Bio

• Carbon biochemistry is all based on carbon backbones (only C and H bonds). Like octane (also called gasoline): C8H18 and glucose C6H12O6
• The important functional groups for biology: (R remainder: could be anything but has to start with C)

  Hydroxyl group: (alcohol) → R-OH 

  Phosphate: (organic phosphate). It’s an energy carrier

  Amino group: NH2-R occurs in amino acids 

  Carbonyl : R-C=O-H or R-C=O (depends on if it’s place at the end or in between two carbons)

  Carboxyl : R-C=O-OH → very important acid, covers most of biology
• The wet weight of our body (muscles, organs, etc everything that isn't bones, hair or teeth) is made of 75% water. Among the remainder are the large molecules (about 24%) and the rest are ions and small molecules. 
• Large molecules (24% of our body) are mostly proteins, nucleic acids (RNA and DNA), carbohydrates (sugars), lipids  (can never be polymers)
• Proteins, nucleic acids and carbohydrates are called macromolecules or polymers because they occur in polymers of thousands of subunits that are linked together. 

  \_ It’s a contrast to lipids that can also be big but can never be linked together, they are always single molecules. 
• Polymerization is the bonding of monomers, the formation of covalent bonds. 

  We distinguish two important processes:

  -Condensation reaction: a monomer comes in and forms a new covalent bond that gets attached to the growing polymer chain. A water molecule is released. 

  -The opposite reaction of polymerization is hydrolysis which means splitting with the help of water. The water helps to break down the covalent bond and forms another covalent bond. 
• Proteins are machines that do important work in our body. They come in all shapes and sizes with different functions (some proteins cut dna, enzymes (proteins that speed up certain reactions), gets rid of alcohol, structural proteins)

  They range in size from a few amino acids to thousands of them (titin = 33000 amino acids). We call them peptides. 

  Proteins are polymers of amino acids.
• There are 20 different amino acids. 
• Basic structure of all amino acids:

  They always start with an amino group (NH3+), then they have a central carbon with a side chain R attached. It’s this remainder that differentiates each amino acid. On the other side is the carboxyl group (COOH-)
• DNA stands for: Deoxyribo Nucleic Acid
• There are three types of amino acids. Nonpolar AA, polar AA and completely charged AA.
• The non polar amino acids mostly have C and H in their side chains.
• The polar amino acids have polar covalent bonds, hydroxyl group. They have a partial charge so they can interact with each other by forming hydrogen bonds.
• The completely charged amino acids have a carboxyl group that gives a charge and can form ionic bonds in the interior of proteins.
• When you form polymers (in this case peptide bond formation), it’s the amino group, the nitrogen atoms that initiate the covalent bond between C and N and it releases one molecule of water.
• Every peptide starts with an amino group and ends with a carboxyl group. 
• The primary structure, determines how proteins can fold and what kind of function it has. 

  As the protein comes out of the ribosome it is completely unfolded but all the information is already present in the sequence of the amino acids. 
• Proteins go from a linear polypeptide (unfolded) to something more functional. 

  The initial folding only involves peptide backbone, there is no sidechain involved. 
• When the protein goes out of the ribosome, hydrogen bonds are formed between the C=O that has a partial negative charge and the H-N that has a partial positive charge on the other side. This is called the secondary structure formation
• Types of secondary structures: The alpha-helix → is a straight rod helix where aa 1 forms a hydrogen bond with aa 4. The hydrogen bond is always in the same direction as the rod and that helps stabilize the structure. The side chains are not involved and are pointed towards the outside, they help with the interactions with other surrounding structures but don’t play a role in the structure.
• Types of secondary structure: The beta pleated sheet → is a plane, is flat. The hydrogen bonds are between the N-H and the O=C. The side chains stick out of the plane upwards or downwards not contributing to the sheet. 
• Proline fits neither alpha or beta. It’s the only amino acid among the 20 that forms a ring structure with the neighboring N atom that belongs to the peptide backbone. There is no H atom because the outermost shell is filled. Therefore it cannot form hydrogen bonds needed to make a secondary structure. The CN bond can't rotate anymore because it has the shape of a ring.
• The side chains determine the tertiary structure. They are formed by low energy interactions such as hydrogen bonds between polar covalent bonds, hydrophobic interactions and Van der Waals interactions, the disulfide bonds, ionic bonds between the amino and the carboxyl group.   

