UNIT 1 - KA2 Flashcards
What is the proteome
The proteome is the entire set of proteins expressed by a genome
What is an organisms genome
- the genome is the total genetic material in a cell
This includes chromosomal DNA and the extra chromosomal and also the RNA in all forms in the cell
Why is the proteome larger than an organisms 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
What is selective gene expression
Not all genes are expressed as proteins in a particular cell
What are genes that do not code for proteins called
Genes that do not code for proteins are called non-coding RNA genes
What do non coding RNA genes include (3)
include those that are transcribed to produce tRNA, rRNA, and RNA molecules that control the expression of other genes.
How can the set of proteins expressed by a given cell type
The set of proteins expressed by a given cell type can vary over time and under different conditions
What are some factors affecting the set of proteins expressed by a given cell type (4)
the metabolic activity of the cell,
cellular stress,
the response to signalling molecules,
and diseased versus healthy cells.
What system do eukaryotic cells
Eukaryotic cells have a system of internal membranes, which increases the total area of membrane
What type of surface area and volume ratio do eukaryotes have
Because of their size, eukaryotes have a relatively small surface area to volume ratio.
What does the endoplasmic reticulum form a network of
The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane
What is the plasma membrane to small to carry out
The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes.
What is the Golgi apparatus a series of
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 transport
Vesicles transport materials between membrane compartments
What are the two types of endoplasmic reticulum
- rough endoplasmic reticulum
- smooth endoplasmic reticulum
What is the main difference between rough and smooth endoplasmic reticulum
- rough ER has ribosomes on its systolic face
- smooth ER lack ribosomes
What are hydrolases
Hydrolases are enzymes that catalyse the cleavage of a covalent bond using water
Describe the function of smooth endoplasmic reticulum
Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane
Where does the synthesis of all proteins begin
The synthesis of all proteins begins in cytosolic ribosomes
Cytosolic
The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol
Transmembrane proteins
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.
What is translation
Translation continues after docking, and the protein is inserted into the membrane of the ER
What happens to the proteins when they are in the ER (after endoplasmic reticulum)
Once the proteins are made at a ribosome on the RER and put into the lumen of the RER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus
What happens to proteins as the they move through the Golgi apparatus
As proteins move through the Golgi apparatus they undergo post-translational modification
How do molecules move through Golgi discs
Molecules move through the Golgi discs in vesicles that bud off from one disc and fuse to the next one in the stack.
What do enzymes catalyse the addition of
Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates.
Which is the major type of post - translational modification
The addition of carbohydrate groups is the major modification
Describe the function of vesicles after the Golgi apparatus
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
What are microtubules
Microtubules are structures that make up the cells cystoskeleton and offer support and a means of transport
Where are secreted proteins translated (SP 1)
Secreted proteins are translated in ribosomes on the RER and enter its lumen. They bud off the RER in a vesicle and go to the Golgi apparatus
What are two examples of substances which are secreted from a cell
- peptide hormones
- digestive enzymes
Where are the proteins packaged (SP2)
The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
What happens to the secretory vesicles (SP 3)
These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell
How are many secreted proteins synthesised as (SP4)
Many secreted proteins are synthesised as inactive precursors and require proteolytic cleavage to produce active proteins
What is proteolytic cleavage
Proteolytic cleavage is another type of post- translational modification.
What is an example of a protein which undergoes proteolytic cleavage
Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.
What determines the structure of a protein
Amino acid sequence determines protein structure
What are proteins polymers of
Proteins are polymers of amino acid monomers
What are amino acids linked by
Amino acids are linked by peptide bonds to form polypeptides
What do amino acids have the same of
Amino acids have the same basic structure, differing only in the R group present
How are amino acids classified
Amino acids are classified according to their R groups: basic (positively charged); acidic (negatively charged); polar; hydrophobic
What do R groups of amino acids vary in
R groups of amino acids vary in size, shape, charge, hydrogen bonding capacity and chemical reactivity.
