Biomolecules 2

1. Biomolecules 2

2. Most biological molecules are made from covalent combinations of six important elements, whose chemical symbols are CHNOPS. Biological molecules, or biomolecules, are mainly built by joining atoms through covalent bonds. Although more than 25 types of elements can be found in biomolecules, six elements are most common. These are called the CHNOPS elements; the letters stand for the chemical abbreviations of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur.

3. C, H, N, O , P, S

4. Valence and Covalent Bonding Each element has a characteristic valence that determines the number of covalent bonds it can form. The ability of an atom to combine with other atoms depends on the number of electrons in the outer shells of the atoms. Some elements, the so-called noble gases, have complete outer shells and do not share electrons. Many elements will share electrons with other elements, such that each element completes its outer electron shell capacity to effectively resemble nobel gasesA shared electron pair is called a covalent bond. The number of covalent bonds that each element can form is called its valence. The CHNOPS atoms are shown above. Each valence position is represented by a stick protruding from the atom.

5. Hydrocarbons, the simplest organic molecules, contain only carbon and hydrogen atoms. • Because carbon can form simultaneous covalent bonds with up to four partners, an enormous number of carbon compounds are possible. Carbon chemistry is called organic chemistry. • Among the simplest organic compounds are those containing only hydrogen and carbon, or hydrocarbons. Hydrocarbons include methane gas, liquid gasoline, and solid paraffin wax in candles. • Simplest molecule is methane, CH4, in which one carbon atom shares electrons with four atoms of hydrogen. The four hydrogen atoms are oriented at the vertices of a tetrahedron.

6. Isomers • Organic molecules exist in three-dimensional space, and the same set of atoms can be put together in many recognizably different ways, resulting in molecules called isomers. • The atoms found in a simple sugar, with the structural formula C6H12O6, can be arranged in over a dozen different ways. • Even though many isomers can theoretically exist, cells are discriminating about which ones they will synthesize and recognize. For example, the sugar glucose (C6H12O6) is very abundant and can be used by almost all organisms as a quick energy source. By contrast, an isomer of glucose called tagatose (also C6H12O6) is rare and is not useful to most forms of life—same atoms, different shapes. • Three situations can lead to the existence of isomers: • Structural isomers: Variations in the position at which different atoms are joined together. • Enantiomers: Left-handed and right-handed variations resulting from the tetrahedral geometry of carbon. • Geometric isomers: Variations in the placement of atoms around carbon atoms joined by double covalent bonds.

7. L-

8. Polarity Many combinations of different elements result in unequal electron sharing, called polar bonding. As was already seen, the sharing of electrons in covalent bonds is not always equal. In a covalent bond, atoms especially such as oxygen contain a higher localization of negative charge density than their atomic partners. As a result, the electron distribution is asymmetric, or polar, and the oxygen atom is said to be electronegative. This asymmetry results in regions of slight negative and positive charge in different regions of the molecule, denoted by the Greek symbol δ, for "partial" charge.

9. The Functional Groups • The properties of different biological molecules depend on certain characteristic groupings of atoms called functional groups. • If you know the properties of some of the functional groups, you will be able to quickly look at many simple biological molecules and get some idea of their solubility and possible identity. The names of the six most important functional groups are: • Hydroxyl • Carbonyl • Carboxyl • Amino • Sulfhydryl • Phosphate

10. The Hydroxyl and Carbonyl GroupsTwo functional groups containing oxygen, the hydroxyl and carbonyl groups, contribute to water solubility.Oxygen occurs in these two common functional groups:Hydroxyl groups have one hydrogen paired with one oxygen atom (symbolized as -OH). Hydroxyl groups are not highly reactive, but they readily form hydrogen bonds and contribute to making molecules soluble in water. Alcohols and sugars are "loaded" with hydroxyl groups.Carbonyl groups have one oxygen atom double-bonded to a carbon atom (symbolized as C=O). Like hydroxyl groups, carbonyl groups contribute to making molecules water-soluble. All sugar molecules have one carbonyl group, in addition to hydroxyl groups on the other carbon atoms.Carbonyl groups exist in two forms:Aldehyde groups, where the C=O group is at the end of an organic molecule. A hydrogen atom is also located on the same carbon atom.Keto groups, where the C=O group is located within an organic molecule. All sugars have either a keto or an aldehyde group.

