on the affinity of haemoglobin for oxygen
decreases affinity for oxygen
what is the effect of increasing the pH on the affinity of haemoglobin for oxygen
increasing pH increases affinity for oxygen
what is the effect of decreasing temperature on the affinity of haemoglobin for oxygen
increases affinity for oxygen
what is the effect of increasing the temperature on the affinity of haemoglobin for oxygen
decreases affinity for oxygen
what does a decrease in pH or an increase in temperature mean
it lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced
what does reduced pH and increased temperature in actively respiring tissue mean
it will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue
what can the addition or removal of phosphate cause
reversible conformational changes in proteins
this is a common form of post-translational modification
what does protein kinases catalyse
the transfer of a phosphate group to other proteins
which phosphate is being transferred to specific R groups in the protein
the terminal phosphate of ATP
what does protein phosphatases catalyse
the reverse reaction of protein kinases
what does phosphorylation bring 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
what happens to proteins by phosphorylation
some are activated while others are inhibited
what does adding a phosphate group result in
adding charges
ionic interactions in the unphosphorylated protein can be disrupted and new ones created
