Biochemistry

1. Biochemistry

2. Atoms - tiny and compose all matter • Niles Bohr created idea that all atoms had an outer cloud of tiny subatomic particles called electrons that have a neg. charge. At centre is a nucleus composed of protons and neutrons. • Each proton carries a positive charge and the number of them equates to the atomic #, whereas neutrons have no charge but when weight added to protons gives atomic mass

3. Electrons and Ions • positive charges of nucleus balanced with neg. charges of electrons • electrons are difficult to pinpoint and as such are said to be in orbitals (an area where the electron may be found) and each orbital can hold only two electrons (p.11). • atoms in which the number of electrons do not equal the number of protons is an ion (charged) • can gain or lose, Na will lose (Na+) and Cl will gain (Cl-)

4. Electrons and Ions • Energy • electrons have energy related to their proximity to the nucleus (potential) • moving an electron out requires energy and moving one in releases energy • shells closest have least energy and ones furthest away have most • lose electron = oxidation, gain electron = reduction (redox reactions)

5. Water • only molecule of the most common ones that exists as liquid at earth's surface temp • allowed movement of other molecules without having to be covalently or ionically bound when earth was first being created (evolutionary important).

6. Polarity of Water • water has ability to form hydrogen bonds = weak bonds with 5 to 10% of strength of covalent bonds which derives from its structure and is responsible for living chemistry • one oxygen and two hydrogens off to the side, no unpaired electrons and no full charge due to electron attracting power of oxygen (electronegativity) it has a slight negative charge and the hydrogen ends therein have a slight positive charge (formation of intermolecular bonds) • positive end of one polar molecule will interact with the negative end of another polar molecule creating the hydrogen bond

7. Solvency of Water • water molecules gather around any molecule that exhibits a charge, full or partial • salt dissolves quickly due to double charge that is picked up by the double charge of the water molecule (hydrogen with chlorine and oxygen with sodium) ~ p. 18 • miscible = liquid that dissolves in another liquid (ethanol and ethylene glycol) • immiscible = liquid that does not dissolve in another liquid • Gasoline and oil are immiscible in water, but miscible with each other.

8. Organelles • Nucleus – nuclear pores, chromatin and nucleolus Ribosome Endoplasmic Reticulum Golgi Apparatus Mitochondrion Lysosome Peroxisome Centrosome Vacuole Cytoskeleton Plastids Cell membrane Cell wall Flagella/Cilia

9. Understanding the Cell Membrane • Via electron microscopy the cell membrane was discovered to have two layers (a bilayer) • Via chemical analysis the bilayer was found to be a phospholipid (two fatty acids and one phosphorous group attached to a glycerol) Allows for a polar “head” and a non-polar “tail” Creates a phospholipidbilayer

10. Cell Membrane Structure • Membrane Activities • Transport raw materials into cell • Transport products and wastes out • Prevent entry of unwanted material • Prevent escape of desired material • All of this needs to be done by each and every cell in our bodies

11. Understanding the Cell Membrane • The Fluid-Mosaic Membrane Model • Mosaic of components throughout the membrane like raisins in raisin bread • Components that comprise the membrane: • Proteins – integral and peripheral • Carbohydrates – glycolipid, glycoprotein • PhospholipidBilayer • Cholesterol can incorporate itself in cell membranes • It makes the membrane less permeable to most biological molecules

12. Cell Membrane Transport • Homeostasis – near constant conditions that our bodies stay in. It is facilitated by a number of passive and active processes • Brownian Motion – random movement of molecules • Temperature Dependent? • Passive transport • Diffusion occurs across a concentration gradient (high to low) • Cell size limits diffusion • If cell is large, substances will need to diffuse too far so this process is not favorable

13. Cell Membrane Transport • Osmosis – the diffusion of water across a selectively permeable membrane • Water in the extracellular fluid (ECF) and the cytoplasm is free to move across the cell membrane. • The water molecules move from an area of high water concentration to an area of lower water concentration across a semi-permeable membrane

