Unit 1: Key Area 2 Flashcards
What is a proteome?
The proteome is all of the proteins made by a genome (genetic sequences of bases found on DNA)
Explain why the proteome is bigger than the genome
The proteome is larger than the number of genes, particularly in eukaryotes, because more than one protein can be produced from a single gene as a result of alternative RNA splicing.
Protein structure
What determines the structure of a protein
The structure of a protein is determined by the sequence of amino acids
Protein structure
What are proteins and what are they made up of
Proteins are polymers made up of amino acid monomers
Protein structure
What are amino acids linked by and what do they form
The amino acids are linked by peptide bonds to form polypeptides
Protein structure
What determines an amino acids characteristics
All amino acids have the same basic structure apart from their R group.
The R group of used to classify each amino acid. They can be described as basic, acidic, polar or hydrophobic.
Protein structure
Describe the characteristics of R groups
The R groups vary in size, shape, change, their ability to form hydrogen bonds and chemical reactivity.
Classifying amino acids
Describe a basic amino acid and what group it contains.
Name 3 examples
Basic- hydrophilic contain anime group (N+H)
Examples: Hisitidine, Lysine & Arginine
Classifying amino acids
Describe an acidic amino acid and what group it contains.
Name 3 examples
Acidic- Hydrophilic contain COOH-
Examples: Aspartic Acid & Glutamic acid
Classifying amino acids
Describe a polar amino acid and what group it contains.
Name 3 examples
Polar- Hydrophilic contains C=O, NH or OH
Examples: Cysteine, Serine & Theronine
Levels of protein structure
What will determine the structure and function of an protein
As the R groups on the amino acids are quite different, the order which they take to form a protein will determine a structure which will dictate its function.
Levels of protein structure
How many different levels of protein structures are there
There are 4 different levels of protein structure
Describe the primary structure in proteins
The primary structure is the sequence in which the amino acids are synthesised into the polypeptide
Describe the secondary structure in proteins
The arrangement of amino acids in the primary structure results in the secondary structure where hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or anti- parallel beta-pleated sheets, or turns
Describe the tertiary structure in proteins
Then the folded tertiary structure is made by interactions between R groups:
The conformation is stabilised by interactions between R groups: hydrophobic interactions, ionic bonds, London Dispersion Forces, hydrogen bonds and disulfide bridges
What are disulfide bridges
Disulfide bridges (covalent bonds between R groups containing sulfur)
In what proteins do quaternary structures exists
Quaternary structure exists in proteins with two or more connected polypeptide subunits
What does the quaternary structure describe
The quaternary structure describes the spatial arrangement of subunits
What is a prosthetic group
A prosthetic group is a non protein unit tightly bound to a protein and necessary for its function.
What is the ability of haemoglobin to bind with oxygen
The ability of haemoglobin to bind oxygen is dependent upon the non protein haem group
What factors affect R group interactions
Temperature and pH are factors which can affect the interactions between R groups
Describe what happens to the R group interactions when you increase the temperature
Increasing temperature disrupts the interactions that hold the protein in shape; the protein begins to unfold eventually becoming denatured.
Describe what happens the the R group interactions in proteins and the charges on acidic and basic R groups by changing the pH
The charges on the acidic and basic R groups are affected by pH. As pH increases and 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 does ligand binding do to a protein
Ligand binding changed the conformation of a protein
What is a ligand
A ligand is a substance that bacon bind to a protein
What can happen to the R groups that are not involved in protein folding
R groups which are not involved in protein folding can allow ligand binding
Describe the R group binding site
The R group binding sites will have a complementary shape and chemistry to the ligand
What happens to the ligand when it binds to a protein binding site
When the ligand binds to a protein binding site the conformation of the protein changes
This change in conformation causes a functional change in proteins
Where do allosteric interactions occur and what does this mean
Allosteric interactions occur between spatially distinct sites. This means a molecule binds at one site and has an effect on another
What do allosteric enzymes contain
Allosteric enzymes contain a second type of site, called an allosteric site
Describe the binding of a substrate molecule to one active site of an allosteric enzyme
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 biologically important because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration
Describe the structure of allosteric proteins
Many allosteric proteins consist of multiple subunits (have quaternary structure)
What do allosteric proteins with multiple subunits show
Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits
What do modulators do
Modulators regulate the activity of the enzyme when they bind to the allosteric site
What happens after the binding of a modulator
Following the binding of a modulator the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
What do positive and negative modulators do to the enzyme’s affinity
Positive modulators increase the enzyme’s affinity for the substrate whereas negative modulators reduce the enzyme’s affinity for the substrate
What does the binding and release of oxygen in haemoglobin show
The binding and release of oxygen in haemoglobin shows co operativity.
