1. DP Chemistry Standard Level Option B.2 By: Alexander Burant

2. Table of Contents (Click where you want to go) Structure of Proteins Condensation Reactions Electrophoresis Secondary Structures

3. B.2 Proteins and Enzymes What you should understand by then end of this presentation: Understand what proteins and amino acids are Understand protein structures How does its shape affect function in metabolic processes How pH, temperature, and heavy metals affect enzyme activity The use of chromotography By the end I should be able to: Deduce structural formulas of reactants and products Explain solubilities and melting points of of zwitterions Apply relationships between charge, pH and isoteric point for amino acids and proteins

4. Terms to keep in mind Zwitterion: a dipolar ion that has both a positive and negative charge but overall neutral. Zwitterions are not dipoles – Zwitterions are commonly called inner salts – Overall, they are neutral but contain regions with positive and negative charges. – Overall, a zwitterion is neutral

5. Terms to keep in mind Amphoteric: can have properties of both acids and bases Buffers: solutions that can resist changes in pH Isoelectric point: a point that is electrically neutral

6. To understand proteins, we need to understand amino acids Amino acids are acids, obviously, that are comprised of an NH 2 and a COOH. Amino acids can be called the building block of nearly all biological structures. What’s so special about them? They form many of the biological structures such as muscles, cells and tissue Most importantly, they can bond together in a condensation reaction to make long chains called a polypeptide. They do this in a condensation reaction

7. Condensation Reactions This are reactions when two molecules come together to make a larger one as a smaller one is released. Notice in this amino acid that in blue, we have an OH molecule. Notice in this amino acid that in blue, we have an H molecule. Notice that the red portion of the molecule on each amino acid has a single bond with the blue. This mean that each amino acid can ditch the other. Notice that the C=O And N-H bonded together This then means that H2O Needs to be released.

8. 2-amino acids The previous example is that of a dipeptide and water If another amino acid was added then it would be tripeptide There are many combinations of these peptide chains which gives us the great variance of amino acids. FYI: 2-amino acids have another name by α – amino acids

9. What Exactly are Proteins? IB Language: Proteins are large macromolecules made up of chains of 2-amino acids formed by condensation reactions. Let’s break this definition down put it in english

10. IB Language: Proteins are large macromolecules made up of chains of 2-amino acids formed by condensation reactions. Macromolecule: a really big molecule Amino acid Condensation Reactions: This is when two typically larger molecules come together and in the process release a smaller molecule (typically water )..

11. What do proteins do? The enzymes of the proteins are a catalyst for man of the reactions in the body Structure in the body Energy source Some are hormones Some are carrier molecules such as hemoglobin that carries oxygen in our cells.

12. Protein Structure Recall that proteins are chains of the 2-amino acids. Imagine that proteins are like headphones and you just put them in your pocket. – What happens to them? – This same concept occurs to proteins The entanglement of proteins give them 3D shapes which affect functions. The structure is affects by the same forces as regular molecules such as hydrogen bonding and van der Waals’ force. – The Primary structure is the condensation reaction itself ie the long chain of amino acids. – Secondary structure of protein bond via intramolecular hydrogen bonding. – Tertiary Structure can be held together by Vander Waals’ force, hydrogen bonding, and ionic attractions due to ionic groups. This controls the function of the protein and can be held together by disulfide bridges and hydrogen bonding

13. Secondary Structures Think of the head phone analogy – Long headphone chords get tangled – So do long chains of enzymes The chains create different structures due to the intramolecular forces we have previously learned about. In secondary structures, this “entanglement” occurs from hydrogen bonding – Remember that hydrogen bonding is not actual bonding but an attraction of hydrogen to highly electronegative molecules.

14. Secondary Structures Continued Remember what a hydrogen bond actually is. The highly electronegative atom, bonded with a hydrogen, “hogs” the electrons which leaves the partially positive hydrogen to be partially attracted to other electronegative atoms. Now image a long chain of amino acids, the lone hydrogens will want to bind somewhere else on the chain which creates the helix formation. This fancy word for this is α-helix. It looks like this

15. Another Type of Secondary Structure Β-pleated sheet is another form of bonding where the atoms form a sheet by hydrogen bonding

16. How do we analyze proteins? In order to analyze, the proteins must be broken down by HCl Paper Chromatography – The unknown amino acid is placed near the bottom of the chromatography paper. – The paper is placed in a solvent which causes the amino acids to rise – Different amino acids move up the paper at different rates Electrophoresis – The structure of the amino acid determines pH which is called the isoelectric point

17. Electrophoresis? Amino acids change structure at different pH levels Lets think this through as to what happens when an amino acid is places in a solution with low pH – What does this mean? – A low pH means a high concentration of H+ or low? – These extra protons latch on to the amino acid What happens at a high pH – A solution with high pH mean more H+ or OH- – What will happen to the protons on the amino acid? Will the soltuion with OH- abundance accept H+ or donate? The solution will accept H+ so it can make water, not donate H+ leaving an unstable oxygen. With this knowledge, we can say that amino acids act as buffers Now each amino acid will find the spot where it finds its unique pH level and this is called the isoelectric point.

18. Electrophoresis Since each amino acid has its own isoelectric point The acids are placed in a gel with a specific pH where a potential difference is applied to it (fancy way of saying it is hooked up to a battery or another source of electricity). The acids move across the gel at different rates. They are sprayed and then identified How do we know which way they move? – Remember that opposites attract – A negatively charged molecule will move toward the positive electrode.