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UNIT 1

UNIT 1. BIOCHEMISTRY. Note: 1) bonds repel each other so that there is the maximum space between them. 2) lone pairs also repel bonds as well as other lone pairs. . Acids, Bases and Buffers (pg. 20). Pure water never only contains only H 2 O molecules

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UNIT 1

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  1. UNIT 1 BIOCHEMISTRY

  2. Note: 1) bonds repel each other so that there is the maximum space between them. 2) lone pairs also repel bonds as well as other lone pairs.

  3. Acids, Bases and Buffers(pg. 20) • Pure water never only contains only H2O molecules • Two H2O in every 550 million react with each other.

  4. Acids and Bases • Compounds other than water can increase or decrease [H3O+] or [OH-] • ACIDS • Increase the concentration of H3O+ ions in a solution. • Acidic solutions: sour taste, ability to conduct electricity. • Contain at least one ionizable hydrogen atom. • BASES • Increase the concentration of OH- ions in a solution. • Basic solutions: bitter taste, slippery feel, conduct electricity. • 2 reactions: • 1) Ionic base containing OH- ion dissociate to produce OH- • 2) Base not containing OH combines with H+ ions

  5. Acids and Bases (2) • Pure water contains equal numbers of hydonium and hydroxide ions • [H3O+] = [OH-]  Neutral • Neutralization reaction: • Acid and base mixed

  6. pH • Concentration of a solute in aqueous solution is measured in moles of the solute per litre of solutions  mol/L • A mole is the amount of any substance that contains 6.02 x 1023 particles of the substance. • A [H3O+] of 2.0 mol/L contains __________________________________ H3O+ ions. • A neutral solution has [H30+] = 1.0 x 10-7 mol/L. • The pH of an aqueous solutions is equal to the negative logarithm of the hydronium ion concentration. • Acidic solutions, 0 < pH < 7 • Basic solutions, 7 < pH < 14

  7. The Chemicals of Life(1.2) • Carbon • Can form four covalent bonds • Attach to each other to form strait and branched chains and ringed structures. • Hydrocarbons: contain only carbon and hydrogen  non-polar. • Functional groups: reactive clusters of atoms containing hydrogen, oxygen, nitrogen, sulfur, and phosporus. • Attach to the carbon backbone. • Bonding Capacity: number of covalent bonds an atom can form.

  8. Functional Groups and Reactivity • FGs are more reactive than the hydrocarbon portions of biological molecules. • Eg. –OH and –COOH are polar due to the electronegative oxygen atom they contain. Therefore, sugars and alcohols are highly soluble in water. • Eg. –COOH makes a molecule acidic. –NH2 makes a molecule basic.

  9. PP, page 27, #1

  10. Biological Macromolecules • Complex carbohydrates, proteins, and nucleic acids are polymers. • Lipids (triglycerides and phospholipids) are not polymers but are relatively large molecules composed of several smaller parts.

  11. For carbs, proteins, and Nas, the subunit can also be called a __________________.

  12. Anabolic Reactions & Condensation Reactions • Anabolic Reaction: result in the construction of large molecules from smaller subunits. • ‘formation’ • Cells use this process to form proteins (ex//cytoskeleton ( strength), carbohydrates (ex//membrane, glycogen for energy storage), lipids (ex//phospholipidbilayer), etc. • Condensation/Dehydration Synthesis: creates a covalent bond between two subunits, removing (forming) a water molecule in the process. • An –OH group is removed from one subunit, an H is removed from another. OH + H  H2O. • Process requires energy.

  13. Catabolic Reactions & Hydrolysis Reactions • Catabolic Reactions: reactions that break macromolecules into smaller units. • ‘digestion’ • Cells may use this process to break apart larger unusable macromolecules into their subunits in order to re-build them into functional/required macromolecules. (Lego) • Hydrolysis: water molecule is used to break a covalent bond holding subunits together. • Release of energy

  14. Hydrolysis and condensation require the assistance of special protein molecules called enzymes – more on enzymes later.