What are the wide range of functions carried out by proteins the result of
The wide range of functions carried out by proteins results from the diversity of R groups
What is the primary structure
The primary structure is the sequence in which the amino acids are synthesised into the polypeptide
Secondary structure
Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure.
What is a peptide bond
A peptide bond is a strong covalent bond between a carbon atom of one amino acid and the nitrogen atom of another amino acid.
What is removed from between two amino acids
Water is removed from between the two amino acids to allow the bond to form
What two groups do amino acids contain
- an amine group
- an acid group
What are the 5 features of amino acids
- central carbon
- an amine
- carboxylic acid
- a hydrogen
- variable R group
Acidic R groups
Negatively charged amino acids are hydrophilic and the key component of their R group is a carboxylic acid group (negatively charged at pH 7)
Basic R groups
Positively charged amino acids are hydrophilic and the key component of their R group is an anime group (positively charged at pH 7)
Polar R groups
Polar amino acids are hydrophilic and the key component of their R group are hydrophilic groups, like carbonyl (c=o) hydroxyl (OH) or amine (NH)
What are the four levels of Protein structure
- primary structure
- secondary structure
- tertiary structure
- quaternary structure
What are the three types of secondary structure
alpha helixes , parallel or anti- parallel beta-pleated sheets, or turns
Alpha helix
The alpha helix is formed by twisting the polypeptide chain into a helix and then stabilising with hydrogen bonding
Where will a hydrogen bond from in an alpha helix
A hydrogen bond will form between every 4th amino acid in an alpha helix
Beta sheet
The second main structure is called beta pleated sheet. The polypeptide chain is arranged In rows are linked with hydrogen bonding
What can beta sheets be
Beta sheets can be either parallel or anti parallel
What is a turn in the secondary structure of a protein
Turns are a third type of secondary structures it is a short section with no a/B structure. They reverse the direction of the polypeptide chain and are stabilised by hydrogen bonds
What does the polypeptide fold into
The polypeptide folds into a tertiary structure
What are disulphide bridges
Disulfide bridges are covalent bonds between R groups containing sulfur.
What are tertiary structures
Tertiary structure refers to the overall folding of the polypeptide and its final shape.
What is folding at the tertiary structure level stabilised by
By many different interactions between R groups of the amino acids
What is tertiary structure brought about by
Tertiary structure is brought about by charge effects such as interactions of the R groups in hydrophobic regions
What are the several possible R group interactions (5)
- hydrophobic interactions
- ionic bonds
- London dispersion forces
- hydrogen bonds
- disulphide bridges
Hydrophobic interactions
- hydrophobic amino acids tend to cluster together on the interior of a protein, away from the surface
- hydrophobic amino acids will predominate at the surface of a soluble protein. This hydrophobic effect is one of the main driving forces of protein folding
Ionic bonding
The COOH and NH2 groups ionise to become COO- and NH3+. These groups are strongly charged and can attract each other
London dispersion forces
Very weak attractions between the electron clouds of atoms
Hydrogen bonding
The weak negative charge of the oxygen of c=o is attracted to the weak positive charge on a hydrogen of an OH or NH2 group
Which proteins does quaternary structure exist in
Quaternary structure exits in proteins with two or more connected polypeptide subunits which are linked by binds between the R groups of the polypeptide chains
What does quaternary structure describe
Quaternary structure describes the spatial arrangement of the subunits.
What is an example of a protein which shows quaternary structure
Haemoglobin consists of 4 domains (polypeptide chains) connected to a haem group
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 to oxygen dependant upon
The ability of haemoglobin to bind oxygen is dependent upon the non-protein haem group.
What can influence the interactions of the R groups
Interactions of the R groups can be influenced by temperature and pH
What is the affect of increasing temperature
Increasing temperature disrupts the interactions that hold the protein in shape;
the protein begins to unfold, eventually becoming denatured
What are the charges on acidic and basic R groups affected by
The charges on acidic and basic R groups are affected by pH
What is the effect of pH on the normal ionic interactions
As 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 will any factor that changes the interactions of the R groups change
Any factor that changes the interactions of the R groups will change the shape of the protein.
