1.2 proteome Flashcards
Proteome definition
The entire set of proteins expressed by a genome
Proteome size comparison with gene number explain
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 gene produce
tRNA, rRNA and RNA molecules which control expression of other genes.
Are all genes expresses as proteins
No some are expressed as RNA molecules.
SER actual name
Soft endoplasmic reticulum
RER actual name
Rough endoplasmic reticulum
What is the purpose of the intracellular membranes
To increase the surface area to volume ratio, to allow for vital cellular functions to take place.
What is the difference between the rough and smooth endoplasmic reticulum
The rough endoplasmic reticulum has ribosomes, and produces protein
Whereas the soft endoplasmic reticulum does not have ribosomes and produces lipids (fats).
Function of the endoplasmic reticulum
The endoplasmic reticulum 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 out post translational modification and send these modified proteins and lipids off to their destination.
Lysosome’s definition
Membrane bound organelles containing hydrolases that digest proteins, lipids, carbohydrates and nucleic acids.
Hydrolase definition
Enzymes which use water to break down substrates such as proteins, fats, nucleic acids and carbohydrates.
What are genes which don’t code for protein called
Non - coding RNA genes
Factors affecting proteins expressed in a cell
Metabolic activity
Cellular stress
Response to signalling molecules
Disease
Vesicles definition
Cell organelles which transport materials between membrane compartments
What are intracellular membranes
They are membranes which inside a cell which increase the cell membrane surface area to volume 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. (Not part of the course but important to remember).
Process of producing a cytosolic protein
mRNA will leave the nucleus and travel to a ribosome in the cytosol.
In cytosolic the ribosome will remain in the cytosol.
A polypeptide chain will be produced by the ribosome.
This will then fold into shape and become a protein.
The protein will remain in the cytosol.
Process of producing a transmembrane protein
An mRNA strand travels from the nucleus to 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 vesicles to be transported to the Golgi apparatus.
The Golgi apparatus then processes and carries out post translational modification.
Then the transmembrane protein is sent onto 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 proteins
Nucleus, mitochondria, chloroplasts
Destination of transmembrane proteins
Plasma membranes
Secretory vesicles
Lysosomes
Secretory definition
Means to be sent outside 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
Examples of secreted proteins
Peptide hormones and digestive enzymes.
What happens after a protein moves through the Golgi apparatus
It’s packaged into a secretory vesicles 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.
Proteolytic cleavage reason
To activate a protein at the correct time.
Example of Proteolytic cleavage
Digestive enzymes
Amino acids definition
The small 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
Amino acid different types
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 acid
Tertiary structure types
Ionic
Hydrophobic
Hydrogen bonding
Disulphide bridge
London dispersion forces.
Ionic tertiary structure
Creates electrostatic forces or 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 temp 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 the 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
Where in a protein with quaternary strucure on one ligand binds to the active site of one sub unit it changes the affinity of all the active sites and allows for ligand to bind to active site.
Examples of co-operativity
Haemoglobin
Rules for temperature and pH on haemoglobin saturation
As pH increases and temp decreases saturation increases
As pH decreases and temp 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 active 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 to proteins by removing a phosphate from ATP forming 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
Pphosphorylated protein +ADP —-> Protein + ATP.
Where does the phosphate bind to a protein
At specific complimentary R groups.
Effect of phosphate group of tertiary structure
Can add negative charges to the protein, disrupting and creating New Ionic interactions.
What varies in 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.
