1. Key Area 2- Proteins Flashcards
Define proteome
The entire set of proteins expressed by a genome
Explain why the proteome is larger than the number of genes particularly in eukaryotes
As more than one protein can be produced from a single gene as a result of alternative RNA splicing
Not all genes are expressed as proteins in a particular cell type. What is the term to describe genes that do not code for proteins?
non-coding RNA genes
What do non-coding RNA genes include?
Those that are transcribed to produce tRNA, rRNA and RNA molecules that control the expression of other genes
The set of proteins expressed by a given cell type can vary over time and under different conditions. What are the factors that affect the set of proteins expressed by a given cell type?
- metabolic activity of the cell
- cellular stress
- the response to signalling molecules
- whether the cell is diseased or healthy
Why do eukaryotes have a relatively small surface area to volume ration?
Because of their size
What is the function of Eukaryotic cells having a system of internal membranes?
Increases the total area of membrane which allows vital functions to be carried out
What is the Endoplasmic reticulum (ER)?
Forms a network of membrane tubules continuous with the nuclear membrane
What is the difference between the rough endoplasmic reticulum (RER) and the soft endoplasmic reticulum (SER)
The RER has ribosomes on its cytosolic face while the SER lacks ribosomes
What is the Golgi Apparatus
A series of flattened membrane discs
What are lysosomes?
Membrane-bound organelles containing a variety of hydrolases (class of enzymes) that digest proteins, lipids, nucleic acids and carbohydrates
What is the function of vesicles?
To transport materials between membrane compartments
What are the two types of vesicles and their functions?
- transport vesicles which move molecules within the cytosol
- secretory vesicles which transport molecules to the plasma membrane
What are the two types of vesicles and their functions?
- transport vesicles which move molecules within the cytosol
- secretory vesicles which transport molecules to the plasma membrane
Where are lipids and proteins synthesised in general
in the endoplasmic reticulum (ER)
Where are lipids synthesised
In the smooth endoplasmic reticulum (SER) and inserted into its membrane
Where does the synthesis of all proteins begin?
In the cytosolic ribosomes
Where is the synthesis of cytosolic proteins completed?
In cytosolic ribosomes and remain in the cytosol
What is the cytosol?
Is the intra-cellular fluid that is present in the cytoplasm
What are examples of cytosolic proteins?
Enzymes of glycolysis, enzymes that attach amino acids to tRNA molecules for use in protein synthesis
Describe the synthesis of transmembrane proteins?
Transmembrane proteins carry a signal sequence which temporarily halts translation and directs the ribosome synthesising the protein to dock with the ER, forming the RER.
Describe what happens after docking
Translation continues after docking and the protein is inserted into the membrane of the ER
How are proteins moved between membranes?
Once the protein is in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus. Molecules move through the golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack
What happens when proteins move through the Golgi apparatus?
They undergo post-translational modification where the major modification is the addition of carbohydrate groups
When vesicles leave the Golgi apparatus where do they take the proteins? and what happens to the vesicles?
To the plasma membrane and lysosomes. Vesicles move along microtubules to other membranes and fuse with them within the cell.
Where are secreted proteins translated?
In ribosomes on the RER and enter its lumen
What are examples of secreted proteins?
Peptide hormones (insulin) and digestive enzymes (pepsin)
Describe the secretory pathway
Secreted proteins are translated in ribosomes on the RER and enter its lumen. 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.
What is the function of proteolytic cleavage?
To produce active proteins
Why do many secreted proteins require proteolytic cleavage?
Due to many secreted proteins being synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
What are examples of proteolytic cleavage?
Digestive enzyme pepsin being secreted as an inactive precursor. The HCl in the stomach causes the removal of a section of the inactive pepsin.
What does the amino acid sequence determine?
The structure of a protein
What are proteins?
Polymers of amino acid monomers
What are the bonds linking amino acids?
peptide bonds which form polypeptides
Amino acids have the same basic structure, so what do they differ by?
R groups
What is a peptide bond?