  They are all formed in the interior of the folding proteins.
• The disulfide bond/bridge is rare, it can occur in keratin for example.

  It is mediated by the covalent bond formation between the two cysteines. Cysteine have this SH sulfide group. If during the folding they come together in proximity then a disulfide bond forms between these two cysteines. It’s the only covalent bond you’ll find outside of the peptide bond, and is the only covalent bond you will find tertiary structure between two amino acids. 
• In large proteins you always find stretches of hydrophobic amino acids and stretches hydrophilic of amino acids. They will automatically rearrange in a way where the hydrophobic stretches point inwards, away from the water to minimize the disruption of the hydrogen bonds, and all the hydrophilic amino acids will rearrange to interact with water and will be on the outside. 
• The coiled coil is a structure you can find in keratin. Multiple alpha helices wrap around each other like ropes. This works because there are hydrophobic amino acids in every 4th position of the alpha-helix.  The stripe of hydrophobic amino acid slowly winds around the helix.  
• Some proteins are not functional after tertiary folding and are not functional as a single polypeptide. 

  It means they have to form a dimer or a tetramer or even higher order structures. This process is called quaternary structure/folding. 
• Sometimes you mutate a single amino acid and that can completely destroy the protein but for other proteins you can make a change and it won’t affect anything → we call that a neutral mutation.
• The experience of heating and cooling a protein showed for the first time that proteins carry everything they need to fold/unfold within their primary structure. All the information is incoded in aa sequence. Also shows that the interactions are fairly weak because you can disrupt them with heat.
• Protein turnover means the breakdown and resynthesis of proteins that occurs constantly in our body. Every protein has a half life. When the half life is reached, half the proteins are broken into individuals aa and form into new proteins.
• Chaperones are specialized proteins that keep proteins from reacting inappropriately with one other. They allow proteins to be separated so they can mature individually and fold before being released.
• Nucleotides are made up of N as the base that gives the identity to the nucleotide. The other parts are the backbone made of a sugar and the phosphate group. 
• Sugars in nucleotides are made up of five C, O, a hydroxyl group and the standard sugar is ribose. The C atoms are labeled into primes (from 1 prime to 5 prime). This is important for how a monomer is attached to the growing peptide chain because it’s always the 5 prime and 3 prime carbons that are involved in the elongation of RNA and DNA.
• The sugar found in DNA is unusual. It is called deoxyribose because it lacks one oxygen. Instead of a hydroxyl group it has just one Hydrogen and that makes it more stable. It’s important for DNA because it is able to store genetic information.
• The nucleotides can occur in monomers and carry one phosphate and they can also be energy carriers so carry one phosphate group or can be biphosphate or triphosphates.
• Nitrogenous bases: 

  The pyrimidines are made up of a single aromatic ring. There’s Cytosine, Uracil, Thymine. 

  The purines have two aromatic rings. There’s Guanine and adenine. 
• To form the bonds the hydroxyl group is always attached to the 3 prime carbon and the phosphate group is always attached to the 5 prime carbon of the incoming monomer. This gives rise to the phosphodiester linkage.
• Base pairing of DNA: 

  Two nitrogenous bases interact and the only way to fit inside DNA is to have three aromatic rings, the purine-pyrimidine pair that limit the base pairing and you can only get Guanine paired with Cytosine and Adenine with Thymine.
• The two strands of DNA are held together only by two hydrogen bonds and are really hard to disrupt.
• All the nitrogenous bases are facing inwards and therefore are protected to avoid mutations because it’s the bases that carry the genetic information. 

  The sugar phosphate backbone is facing towards the outside and is interacting with surrounding water.