14. Cell Membrane Transport • Isotonic solutions – water concentration inside the cell equals that outside • Hypotonicsolutions – water concentration outside the cell is greater then inside (water moves into cell) • Can cause lysis • Hypertonic solutions – water concentration inside the cell is greater then outside (water moves out of cell) • Can cause plasmolysis

15. Cell Membrane Transport • Facilitated Diffusion • A carrier protein facilitates the movement of large particles (glucose) from a region of high to low concentration • Depends on 3D shape of protein and molecule to complete process • Due to the fact this is driven by a concentration gradient is it considered diffusion Channel Proteins – work the same way however they transport ions. Channel has to have a different charge than ion being moved.

16. Cell Membrane Transport • Active Transport • The cell expends energy to move substances in or out • Often involves moving substances against a concentration gradient • A resting person uses up to 40% of their energy on active transport The system that allows this to occur is an integral protein called a pump

17. Cell Membrane Transport • Endocytosis – process by which larger molcules are accepted into the cell • Pinocytosis – small droplets of ECF are accepted into the cell • Phagocytosis – large droplets of ECF are accepted into the cell • Receptor-assisted endocytosis – membrane receptors attach to special materials in the ECF and accept them into the cell • Exocytosis – reverse of endocytosis

18. Chemical Basis of Life Chemical Fundamentals (p. 24 - 55)

19. Carbon • Carbon atoms can form straight and branched chains as well as ring structures of various sizes and complexity. These act as backbones for biological molecules. • hydrogen, oxygen, sulfur and phosphorous can attach to the carbon backbone to form reactive clusters known as functional groups (p. 25). • Bonding capacity is the number of covalent bonds an atom can form with a neighbouring atom (p. 26).

20. Chemical Building Blocks • molecules formed by living organisms contain carbon and are called organic molecules and have carbons at centre and functional groups extending out (-OH is hydroxyl, -COOH is carboxyl). • most chemical rxns in body are transferring functional groups or breaking carbon bonds • some molecules are simple and others are quite complex and play a structural role or store information for the organism and are called macromolecules • there are 4 main types which are made up of smaller subunits: carbohydrates, lipids, proteins, nucleic acids

21. Polymers - a molecule built of a long chain of similar molecules called monomers.

22. Creation and Destruction of Macromolecules(fig. 5 p. 28) • The four macromolecules that exist all are put together in the same way. • Hydroxyl from one subunit and hydrogen is removed from the other (dehydration synthesis or condensation). Absorption of energy occurs. Referred to as anabolic reactions because large molecules are being made from smaller ones. • requires the correct chemical bonds being broken and is facilitated by catalysts which are special proteins called enzymes

23. Creation and Destruction of Macromolecules (fig. 5 p. 28) • breaking substances down is just as important and it involves the addition of water (hydrolysis reaction) to an area where a covalent bond has been broken ~ essentially the undoing of a condensation reaction. • Referred to as catabolic as macromolecules are broken down into smaller subunits which usually occur during digestion.

24. Carbohydrates • molecules that contain C:H:O in a 1:2:1 ratio • good for energy storage because they contain many C-H bonds which are most often broken by organisms to obtain energy • energy source; building materials; cell surface markers

25. Sugars • simplest are monosaccharides (taste sweet) and the most important of which is created by plants (C6H12O6) • can exist in straight form but when in water solution, almost always form rings • primary energy store in living organisms is glucose with 6 carbons • monosaccharides have an aldehyde (end) or ketone (middle) functional group attached to their carbon backbone (p.29)

26. Sugars • ISOMERS = molecules with the same chemical formula but a different arrangement of atoms (glucose, galactose, fructose) • disaccharides or trisaccharides (oligosaccharides) are formed to allow easier transport throughout the body • sucrose (table sugar) is glucose + fructose • polysaccharides are several hundred monosaccharides linked together • serve as energy storage (starch and glycogen) and structural support (cellulose and chitin)