A covalent bond formed between two amino acids
What do R groups of amino acids vary in? (5 factors)
- size
- shape
- charge
- hydrogen bonding capacity
- chemical reactivity
What are the different types of R group classification? (4)
- basic (positively charged)
- acidic (negatively charged)
- polar
- hydrophobic
What do the wide range of functions carried out by R groups result from?
The diversity of R groups
What are the 4 levels of structure of a protein?
primary, secondary, teritary, quaternary
Describe the primary structure of a protein
The sequence in which the amino acids are synthesised into the polypeptide
What is the bonding in the primary structure of a protein?
peptide bonds between amino acids to form a polypeptide
Describe the secondary structure of a protein
Folding of the amino acids chain results in regions of secondary structure: alpha helices, parallel or antiparallel beta pleated sheets, or turns
What is the bonding in the secondary structure of a protein?
Hydrogen bonding along the backbone of the protein strand
Describe the tertiary structure of a protein
Further folding of the polypeptide into a tertiary structure giving a 3-dimensional shape
What is the bonding in the tertiary structure of a protein?
This conformation is stabilised by interactions between R groups: hydrophobic interactions, ionic bonds, LDFs, hydrogen bonds, disulphide bridges and covalent bonds between R groups containing sulfur
Describe the quaternary structure of a protein
This exists in proteins with two or more connected polypeptide subunits
What is the bonding in the quaternary structure of a protein
Further bonding between R groups on the different polypeptides that make up the subunits
Define a prosthetic group
A non-protein unit tightly bound to a protein and necessary for its function
What factors influence the interactions of R groups?
Temperature and pH
What effect does an increased temperature have on R groups
Increasing the temperature disrupts the interactions that hold the protein in shape, the protein begins to unfold and eventually becomes denatured
What effect does a change in pH have on R groups?
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 substance that can bind to a protein
Which R groups can bind to ligands?
R groups not involved in protein folding
What is the result of ligand binding?
As a ligand binds to a protein-binding site, the conformation of the protein changes thus causing a functional change in the protein
What allows ligand binding?
R groups not involved in protein folding can allow binding to ligands
What do binding sites have to allow a ligand to bind?
complementary shape and chemistry to the ligand
Where do allosteric interactions occur?
Between spatially distinct sites
What do many allosteric proteins consist of?
Multiple subunits as they have quaternary structures
What is the effect of the binding of a substrate molecule to one active site of an allosteric enzyme? And why is this biologically important?
It increases the affinity of other active sites for bonding 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 is the second type of site on an allosteric enzyme called?
An allosteric site
What is the second type of site on an allosteric enzyme called?
An allosteric site
What regulates the activity of the enzyme when they bind to the allosteric site?
Modulators
What occurs 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 effect does positive modulators have on an enzymes affinity?
Increases the enzymes affinity for the substrate
What effect does negative modulators have on an enzymes affinity?
Reduces the enzymes affinity for the substrate
What do allosteric proteins with multiple subunits show?
Co-operativity in binding in which changes in binding at one subunit alters the affinity for the remaining subunits
What is an example of binding which shows co-operativity?
The binding and release of oxygen in haemoglobin. Changes in binding of oxygen at one subunit alters the affinity of the remaining subunits of oxygen
Describe the influence temperature and pH have on the binding of oxygen
A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen so the binding of oxygen is reduced.
What is the physiological impact a reduced pH and increased temperature have in the binding of oxygen to haemoglobin?
A reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to muscle cells
What is phosphorylation?
The addition or removal of phosphate
What effect does phosphorylation have on proteins?
Can cause a reversible conformational change in proteins and is a common form of post translational modification
What is the function of protein kinases? What is an example of this
Catalyse the transfer of a phosphate group to other proteins. An example of this the terminal phosphate of ATP is transferred to specific R groups
What is the function of protein phosphatases?
Catalyse the reverse reaction of phosphorylation
What does the process of phosphorylation bring about? And how does it affect the activity of proteins?
Brings about conformational changes which can affect a protein’s activity. The activity of many cellular proteins are regulated this way.
How does phosphorylation have different effects on proteins?
Some proteins are activated by phosphorylation while other are inhibited. Adding a phosphate group adds a negative charge. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created.