What is a ligand
A ligand is a substance that can bind to a protein
What type of groups can allow binding to proteins
R groups not involved in protein folding can allow binding to ligands
What features of binding sites are complementary to the ligand
Binding sites will have complementary shape and chemistry to the ligand
What happens as a ligand binds to a protein binding site
As a ligand binds to a protein-binding site the conformation of the protein changes
What happens as a result of the confirmation of a protein changing
This change in conformation causes a functional change in the protein
What is an allosteric enzyme
An allosteric enzyme is an enzyme whose activity is regulated by altering its conformation
What do allosteric interactions occur between
Allosteric interactions occur between spatially distinct sites
What do allosteric enzymes contain along side an active site
Allosteric enzymes contain a second type of site called an allosteric site
Draw a simple diagram to explain what the allosteric site of an enzyme is
Check jotter
Active site =
Allosteric site =
Active site = substrate joins
Allosteric site = substance other than substrate joins
What does the binding of a substrate molecule to one active site of an allosteric enzyme increase
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
What can happen to the activity of allosteric enzymes
This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.
What do many allosteric proteins consist of
Many allosteric proteins consist of multiple subunits (have quaternary structure)
How can the rate of product formation be regulated
The rate of product formation (rate of reaction) by a metabolic pathway can be regulated by raising or lowering the activity of just one enzyme in the pathway
Where do modulators bind in allosteric enzymes
In allosteric enzymes modulators bind at secondary binding sites (allosteric sites)
How do modulators regulate the activity of the enzyme
Modulators regulate the activity of the enzyme when they bind to the allosteric site
What happens following binding of a modulator
Following binding of a modulator, the conformation of the enzyme changes and this alters the affinity of the active site for the substrate
Positive modulators
Positive modulators increase the enzyme’s affinity for the substrate and increase enzyme activity
Negative modulators
Negative modulators decrease the affinity of the enzyme for the substrate and so decrease the enzyme activity
What does the binding and release of oxygen in haemoglobin show
The binding and release of oxygen in haemoglobin shows co-operativity
What do some proteins with quaternary structure show
Some proteins with quaternary structure show cooperatively between their polypeptide subunits
What do changes in binding of oxygen at one subunit alter the affinity of
Changes in binding of oxygen at one subunit alter the affinity of the remaining subunits for oxygen. (Increases the ligand affinity of remaining subunits
What is the effect of a high temperature on haemoglobins affinity for binding 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 effect of low pH on haemoglobins affinity for binding oxygen
As pH decreases haemoglobin affinity for oxygen decreases
What can the addition or removal of phosphate cause in proteins
The addition or removal of phosphate can cause reversible conformational change in
proteins
What is a common form of post translational modification
The addition or removal of phosphate can cause reversible conformational change in
proteins. This is a common form of post-translational modification
What is the effect of protein kinase on protein
Protein kinases catalyse the transfer of a phosphate group to other proteins
What is the effect of protein kinase on ADP/ATP
The terminal phosphate of ATP is transferred to specific R groups
What is the effect of protein phosphate on proteins
Protein phosphatases catalyse the reverse reaction
What is the effect of protein phosphatase on ADP/ATP
They catalyse the transfer of a phosphate group from proteins onto ADP to regenerate ATP
What type of changes does phosphorylation bring about
Phosphorylation brings about conformational changes which affect a proteins activity
How is the activity of many cellular proteins, such as enzymes and receptors regulated
Through phosphorylation which brings about conformational changes and affects a proteins activity
What are the two ways proteins are activated
Some proteins are activated by phosphorylation while others are inhibited
What type of charge do phosphate groups add
Adding a phosphate group adds negative charges
What can happen to ionic interactions in unphosphorylated proteins
Ionic interactions in the unphosphorylated protein can be disrupted and new ones created