Changes in binding of oxygen at one subunit alters the affinity of the remaining subunits for oxygen
Describe the influence and physiological importance of temperature on the binding of oxygen
An increase in temperature lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced
An increase of temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue
Describe the influence and physiological importance of pH on the binding of oxygen
A decrease in pH lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced
A decrease of pH in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue
How does the addition or removal of phosphate affect proteins
The addition or removal of phosphate can cause reversible conformational change in proteins
This is a common form of post translational modification
What do protein kinases catalyze
Protein kinases catalyze the transfer of a phosphate group to other proteins
ATP —> ADP + Pi
What happens to the terminal phosphate of ATP
The terminal phosphate of ATP is transferred to specific R groups
What does protein phosphatases catalyze
protein phosphatases catalyses the reverse reaction
Removes phosphate from molecule
ADP + Pi —-> ATP
What does phosphorylation bring about
Phosphorylation brings 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 does phosphorylation do to proteins
Some proteins are activated by phosphorylation while others are inhibited
This is because adding a phosphate group adds negative charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.
Are all genes expressed as proteins in a cell. Explain why?
Not all genes are expressed as proteins in a particular cell type
Genes that do not code for proteins are 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
What affects the set of proteins produced by a given cell
The set of proteins expressed by a given cell type can vary over time and under different conditions
Some factors affecting the set of proteins expressed by a given cell type are the metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells.
Describe the structure of eukaryotic cells
Eukaryotic cells have a system of internal membranes, which increases the total area of membrane
Because of their size, eukaryotes have a relatively small surface area to volume ratio. The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes.
What does the endoplasmic reticulum (ER) form
The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane
What is the Golgi apparatus
The Golgi apparatus is a series of flattened membrane discs
What are lysosomes
Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates
What do vesicles do
Vesicles transport materials between membrane compartments
What do Rough ER (RER) and smooth ER (SER) contain
Rough ER (RER) has ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes.
Where are Lipids synthesized and what happens to it afterwards
Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
Where does the synthesis of all proteins begin and where do cytosolic proteins finish synthesis
The synthesis of all proteins begins in cytosolic ribosomes
The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol
What do transmembrane proteins carry and what does it do
Transmembrane proteins carry a signal sequence, which halts translation and directs the ribosome synthesising the protein to dock with the ER, forming RER
What is a signal sequence
A signal sequence is a short stretch of amino acids at one end of the polypeptide that determines the eventual location of a protein in a cell.
When does translation continue and what happens to the protein
Translation continues after docking, and the protein is inserted into the membrane of the ER
What happens once the proteins are in the ER
Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
What happens as the proteins move through 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 in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.
What does the addition of a carbohydrate group do
The addition of carbohydrate groups is the major modification
What do vesicles that leave the Golgi apparatus do
Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes
Vesicles move along microtubules to other membranes and fuse with them within the cell
Where ate secreted proteins translated
Secreted proteins are translated in ribosomes on the RER and enter its lumen
Name examples of secreted proteins
Peptide hormones and digestive enzymes are examples of secreted proteins.
What happens to the proteins once they are translated
The proteins 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
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
What is proteolytic cleavage and name an example of a certain types of secreted proteins that require proteolytic cleavage to become active.
Proteolytic cleavage is another type of post- translational modification. Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.
