BCHM 307 1st Edition Exam 1 Study Guide Lectures 1 15 Lecture 1 January 14 Water and Organic Chemistry What is a covalent bond A covalent bond is the strongest biochemical bond It requires an input of energy to break it The two molecules in a covalent bond have shared pair s of electrons What is a dipole A dipole forms due to differences in electronegativities between atoms and their geometry Partial dipole charges can cancel each other out to create no net dipole The H atoms in water are dipole positive and the Oxygen atom is dipole negative Some basic electronegativities to know are Fluorine 4 Oxygen 3 5 Nitrogen 3 Carbon 2 5 and Hydrogen 2 1 What are some properties of water Water is a solvent It can form hydrogen bonds with other water molecules It can dissolve hydrophilic and polar molecules Water has a high boiling point The hydrogen bonds keep the 3 D structure stable List the common functional groups of biochemistry CH4 Methane RCH4 Methyl RCH2R Methylene RCH CHR Methene RCX O Carboxylic Acid RCHR OH Alcohol RCH O O C O Carbon Dioxide Aldehyde RCR O Ketone Lecture 2 January 16 What is oxidation and how can carbon become more oxidized Oxidation refers to what happens when a molecule loses electrons Carbon becomes more oxidized with added oxygen bonds Carbon dioxide is the most oxidized form What are hydrophobic and hydrophilic molecules Hydrophilic molecules are polar and can form hydrogen bonds with water They are water loving molecules Examples are sugars and salts Hydrophobic molecules are nonpolar and fear water They can t form hydrogen bonds because they lack certain functional groups They hydrophobic effect refers to the segregation of hydrophobic molecules in water The hydrophobic molecules will bond with each other Water will surround the molecules and form a cage around it What are amphiphilic molecules Fatty acids are an example They have polar heads and nonpolar tails They will form a sphere in water with the heads facing outwards Detergents work due to their amphiphilic properties Acid and Basic Chemistry What is the equilibrium constant It is equal to the concentration of hydrogen times the concentration of hydroxide atoms divided by the concentration of water in the solution Water dissociation will break into equal concentrations of hydrogen and hydroxide ions What is pH pH log H Each pH unit equals a 10 fold increase in acid or base properties What is a conjugate base A conjugate base is a compliment to the acid When the acid loses a proton it forms the conjugate base What are Ka and pKa Ka concentration of hydrogen time concentration of dissociated acid over concentration of original acid pKa log Ka A strong acid has a large Ka and a small pKa A large pKa means a stronger base What is a buffer Buffers help a system to maintain a constant pH They bind or release protons based on the need The maximum buffer capacity is reached within one pH unit of the pKa Lecture 3 January 21 Amino Acids What is an amino acid Amino acids are the basic building blocks of proteins All contain a basic amino group an acidic carboxyl group an alpha carbon attached to a hydrogen and a variable R group The R group gives the amino acid its unique properties There are 20 amino acids What is chirality and stereoisomers Chiral means when there are 4 different substituents attached to the alpha carbon Enantiomers are stereoisomers that are mirror images of each other Enzymes that have specific binding sites are stereospecific Proteins are made from L Amino Acids How are amino acids characterized Amino acids are grouped into three categories based on their R groups The hydrophobic nonpolar group is one They avoid interactions with water and often have C C or C H bonds The polar uncharged amino acids cannot accept or donate a proton in a solution at a physiological pH Polar charged amino acids can donate or accept a proton Lecture 4 January 23 What are the specific properties of different amino acids Glycine is the only non chiral amino acid Methionine is used to initiate polypeptide chains Proline has a rigid backbone and will form a kink in a polypeptide chain Phenylalanine and tryptophan are aromatic amino acids Serine can be modified by kinases Tyrosine absorbs light at 280 nm and can be phosphorylated Cysteine can make disulfide bonds Aspartate and glutamate are negatively charged Lysine arginine and histidine are all basic amino acids Lecture 5 January 26 What is the shikimic acid pathway It is a long and complex pathway that bacteria plants and yeasts use to make aromatic amino acids Humans cannot perform this due to our diet What are essential amino acids Essential amino acids are the 10 amino acids that cannot be naturally made in our bodies What is EPSP synthase It is an enzyme that all plants have which blocks the production of aromatic amino acids and is in herbicides Ascorbic acid is required for the hydroxyproline and hydroxylysine to be produced A deficiency in vitamin C leads to scurvy Why are acidic and basic amino acids important Shifting the pH will cause different protein interactions to happen What is a zwitterion It is an amino acid at a neutral pH that does not have a charged R group but have an overall net charge What happens to charged molecules at different pH values Using alanine as an example of this At a low pH the charge will be 1 At a neutral pH the charge will be 0 At a high pH the charge will be 1 Amino acids also have pKa values Lecture 6 Janurary 28 How are amino acids linked together Peptide bonds are formed through the removal of water to link together amino acids They are formed the carboxyl and amide groups of two amino acids Peptides don t have to have structure and are normally less than 100 amino acids long They do have direction with an N amino terminus and a C carboxy terminus The peptides form a protein s backbone What are some important biological peptides and their functions Insulin regulates the uptake of glucose in the body and is involved with signaling Endorphins are neurotransmitters Oxytocin is a cyclic peptide hormone that has disulfide bridges and intramolecular crosslinks Antibodies are involved in defense HDL and LDL are used for storage and transport Actin is involved in movement What is a protein s primary structure The primary structure is the sequence of amino acids along the peptide backbone It dictates the protein s shape and therefore function as well It can be described as which amino acids are present or composition or by