27. Starches • storage of glucose as an insoluble form by joining them together into long polymers called polysaccharides (if side chains off the main, even less soluble) • starches are polysaccharides formed from glucose • examples are amylose, amylopectin and glycogen (animals) which is formed if there are too many glucose molecules within our bodies

28. Cellulose • as compared to starch, in which all chains are attached to one side of the main chain, cellulose has the subunits of glucose switching back and forth making a more linear arrangement • because cellulose is not easily broken down, it works well as a biological structural material and occurs widely in this role in plants • good source of energy if you can break it down but not many organisms can. Cows break it down using bacteria in their stomachs and human need it to assist digestion • structural material in insects, fungi and other organisms is called chitin (adds nitrogen) = very difficult to digest as it is tough, resistant surface (p.34).

29. Lipids • insoluble in water (hydrophobic), but soluble in oil • contain fewer polar O-H bonds but more non-polar C-H bonds in comparison to carbohydrates • storage of energy, insulation, building membranes and chemical signaling molecules. • Fats, phospholipids, steroids, waxes

30. Lipids - Fats • long term insoluble storage molecules that contain more C-H bonds then normal carbohydrates • starches are insoluble due to long polymers but fats are insoluble because they are non-polar therein fat molecules will cluster together and are not soluble in water • 1 gram of fat = 38kJ of chemical energy • 1 gram of carbohydrate or protein = 17kJ of chemical energy • SI units = 1 cal (on food labels) equates to 4.18kJ

31. Lipids - Fats • Fat molecules are built from two different kinds of subunits: 1. Glycerol - 3 carbon alcohol with each carbon bearing a hydroxyl (OH) group, backbone to which three fatty acids are attached 2. Fatty Acids - long hydrocarbons ending in carboxyl (COOH)

32. if there are three fatty acids attached to the backbone the resulting structure is a triglyceride • they vary in length between 14 and 20 carbons and if all carbons are all single bonds they are called saturated, if double bonds there is fewer then maximum number of hydrogen atoms and are called unsaturated • saturated fatty acids fit together closely and utilize van der Waals forces which increase the attraction between molecules and allow these molecules to be solids at room temperature.

33. if a fat has more than one double bond it is said to be polyunsaturated and have low melting points due to the fat molecules not being closely aligned • a liquid fat is called an oil but can be converted to solid by adding hydrogen (p.b.) • fats are much more efficient at storing energy and will yield twice as much chemical energy as carbos • esterification = glycerol is linked to fatty acids creating ester linkages (p. 37).

34. Lipids - Phospholipids • - glycerol, two fatty acids and a highly polar phosphate group (polar) (p.38)

35. Sterols (Steroids) • hydrophobic molecules containing four fused hydrocarbon rings and different functional groups. • cholesterol is a type of lipid called a steroid which when too much is ingested causes • plaques (atherosclerosis) to form which block blood vessels which may lead to blockage, high blood pressure, stroke or heart attack. • cells convert cholesterol into a number of compounds (vitamin • D, bile salts) • sex hormones for males and females are also steroids • membranes of cells are phospholipids, terpenes make up photosynthetic pigment carotene and light absorbing pigment carotene retinol found in your eyes

36. Lipids - Waxes • lipids with long-chain fatty acids linked to alcohols or carbon rings • hydrophobic with a firm, pliable consistency = good for waterproofing (i.ecutin on plants or feathers of birds)

37. Proteins • most important proteins are enzymes which allow rxns to occur more quickly but remain unaffected or unaltered themselves (catalysts) • cartilage, bones, tendons, keratin, peptides (brain) all are made up of proteins • all are a long polymer chain of amino acid subunits linked end to end • structural building blocks and functional molecules which are what our DNA codes for

