Exam 1 Final Exam Review Sheet 4 types of biomolecules Nucleotides these make up DNA RNA and polymers of these are nucleic acids Nucleic acids have 4 monomers Adenine Thymine replaced with urasil in RNA Cytosine and Guanine Amino Acids 20 naturally occurring amino acids Amino acids are made up of two functional groups Amino groups and carboxylic acids Polymers of amino acids are proteins Proteins are used for signal molecules enzymes cell structure and function and catalysts Carbohydrates important for energy energy storage and cell to cell recognition Polymers of carbs are polysaccharides Polysaccharides important for energy storage Lipids hydrocarbons that are insoluble in water Usually have a hydrophobic and hydrophilic component This is the only biomolecule that does not have a polymer 3 types of biopolymers nucleic acids proteins polysaccharides Water properties polarity H bonding non covalent interactions hydrophobic effect Hydrogen bonding occur due to electron arrangement This is the attraction of partial positive and negative charges Hydrogen and an electronegative species Hydrophobic effect phenomenon that occurs when polar and non polar molecules come into contact Non covalent interactions van der waals hydrogen bonding ionic interactions Polarity how equal bonding electrons are shared Leads to a dipole moment Buffers Henderson Hasselbalch problems practice problems from class exams Amino acids if given a structure classify it as hydrophobic polar charged ID peptide bonds N C termini in aa chain Levels of protein structure Primary basic amino acid sequence made only of peptide bonds Secondary occur in amino acids that are in close proximity to each other Tertiary Structure amino acids that are not in close proximity to each other interact with one another Only deals with covalent bonds Exam 2 Hemoglobin myoglobin what is p50 difference between sigmoidal hyperbolic p50 is the pressure that allows for 50 of protein saturation The lovwer the p50 the stronger the affinity Myoglobin has a lower p50 than hemoglobin so it has a stronger affinity This makes sense because it stores oxygen and holds onto it rather than transporting it like hemoglobin T vs R state of hemoglobin describe and explain importance T state is the tense state and this is when no oxygen is bound to the iron It has 5 but it wants 6 and it has a low affinity for oxygen The T state is more stable because it is trying to work and stabilize itself The R state is the relaxed state Fully bound with oxygen Has a higher affinity because all parts are bound The shape of the R state changes the overall shape Bohr effect effect of BPG binding to hemoglobin The bohr effect states that hemoglobins ability to bind to oxygen also depends on the pH Lungs the lungs need a higher pressure of oxygen in order to get it back CO2 is released and then converted into a bicarbonate which increases the pH The pH and pressure in the lungs is higher Tissues the tissues need a low pressure and lower pH so oxygen can be released Low pressure and pH lowers the affinity 2 3 BPG binds in the T state and stabilizes hemoglobin when there is no oxygen bound It keeps the affinity low in the tissues and has no effect in the lungs It decreases affinity for oxygen in the tissues so it will be released and it keeps oxygen in the tissues 3 types of enzyme catalysis allosteric inhibition regulate the flux of biochemical through metabolic pathways Multisubunit enzyme that binds one unit and conformation effects binding Associated with feedback inhibition Regulates allosteric enzymes Covalent modification of enzymes adding phosphate groups Ubiquination tag put on proteins to be destroyed Proteolytic in order for some enzymes to be active they must be cleaved This is necessary because we don t want enzymes to be active everywhere all the time An example of this is lysozyme We add mostly phosphate groups to modify so they are not active everywhere Lock key vs induced fit model for substrate binding to enzyme importance of weak interactions Lock and Key model the substrate is a perfect compliment to the enzyme Induced fit model complimentary to the transition state The substrate and the enzyme are not a perfect fit so it must change shape to enter the transition state The enzyme and substrate are held together by non covalent interactions Non covalent interactions allow the enzyme and substrate to be held together but yet break easily Enzyme kinetics know Michaelis Menton eq calculate kinetic parameters from Lineweaver Burke plots practice problems from class exams ID competitive mixed non competitive inhibitors from Lineweaver Burke plots kcat specificity constant Exam 3 Saturated unsaturated and Trans fats Saturated fats contain no double bonds and are fully saturated with hydrogens Unsaturated fats contain double bonds and do not have a full compliment of hydrogens They can be in the cis or trans conformation Trans fats act a lot like saturated fats because they can stack easily where as cis unsaturated fats created a kink in the structure Cis are usually liquid at room temperature Trans are usually solid Recognize general lipid types be able to indicate structures of glyercophospholipids sphingolipids glycolipids glycoproteins Passive vs active membrane transport Passive transport requires no input of energy and it follows the concentration gradient This differs from active transport because active goes against the gradient and requires energy Facilitated diffusion is an example of passive transport A protein is added to assist in the transport across membrane Membrane Proteins Integral membrane proteins embedded in the membrane hydrophobic interactions hold them together Also contain alpha helices and beta sheets These allow for movement by creating a hole in the membrane Peripheral membrane proteins only attached to one side of the protein usually polar and charged Have no contact with the hydrophobic region Tight association Non covalent interactions hold them together Lipid linked membrane proteins attach to the hydrophobic region usually a fatty acid can be attached to the n terminis myristolated or the c terminis prenylated N linked lipid proteins are only attached to the amino acid always a cysteine attached to an asparagine O linked are usually isoprene groups Form thioester bonds and only involve amino acids that have an OH group Define catabolism anabolism A B C D Anabolic Builds up Catabolic Degrades Thermodynamics calc G G Keq