1.2 - The Proteome Flashcards
Unit One
Proteome definition
The entire set of proteins expressed by a genome
Size comparison of proteome and gene number
The proteome is drastically larger than the number of genes in the genome, particularly in eukaryotes, because more than one protein can be produced from each gene due to alternative splicing, and post translational modifications.
What do non-coding RNA genes produce
tRNA, rRNA and RNA molecules which control expression of other genes
Are all genes expressed as proteins
No, some are expressed as RNA molecules
Full name of SER
Smooth Endoplasmic Reticulum
Full name of RER
Rough Endoplasmic Reticulum
What is the purpose of the intracellular membrane
To increase the surface area to volume ratio, to allow for vital cell functions to take place
What is the difference between the RER and the SER
The rough endoplasmic reticulum has ribosomes and produces proteins while the smooth endoplasmic reticulum does not have proteins and produces lipids (fats)
Function of the endoplasmic reticulum
The ER creates a network of membrane tubules continuous with the nuclear membrane to produce lipids and proteins
Golgi apparatus
The cell organelle which receives proteins and lipids from the ER. Consisting of a series of flattened discs to process, carry outpost translational modification and send those modified proteins and lipids off to their destination
Lysosome definition
Membrane bound organelles containing hydrolases that digest proteins, lipids, carbohydrates and nucleic acids
Hydrolase definition
Enzymes that use water to break down substrates such as proteins, fats, nucleic acids and carbohydrates
What is the name of genes that don’t code for proteins
Non-coding RNA genes
Factors affecting proteins expressed in a cell
Metabolic activity, cellular stress, response to signalling molecules or disease
Vesicle definition
Cell organelles which transport materials between membrane compartments
What are intracellular membranes
They are membranes inside a cell which increase the cell membrane surface area to ratio
Lysosome pH
Acidic to allow for optimum enzyme activity
What is cytosol
Cytosol is part of the cytoplasm where the new cell organelles are suspended
Process of producing a cytosolic protein
- mRNA will leave the nucleus and travel to a ribosome in the cytosol
- the ribosome will remain in the cytosol
- a polypeptide chain will then be produced by the ribosome
- this will then fold into shape and become a protein will remain in the cytosol
Process of producing a transmembrane protein
- an mRNA strand travels from the nucleus to the cytosolic ribosome
- the cytosolic ribosome produces a polypeptide chain containing a signal sequence
- the cytosolic ribosome then travels to the endoplasmic reticulum and docks with it forming the RER
- translation then continues at the RER and is then packaged into a vesicle to be transported to the Golgi apparatus
- the Golgi apparatus then processes and carries out post translational modification
- then the transmembrane protein is sent out to its destination
How do proteins travel away from the rough endoplasmic reticulum
They use vesicles which bud off the endoplasmic reticulum and fuse to the Golgi apparatus
signal sequence definition
The sequence of amino acids that informs the ribosome that it needs to dock with the endoplasmic reticulum
Destination of cytosolic ribosomes
Nucleus, mitochondria, chloroplasts
Destination of transmembrane proteins
Plasma membranes, secretory vesicles, lysosomes
Secretory definition
Means to be sent out the cell
Post Translational Modification
Where a molecule or group is added to the protein in the Golgi apparatus after translation
What is the major post translational modification
The addition of a carbohydrate
How do vesicles travel to different locations
By using the micro tubules of the cytoskeleton
Examples of secreted proteins
Peptide hormones and digestive enzymes
What do secretory vesicles do
They leave the Golgi complex and fuse with the plasma membrane - releasing the protein out of the cell
What happens after a protein moves out of the Golgi apparatus
Its packaged into a secretory vesicle and transported to the plasma membrane, a lysosome or transported out of the cell
Proteolytic cleavage definition
A form of post translational modification where a section of a polypeptide chain is removed from a protein to activate the protein
Reason for proteolytic cleavage
TO activate a protein at the correct time
Example of proteolytic cleavage
Digestive enzymes
Amino acids definition
The smaller monomer molecules which make up a protein
Proteins definition
Large polymer molecules consisting of many amino acids linked by peptide bonds
Amino Group
NH2 in isoelectric
Carboxyl group
C=OOH
Peptide bond
C=ONH
Amino acid structure
NH2-CHR-C=OOH
Different types of amino acids
Basic, acidic, hydrophobic, polar
