Cells/Proteins KA2 Proteins Flashcards
What is the proteome?
The entire set of proteins expressed by a genome
Why is the proteome larger than the number of genes?
Due to alternative RNA splicing and post translational modification
Not all genes are expressed as…
Proteins in a particular cell
What does amino acid sequence determine…
Protein structure
Proteins are polymers of…
Amino acid monomers
What do amino acid link by? What does this form?
AA link by peptide bonds to form polypeptides
What is the primary structure?
The sequence in which the amino acids are synthesised into the polypeptide
Hydrogen bonding along the … results in … ?
Along the backbone of the protein strand results in regions of secondary structure
Name the types of secondary structure;
Alpha helices
Parallel or anti-parallel beta sheets
Turns
Identify the structure of amino acids;
Basic - positively charged
Acidic - negatively charged
Polar - hydrophobic
Polypeptide fold into a … ? What causes this confirmation?
Folds into a tertiary structure
This conformation is caused by bonding - such as interactions of the R groups in hydrophobic regions, ionic bonds, van der waals interactions - including hydrogen bonds and disulphides bridges
What is a prosthetic group?
A non-protein unit tightly bound to a protein necessary for its function
When does quaternary structure exist?
In proteins with several connected polypeptide subunits
What can interactions of the R groups be influenced by?
Temperature and pH
What do R groups at the surface of a protein determine?
Its location within a cell
Hydrophilic R groups will predominate…
What will hydrophobic R groups do in these proteins?
At the surface of a soluble protein found in the cytoplasm
Hydrophobic R groups may cluster at the centre to form a globular structure
Describe the fluid mosaic model…
?
What do regions of hydrophobic R groups allow for?
Allow strong hydrophobic interactions that hold integral proteins within the phospholipid bilayer
Some integral proteins are … ?
Give some examples
Transmembrane
For example, channels, transporters and many receptors
Peripheral proteins have fewer… ?
Hydrophobic R groups interacting with the phospholipids
What is a ligand?
A substance that can bind to a protein
R groups not involved in protein folding can allow binding to these other molecules
DNA binds to…
A number of proteins
What do positively charged Histone proteins bind to?
Negatively charged sugar-phosphate backbone of DNA in eukaryotes
The DNA is wrapped around histones to form nucleosomes packing the DNA in chromosomes
Other proteins have binding sites that are specific to…
Particular sequences of double stranded DNA and when bound to can either stimulate or inhibit initiation of transcription
As a ligand binds to a protein binding site or as a substrate binds to an enzyme’s active site, what happens?
The conformation of the protein changes, this change in conformation causes a functional change in the protein
When does induced fit occur in enzymes?
When the correct substrate starts to bind resulting in a temporary change in shape of the active site increasing the binding and interaction with the substrate
(During induced fit) what happens to the conformation of the enzyme?
The conformation of the enzyme changes and this alters the affinity of the active site for the substrate
In enzymes, what is related to induced fit? What does the chemical environment do?
Specificity between the active site and substrate is related to induced fit
The chemical environment produced lowers the activation energy required for the reaction
Describe the difference between positive and negative modulators with relation to the substrate
Positive modulators increase the enzyme affinity whereas negative modulators reduce the enzyme’s affinity for the substrate
Once catalysis takes place, what happens to the original enzyme?
The original enzyme conformation is resumed and products are released from the active site
What do some proteins with quaternary structure show?
Shows cooperativity in which changes in binding at one subunit alter the affinity of the remaining subunits
Describe cooperativity in the binding and release of oxygen in haemoglobin and the influence of temperature and pH
?
Describe the effect of temperature on haemoglobin’s ability to bind oxygen
As temperature increases, affinity for oxygen decreases
This is because hardworking tissues produce heat
Describe the effect of pH on haemoglobin’s ability to bind oxygen
As pH decreases, affinity for oxygen decreases
This is because hardworking tissues make carbon dioxide which decreases the pH
As a result oxygen is released to tissues
The addition or removal of phosphate from particular R groups can be used for?
Used to cause reversible conformational changes in proteins
The addition or removal of phosphate from particular R groups is a common form of?
Post translational modification
In this way the activity of many cellular proteins such as enzymes and receptors are regulated
What is kinase responsible for?
Often responsible for phosphorylation of other proteins
What is the role of phosphatase?
Phosphatase catalyses dephosphorylation
Some proteins (ATPases) use ATP for ?
Phosphorylation
Give an example of how ATPases use ATP for their phosphorylation
Eg. Myosin has heads that act as cross bridges as they bind to actin
When ATP binds to myosin, the myosin head detaches from actin, swings forwards and rebinds
The rebinding releases ADP and a phosphate ion drags the myosin along the actin filament
