Unit 1- Binding to Ligands and Conformational Change Flashcards
What is a ligand?
A ligand is a substance that can bind to a protein.
Give examples of proteins which the ligand DNA can bind to?
Histone proteins can bind to DNA allowing it to be packaged- these ligands have positively charged R groups allowing it to bind to the negative sugar-phosphate backbone of the DNA.
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.
Define allosteric enzymes
An allosteric enzyme is an enzyme that contains a region to which small, regulatory molecules may bind in addition to and separate from the substrate binding site and thereby affect the catalytic activity.
What do modulators do to enzymes?
Cause a change in conformation which will either increase the enzymes affinity for its substrate (positive modulator) or decrease its affinity for its substrate (non-competitive inhibitor/negative modulator)
What is meant by cooperativity in proteins?
Changes in binding of a ligand at one subunit alter the affinity of the binding of ligands at the remaining subunits eg. haemoglobin.
How does haemoglobin show cooperativity
When an oxygen molecule binds to one subunit, it changes the conformation of the subunit. This changes the conformation of the other subunits, increasing the oxygen affinity of these other subunits. As the oxygen affinity of a haemoglobin molecule increases further as oxygen binds to each subunit, oxygen collection is therefore maximized where oxygen levels are high. Conversely when oxygen levels are low the release of an oxygen molecule from one subunit decreases the oxygen affinity of the other subunits. In low oxygen areas (working tissues) the release of oxygen from each subunit decreases the oxygen affinity of the other subunits, thus maximizing the release of oxygen where it is needed.
What environmental factors can affect the binding of oxygen to haemoglobin
pH and temperature
What does a high temperature and low pH cause haemoglobin to do?
Haemoglobin has a lower affinity for oxygen this is because these conditions will be present in working tissues so this allows oxygen to be more readily offloaded to these tissues.
Why does the oxygen dissociation curve move to the right as the size of the mammal decreases?
Mammals that are smaller have a bigger surface area to volume ratio and therefore need to be able to carry out more respiration to maintain body temperature so need to be able to offload oxygen more readily.
What enzymes catalyse phosphorylation and dephospho rylation?
1) Kinases catalyse phosphorylation, which is the transfer of a phosphate from ATP to the protein.
2) Phosphatases catalyse dephosphorylation, which is the removal of phosphate from a molecule.
What are ATPases?
A group of transmembrane enzymes that use the phosphate from ATP to phosphorylate themselves, rather than their substrate. The phosphate binding changes their conformation and so alters their function.
What are the steps in muscle contraction?
1) Myosin heads are bound to actin to form cross bridges.
2) The binding of ATP to the myosin causes a conformational change. This makes the myosin head detach from the actin and swing forwards.
3) The ATP is broken down to ADP and phosphate. These stay bound to myosin and cause a second conformation change so..
4) …the myosin head rebinds to the actin which causes yet another conformational change in the myosin so…
5) …the ADP and phosphate are released from the myosin. The myosin head swings back to its first conformation, dragging the actin filament along. And then the cycle is ready to start again.
What does myosin act as?
An ATPase
Why is it important for DNA to be able to be packaged?
Allows efficient transcription
