Chapter 3 Biochemistry

1. AC Chapter 3 Biochemistry Here- Bio molecule art by David Goodsell, creates hyperrealist paintings the molecular world Here,a depiction of HIV shown in cross-section- the structural biology & electron microscopy — gives a much -maligned pathogen a unique artistic quality.

2. Examples of bio molecules: Hemoglobin • the oxygen-carrying molecule of erythrocytes, formed by developing erythrocytes in the bone marrow; • a protein made up of 4 polypeptide chains that contain 141 - 146 amino acids each.

3. Examples of biological molecules: • The Helicase enzyme unzips the DNA molecule, to expose the nitrogenous bases so we can read the genetic code & do everything that is in the instructions for life.

4. Inside leaves, solar energy is transferred to the chemical bonds in biological molecules like GLUCOSE – food.

5. Examples: Biological molecules • Hormones are chemical messengers that regulate imperative bodily functions in living organisms. • For example pheromones are hormones used by ants & other insects as a communication system to send messages among one another or to attract the opposite sex. http://www.reciprocalnet.org/edumodules/commonmolecules/biochemical/index.html

6. Examples: biological molecules • Other examples of biomolecules are poisons found in animals. Batrachotoxin, a poison at the skin of the golden poison frog • Phyllobatesterribilis is considered to be one of the most deadly poisons to humans, however it is harmless to predator, the snake Liophisepinephelus . bio.davidson.edu

7. Before you can study any of these complex systems, you must understand the molecules that are behind all the wonder…..

8. Remember! CHNOPS: the 6 most common elements in living things • Biological molecules, are built by joining atoms through covalent bonds. • Although more than 25 types of elements can be found in biomolecules, 6 elements are most common. These are called the CHNOPS

9. All compounds can be classified into 2 broad categories: Organic compounds made primarily of carbon atoms. Most matter in living organisms that is not water is made of organic compounds. Inorganic compounds Compounds that, with a few exceptions, do not contain carbon atoms. (an exception is CO2- not organic!) water is ex. of an inorganic compound.

10. What do people think organic means? • A survey showed most people think “organic” refers to organic foods (limited use of synthetic materials during growth & production), and only a few science majors said carbon compounds. • Organic chemistry is - the study of the structure, properties, and reactions of carbon compounds.

11. I.Whatis anOrganic Compound? • Contains carbon atoms • Even though organic chemistry focuses on carbon, many organic compounds also contain hydrogen (H), nitrogen (N)-, oxygen (O), phosphorous (P) or other elements. • Carbon molecules make up the bodies of all living things and have many different functions; • They are also commonly used in medicine, food, paints, and gasoline.

12. Where is Carbon on the Periodic Table? It forms4 covalent bonds

14. Carbon has 4 electrons in its outmost electron shell. (It has a valence of 4) • it forms4 covalent bonds

15. A. Carbon Bonding: C atoms form many different shaped molecules: • It can form straight chains, branched chains with a single bond. • A carbon atom can also share two or even three pairs of electrons with another atom.

16. Carbon bonds: Chains, Branched, RingsEach line represents a single covalent bond

17. Carbon also forms double & triple bonds A good site for more explanation: www.biologyjunction.com

18. Examples: carbon bonding in molecules

19. B. Functional Groups - A specific group of atoms that gives a known type of behavior to molecules – changes the characteristics of the compound- (See page 52 in your textbook for more on functional groups) Hydrocarbons - C and H only Alcohols - OH Acids - COOH Amines - NH2 An excellent site to look more closely at functional groups: http://www.phschool.com/science/biology_place/biocoach/biokit/function.html

21. More Functional groups

22. Example -adding a hydroxyl group – makes ethane into an alcohol- Example - adding an amino group - makes methane or ethane into- an amine

23. C. Naming Hydrocarbons The simplest organic compounds are hydrocarbons. Hydrocarbons are compounds that consist of hydrogen and carbon atoms. When naming hydrocarbons, the prefixes vary depending on the number of carbons in a compound, the prefixes are: http://chemwiki.ucdavis.edu/index.php?title=Organic_Chemistry/Case_Studies/What_is_Organic%3F#Carbon-containing_Compounds

24. Methane- the simplest carbon compound- 1 Carbon & 4 hydrogen atoms

25. Other simple organic molecules • Butane cyclohexane

26. D. Drawing Molecules: ways that a molecule can be drawn: 1. Skeletal Structure (Kekulé Structure) • In this form of representation, atoms are placed on a plane and lines are drawn between atoms to represent bonding electrons.

