Unit 1 - Proteomics Flashcards
Genome
An organism’s complete set of DNA including both protein-coding genes and non-coding RNA genes (that produce tRNA, rRNA and RNA molecules that control other genes).
Proteome
The entire set of proteins that can be expressed from a genome.
Alternative RNA splicing
Different mature mRNA transcripts are produced, depending on which RNA segments are treated as exons and introns in a primary RNA transcript.
Factors affecting gene expression
Cell type - proteins characteristic for that type of cell are produced, along with essential proteins (eg. proteins involved in respiration).
Also, metabolic activity of the cell, cellular stress and response to signalling molecules.
Proteins produced by a cell can be changed by disease and can act as early indicators.
Prokaryotic cells
Bacteria and archaea.
Much smaller than eukaryotic cells (1-5 micrometres in size, compared to 10-100 micrometres for eukaryotes) due to the absence of intracellular (internal) membrane structures (including the absence of a true membrane-bound nucleus).
Eukaryotic cells
Contain a system of internal membranes to increase the total area of membrane available for vital metabolic processes.
They have a true membrane bound nucleus and organelles.
Endoplasmic reticulum (ER)
A network of membrane tubules continuous with the nuclear membrane.
Used for lipid (smooth ER) and protein (rough ER) synthesis.
Vesicles
Sacs made of membrane that transport materials between compartments or to the plasma membrane.
Lysosomes
Membrane bound organelles containing hydrolase enzymes that digest proteins, lipids, nucleic acids and carbohydrates.
They digest damaged organelles to allow component molecules to be recycled by the cell.
They are involved in phagocytosis by white blood cells in the immune system.
Golgi apparatus
A series of flattened membrane discs where proteins undergo post-translational modification.
Cytosol
The liquid component of the cytoplasm.
The ribosomes and organelles are suspended in the cytosol, forming the cytoplasm.
Cytosolic ribosomes
Synthesise proteins and release them directly into the cytosol.
Signal sequences may direct the proteins to chloroplasts, mitochondria or the interior of the nucleus.
Smooth endoplasmic reticulum (SER)
Used for synthesis of lipids (oils, phospholipids and steroid hormones).
These are made by enzymes embedded in the SER. Phospholipids are inserted directly into the SER membrane.
The SER has no ribosomes attached to it.
Glycoprotein
Made by enzymes in the Golgi apparatus that attach sugars to polypeptides in multiple steps as they move through the flattened discs.
Most secreted proteins are glycoproteins, and they are important for ‘self’ recognition by the immune system.
Rough Endoplasmic reticulum (RER)
Used for the synthesis of transmembrane proteins.
Cytosolic particles attached to partially completed polypeptides (at the signal sequence) cause cytosolic ribosomes to dock with protein pores in the ER, forming RER.
Translation is completed, the cytosolic particle is removed and the polypeptide chain is inserted directly into the ER membrane.
Inactive precursor
Many secreted proteins are synthesised in an inactive form as precursors, which require proteolytic cleavage to produce active proteins. eg. insulin, pepsin.
Secretory vesicles
Bud off the Golgi apparatus. Used to package proteins which are to be secreted out of the cell.
The vesicles move along microtubule pathways before fusing with the plasma membrane, releasing the proteins out of the cell.
Polypeptide (Higher version)
An amino acid polymer. The sequence of amino acids determines the structure of a protein.
Amino acid
Join together to create a polypeptide.
Have a central carbon atom with 4 groups bonded to it : NH2 (amine group); COOH (carboxylic acid group); hydrogen and a variable ‘R’ group.
R group
The variable part of an amino acid, containing different types of functional group.
They vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity, and this leads to a wide range of protein functions.
They are vital in determining the structure and location of proteins.
Acidic amino acids
These become negatively charged due to the extra carboxylic acid in the R group.
When the R group interacts with the aqueous solutions inside the cell, the carboxylic acid group (COOH) becomes negatively charged (COO-)
eg. aspartic acid
Basic amino acids
These become positively charged due to the extra amine group in the R group.
When the R group interacts with the aqueous solutions inside the cell, the amine group (NH2) becomes positively charged (NH3+)
eg. lysine
Polar amino acids
Polar R groups (eg. those containing OH) have groups which are slightly charged and can form hydrogen bonds with other molecules such as water.
eg. serine
Hydrophobic amino acids
These amino acids carry no charge so do not form hydrogen bonds with water. They do not mix readily with water.
