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IB BIOLOGY Topic 2.1- 2.5 Molecular Biology Biochemistry • Branch of organic chemistry that attempts to explain chemical characteristics and reactions that occur in living organisms. • Biomolecules: – – – – Carbohydrates Lipids Proteins Nucleic Acids Molecules to Metabolism • Metabolism – – Collection of chemical reactions involving biomolecules, that occur during living processes – Reactions occur in predictable patterns • Ex: Insulin – Insulin is a protein hormone that facilitates the movement of glucose from the blood to the inside of the cell – Binds to hormone receptor outside of cell glucose channels open – Glucose in high concentration outside of cell glucose continues to diffuse into cell – Receptor molecule and protein channel are both coded for by DNA Carbon-based Life • Organic moleculecontains carbon • Ex: CO2 • Inorganic molecule- no carbon • Ex: H2O • All biomolecules are organic • Carbon always forms 4 covalent bonds with other elements • Other elements common to organic molecules: – H, O, N, P Biochemical Compounds • Polymers of biomolecules are composed of monomers. • Pg. 54 • Fill in charts provided, both Table 2.1 and 2.2 Metabolism Controlled by Enzymes • Molecular movement in an aqueous environment causes collisions among molecules • All reactions within cells-metabolism • Determining factors of Reactions: – Identity of colliding molecules – Orientation of colliding molecules – Speed of colliding molecules • Enzymes increase odds of collisions reaction Enzymes • Enzymes are proteins • Ex: Formation of ATP that catalyze chemical – ADP + Pi ATP reactions – Binding a phosphate takes energy (food, • There are sites on the sunlight) enzyme that are specific – ATP synthase increases to the binding of a the odds of a collision particular reactant, or reaction substrate – Facilitated the covalent bond (adding the phosphate) Enzymes, cont. • Enzymes are used in the following: – – – – – – Replication of DNA Synthesis of RNA Synthesis of proteins Cellular respiration Photosynthesis Digestion Catabolism and Anabolism • Catabolic reactions: – Break molecules down – Break polymers to monomers • Hydrolysis: – Breaking molecules using an H2O molecule • Anabolic reactions: – Build molecules – Add monomerspolymers • Condensation: – Building molecules by removing H2O molecule https://www.youtube.com/watch?v=D hHoz-W_3Rk Catabolic Reaction Anabolic Reaction Water • Water is solvent of life • Living cells are in aqueous environment • Structure: – Covalent bonding of H to O – Result: partially positive and partially negative poles – Hydrogen bonding does occur between hydrogens of H2O molecules • Ephemeral • Polarity– Partially positive and partially negative poles – Affects orientation of molecule in solution https://www.youtube.com/watch?v=nSENolWbyYQ Water, cont. • Cohesive properties: – Attracted to each other – Hydrogen bonding occurs • Locked into place ice • Liquid water lots of movement between molecules • Ephemeral H Bonding: – Why H2O forms droplets – Why H2O has surface tension – Why H2O moves in a column in plant tissues Water, cont. • Adhesive Properties: – Attraction between two unlike molecules – Water “beads” on many surfaces – Adhesion keeps water column in plants from dropping • Attraction of H2O to cellulose Water, cont. • Thermal Properties – High specific heat • Can absorb or give off lots of heat without affecting H2O temperature • Heat stabilizing – High heat of vaporization • Absorbs lots of heat as it evaporates – Ex: perspiration Water, cont. • Solvent properties: – Like dissolves like – Medium of biochemistry • Animals: – Blood • High water content • Solutes in blood: – – – – Glucose Amino acids Fibrinogen( clotting) Hydrogen carbonate ions(transport of CO2) • Plants: – Vascular tissue: • Xylem- carries H2O up from roots • Phloem- carries dissolved sugars down from leaves to rest of plant Water, cont. • Hydrophylic- H2O loving – Polar – Majority of biochemically important molecules are polar – Polar solvent easily dissolves polar solute – Ex: carbohydrates soluble due to hydroxyl (alcohol) groups • Hydrophobic- H2O hating – Non-polar – Mainly C and H compounds • Ex: lipids, methane • Proteins-differentially polar depending on arrangement Table 2.4 pg 66 • Complete chart provided Carbohydrates and Lipids • Monosaccharides – Building blocks of polysaccharides – Most common: • Trioses C3H6O3 • Pentoses C5H10O5 • Hexoses C6H12O6 • Condensation reactions in monosaccharides – Joins monomer larger polymer Functions of Major Polysaccharides • Cellulose: • Glycogen: – Major component of plant cell walls, gives rigidity and support to roots, leaves, stems – Not digestible in humans • Dietary fiber • Starch: – Organic product of photosynthesis, stored as granules in chloroplasts, or roots (storage structure) – Two subcomponents: • Amylopectin • Amylose – 3 glucose carb is straight chained – Excess glucose stored in liver and muscle – Only 24 hour supply stored – Requires enzymes to break it down to glucose for cellular use • All: monomer-glucose Fatty Acids • All have carboxyl group – (-COOH) at end • All have methyl group – CH3 at other end • All have multiple CH2 groups in between • Saturated Fatty Acids: – All carbons are saturated with hydrogen, no bends in the chains – Animal products; • Butter, bacon, fat in red meat • Solid at room temperature Fatty Acids, cont. • Monounsaturated FAs – One double bond in chain • Polyunsaturated FAs – At least 2 double bonds – Plant based: olive oil – Liquid at room temperature Fatty Acids, cont. • Hydrogenation: cis and trans fatty acids – Double bonds eliminated, totally or partially by adding hydrogens during processing – Straightens out bent shape – Naturally curved: cis FAs – Hydrogenated: trans Fas – Trans FAs behave like saturated fats • Omega-3 – Cis FA – Fish oils Condensation Reactions • Formation of triglyceride lipids: – Fats in animal cells, oils in plant cells – Vary greatly Energy Storage in Humans • Glucose glycogen in liver and muscle tissue • Triglyceride lipidsadipose tissue – Twice the energy per gram – Insoluble in water – Do not upset osmotic balance • Glucose stored in cells would attract water due to concentration gradient difference Chylomicrons • Small particle made of fat and protein • Produced in alimentary canal and released into the bloodstream • Transport fats to the liver and other tissues • LDL- low density lipoproteins • Elevation of these LDL levels is undesirable for health Calculating BMI • Uses weight and height • Formulas: – Metric: weight(kg) / height(m) – Imperial: weight(lb.) / height(in) x height(in) x 703 Proteins • Formation of polypeptides: – Cells use 20 naturally occurring AA to make proteins – Polypeptide encoded by DNA – Genes can be expressed differently for different cellular proteins • Pancreas- translates DNA sequence that encodes insulin • Humans: – 20,000-25,000 genes per cell – Grape plants- 30,000 – Chickens- 17,000 • All genes encode for possible polypeptides found in that organism Proteins, cont. • Synthesis of polypeptides: condensation reaction – Sequence of AAs determined by DNA, but reactions are identical. • Variability of Polypeptides: – Each has own AA sequence and own folding pattern Proteins, cont. • Levels of polypeptide and protein structure – (Complete Table 2.8 with grid provided ) – Primary structure: • Sequence of AAs – Secondary structure: • Repetitive shapes of either helixes or pleated sheets – Tertiary structure: • A globular shape (enzymes) – Quaternary structure: • Two or more polypeptides combine to make a single functional protein (hemoglobin) Proteins, cont. • Proteins vs. polypeptides: – Proteins are organic substances consisting of covalently bonded amino acids, ready to carry out function – Polypeptides are single AA chains with its own primary structure that may or may not be able to serve a biochemical function without further modification • Genome: – Unique DNA sequence of one individual • Proteome: – Unique set of proteins for each individual Denaturing Proteins • Intramolecular bonds that determine protein shape can be altered by temperature and pH. – Alteration of unique 3-D shape renders them useless in biochemical reactions – Can be reversible if most covalent bonds remain when temperature and pH return to normal