27. 2. Condensed Structure • A simplified version of the bond-line structure that omits the lines. When there are 2 or more of the same kinds of atoms attached to a central atom, a subscript is used to indicate how many of these atoms are attached. 3. Lewis Structure • valence electrons are represented as dots. This structure shows what atoms are bonded together, which electrons are involved in bonding, lone pairs, any formal charges.

28. E. Isomers- same chemical formula, different structure! • Organic molecules are three-dimensional • the same set of atoms can be put together in different ways, resulting in “isomers” • Example: The atoms found in a simple sugar, with the structural formula C6H12O6, can be arranged in over a dozen different ways. sonefe.org

29. F. Polarity: Unequal electron sharing • In covalent bonds e sharing is not always equal. • Example: Water - oxygen contains a higher negative charge density than hydrogen. So electron distribution is asymmetric, or polar, and the oxygen atom is said to be electronegative. • This asymmetry results in regions of slight negative & positive charge in different regions of the molecule, denoted by the Greek symbol δ (delta), for "partial" charge.

30. Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons • Oxygen is a very electronegative atom & pulls electrons to itself. • That would leave the oxygen side of a molecule fairly negative and the carbon fairly positive. http://www.chemguide.co.uk/basicorg/bonding/eneg.html

31. G. Sizes of Molecules 1. Monomers-small simple molecules 2. Polymers-big molecules formed when monomers bonded to each other

32. 3. Reactions to build or break down molecules • Condensation Reaction • 2 monomers join together- a water is released (an H from 1 end and an OH from the other end are cut loose when the monomers join.) • Hydrolysis Reaction • polymers are broken back down- they need a wateradded.

33. Hydrolysis of sucrose

34. Condensation Reactions (also called dehydration synthesis) -builds monomers into polymers http://nhscience.lonestar.edu/biol/dehydrat/dehydrat.html

35. Hydrolysis Reactions- break down polymers into monomers by adding water

36. H. Energy from ATP • Life needs a constant supply of energy • Chemical bonds store energy. • One molecule that living things use to store energy is in the bonds of the ATP molecule • Adenosine Triphosphate

37. Adenosine Triphosphate Blue = ribose (a 5-carbon sugar)Green = adenine (a nitrogenous base) Yellow = phosphate groups Energy is stored in bonds joining thephosphate groups

38. ATP-ADP Cycle. The energy is released when the last P is taken off Energy is stored in ATP (ADP + P) Energy is used as needed & ATP is converted back to ADP + phosphate.

39. ATP further explained • A nitrogen-containing compound, adenine, is represented by the two rings & The three linked phosphate groups, -PO4- are represented by the small circles with a “P.” • Because the phosphate groups are close together and have negative charges. When a bond between the phosphate groups is broken, energy is released. • This hydrolysis of ATP is used by the cell to provide the energy needed to drive the chemical reactions in an organism

40. II. Four Classes of Organic Molecules • Much of biochemistry deals with the structures, functions and interactions of cellular components, basically: • Carbohydrates • Proteins, • Lipids • Nucleic Acids

41. Monomers & Polymers • Each group has small molecules(monomers) • linked to form larger macromolecules (polymers) three to millions of subunits.

42. Carbohydrates the most important energy source for cells • short-term energy storage (sugar) • intermediate-term energy storage • starchfor plants • glycogenfor animals • as structural components in cells • cellulosecell walls of plants • chitin-exoskeleton of insects

43. Monomers & Polymers 1.   Monosaccharides - single sugar unitsglucose 2.   Disaccharides - twomonosaccharides. Lactose, maltose 3.   Polysaccharides - linking many sugar units together Examples: starch, glycogen, cellulose

44. Carbohydrates • General formula [CH2O]n • where n is a number between 3 and 6. • Ex- glucose= C6H12O6

45. Maltose & Lactose are examples of disaccharides What does it mean to be “lactose intolerant”?

46. Got Milk?- milk’ssugar is lactose • Infant mammals are fed on milk from mom • Enzyme lactasedigests the molecule into its two subunits for absorption. • in most species, including humans, the production of lactase gradually ceases with maturity, & they are then unable to metabolize lactose… becoming “Lactose intolerant”

47. A Polysaccharide Lots of monomers linked together

48. B. Proteins • Important as control and structural elements. • Control –enzymes, hormones. • Structural -cell membrane, muscle tissue, etc. • Amino acids are the building block of proteins • All living things (and even viruses) use various combinations of the same 20 amino acids.

49. 1. An Amino Acid • an amino end(NH2) • a carboxyl end (COOH). • R is the variable (R-group) of each amino acid.