Macromolecules - Large biological molecules like protein and nucleic acids; polymers of subunitsWater- 80% of planet, 70% of cell is water; all reactions occur in the context of water- Not just a medium for reactions, but part of the reactions and part of the structure of the entire cell- Water a polar molecule, so can form hydrogen bonds, which can clump water molecules together in specific structures (book, castle, etc.)o Leads to emergent properties of water like surface tension, high specific heat (must break hydrogen bonds)o Hydrophilic and hydrophobic properties Philic – will dissolve in water; polar molecules; ex. NaCl integrates into the water structure (hydration shell) Phobic – won’t dissolve in water; non-polar; oils, hydrocarbons- 3D structure of proteins and other molecules is due to the power of watero Example – amphipathic cellular membranes (fatty acids); phospholipid bilayer  Hydrophilic head, hydrophobic tail Can form 3D sphere structure or form a plane (bilayer) structureProteins- X-ray crystallography – methods used to determine protein structureo First, must crystallize the protein in question; purify the protein and let it evaporate in vacuum environment to form crystals; atoms in the protein arrange and align themselves in a stacked patterno Crystal put into the machine; x-rays directed towards the protein crystal; the stack of atoms is hit with the x-ray, it is diffracted and this diffraction is captured electronically, telling us where the atoms of the protein areo X-ray crystallography by Rosalind Franklin in 1953 helped predict the structure of DNA- Electron microscopy – 1,000,000-5,000,000 fold increase in magnification; equivalent of taking a single cell and amplifying it to the size of an Olympic swimming pool - Average protein size – 300 amino acidso Small hormones (oxytocin/vasopressin) – 9 aao Largest – 27,000 - Amino acids link together through peptide bonds – amino group links with the carboxylic acid of different amino acids – produces water as a by-product- Primary structure – amino acid sequence; all proteins in our body have different primary structures and functionso If there are 20 amino acids, there are 160,000 possible combinations for any 4 amino acid sequenceo 20^n where n=length of amino acid sequence will give you how many possible combinations and sequences of amino acids you can have- Secondary structure – way that the amino acid sequence can fold up; particular folding pattern has strong relationship with that particular protein’s functiono Particular folding pattern is a function of amino acid sequenceo Happens in water spontaneously - Learn to draw one of each category – non-polar, polar, acidic, basico Be able to look at a structure and be able to say which one belongs to which category- Forces that determine and support the correct 3D structureo Hydrophilic/hydrophobic interactions of the R groupso Bonds/interactions between the R groupso Interactions between nearby peptide bondso Prolineo Cofactors like Mg2+ and Zn+ Non-amino acid elements- 2 cysteine amino acids can covalently bond together – only example of two R groups forming covalent bonds with each othero Other cases of bonding between R groups are ionic bonds or hydrogen