Protein Function Flashcards
Biological properties of a protein depends on binding to another molecule -> what kind of general functions can you think of?
- Antibodies attach to viruses and bacteria to defend the body
- Specific enzymes catalyze chemical reactions
- Actin molecules bind to one another to form stable filaments
What grants proteins their specificity in binding? (+how do we call the components of binding)
- Ligand = molecule that binds to the protein (“ligare” = to bind)
- Binding site = cavity at the surface of the protein which receives a ligand
- additionally some surface parts may be there to attract or attach protein to a particular part of the cell - Specificity depend on weak noncovalent bonds (hydrogen, electrostatic, van der Waals, hydrophobic) -> since weak they will work ONLY if the ligand fits perfectly to the binding site
-> prevents incorrect binding, allows tight bonding when a match is found
What are antibodies? What is their function?
= immunoglobin proteins produces by the immune system in response to a foreign substance (e.g. virus)
- By binding they either directly inactivate the target or mark it as “need to destroy”
- target molecules = antigens
What is the general structure of an antibody?
- Y-shaped molecules with 2 identical antigen binding sites, which are formed from several loops of polypeptide chain
- difference in length of the loops and amino acid sequence present there determines their specificity
What produces antibodies? How does it react to the antigens?
Antibodies are produced lyphocytes, or B cells
- each carries a different membrane-bound antibody -> encounters antigen that fits -> stimulated to divide and produce free antibodies
Where do we get antibodies in a lab?
Antibodies can be aquired from animals like mice, rabbits, sheep -> inject them with antigen A repeteadly over multiple weeks -? will activated specific B cells that produce anti-A antibodies
- We can then also fuse B cell with tumor cell => we get a specific B cell that can keep on dividing
How can antibodies help us viasulize certain molecules?
What do enzymes do?
Enzymes are specific types of proteins that bind to one or more ligands=substrates and convert them into chemically modified products => catalyze chemical reactions
Explain funtion of each of the following groups of enzymes: hydrolase, nuclease, protease, ligase, isomerase, polymerase, kinase, phosphatase, oxido-reductase, ATPase
What is the main function of lysozyme and where do we find it?
= enzyme that acts as a natural antibotic
- it severs the polysacharude chain of the cell wall of bacteria -> since bacteria is already facing strong forces of osmosis in the case of even a small cell wall damage it ruptures
- present in saliva, tears, egg whites
How exactly in chemical terms does lysozyme do its job?
Reaction catalyzed = hydrolysis
- In normal aquetous environment polysaccharide chains do NOT undergo a change because they would need to be in a spacific geometrical shape = transitional state -> that state requires a lot of energy = activation energy
-> a simple H2O cannot achieve that
BUT lysozyme can bind to active sites at the polysacharide chain -> forces it into the transitional state
-> the bond to be broken is held close to glutamic acid and aspartic acid -> conditions reduce activation energy needed for hydrolysis -> adds a H2O molecule to a single bond between 2 adjuscent sugar groups in a polysaccharide chain -> bond breaks
- breakage is favourable because it would take more energy to keep it together
Look at possible enzyme actions:
Where can we also encounter enzymes?
Drug development -> there are multiple treatment options that inhibit a specific enzyme connected to the disfunction of interest
- E.g. Methotrexate shuts down enzyme dihydrofolate reductase which produces coumpound for DNA synthesis during cell division => attacks cancerous cells
Is the order of amino acids all that’s needed to grant proteins such immense versatility in function?
No. Sometimes they also emply some small non-protein molecules which allow them to do something that amino acids are not capable of doing
- Enzymes do it as well, often associated with a small metal atom
- E.g. Photoreceptor rhodopsin forms a covalent bond with Retinal that is capapble of detecting changes in light -> if proton is absorbed -> retinal changes conformation -> amplified by rhodopsin -> cascade of events
- we need to consume vitamine A to synthesize Retinal
What levels of protein control can you think of?
1) Cell controls the amount of protein made (via genetic expression) and degraded
2) Control over enzymes by enclosing them into specific subcellular compartments
3) Level of the protein itself
What is meant by “enzymes generate a complex web”?
There is an abundancy of enzymes within the cell and together they create metabolic pathways - chains of chemical reactions in which product of one enzyme will be the substrate for another
- sometimes enzymes can even compete for substrates - decisions have to be made
So what kind of positive/negative mechanisms regulate the enzymatic activity?
1) Negative regulation = enzyme is supressed
- Feedback inhibition = the activity of enzyme 1 will altered/decreased by a binding (to regulatory site) product later in the metabolic pathway
2) Positive regulation = enzyme is activated
- product in one metabolic pathway stimulates an enzyme from another
Why did we start calling enzymes “allosteric” -> how did we resolve the “issue”? What does it depend on?
At the beginning - it was discovered that reculatory molecules had different shapes than the enzymes preferred substrate -> “allo” = other, “stere” = solid => allosteric
Later on realized that enzymes seem to have multiple binding sites - one for regulatory molecules, one for substrates => allows them to “communicate”
- actually all depends on the conformation (which shifts based on binding) i.e. if regulatory molecule binds -> conformation change -> makes the active site for substrate less favourable
Fill in: The difference between allosteric inhibition and orthosteric inhibition is that…
The orthosteric inhibitor binds at the same place as the substrate and the allosteric inhibitor binds at a distant place.
How may protein phosporylation aid the control of proteins? In general
Adding covalently one or more phospotate groups to protein’s amino acid chains -> provides negative charges -> attracts positive amine acids of the same proteion -> conformation change -> altering in the ligand binding sites
- could be removed by another enzyme = reversible
How may protein phosporylation aid the control of proteins? In detail
Enzyme-catalyzed transfer of the terminal phophate group of ATP to hydroxyl group on a serine, threonine, or tyrosine side chains
= catalyzed by Protein Kinase
Dephosphorylation = removal of the phosphate group is catalyzed by Protein Phosphotase
Learn: Cells contain hundreds of different protein kinases that can inhibit or stimulate specific proteins (depending on conformation). Similarly, protein phosphotases also have different forms - some that affect specific proteins, some that wide ranges => balance between these 2
For many proteins phosphate groups are added and removed in a continuous cycles -> can switch rapidly, the faster the cycle “turns” the more rapid changes can be observed in response to a stimulus
What else can phosphorylation enable? You may provide an example
It can also create a doscking sites where other proteins can bind -> create complex protein systems
E.g. binding of a ligand to receptor tyrosine kinases (transmembrane proteins) -> phosphorylation of receptor proteins on tyrosines -> allows for binding of intracellular signaling proteins
Is phosphorylation the only form of covalent modification that allows a change in the protein’s activity?
No the same can be sometimes achieved by acetyl group to lysine side chain, fatty acid to a cysteine chain, protein ubiquitin that labels the target for degradation
- There could be multitude of different modifications happening at the same time -> amount and type determines protein’s behavior