11. The Carboxyl Group: AcidsCarboxyl groups are weak acids, dissociating partially to release hydrogen ions.The carboxyl group (symbolized as COOH) has both a carbonyl and a hydroxyl group attached to the same carbon atom, resulting in new properties.Carboxyl groups frequently ionize, releasing the H from the hydroxyl group as a free proton (H+), with the remaining O carrying a negative charge. This charge "flip-flops" back and forth between the two oxygen atoms, which makes this ionized state relatively stable. (Hydroxyl groups sometimes ionize momentarily, but the resulting ionic forms are not stable and the ions immediately rejoin.)Molecules containing carboxyl groups are called carboxylic acids and dissociate partially into H+ and COO−. Carboxyl groups are common in many biological molecules, including amino acids and fatty acids.Asimple 2-carbon acid found in vinegar is acetic acid (below). The carboxyl group ionizes and the resulting ionized group is stabilized by the negative charge flip-flopping between the two oxygen atoms.

12. The Amino Group: Bases • Nitrogen in biological molecules usually occurs in the form of basic amino groups. • Nitrogen is another abundant element in biological molecules. Having a valence of 3, nitrogen normally forms three covalent bonds, either single, double, or triple bonds. • By convention, nitrogen atoms are represented by blue spheres in molecular models. • Amino groups (-NH2) are common functional groups containing nitrogen. Amino groups become often ionized by the addition of a hydrogen ion (H+), forming positively charged amino groups (-NH3+).

13. 1s22s22p63s23p4  • The Sulfhydryl Group • Sulfur is found mainly in proteins in the form of sulfhydryl groups or disulfide groups. • Like oxygen, sulfur typically has a valence of 2, although it can also have a valence of 6, as in sulfuric acid. • Sulfur is found in certain amino acids and proteins in the form of sulfhydryl groups (symbolized as -SH). Two sulfhydryl groups can interact to form a disulfide group (symbolized as -S-S-). • By convention, sulfur atoms are represented by yellow spheres in molecular models. • The figure above illustrates two molecules: one with a sulfhydryl group and one with a disulfide group.

14. The Phosphate Group • In biological molecules, phosphorus occurs mainly in the form of acidic phosphate groups. • Phosphorus normally has a valence of 5. Its most common functional group in organic molecules is as a phosphate group (symbolized as -PO42−). Phosphorus is covalently paired to 4 oxygen atoms in phosphate groups: one P=O bond and three P-O− bonds. • In molecular models, phosphorus atoms are represented by orange spheres. • The compound H3PO4 is phosphoric acid, a strong acid that ionizes readily to give H2PO4− and hydrogen ion (H+). This compound can further ionize to HPO42− and H+, and still further to PO43− and H+. • Although all these chemical forms coexist in equilibrium in water, the convention in biology is to represent the phosphate ion in its doubly charged form HPO43−, often abbreviated by the symbol Pi, "inorganic phosphate." This form is shown in the figure below. • Phosphate groups are found in DNA and RNA, and in certain lipids. They are involved in the biological storage and release of energy.

15. 1. Which of the following elements is not one of the six most abundant elements found in all living cells? a. oxygen b. nitrogen c. sulfur d. potassium e. carbon

16. 2. What is the valence of carbon? • 1 • 2 • 3 • 4 • 5

17. 3. The correct shorthand to symbolize a carboxyl group is: • -NH2 • -COOH • -OH • -C=O • -SH

18. 4. Which of the following functional groups is acidic (ionizes to liberate H+ ions)? • H3PO4 • -COOH • -OH • all of the above • a and b, but not c

19. 5. Which functional group(s) are basic (accept H+ ions)? • carboxyl groups • hydroxyl groups • keto groups • amino groups • sulfhydryl groups

20. 6. Which of the following molecules contains a triple bond? • NH3 • HCCH • CH4 • C(H3)C(H2)CH3 • all of the above

21. 7. A substance that is polar: • is able to dissolve in water • contains an asymmetric distribution of electrical charge • involves unequal sharing of electrons • can be involved in hydrogen bonding • all of the above

22. 8. Which of the following types of chemical groups is not polar? • -OH • -COOH • -NH2 • -CH3 • phosphate group

23. Macromolecules Inorganic molecules USUALLY do not have carbon. i.e. H2O, NaCl Carbon dioxide (CO2) is the exception. It has carbon but is inorganic As said, living things are made of 5 main atoms carbon, hydrogen oxygen, nitrogen, phosphorus “Large” molecule Formed by monomers (small molecules) bonding together Large molecule with many monomers is a polymer

24. There are four main macromolecules in living things Carbohydrates, lipids, nucleic acids, proteins Carbohydrates Sugars and starches Made of 3 atoms: carbon, hydrogen and oxygen Most carbohydrates have a C1:H2:O1 ratio (1:2:1) Monosaccharides are the monomer. Simple Sugars such as Glucose (C6H12O6)

25. Monosaccharides bond together to form polysaccharides Disaccharides SUCROSE • Two molecules together • Ex) Maltose, lactose • Formed from dehydration synthesis

27. Carbohydrates have two main functions. 1. Usable (short-term) energystorage 2. Structure and support Sugars (monosaccharides) are usable energy for cells. (glucose, fructose, sucrose) Glucose most common sugar in cells

28. Energy Storage Polysaccharides provide short term energy storage. Plants use starch (in roots and stems) Animals store glycogen in the liver.

