Biomolecules

1. Biomolecules

2. Our journey begins here with molecules. Simple to Complex – Life’s Levels of Organization

3. When atoms come together by sharing electrons the bond is a covalent bond. A molecule is formed when two or more atoms are bound together covalently. Note outer shell of each atom now is full H2

4. (for CH4) Drawing It Out The sharing of a pair of electrons between atoms (a covalent bond) is shown as: H-H (for H2) Structural formula Chemical formula or H-O-H (for H2O) Structural formula Chemical formula or Structural formula Chemical formula

5. Water - A Most Important Molecule Note how bonding fills all outer electron shells.

6. Molecular Shape Molecules have distinct shapes – and shape matters.

7. Molecular Shape A regulatory protein molecule (yellow) binding to DNA. Without complementary shapes, binding would not occur.

8. Biological Chemistry Takes Place in Solutions Molecules are often described as hydrophilic (water-loving) or hydrophobic (water-fearing) on the basis of their solubility in water.

9. The Role of Carbon in Organisms Organic compounds contain carbon A carbon atom has four electrons available for bonding in its outer energy level. In order to become stable, a carbon atom forms 4 covalent bonds that fill its outer energy level.

10. The Role of Carbon in Organisms Carbon compounds vary greatly in size. When carbon atoms bond to each other, they can form straight chains, branched chains, or rings.

11. Cells make a huge number of large molecules from a small set of small molecules

12. Most of the large molecules in living things are macromolecules called polymers Polymers are long chains of smaller molecular units called monomers (building blocks) A huge number of different polymers can be made from a small number of monomers SIZE: monomer<polymer<macromolecule • 4 types of macromolecules: • carbohydrates, lipids, proteins, & nucleic acids • (poly ~ many ; mono ~ one)

13. Making and Breaking of POLYMERS Cells link monomers to form polymers by dehydration synthesis(building up); also called condensation reaction Short polymer Unlinked monomer Removal ofwater molecule Longer polymer

14. Making and Breaking of POLYMERS Polymers are broken down to monomers by the reverse process, hydrolysis (hydro ~ add water; lysis ~ to split) Addition ofwater molecule

15. Isomers Molecules that have the same simple chemical formula but have different structural formulaare called Isomers (both have the chemical formula C6H12O6)

16. CARBOHYDRATES composed of carbon, hydrogen, and oxygen with a ratio of about two hydrogen atoms and one oxygen atom for every carbon atom.

17. The structure of carbohydrates The monomer (building block) of a carbohydrate is a simple sugar called a monosaccharide* (mah noh SA kuh ride). (ie. glucose, fructose) are the fuels for cellular work *(Mono ~ one; sacchar ~ sugar)

18. Monosaccharides can join to form disaccharides*, such as sucrose (table sugar) and maltose (brewing sugar) *di ~ two; sacchar ~ sugar

19. Polysaccharides are long chains of sugar units polymers of hundreds or thousands of monosaccharides linked by dehydration synthesis

20. Polysaccharides are long chains of sugar units Function as Energy storage Starch (plants) Glycogen (animals) Structure Cellulose (plants cell walls) Chitin ( insects)

22. Chitin Structural polysaccharide Structural componemt of cell walls in fungi Exoskeleton of invertebrates like insects, crustaceans like crawfish, shrimp etc. Suture material for surgery (breaks down as wound heals)

23. Lipids composed largely of carbon and hydrogen They are not true polymers • They are grouped together because they do not mix with water (Nonpolar) • (ie. fats, oils, • waxes, steroids)

24. Lipids include fats and oils, Fats and oils are lipids whose main function is long term energy storage Other functions: Insulation in higher vertebrates “shock absorber” for internal organs Fatty acid Fatty acid

25. Lipids include fats like a triglyceride, Fatty acid Fatty acid

26. Saturated & Unsaturated fats fatty acids of unsaturated fats (plant oils) contain a double bond. These prevent them from solidifying at room temperature Saturated fats (lard) lack double bonds They are solid at room temperature

27. Saturated & Unsaturated fats No double bonds between carbon and carbon One or more double bonds between carbon and carbon

28. Phospholipids Partial exception to the hydrophobic (non-polar) lipid rule Have a polar region and a nonpolar region on each molecule Polar Region Compared to a Triglyceride Phosphate group replaces 3rd fatty acid Nonpolar Region

29. Phospholipids Major component of all cell membranes! Phospholipids form a double layer in each cell membrane. The polar heads are oriented towards the aqueous areas and the nonpolar fatty acid tails form a nonpolar lipid barrier between the inside and outside of the cell. Thus, membranes have two sides, each facing the aqueous environment inside and outside of the cell.

