9-3-13- Free radicals= highly reactive particles. Chain reaction nuclaeic acids and cell membranes do a lot of damage. Peroxisomes get rid of these. Peroxisomes also help with lipid metabolism BINDING SITE- Will so closely interact with a ligand- 2 main characteristicso shapeo distribution of charge - something smaller like a protein or something will interact with this siteo chemical mesangero something enzyme will act on o etc- most of what proteins do (not all) will be due to its interaction with an enzyme like basic chemistryo binding site & substrate = ligand whereaso binding site and ligand = all- 4 main things to look at in binding siteo specificity- if we had a lock and a key (which the binding site ligand islike that) you have to have the right key to fit in the lock for it to work but you don’t have have to have 1 unique key but maybe a small group of chemicals of related shapes that are gonna fit in due to the shape and charge distribution for example: on hemoglobin mole cule; binding site for oxygen carbon dioxide wont fit but carbon monoxide will so it can bindwith those 2 things! *** FIGURE 3.28o Affinity- if its gonna bind how easy is it to get that binding how long does that binding last. So the binding is temporarty connection NOT GONNA USE COVALENT BINDING. Three things will influence affinity: Charge The right shape Concentration- if I increase the concentration will increase the likelihood of the binding  ***can still have a binding site with low affinity  ***FIGURE 3.29 so like a positive and a positive with the right shapes will have low affinity but a negative and a positive with the right shapes will have a high affinity o saturation- if I have a protein with a binding site and that protein is one of the transporters in a plasma membrane (with the lipids) and a transmembrane protein and I wanna bind to this binding site and im gonna change the shape of this protein so that binding site is exposed to the other side of the (so I change the shape) the time to do all of this9-3-13will limit the time if all of the binding sites are full if they are all saturated I reach a MAXIMAL CAPACITY ***FIGURE 3.30 if ive reached saturation I can make some more proteins  saturation does lead to a maximal physiological characteristic but I can change that with increasing the amnt of proteins (can also decrease the amnt of proteins)o competition- occurs when I have different ligands. If I have more thanone ligand that will fit and bind then theres a competition between them. The one with higher affinity will win. The lower affinity one will bind just not as much. And how much the lower affinity one binds depends on the amount of difference between the competition  hemobglin example: - the room has like 20% oxygen in the room and the hemoglobin pulls it into body blood etc- if I have less oxygen then carbon monoxide we will die because the affinity for carbon monoxide has the higher affinity so we would die because the oxygen wont get to tissues and braino can pump oxygen into air to get more oxygen to us o and decrease the amount of carbon monoxide by pumping it out  can manipulate the competition two ways by- changing the relative concentration of proteins - changing the number proteins- changing the shape of proteinsHOW IM GONNA CONTROL PROTIENS……- all the proteins are coded by the DNA so all the proteins aren’t activated by a given number of cell- protein has to be coded in dna - first of all we need to have the right DNA (PROCESSING OF DNA)o genetically modified organisms- like put something in strawberries to not let it die when it freezes; basically we can modified what coding we can doo **figure 3.19o first we need the exons vs the introns (thing we don’t need) o then we copy the code on hthe RNA, = primary RNA transcription can turn this off and on with proteins == this is one place for control o then we splice- nucleus acts on ??? = cut out the introns and put together the exons9-3-13 we can also control splicing- can take the same dna and create different proteins.  So we can regulate which proteins are in the cell with this splicingo This piece will go out to the nucleus and bind to a ribosome and do translation Can turn this one on and aoff= we can regulate this process If we need a protein fast we should control it at this level because its faster than transcription - Posttransational modification= things that happen after the translationo i can make it in an active form or an inactive form o splitting= ooccurs in the cytoplasm or the out side of the cell not nucleus ** fig 3.23 by cutting off a part of the chain we change the 3-d shape which will change how that protein will interact with other things like ligands can be a single or multiple  can occur immediately after translation or a long time after  can occur in totally different part of your body- were gonna have some proteins made in your liver that the splitting will happen in the kidneys or lung because that’s where the enzymes that do it are locatedo methylation- were gonna take this protein and stick methyl on it on certain spots. It can change the activity of that protein, and can help localize. Its basically the address for where the cell needs to go  important in nuclear proteins for the RNA and DNA - made in the ribosome makes sure it goes back to the nucleuso glycosalation- ^same but with a sugaro covalent modulation- manipulating the shape of the binding site.**fig 3.32 SINGLE binding site but have phosphate added on = phosphorlation (chemical reation) (covalently add a phosphate which comes from an ATP) which changes that functional site. So in this case phosphorlation turns the protein on BUT CAN TURN OFF BUT USUALLY TURNS ON - Dephosphorlation- taking the phosphate off - Way we control this is with an enzyme (which speeds up the rate of the reation but does not control the direction of the chemical reaction that’s up to concentration) - Kinase- enzyme for PHOSPHORLATION- Phosphotace- enzyme for DEPHOSPHORLATION9-3-13o allosteric modulation- manipulating the shape of the binding site. This one I need two  functional site- enzyme site. Transport site regulatory site- bind metabolic process site or chemical messanger . this site will change the shape of the functional site- when change the shape turn the protein on (or off) then will increase the