29. Structural Support Polysaccharides can also support both plants and animals. Cellulose is in the cell wall of plant cells to make them stronger. (indigestible) Chitin is a polysaccharide used in the exoskeletons of insects and crabs

31. LIPIDS All lipids do not dissolve in water = hydrophobic • Long term energy storage/insulation & padding (fats). Six times more energy storage than carbohydrates. (fats, oils, waxes) • Cellular Membranes- phospholipids • Chemical Messengers- steroids and cholesterol (hormones)

32. Types • Fatty Acids • Chain of carbons ending in COOH • Fatty acids can be saturated, unsaturated, or polyunsaturated • Saturated Fatty Acids • Solid at room temperature • Bad for health • Unsaturated Fatty Acids • Contain double bonds • Liquid at room temperature Saturated fats have only single bonds between the carbons on the long fatty acid chains. Found in animals Solid at room temperature

33. Types • Triclycerides • Neutral Fats • Glycerol + 3 Fatty Acids • Can be saturated or unsaturated

34. Polyunsaturated Fats • Polyunsaturated fats have two or more double bonds between the carbons on the long carbon chain of the fatty acid.

35. Unsat. & PolyunsatFats • Found in plants • Called oils • Liquid at room temperature • Better for you, but don’t taste as good.

36. Phospholipids • Found in cell membrane • Same structure as triglyceride but one fatty acid is replaced with a phosphate group (polar) • Hydrophilic phosphate head, hydrophobic fatty acid tail

37. Phospholipids • Phospholipids are found in a bilayer (two layers). • The long carbon chains face the middle and the phosphate groups face the outsides.

38. Steroids • Ringed structures made from cholesterol • Chemical messengers and form hormones • Ex) Cholesterol, Testosterone, Estrogen

39. Proteins • Structure • Keratin and collagen • Movement • Actin and myosin • Enzymes • Speed up chemical reactions • Transport • Hemoglobin to carry oxygen in blood, proteins across cell membrane • Antibodies • Fight disease • Hormones • Maintain cell function – insulin

40. Structure of Proteins • Made of Amino Acids • Amine (NH3); Acid (COOH) • 20 different amino acids have different R groups

41. Structure of Proteins • Amino acids undergo dehydration synthesis to form • Dipeptides (2 amino acids) • Polypeptides (~3-20 amino acids) • Proteins (many amino acids) • Peptide bond is formed (polar)

42. Structure of Proteins (4 Levels) • Primary Structure • Linear sequence of amino acids • Secondary Structure • Hydrogen bonding between amino acids • Causes folding • Alpha helix and beta sheets

43. Tertiary Structure • 3D arrangement of amino acid chain • Caused by covalent, ionic, and hydrogen bonding between R groups • Precise shape = specific function • Quaternary Structure • More than one polypeptide chain grouped together

44. Denaturing Proteins • Cause protein to lose shape = not function • pH, temperature, chemicals and heavy metals disrupt bonds • Ex Heating an egg, adding vinegar to milk

45. Proteins • When you look at someone, the main things you see are proteins. • Proteins do many jobs for living things • Structure- found in hair, horns and spider’s silk. • Transport- moving materials • Defense- antibodies • Enzymes- helping chemical reactions

46. Nucleic Acids DNA and RNA

47. Nucleic Acids • Nucleic Acids have two main functions- • Genetic material for all life forms (DNA, RNA) • Energy for all life forms (ATP)

48. Nucleic Acids The monomer for a nucleic acid is a nucleotide. Nucleotides made of three parts • phosphate group • 5 carbon (pentose) sugar • Nitrogenous Base

49. DNA • Deoxyribonucleic acid • Stores genetic information • Codes for the order of amino acids in proteins • Made of nucleotides • 5 carbon sugar (deoxyribose) • Phosphate • Nitrogenous bases • Adenine (A) • Thymine (T) • Cytosine (C) • Guanine (G)

50. DNA Structure • The sugar and phosphate bond to form a backbone • Bases stick out and hydrogen bond with a second strand – antiparallel • Strands wind around in a double helix