38. Amino Acids • contain an amino group (-H2N) a carboxyl group (-COOH) a hydrogen atom and a functional group (R), all bonded to a central carbon atom (fig. 28, p. 41) • identity of each AA is linked to R group, 20 different R groups so 20 different AAs (p.49) • grouped into 5 chemical classes based on chemical nature of side groups • AA are amphiprotic which means they possess acidic (carboxyl) and basic (amino) R groups. • when ionized a positive amino (NH3+) at one end and a negative carboxyl (COO-) at the other which can allow a covalent bond to form between two amino acids called a peptide bond • 8 essential AA (must be obtained from food) and 12 we can create ourselves

39. Polypeptides (fig. 30, p. 43 & fig.31, p. 44) • name given to long chain of amino acids linked end to end using peptide bonds • each protein has a sequence of steps that it goes through in its formation (occurring in cytoplasm): • Primary Structure • simple linking of AA together in a linear chain (peptide bond) • amino terminus (A-terminus) & carboxyl terminus (C-terminus) • completed by protein synthesis, one altered base pair could render protein useless

40. Secondary Structure • - each AA interacts with neighbors due to R chains and H bonds are created that allow B-pleated sheets and helices to be formed

41. Tertiary Structure • - depends a great deal on the secondary structure but is a folding back upon itself of the chain and • sheets and helices due to whether the R groups are polar or non-polar. • h-bonds, ionic bonds and van der Waals forces keep the polypeptide folded in its shape • cysteine has S in its R group and when near each other will form a disulfide bridge

42. Quaternary Structure • two polypeptides associate to form a functional unit, do not all need to be identical to come together (protein hemoglobin: 2 of type A polypeptide, 2 of type B polypeptide)

43. Types of Proteins • Globular Proteins • = carry out chemical reactions, antibodies (infection) are also globular • = composed of one or more polypeptide chains and are round • Structural Proteins • = keratin in hair, actin and myosin in muscles, most abundant (collagen)

44. Denaturing • environment matters (pH, temperature, ionic concentration, chemicals) • usually return to normal when agent is removed provided polypeptide is still intact • Gastrin = enzyme in stomach works at a pH of 2, once in small intestine the pH is 10 so it denatures • Chaperone proteins = aid the growing polypeptide to fold into its tertiary structure

45. Nucleic Acids • are long information storage polymers made up of repeating subunits called nucleotides • nucleotides are each made up of 3 smaller building blocks (fig. 42, p. 53): • 5-carbon (pentose) sugar • phosphate group (PO4-) • organic nitrogenous base • sugars are linked together in line by the phosphate groups creating a phosphodiester bond in which the phosphate group of one sugar binds to the hydroxyl group of the next sugar.

46. Nucleic Acids • the nitrogenous bases protrude out from the sugar and can be of 4 different types when dealing with DNA sequencing (guanine = cytosine, adenine = thymine) • DNA is a double chain (strand) of these nucleotides wrapped in a helix held with hydrogen bonds. The two strands are said to run antiparallel.

47. Nucleic Acids • - order codes genetic information and more directly the order and type of proteins that are going to be created and therein the distinctive traits in the body • DNA is also the unit that permits the transmission of hereditary information to offspring, master copy, but also RNA (ribonucleic acid) that is a temporary copy of sections of DNA that allows the aforementioned proteins to be created

48. Nitrogenous bases broken down into purines and pyrimidines (fig. 42, p.53) • Pyrimidines = small single rings  cytosine, thymine (DNA), uracil (RNA) • Purines = large double ring compounds  guanine, adenine • Nucleotides are also important intermediaries in a cell’s energy transformations • ATP = adenosine triphosphate ~ drives all of cell’s energy reactions • NAD+ = nicotinamide adenine dinucleotide ~ nucleotide derivative used in making ATP • NADP+ = nucleotide similar to NAD+ is used as a coenzyme in photosynthesis

50. Chemical Basis of Life Metabolism (p. 58 - 67)