30. THE STEROIDS Fused Rings Found in all steroid compounds Cholesterol: Precursor in living organisms for: sex hormones ( testosterone in male, estrogen and progesterone in female) Corticosteroids from adrenals Vitamin D Bile salts Important part of cell membranes Obtain in diet and make it in the liver. Anabolic steroids: Testosterone mimics

31. PROTEINS Essential to the structures and activities of life Make up 50% of dry weight of cells Contain carbon, hydrogen, & oxygen PLUS nitrogen and sometimes sulfur Proteins are involved in Cellular structure Movement (muscles) Defense (antibodies) Transport (blood) Communication Monomers are called amino acids

32. The structure of proteins 20 common amino acids that can make literally thousands of proteins. Their diversity is based on different arrangements of amino acids R = variable group- which distinguishes each of the 20 different amino acids

33. Amino acids can be linked by Peptide Bonds Cells link amino acids together by dehydration synthesis (condensation reaction) The bonds between amino acid monomers are called peptide bonds PEPTIDEBOND Amino acid Amino acid Dehydrationsynthesis Dipeptide

34. A protein’s specific shape determines its function A protein consists of polypeptide chains folded into a unique shape The shape determines the protein’s function A protein loses its specific function when its polypeptides unravel

35. Enzymes Enzymesare proteins that catalyze (i.e., increase the rates of) chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products.

36. Enzymes Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

37. LEVELS OF STRUCTURE IN PROTEINS: Function of a protein is determined by its overall conformation. (Failure to achieve the proper confirmation can result in a non-functioning protein, with disastrous results.) PRIMARY LEVEL (Primary Structure) - the specific sequence of amino acids joined together

38. LEVELS OF STRUCTURE IN PROTEINS: SECONDARY LEVEL (Secondary structure) This level is defined as the way the polypeptide chain is coiled and folded upon itself. Two Types of Secondary Structures: Alpha Helix Beta pleated sheet Alpha Helix Beta pleated sheet

39. LEVELS OF STRUCTURE IN PROTEINS: TERTIARY LEVEL (tertiary structure) the overall 3-D conformation of a protein tertiary structure

40. LEVELS OF STRUCTURE IN PROTEINS: QUATERNARY LEVEL (quaternary structure) Found only proteins composed of two or more polypeptide chains (each with its primary, secondary, tertiary structure). REMEMBER: Without correct conformation, protein will be dysfunction or non-functional.

41. LEVELS OF STRUCTURE IN PROTEINS: DENATURATION OF PROTEIN: loss of native conformation -unfolding of tertiary and secondary structures -biologically inactive in this state Proteins are sensitive to: temperature pH salt concentration solvent Effect of denaturing agent: Proteins will unfold and lose conformation.

42. PRIONS Prions – abnormally folded proteins In some diseases, these agents have the ability to subvert normal proteins to unfold and refold abnormally See this in some forms of: Alzheimer’s Kuru Scrapie Creutzfeld-Jakobs Bovine spongiform encephalopathy (Mad cow disease) Transmissible mink encephalopathy

43. Nucleic acids A nucleic (noo KLAY ihk) acid is a complex biomolecule that stores cellular information in the form of a code. DNA (deoxyribonucleic acid) contains the instructions used to form all of an organism’s proteins. RNA (ribonucleic acid) forms a copy of DNA for use in making proteins. They ultimately control the life of a cell

44. Nucleic acids The monomers of nucleic acids are called nucleotides Each nucleotide is composed of a sugar, a phosphate, and a nitrogenous base Nitrogenousbase (A) Phosphategroup Sugar

45. Basic Structure of Nucleotide One5 carbon sugar One Phosphate group One Nitrogen base For a given nucleic acid, the phosphate groups are identical in each nucleotide. The sugars differ between DNA and RNA. The real difference is in the nitrogen bases. Therefore each type of nucleotide is named for the nitrogen base it contains.

46. The DNA and RNA nucleotides differ in the 5-carbon sugar: DNA – deoxyribose, RNA – ribose In DNA, the hydroxyl group on C2 has been replaced by a hydrogen. In other words, an oxygen is missing at that site. (deoxyribose has one carbon without a hydroxyl group) Hence, the name: Deoxyribose. In RNA, the ribose has the hydroxyl group on C-2.

47. There are two main groups of bases with five types of bases. The nitrogen bases: A,G, C are found in all Nucleic acids. T is found only in DNA. U is found only in RNA.

48. Condensationreaction or dehydration synthesis joins nucleotides between the phosphate group on one nucleotide and the sugar on the other nucleotide. This linkage is referred to as : The “Sugar-Phosphate” backbone of the nucleic acid.

50. ATP - Adenosine Triphosphate Energy source used by all Cells Organic molecule containing high-energy Phosphate bonds