Unit 1 : Cells and Proteins Key Area 2 Flashcards
Genome
An organisms complete set of DNA (not all this DNA codes for proteins)
Proteome
Entire set of proteins that can be expressed by an organisms genome (much larger than no. Of genes)
Describe alternative RNA splicing and how it allows many proteins to be produced form a single gene
Different combinations of exons can be left in or removed during transcription to produce different mature RNA transcripts.
number/type of protein produced by a cell can vary over time and can be affected by factors such as ;
Metabolite activity of the cell, cellular stress, in response to signalling molecules, diseases vs healthy cells
Eukaryote
Cells which have a clearly defined nucleus
what are cell membranes called specifically in eukaryotic cells?
plasma membranes
what is the result of eukaryotes having a small surface to volume ratio?
There’s not enough membrane to preform all the vital functions
What does a series of intracellular membranes help with?
protein synthesis and transport in the cell
Name 4 organisms that have intracellular membranes?
Endoplasmic reticulum, golgi appartus, vesicles and lysosomes
Endoplasmic reticulum
a series of membrane tubules that extend from the nuclear membrane.
whats the difference between the rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER)
RER has ribosomes dotted along its surface whereas the SER doesnt.
Golgi apparus
a series of flattened membrane disks that proteins can pass through to be modified.
Lysosomes
Membrane-bound organisms that contain hydrolases which are enzymes.
What do hydrolases do?
They break down proteins, lipids, nucleic acids and carbohydrates - they use water to break covalent bonds in these substances.
Vesicles
membrane-bound organelles that transport proteins and other substances around the cell.
What are membranes composed of?
Both lipids and proteins - synthesised in the cells at the endoplasmic reticulum
Cytosolic proteins
They remain in the cytosol
Transmembrane proteins
They are permanently attached to a membrane.
What part of the phospholipid bilayer does lipids form?
Hydrophobic lipid tails
Where are lipids synthesised?
Synthesised in the smooth endoplasmic reticulum + inserted into its membrane.
Cytosol
the fluid in which the organelles are suspended
cytoplasm
cytosol and all the organelles (not the nucleus) within the plasma membrane.
How do proteins move through the golgi apparatus for post-translational modifications
Proteins move from one disk to the next in vesicles that bud off and fuse with the next membrane.
Give an example of a major post-translational modification that occurs in the golgi?
The addition of carbohydrates to form a glycoprotein.
Enzyme catalyse the addition of various sugars in multiple steps to form the carbohydrates
Summarise the movement and modification of transmembrane proteins after the insertion of proteins into the RER membrane?
Transport vesicles carrying protein leave the RER membrane + fuse with the golgi.
post-translational modifications (ie. the addition of carbohydrate) occurs.
vesicles that leave the golgi apparatus take proteins to the plasma membrane + lysosomes.
describe the movement of proteins between membranes and the modifications they may undergo.
After insertion into the RER membrane, transmembrane proteins are carried in transport vesicles to the golgi apparatus.
These vesicles move along the golgis flattened membrane disks by budding off one disk + fusing with the next.
This is where post-translational modifications occur. The major one being the addition of carbohydrates. Once completed proteins are packaged into vesicles them to either the plasma membrane or lysosomes.
what are many proteins that are destined to be secreted from the cell synthesised as?
inactive precursors, and require proteolytic cleavage to produce active proteins. (this is an example of post-translational modifcation in secreted proteins)
Summarise the secretory pathway.
- proteins are synthesised at the RER and then enter the lumen of the RER where they’re packaged into transport vesicles.
- Proteins move through the golgi apparatus and undergo modification such as addition f carbohydrates and proteolytic cleavage.
- Once modificed, proteins are packaged into secretory vesicles which tavel and fuse with the plasma membrane, releasing the protein out of the cell.
If amino acids are monomers what polymer do they join together?
proteins
What are long chains of amino acids joined together with?
peptide bonds
what are the R-groups
the variable section of the amino acid - this is what gives rise to many different amino acids.
Amino acids join together with a peptide bond between what two groups?
The ‘c’ of the carboxyl group of the 1st amino acid and the ‘N’ of the amine group
What is the amino acids being joined together descibed as.
