Cell Biology Write down those examples! Theyre important.

Midterm supposed to be on a Wednesday, not a Thursday 4 major groups, carbohydrates, nucleic acid, amino acid, fatty acid Today is amino acid and protein. Perhaps introduce nucleotides and nucleic acid. Fatty acid next tine. What are amino acids? Building blocks, monomers, of protein. Understand terminology of structure. Amino group, carboxyl group, an incredibly alpha carbon, side chain R group could be metal, ring structure. Depending on what goes inside R group, it truly dictates the characteristic of amino acid and perhaps the protein. Amino acid has the ability to become ionized. If you have this in the water, ability to become ionized. It will now have a charge. Amino terminus and carboxy terminus. NC There are 20 amino acids that ccan be found anywhere. Every single one is designated for who they are because of the R group. Amino acids: you NEED to know this table! Why is an amino acid negative, which one is it? An amino acid with a negative charge on the side change aspartic acid, glutamic acid. Hydrogen bonds, need N or O or C. an absence of these polar bonds means a nonpolar a-acid. Number of carbons determine hydrophobic or philic Glycine has a carboxyl and amino right in the corner which makes it very polar. So can form hydrogen bonds. Has ability to do some for of hydrogen bonding and be polar. 1. the characteristic of the amino acid is almost always dictated by the R group. 2. an R group that has an oxygen or a nitrogen is considered to be polar. Wy? It has the ability to form hydrogen bonds, and that makes it polar. 3. an amino acid that has a positively charge R group is considered basic. An amino acid that has a negatively charged R group is considered acidic. Have the ability to become phosphorilatyed Only 3 of them have the ability to become phosporolated: Thre-, Ser-, Ar-, When you are adding on to something, you need a kinase to put a phosphate group to these amino acids. Only aa with a hydroxyl group has ability to phospohrate AA. Need that and kinase. Significance of phosphorylation Controls enormous amount of signaling cascade. Tyrosine, Threonine, Serine Polypeptides Chain: A glucose is good but it can only do so much. You need to make a polymer for it to be useful!

A very similar thing here. You have AA which are the building blocks for proteins. The question is how is this protein being formed using these AA. In order to form a polypeptide, you need to form a peptide bond. A peptided bond, what is it? When you remove a molecule of water to bond them together, what is it called? Condensation Very similar thing as to the carbs. You remove a molecule of water, and what tyou are forming is a dipeptide. Two amino acids. The key yto remember is the peptide bond right here. You got a C C N. that is a peptided bond. It can grow to be literally thousands in some cases. As many as a hundred amino acid or as many as ten thousand amino acid. A thousand different AA linked together by a peptided bond and most imporatnyl each of these has a different R group. Each r group will dictate to the protein to behave based on their characteristics. Lets say an amino acid like P53. Its a very popular tumor suppressor gene. There are about 1200 amino acid. Out of them each hAA dictates P53 to be like that specific AA. It is a combination of many different AA that gave rise to the properties of that protein. When you have a chain of polypeptideds, right here, recognize the peptide bond, CCN, CCN, or N and C but CCN is the safest. What you need to do is again theres a direction. You got N terminus, carboxy terminus. N terminus is known as C terminus. Carboxy terminus known as C terminus. The R group dictates the property of that protein. So now that you know AA are very complicated by default because of their R group, also AA can be put together with polypeptide to make larger pieces of protein, but they have to have a way to fold themselves, to get a confirmation, which is truly the least amount of energy required. Cell us a very efficient system. They dont like to waste energy. They will find very specific way to make sure AA is folded to be comfy and happy but very low amount of energy. Folding takes place among the R group. Folding of protein usually or almost always is predicted because of the R groups. The R groups make whether the protein should fold this way or that way. There are also tiny little proteins called chaperones that have the ability to help navigate the r group where they should go. Lets pick a few of these, lets dive in and see what are some of the folding criteria. What needs to take place in order for protein to fold itself into the right position. Here is the amino acid. Here is potentially another amino acid. Multiple bonds that could take place. Ionic bonds, literally steal an electron, there are ydrogen bonds (last week), there are vanderwaals attractions (not really bonds but because of AA you tend to have very temp short charge. Tiny snapshot of positive or negative. Potentially allows for vanderwaals). In some cases covalent bonds. Which amino acid forms covalent bonds? Cystine. Its the only one. Which amino acid has cystine in it? Methionine. Only AA with ability for covalent bonds and disulfide bonds. In adition to that, there is disulfide bonding that is happening between AA that has sulfur in them. Globular proteins: Here is what happens to the metal group. If you have a protein unfold. Now you really truly have to acknowledge all these R groups forming properly. Inside the R group folding is unequivocably

