1 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)2 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 Bilayer3 Nucleic Acids Bases Purines (Adenine and Guanine) Pyrimidines (Cytosine, Uracil, Thymine) Nucleoside (sugar + base) vs Nucleotide (sugar + base + phosphate) Base-pairing (Watson-Crick) Nucleoside4 Chemistry Review Thermodynamics vs Kinetics Thermodynamics G = H - TS G = G + RTlnQ G = -RTlnKeq 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 H S -TΔS - + - Spontaneous at all temperatures + - + Non-spontaneous at all temperatures - - + Spontaneous at low temperatures + + - Spontaneous at high temperatures G<0 Keq>1 G>0 Keq<1 G=0 Keq=1 Keq Meaning K >> 1 Products favored at eq. K << 1 Reactants favored at eq. K ~ 1 Considerable Prod/React present at eq. G < 0 Spontaneous (exergonic) G > 0 Non-spontaneous (endergonic) G = 0 Equilibrium5 Enzyme Kinetics Michaelis-Menton Kinetics Higher Km, lower affinity for substrate Substrate Specificity Feedback Inhibition 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 ][][maxSKSVVm6 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 peptides7 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. Eukaryotes8 Organelle Function Nucleus 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) Ribosomes Translation of mRNA into proteins (present in both pro- and eukaryotes) Rough ER ER associated with ribosomes that is involved in synthesis and glycosylation of peptides to form glycoproteins destined for secretion or integration into the membrane Smooth ER Synthesis of lipids (membrane) and hormones often for export from the cell Breakdown of toxins in liver cells Golgi Apparatus Modification (glycosylation) and ‘packaging’ of proteins into vesicles for secretion or transport to cellular destinations (like lysosomes) Mitochondria 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 Lysosomes 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 Peroxisomes 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 Centrioles Source of the spindle apparatus used for cell division (acts as a microtubule organizing center a.k.a. MTOC) Not present in plant cells Vacuoles 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) Chloroplasts 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 side9 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 =