They contain hydrocarbons in the R group eg. CH3 or benzene rings.
eg. alanine
Polypeptide (AH version)
Formed when amino acid monomers are linked together using an enzyme which causes a condensation reaction.
A water molecule is removed when the OH of the COOH of one amino acid joins to a hydrogen from the NH2 of another, forming a peptide bond.
Primary structure
The sequence in which amino acids are synthesised into a polypeptide chain during translation.
It runs from the N-terminus (NH2 end) to C- terminus (COOH end) of the polypeptide chain, as all amino acids are lined up facing the same way before being joined together.
Primary structure determines the structure of the protein, as R-groups of the individual amino acid residues (amino acids with water removed) interact with the environment.
The structure of the protein determines its function
Secondary structure
A polypeptide strand is folded and stabilised by hydrogen bonds between different peptide bonds in the chain.
N-H in one bond (weak positive) is attracted to C=O (weak negative) in another.
There are 3 types - alpha helix, beta pleated sheet and turns (where the chain folds back on itself)
Alpha helix
A type of secondary protein structure.
It is a spiral with R-groups sticking outwards.
Beta-pleated sheet
Parts of the polypeptide chain run alongside one another, to form a corrugated (ridged) sheet with the R-groups sitting above and below.
They are usually anti-parallel with chains running in the opposite direction, but can be parallel with chains running in the same direction (with respect to N-C polarity).
Tertiary structure
The final folded 3-D conformation of a protein.
It contains regions of secondary structure, stabilised in position by interactions between R-groups of the amino acids, which come close together as the chain folds.
These bonds are affected by changes in temperature and pH, causing the protein to denature as its conformation changes.
R-group interactions
Include hydrophobic interactions, ionic bonds, London dispersion forces, hydrogen bonds and disulfide bridges.
Quaternary structure
The spatial arrangement of polypeptide subunits in a protein containing more than one subunit, such as haemoglobin.
Subunits are connected by bonding between their R-groups.
Prosthetic group
A non- protein group which is tightly bound to a polypeptide, and is essential for its function.
Myoglobin and haemoglobin contain the prosthetic group haem.
Ligand
The general term for any substance that binds to a protein.
Protein folding produces ligand binding sites on the surface of the globular protein, which have a complementary shape and chemistry to their ligand.
Ligand binding results in conformational change, which is crucial for protein function.
Allosteric site
A spatially distinct site on the same protein. eg. an enzyme may have an active site and an allosteric site.
Modulators
Regulate the activity of an enzyme when they bind to the allosteric site.
Binding of a modulator leads to conformational change which alters the affinity of the active site for its substrate, thus affecting the enzyme’s activity.
Positive modulator
Increase the affinity of an enzyme for it’s substrate by altering its conformation.
Negative modulator
Decrease affinity, and therefore the enzyme’s activity. (eg. non-competitive inhibitors).
Cooperativity (general)
Allosteric proteins made of multiple subunits show cooperativity, where binding at one subunit affects the affinity of the other subunits.
Cooperativity in haemoglobin
Oxygen binds to the 1st subunit causing conformational change, and triggering conformational change in the remaining subunits, thus increasing their affinity for oxygen.
Leads to rapid oxygen uptake when there is a small increase in oxygen concentration, and produces an S-shaped curve when plotting % saturation of haemoglobin against oxygen concentration of the tissues.
Protein kinases
Enzymes that catalyse phosphorylation - the transfer of a phosphate group from ATP tp other proteins.
Adding a phosphate adds negative charges, which disrupts ionic interactions.
Protein kinases are mostly dephosphorylated and inactive. They need to be activated by other kinases, which phosphorylate them. This is important in signal transduction cascades and control of the cell cycle. (See later sections)
Protein phosphatases
Enzymes that catalyse de-phosphorylation (the removal of phosphate from a molecule).
De-phosphorylation is the reverse of phosphorylation by kinases.
ATPases
A group of transmembrane enzymes that hydrolyse ATP and use the phosphate to phosphorylate themselves, rather than their substrate.
The binding of phosphate changes their conformation, and alters their function.
eg. the sodium-potassium pump (Na+/K+ATPase).
Reversible conformational change
A change in shape caused by the addition or removal of a phosphate.
Important method for regulating the activity of many cellular proteins, eg. enzymes.
