Biology Day 1 Biomolecules Chemistry Review Enzymes and Metabolism Carbohydrates Monosaccharides glucose fructose galactose Oligosaccharides sucrose glu fru lactose gal glu and maltose glu glu are disaccharides Polysaccharides starch glycogen cellulose chitin etc Storage and structural polysaccharides Starch glucose polymer functioning as energy storage in plants Glycogen glucose polymer functioning as energy storage in animals Cellulose glucose polymer functioning as a structural polysaccharide in plant cell walls Chitin N acetylglucosamine polymer functioning as a structural polysaccharide in insect exoskeletons and fungal cell walls Proteins Amino Acids Polar hydrophilic vs nonpolar hydrophobic side chains Acidic vs basic side chains Asp and Glu are acidic negatively charged at pH 7 Lys and Arg are basic positively charged at pH 7 some include His as basic but not positively charged at pH 7 1 Lipids Cholesterol Increases membrane fluidity at low temperatures Decreases membrane fluidity at high temperatures Steroid precursor Triacylglycerols triglycerides 3 fatty acids bonded to glycerol via ester linkages Phospholipids Lipid Bilayer 2 Nucleic Acids Bases Purines Adenine and Guanine Pyrimidines Cytosine Uracil Thymine Nucleoside sugar base vs Nucleotide sugar base phosphate Nucleoside Base pairing Watson Crick 3 Chemistry Review Thermodynamics vs Kinetics Thermodynamics G H T S G 0 Spontaneous exergonic G 0 Non spontaneous endergonic G 0 Equilibrium H S T S Spontaneous at all temperatures Non spontaneous at all temperatures Spontaneous at low temperatures Spontaneous at high temperatures G G RTlnQ G RTlnKeq G 0 Keq 1 G 0 Keq 1 G 0 Keq 1 Keq K 1 K 1 K 1 Meaning Products favored at eq Reactants favored at eq Considerable Prod React present at eq Kinetics Catalyst 1 Speeds up a reaction 2 Lowers the activation energy in both directions 3 Provides an alternate mechanism pathway for the reaction to occur 4 Is not consumed in a rxn 5 Does not shift the equilibrium Reaction Coordinate Diagrams 4 Enzyme Kinetics Michaelis Menton Kinetics Higher Km lower affinity for substrate Substrate Specificity Feedback Inhibition V Vmax S Km S Competitive Inhibition Inhibitor binds to the active site Increases Km Does not change Vmax Non competitive Inhibition Inhibitor binds somewhere other than the active site Decreases Vmax Does not change Km 5 Cooperativity Sigmoidal curve Hemoglobin vs myoglobin Bohr Effect H and CO2 decrease the affinity of hemoglobin for O2 Enzyme Regulation 1 Allosteric Regulation ex feedback inhibition 2 Phosphorylation covalent modification Ser Thr and Tyr residues can be phosphorylated by kinases use ATP hydrolysis or phophorylases Phosphatases dephosphorylate enzymes Phosphorylation can either activate or inhibit an enzyme depending upon the enzyme 3 Zymogens inactive precursors that become active upon proteolytic cleavage 4 Cofactors involvement of metal ions or organic molecules coenzymes 5 Association with other peptides 6 Cellular Structure Prokaryotes Single circular dsDNA genome and possibly the presence of a plasmid s No nucleus membrane bound organelles or mitotic apparatus Coupled transcription and translation Eukaryotes 7 Organelle Nucleus Ribosomes Rough ER Smooth ER Golgi Apparatus Mitochondria Lysosomes Peroxisomes Centrioles Vacuoles Chloroplasts Function DNA storage and site of transcription Surrounded by a nuclear envelope 2 lipid bilayers through which nuclear pores regulate traffic of large molecules Contains the nucleolus dark spot which is the site of rRNA synthesis Translation of mRNA into proteins present in both pro and eukaryotes ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to form glycoproteins destined for secretion or integration into the membrane Synthesis of lipids membrane and hormones often for export from the cell Breakdown of toxins in liver cells Modification glycosylation and packaging of proteins into vesicles for secretion or transport to cellular destinations like lysosomes Site of ATP synthesis via ATP Synthase as a result of oxidative phosphorylation PDC Kreb s cycle and the Electron Transport Chain Site of fatty acid catabolism oxidation Have their own DNA circular and ribosomes for self replication Contains acid hydrolases digestive enzymes and have pH 5 Degradation of old organelles or phagocytosed materials Produced from the Golgi Apparatus Not present in plant cells Involved in the breakdown involving hydrogen peroxide of many substances including fatty acids amino acids and various toxins Carry out the glyoxalate cycle in germinating plant seeds Source of the spindle apparatus used for cell division acts as a microtubule organizing center a k a MTOC Not present in plant cells Fluid filled membrane bound vesicles used for transport storage of nutrients and other substances pumping excess water out of a cell and cell rigidity in plants Site of photosynthesis in plant cells Animal cells have lysosomes and centrioles not present in plant cells Plant cells have cell walls chloroplasts and a central vacuole not present in animal cells Mitochondrial Structure PDC and Citric Acid Cycle occur in the matrix ETC Complexes are located in the inner membrane Proton s are pumped actively from the matrix to the intermembrane space ATP synthase is located in the inner membrane and synthesizes ATP on the matrix side 8 Metabolism Catabolism breakdown of molecules to release energy Anabolism construction of molecules requires energy Oxidation Reduction Catabolism of Glucose oxidation of glucose C6H12O6 6O2 6CO2 6H2O Highly exergonic G is negative Anaerobic Catabolism of Glucose 1 Glycolysis cytosol substrate level phosphorylation 2 Fermentation cytosol Glycolysis NAD NADH reduction glucose 2 pyruvate oxidation initial investment of 2 ATP followed by production of 4 ATP net of 2 ATP formation of ATP here is referred to as substrate level phosphorylation Regulation inhibited by ATP feedback inhibition and glucagon low blood sugar hormone response activated by AMP other reactants and insulin high blood sugar hormone response Fermentation occurs when aerobic respiration isn t possible regenerates NAD for more glycolysis NADH NAD pyruvate ethanol and CO2 pyr lactate Pyruvate CO2 acetaldehyde ethanol oxidation reductions Alcohol Fermentation obligate anaerobe can t survive in the presence of O2 carry out only fermentation or anaerobic respiration facultative anaerobe capable of fermentation or aerobic