hydrophobic. The protein needs to do a lot of diff maneuvering to make sure this happens (protein folding slide). Final shape has to be at the lowest free energy possible. Protein can potentially be denatured and go back and renature because of the hydrogen bonds they have ability to break very easily. Can be broken by heat, ph, chemical compounds. SDS can break down many things. Another one: reeeeeally nasty. Called BME. Beta __ Ethanol. BME is a reducing agent with ability to break bonds and it stinks. Urea also has ability to denature proteins. 3 different possibilities: SDS BME Urea These are the three potential ompounds that can denature protein. Heat can denature protein too but those are only the hydrogen bonds that get denatured with heat. How proteins actually fold, how they get their shape. Linus Poling, very intelligent chemist frfom Cambridge. Got two nobel prizes. One for chemistry and peace. Got nobel prize for chemical bonds. He identified the structure of protein as well as chemical bonds. AA can line up and potentially have (now again dont worry about what they are) but basically form hydrogen bonding in a way where it will take a helical shape. You can have parallel or anti parallel beta sheets. Alpha helix, beta sheets, loops for none of the above The overall structure of AA: At least 4 level of how AA can potentially organize itself. That org is ahat dictates the overall characteristic of a protein. 1. primary. P 2. secondary: where the hydrogen bonding comes into play. alpha helix and the beta sheet. They are not primary. Have actual confirmation. Have actual hydrogen bond that allows them to take confirmation of alpha helix or beta sheet. 3. tertiary is a bit more involved. In addition to bonding there is non covalent bonding going on in between R groups. The alpha helix and the beta sheets now are somehow, the R groups are now forming specific bonds. The R groups of the secondary structure have ability to do some form of interaction.completly 4. quanternary is most complicated and always include more than one peptide. mature protein or mmature polypopetides come together and form 4th. The tertiary structure of hemoglobin (there are 4 of them) has ability to bond to HEM, that contains iron. What does hemoglobin do>? Carries oxygen throughout the body. Picks it up at the lungs.in order for the most fundamental physiology in system to work, must have a properly functional quanternary structure of protein.

Sickle cell anemia deficiency in the hemoglobin structure. Coillapse of red blood cell. Cant travel freely. What is being anemic? (always exhausted lack of oxygen due to less iron) Domains C beta sheets into beta barrels. Give rise to specific channels in bacteria. You can have more than one beta barrel and they can attach to each other. Another really truly good example of the importance of how ther teriarty structure of proteins is critically is the example from before, cystic fibrosis. If you dont understand significance of protein folding, not worth much. The most important job of the CFTR is to take chlorine out and bring sodium in. its a sodium chloride channel. It can go either way if im not mistaken. For CFTR what is happening is something hass to go in, something has to go out. Specifically used for sodium chloride channel. Normal person with normal teriary protein of CFTR makes a nice channel where chloride goes out and eventually outside and sodium goes in. keeps homeostasis. Maintained from the going back and forth. If you break this, the chlorine gets accumulated inside and sodium outside. Why does that happen? One of the most common is a delta 508 mutation. 90% of people wit CF have a delta 508 mutation. Does not allow protein to fold properly. One AA makes such a difference that it changes confirmation and closes the channel. Mutation changes concentration of mucus outsided of the cell. It enhances bacterial infections. Whats the importance of protein folding? One example. CF or hemoglobin. Protein has 4 structures. 4th is important, has hemo, blah blah. 3rd is important because CF blockage changes environment. Mucus accumulation cause bacterial infection and death.

Cystine makes double bond with sulfide. Proteins are identified with xray crystallography. Have to do it in very cold weather. What are proteins functions? PROTEIN FUNCTIONS IN THE CELL 15% of cell They are the majority of the enzyme in the cell are made out of protein. Some made of rna but far and few in between. You cant do anything without enzymes in the cell. Signaling how does the cell know to do anything? Have to have a proper signaling mechanism. Majority of signaling molecules are proteins. Gene regulation. None f the gene expression will take place unless you have proteins that are transciptioin factors. Have to have these for gene of interest to become activated.

GLYCOPROTEINS Serine and threonine get specific glycosolation called O-linked glycosilation. You can only add o-linked sacharides that you can add onto them.

Another type of glycosilation known as N-linked asparagine (ASN) Dna is a helix but three shapes that are all together. Triple helix. Francis crick and james Watson distance between ~2nm. ~3.4nm. Hooray crystallography! Only way they figured it out was based on distance. There monophosphate, diphosphate, triphosphate. There are two types of sugar. The DNA has a deoxyribo (missing a hydroxyl group at position #2) A DNA has the exact same structure as the one in RNA but it is missing a hydroxyl group. Only has a hydrogen. Did life start with RNA? What is most important part of replication? The RNA primer! Why? Because it has a free hydroxyl group. Cannot extend dna unless youhave a free hydroxyl group. Has to provide that at the 3 end. Makes RNA very totes complicated. There are two (dna and rna) dna has deoxyribo and rna has ribose. In dna nitrogenous bases are cytosine and thymine and guanine and adenine. RNA has uracil instead of thymine. Cyclic AMP: messenger. No only can nucleotides give rise to dna and rna but also enzymes and coA and ATP and other things. Just like aa give rise to proteins Sugar gives rise to carbs Nucleotideds give rise to nucleic acids ALL THROUGH CONDENSATIOOOOOONNNN Formed with phosphodiester bonds Here is an ester bond. Since you have two they are a phosphodiester bond. It is formation of that that gives rise to a nucleic acid. Phospho bond can only happen at 3 group. Grows from 5 to 3. Keep adding a new base with the sugar with the phosphate at the 3 hydroxyl group. Since dna is double stranded it has too have other basses going from 5 to 3. When you put sugar backbone outside and bases inside, theres incredible opportunity for hydrogen bonding between the hydrogenous bases. ATP AND ADP CONVERSION

A few pointers from this lesson: By far most important is the amino acidsd. The overall structure is totally dependednt upon the r group. Characteristic of r group that dictates the primary, 2 3 4 structure of the protein. Protein can take those structures because of alpha beta and sometimes loops. Once you have those structures they can act as enzymes, channels, receptors, etc. You need to understand at least the basis of importance of AA and polypeptides and good example for each one. (CF and hemo) DNA quick review. May wanna learn about nucleotides, rna and dna difference, how was dna discovered. Critical thing that was required was actual distance between the helix. The 2nma dn 3.4nm

And couple of stuff on the last slide.