  15. Carbohydrates (in detail)(pg. 29) • Millions of tonnes are produced by plants and algae every year through process of ___________________________. • Functions: • Sources/storage of energy for organisms. • Building materials • Cell surface markers for cell-to-cell identification. • Types (“saccharide”  sugar) • Monosaccharide • Oligosaccharides • Polysaccharides

  16. Monosaccharides • “mono” + “saccharide”  single sugar. • Contain a single chain of carbon atoms to which hydroxyl groups and a carbonyl group is attached. • Can be distinguished by • the carbonyl group they possess: aldehyde or ketone. • Aldoses: contain aldehyde • Ketoses: contain ketones. • Number of atoms in their backbone. • Pentose: five carbons • Hexose: six carbons. • Etc.

  17. Common Monosaccharide Uses • Trioses • Glyceraldehyde (intermediate compound in carbohydrate metabolism) • Dehydroxyacetone (ingredient in sunless tanning products) • Pentoses • Ribose (component of RNA) • Ribulose (used in photosynthesis) • Hexoses • The hexoses are isomers: contain same chemical formula but with a different arrangement of atoms. Possess different shapes and different physical and chemical properties. • Glucose (source of energy in cells) • Galactose (component of lactose, milk sugar) • Fructose (fruit sugar).

  18. Shapes of Monosaccharides • Monosaccharides with five or more carbons are linear molecules in the DRY state. • Ring structure: when dissolved in water. • Ex// Glucose: carbons 1 & 5 react. • Hydroxyl group at carbon 1: below plane of ring. • α – glucose • Hydroxyl group at carbon 1: above plane of ring: • β - glucose

  19. Oligosaccharides • Contain two or three simple sugars. • Attached by special condensation rxn: glycosidic linkage. • Disaccharides: contain two monosaccharides. • Important dissacharides • Maltose: α–glucose + α–glucose (α 1-4 glycosidic linkage) • Found in grains – use in the production of beer. • “maltose” • Sucrose: α–glucose + α-fructose (α- 1-2 glycosidic linkage) • Table sugar • Use by many plants to transport glucose from one part of a plant to another. • Found in high concentrations in sugar cane, sugar beet, and sugar maple trees. • Lactose: α-glucose + α-galactose • Sugar found in milk.

  20. Polysaccharides • ‘complex carbohydrates’ • Monosaccharide polymers  several hundred to several thousand monosaccharides. • Energy storage and structural support. • Starch: _________________________(amylose + amylopectin) • Glycogen: _____________________________ • Cellulose: _____________________________ • Chitin: ________________________________

  21. Amylose • Unbranched • α-glucose polymer • α 1-4 glycosidic linkages Amylopectin • Branched • α-glucose polymer • Main-chain: α 1-4 linkages • Brances: α 1-6 linkages Angles of glycosidic linkages causes polymers to twist into coils: insoluble in water. AMYLOSE + AMYLOPECTIN = STARCH

  22. Plants and Polysaccharides • Plants store the Sun’s energy mostly in the form of glucose by photosynthesis. ______________________________________________ • Glucose is then broken down when energy is needed by the plant: for anabolism, catabolism (formation of proteins, carbs, other processes) • Usually produce more glucose than needed. • Enzymes link together glucose into amylose and amylopectin (polysaccharides), which mix to form starch. • Potato: “starchy”. • Roots in the winter: deciduous trees store energy in roots during the winter so when spring bloom arrives, they are ready to use energy to bud new leaves (beginning photosynthesis!)

  23. Heterotrophs use enzymes to hydrolyze amylose and amylopectin into individual glucose molecules and then respirate to extract energy to glucose: Cellular Respiration: ______________________________________________ • Excess glucose molecules are linked to one another to form glycogen. Glycogen • Similar to amylopectin (same linkages and branched), but more branches. • Stored in muscle and liver cells. • Depleted in about a day if not replenished.