A water molecule is lost, this is descibed as a condensation reaction.
The structure of the R-groups determines what?
the properties of amino acids
R-groups can be (4 types)
Acidic, basic, polar and non-polar (hydrophobic)
are acidic R-groups hydrophobic or hydrophilic?
hydrophilic
whats the charge of the acidic R-groups?
negative
whats the key component of the acidic R-groups?
a carboxylic acid group (COOH)
are basic R-groups hydrophobic or hydrophilic?
hydrophilic
whats the charge of the basic R-groups?
positive
whats the key component of the basic R-groups?
an amine group (NH2)
are polar R-groups hydrophobic or hydrophilic?
hydrophilic
whats the charge of the polar R-groups?
neutral
whats the key component of the polar R-groups?
Carbonyl groups (CO), hydroxyl (OH) or amine (NH2) groups or a sulphdyl group (SH)
whats the key component of the non-polar R-groups?
hydrocarbon groups, usually in long chains or rings.
are non-polar R-groups hydrophobic or hydrophilic?
hydrophobic
whats the charge of the non-polar R-groups?
neutral
what is the primary structure of a protein?
the sequence in which amio acids are synthesised into the polypeptide - the order of amino acids.
what is the secondary structure of a protein?
Hydrogen bonding along the backbone of the protein strand results in regions of second structure.
what is the tertiary structure of a protein?
the overall shape of the folded protein that is stabilised by R-group interactions.
Hydrophobic r-group interaction
when hydrocarbon groups come close together
LDF r-group interactions
when hydrocarbon groups come close together - van der waals force.
ionic bonds r-group interactions
electrostatic attraction between oppositely charged ions, can be disrupted by changing the pH or additon of charged molecules ie. the addition of phosphate.
Disulphide bonds r-groups interactions
strong covalent bonds formed between sulphur containin r-groups.
hydrogen bonds r-groups interactions
weak electrostatic attraction between hydrogen + a nearby oxygen or nitrogen atom.
What does the quaternary structure descibe?
the spacial arrangement of the subunits.
what are prosthetic groups and what are they used for?
non-protein subunits, they are neccesary for its function.
whats an example of a prosthetic group?
haemoglobin - has a non-protein haem group that allows oxygen to bind.
How does temperature affect protein structure?
increasing temp disrupts the interactions that hold the protein in shape, the protein begins to unfold, eventually becoming denatured.
How does pH affect protein structure?
The charges on acidic or basic R-groups are affected by pH.
as pH increases/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?
substance that binds to a protein at sites that have complementary shapes and chemistry to the ligand. These binding sites are R-groups that aren’t involved in protein folding.
what does ligand binging cause?
Causes a conformational change (shape) which causes a functional change (job)
many proteins that have multiple subunits are allosteric, what does it mean?
their activity is regulated by altering their conformation. Allosteric interactions occur between spatially distinct sites on a proteins surface.
what are modulators?
modulators bind to allosteric sites and change the conformation of the active site.
they can be either positive or negative.
how does positive modulators affect the allosteric enzyme?
increases the enzyme’s affinity for the substrate
how does negative modulators affect the allosteric enzyme?
reduce enzymes affinity for the substrate
what happens when a ligand binds to one subunit of an allosteric protein
can change the affinity of the remaining subunits
describe the co-operativity of haemoglobin
when an oxygen molecule binds to one of four binding sites, this changes the conformation of the remaining 3 binding sites, increasing the affinity of the remaining subuits for oxygen.
What does the additon or removal of phosphase groups cause?
conformational change in proteins. this process is reversible and is an example of a post-translational modification that is not limited to the golgi.
How can protein activity can be regulated?
phosphorylation and this process can activate or inhibit proteins.
What are the steps involved in the phosphorylation and dephosphorylation of a protein
- kinase removes the terminal phosphate group from a molecule of ATP reducing it to ADP.
- kinase then add that phosphate group to the protein, this changes the conformation and function of that protein.
- phosphate removes the phosphate group from the proteins and adds it back on the ADP regenerating it into ATP.
- this changes the conformation of the protein back to the original conformation
