Unit 1 - Proteins Flashcards
What is the proteome?
The proteome is the entire set of proteins
expressed by a genome
Why is the proteome larger 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.
What are genes that do not code for proteins called?
Non-coding RNA genes
What do the Non-coding RNA genes code for and what do they do?
tRNA, rRNA and RNA molecules. These control the expression of other genes.
What are the factors affecting the set of proteins expressed by a cell?
- metabolic activity of the cell
- cellular stress
- the response to signalling molecules
- diseased versus healthy cells
What do eukaryotic cells have?
A system of internal
membranes
What does the system of internal membranes do for eukaryotic cells?
increases the total area of membrane
Because of their size, what do eukaryotic cells have?
A small surface area to volume ratio.
What does the small surface area to volume ratio of the eukaryotic cells cause?
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 do?
forms a
network of membrane tubules continuous
with the nuclear membrane
What does the Golgi apparatus do?
is a series of flattened
membrane discs
What do lysosomes do?
are membrane-bound organelles
containing a variety of hydrolases that digest
proteins, lipids, nucleic acids and
carbohydrates
What do vesicles do?
transport materials between
membrane compartments
Where are proteins and lipids synthesised?
In the ER
What is the difference between the RER and SER?
Rough ER (RER) has ribosomes on its
cytosolic face while smooth ER (SER) lacks
ribosomes.
Where are lipids synthesised and what happens to them?
Lipids are synthesised in the smooth
endoplasmic reticulum (SER) and inserted
into its membrane
What does synthesis of all proteins take place?
Cytosolic ribosomes.
What happens during the synthesis of cytosolic proteins?
The synthesis of cytosolic proteins is
completed in the cytosolic ribosomes, and these proteins remain in the cytosol
What do transmembrane proteins do during synthesis?
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 does the amino acid sequence determine?
determines protein
structure
What are proteins polymers made up of?
amino acid monomers
How are amino acids linked?
Amino acids are linked by peptide bonds
What do linked amino acids form
to form polypeptides
How are amino acids similar?
Amino acids have the same basic structure
How are amino acids different?
differing only in the R group present
How are R groups different?
R groups of amino acids vary in size, shape,
charge, hydrogen bonding capacity and
chemical reactivity
How are amino acids classified?
Amino acids are classified according to their R groups
What does it mean if an amino acid is basic?
It is positively charged
What does it mean if an amino acid is acidic?
It is negatively charged
What does it mean if an amino acid is polar?
It has differing charges
What does it mean if an amino acid is hydrophobic?
It hates water
If an amino acid is basic, what molecules will it have attached to it?
NH2 or NH3
If an amino acid is acidic, what molecules will it have attached to it?
COO or COOH
If an amino acid is polar, what molecules will it have attached to it?
OH
If an amino acid is hydrophobic, what molecules will it have attached to it?
Hydrocarbon
Other than shape, what else determines the function of the protein?
The wide range of functions carried out by
proteins results from the diversity of R groups
What is the primary structure of a protein?
The primary structure is the sequence in
which the amino acids are synthesised into
the polypeptide
What is the secondary structure of a protein?
Hydrogen bonding along the backbone of the
protein strand results in regions of secondary
structure
What type of bonding is involved in secondary protein structure?
Hydrogen bonding
What are examples of secondary structure?
alpha helices, parallel or antiparallel beta-pleated sheets, or turns
What does a polypeptide fold into?
Tertiary structue
What is the bonding tertiary structures?
Interactions between R groups involving hydrophobic interactions, ionic bonds, London dispersion forces, hydrogen bonds; disulfide bridges
What are disulfide bridges?
Disulfide bridges are covalent bonds between
R groups containing sulfur.
What are quaternary protein structures?
Quaternary structure exists in proteins with
two or more connected polypeptide subunits
What does quaternary structures describe?
Quaternary structure describes the spatial
arrangement of the 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 does the binding of haemoglobin to oxygen depend on
non-protein haem group
What does increasing the temperature do to the protein structure?
Increasing temperature disrupts the
interactions that hold the protein in shape;
the protein begins to unfold, eventually
becoming denatured.
What causes the changes to acidic and basic R groups?
pH
What does increasing/decreasing pH from optimum do to the protein structure?
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 is a ligand?
A ligand is a substance that can bind to a
protein
Where can ligands bind to in a protein?
R groups not involved in protein folding can
allow binding to ligands
How do ligands bind to proteins?
Binding sites will have complementary shape
and chemistry to the ligand
What happens to a protein when a ligand binds to it?
As a ligand binds to a protein-binding site the
conformation of the protein changes
What does the binding of the ligand affect as a result of the conformational change?
This change in conformation causes a
functional change in the protein
What are allosteric interactions?
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.
Why are allosteric interactions important?
This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration.
What is co-operativity?
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 when a modulator binds to an enzyme?
Following 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 modulators do?
Positive modulators increase the enzyme’s
affinity for the substrate
What do negative modulators do?
negative
modulators reduce the enzyme’s affinity.
How does the binding of oxygen in haemoglobin show co-operativity?
Changes in binding of oxygen at one subunit
alter the affinity of the remaining subunits for
oxygen
What conditions result in the reduced binding of oxygen in haemoglobin?
A decrease in pH or an increase in temperature lowers the affinity of haemoglobin for oxygen, so the binding of oxygen is reduced.
What conditions result in increased oxygen delivery?
Reduced pH and increased
temperature in actively respiring tissue will
reduce the binding of oxygen to haemoglobin
promoting increased oxygen delivery to tissue
What does the addition or removal of phosphate cause?
The addition or removal of phosphate can cause reversible conformational change in proteins
What is the addition or removal of phosphate known as?
This is a common form of post-translational
modification
What do protein kinases catalyse?
Protein kinases catalyse the transfer of a
phosphate group to other proteins
What happens to the phosphate group when it is added to the protein?
The terminal phosphate of ATP is transferred
to specific R groups
What do protein phosphatase catalyse?
The removal of a phosphate group from a protein.
What does phosphorylation do to the structure of the protein and what does it affect?
Phosphorylation brings about conformational
changes, which can affect a protein’s activity
What happens when a phosphate group is added to a protein?
Adding a phosphate group adds negative
charges. Ionic interactions in the
unphosphorylated protein can be disrupted and new ones created.
How do molecules move through 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 to the proteins that move through the Golgi apparatus?
undergo post-translational
modification
What is the major modification during post translational modification?
The addition of carbohydrate groups is the
major modification
How do the proteins leave the Golgi apparatus?
Proteins leave in vesicles that take proteins to the plasma membrane and lysosomes
How do vesicles move around in the cell?
Vesicles move along microtubules to other membranes and fuse with them within the cell
What happens to the proteins once they 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
Where are secreted proteins translated and what happens to them?
Secreted proteins are translated in ribosomes
on the RER and enter its lumen
What are examples of secreted proteins?
Peptide hormones and digestive enzymes
are examples of secreted proteins.
What happens to the secreted proteins at the Golgi apparatus?
The proteins move through the Golgi apparatus and are then packaged into secretory vesicles
What happen to the secretory vesicles after the Golgi apparatus?
These vesicles move to and fuse with the
plasma membrane, releasing the proteins out
of the cell
What might be required for secretory proteins to work?
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. Digestive enzymes are one example of secreted proteins that require proteolytic cleavage to become active.
What do enzymes do in the Golgi apparatus?
Enzymes catalyse the addition of various sugars in
multiple steps to form the carbohydrates.