  24. Cellulose • Primary structural polysaccharide of plants. • Major component of cell walls. • Most abundant organic substance on Earth. • Strait-chain polymer of β-glucose held together by β1–4 glycosidic linkages • Neither coiled nor branched. • Strait shape allows hydroxyl groups of parallel monomers to form many hydrogen bonds, producing microfibrils.

  25. Corn in your Poop? • Humans do not have the digestive enzymes able to break linkages between β-glucose subunits. • Therefore, can not digest cellulose. • Animals such as cows, sheep, and rabbits can digest cellulose • Symbiotic bacteria and protists in digestive tract produce enzymes that break the linkages. • Roughage • Cellulose fibres – found in fresh fruit, vegetables, and grains – we are unable to digest. • Pass through our DT undigested  scrape walls of DT  stimulates intestinal cells to secrete mucus  lubricates feces and aids in elimination of solid waste (decreases chance of back-up).

  26. Chitin • Exoskeleton of insects and crustaceans and cell walls of many fungi. • Monomer is a glucose molecule with a nigrogen-containing group attached to carbon 2. • Second most abundant organic material found in nature. • Used in contact lenses and biochemical stitches.

  27. Building Carbohydrates with Molecular Modelling Set

  28. Building Carbohydrates with Molecular Modelling Set

  29. PPs, page 34. # 2-10

  30. Lipids (in detail) (page 35) • Hydrophobic – composed of H, C and O • Insoluble in water but soluble in other nonpolar substances. • Functions • Long-term storage of energy (more than twice the amount of energy in carbohydrates). • In animals, excess carbohydrates are converted into fat and stored as droplets in the cells of adipose (fat) tissue. • Thermal insulation: layer of fat under skin (penguins, polar bears, walruses, etc). • Plants also store energy in the form of fat: triglyerides. • Main types: • Triglycerides • Phopholipids • Sterols • Waxes

  31. Triglycerides • Made of: • A glycerol (3-C molecule with three hydroxyl groups) • Three fatty acids (long H chains containing –COOH) • Usually even number of Cs and around 16-18 C long. • Saturated FAs: all single bonds, max # H • Unsaturated FAs: one or more C=Cs, not max # H.

  32. Condensation reaction between glycerol and fatty acid: ester linkage.

  33. Saturated Fatty Acids • Examples: animal fats: butter and lard. • Contain only saturated fatty acids. • Strait hydrocarbon chains allow for many van der Walls attractions • Dipole-dipoles, dispersion forces • Solid consistency at room temperature. • More difficult to catabolize.

  34. Unsaturated/Polyunsaturated Fatty Acids • Examples: plant oils: olive oil, corn oil, peanut oil. • Bent at double bonds. • Reduced number of van der Waals attractions. • Liquids at room temperature. • Hydrogenation: process of adding hydrogen atoms to double bonds in unsaturated triglycerides to form semisolid material (margarine).

  35. Phospholipids • Glycerol molecule + two Fas + highly polar phosphate group. • Polar head (hydrophillic) • Non-polar tails (hydrophobic). • When added to water, phospholipids form spheres called micelles. • Hydrophyllic heads orient themselves towards the water while the hydrophobic tails orient towards themselves.

  36. PhospholipidBilayer • Separate two water compartments (extracellular fluid and cell’s cytoplasm/intracellular fluid). • Heads can mix with water and tails can mix with one another in the center of the bilayer. • Water/polar molecules: can not pass through bilayer due to the highly nonpolar center. • Proteins and hydrophillic pores form channels through which charged materials can pass.

  37. Sterols • Also called steriods • Compact hydrophobic molecules containing four fused hydrocarbon rings and several different functional groups. • Cholesterol: important in cell membrane  aid in fluidity. • Cholesterol in bloodstream and diet rich in saturated fats  artherosclerosis. • Fatty deposits (plaque): line blood vessels and block the flow of blood to tissues • Body tissue dies • Heart tissue: heart attack • Brain: stroke. • Other Sterols: • Sex hormones: testosterone, estrogen, and progesterone.

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