Basic amino acids
Amino acids with a positive charge on the R group
Acidic amino acids
Amino acids with a negative charge on the R group
Polar amino acids
Amino acids which are hydrophilic and contain functional groups such as carbonyl, hydroxyl or amine groups
Hydrophobic amino acids
Amino acids which are non polar and have an R group consisting of large numbers of carbon and hydrogen
Protein structure primary sequence definition
The sequence of amino acids that are synthesised into a polypeptide chain
How is the secondary structure formed
By some amino acids forming hydrogen bonds with other amino acids peptide bonds
secondary structure types
alpha helix, b-sheet, turns
secondary structure definition
the polypeptide chain folded into a specific shape using hydrogen bonding
types of B-sheet
parallel - 2.5 beta sheets
antiparallel - two beta sheets
turns definition
the third type of secondary structure which changes the direction of the polypeptide chain and connect other secondary structures
tertiary structure definition
the structure of a protein influenced by the R groups of the amino acids
tertiary structure types
ionic, hydrophobic, hydrogen bonding, disulphide bridge, London dispersion forces
Ionic tertiary structure
creates electrostatic forces of attraction due to oppositely charged R groups
Hydrophobic tertiary structure
creates a cluster on the interior of the protein and affects protein solubility
hydrogen bond tertiary structure
an electrostatic attraction between a hydrogen atom and N. O. F. on a protein
Disulphide bridge tertiary structure
a covalent bond between two thiol (SH) groups on a protein
London dispersion forces tertiary structure
a temporary attractive force which causes dipoles on a protein
Quaternary structure of proteins
the number and spatial arrangement of polypeptide subunits in a protein
prosthetic groups
a non protein unit tightly bound to a protein, which is necessary for its function
pH and temperature effect on a protein
denaturation
how does pH denature
it changes the charges of the R groups of the amino acids and means normal ionic interactions are altered
how does temperature denature
it disrupts the interactions that holds the protein in shape
ligand definition
a substance that can bind to a protein
how do ligands bond to proteins
R groups not involved in protein folding and structure bond with ligands
what is a conformational change
a change in the shape and function of a protein due to a ligand binding to the protein
allosteric proteins definition
proteins with quaternary structure which allow ligands to bond to spatially distinct sites away from the active site, allowing for conformational change to occur within the protein
cooperativity
when a protein with quaternary structure on one ligand binds to the active site of one sub unit it changes the affinity of all the active sites and allows the ligand to bind to the active site
examples of cooperativity
haemoglobin
rules for temperature and pH on haemoglobin saturation
as pH increases and temperature decreases saturation increases
as pH decreases and temperature increases saturation decreases
allosteric enzymes definition
an enzyme which changes conformation upon binding to a modulator at a secondary binding sites
negative modulator
a molecule binding to the allosteric site in a protein causing conformational change to the protein decreasing active site affinity
positive modulator
a molecule binding to the allosteric site in a protein causing conformational change to the protein increasing site activity
allosteric inhibitor
negative modulator
allosteric activator
positive modulator
phosphorylation definition
a form of post translational modification where a phosphate group is added or removed from a proteins R group causing conformational change
why does phosphorylation occur
to allow for reversible conformational changes in proteins to occur and to activate the protein
which phosphate is removed in ATP
the terminal (third) phosphate
protein kinase
an enzyme which catalyses the transfer of phosphate groups by removing a phosphate from ATP to form ADP
phosphatase
the enzyme which catalyses the removal of a phosphate from a protein and adds it to ADP producing ATP
Phosphorylation activation rule
Most proteins are activated by phosphorylation but some are deactivated
Protein kinase process
Protein + ATP —-> Phosphorylated protein + ADP
Protein phosphorylase process
Phosphorylated protein + ADP —-> Protein + ATP
Where does the phosphate bind to a protein
at specific complimentary R groups
the effect of a phosphate group on tertiary structure
can add negative charges to the protein, disrupting and creating new ionic interactions
what varies between R groups
size, shape, charge, hydrogen bonding capacity, chemical reactivity
why is there such a high diversity of proteins
Because there is a wide range of R groups
