1 Topic 2.1- 2.4 Molecular BiologyIB BIOLOGY HL Topic Molecular Biology

2 Biochemistry Branch of organic chemistry that attempts to explain chemical characteristics and reactions that occur in living organisms. Biomolecules: Carbohydrates Lipids Proteins Nucleic Acids

3 Molecules to MetabolismCollection 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

4 Carbon-based Life Organic molecule- contains carbon Ex: CO2Inorganic 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

5 Biochemical CompoundsPolymers of biomolecules are composed of monomers. Pg. 54 Fill in charts provided, both Table 2.1 and 2.2

6 Metabolism Controlled by EnzymesMolecular 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

7 Enzymes Enzymes are proteins that catalyze chemical reactionsThere are sites on the enzyme that are specific to the binding of a particular reactant, or substrate Ex: Formation of ATP ADP + Pi  ATP Binding a phosphate takes energy (food, sunlight) ATP synthase increases the odds of a collision reaction Facilitated the covalent bond (adding the phosphate)

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9 Enzymes, cont. Enzymes are used in the following: Replication of DNASynthesis of RNA Synthesis of proteins Cellular respiration Photosynthesis Digestion

10 Catabolism and AnabolismCatabolic reactions: Break molecules down Break polymers to monomers Hydrolysis: Breaking molecules using an H2O molecule Anabolic reactions: Build molecules Add monomerspolymers Condensation: Building molecules by removing H2O molecule

11 https://www.youtube.com/watch?v=DhHoz-W_3Rk Catabolic ReactionAnabolic Reaction

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13 Water Water is solvent of life Living cells are in aqueous environmentStructure: 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

14 https://www.youtube.com/watch?v=nSENolWbyYQ

15 Water, cont. Cohesive properties: Ephemeral H Bonding: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

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17 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

18 Water, cont. Thermal Properties High specific heatCan 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

19 Water, cont. Solvent properties: Animals: Plants: Like dissolves likeMedium 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

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21 Water, cont. Hydrophylic- H2O loving Hydrophobic- H2O hating PolarMajority 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

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23 Table 2.4 pg 66 Complete chart provided

24 Carbohydrates and LipidsMonosaccharides Building blocks of polysaccharides Most common: Trioses C3H6O3 Pentoses C5H10O5 Hexoses C6H12O6 Condensation reactions in monosaccharides Joins monomer larger polymer

25 Functions of Major PolysaccharidesCellulose: 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 Glycogen: 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

26 Fatty Acids All have carboxyl group All have methyl 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

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28 Fatty Acids, cont. Monounsaturated FAs Polyunsaturated FAsOne double bond in chain Polyunsaturated FAs At least 2 double bonds Plant based: olive oil Liquid at room temperature

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30 Fatty Acids, cont. Hydrogenation: cis and trans fatty acids Omega-3Double 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

31 Condensation ReactionsFormation of triglyceride lipids: Fats in animal cells, oils in plant cells Vary greatly

32 Energy Storage in HumansGlucose glycogen in liver and muscle tissue Triglyceride lipidsadipose 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

33 Chylomicrons Small particle made of fat and proteinProduced 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

34 Calculating BMI Uses weight and height Formulas:Metric: weight(kg) / height(m) x height(m) Imperial: weight(lb.) / height(in) x height(in) x 703

35 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

36 Proteins, cont. Synthesis of polypeptides: condensation reactionSequence of AAs determined by DNA, but reactions are identical. Variability of Polypeptides: Each has own AA sequence and own folding pattern

37 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)

38 Proteins, cont. Proteins vs. polypeptides: Genome: Proteome: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

39 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