Biochemistry

1. Biochemistry Chapter 3.0-3.16

2. Learning Objectives • Explain organic compounds and hydrocarbons. • Draw the structural formula for methane, propane, butane, and benzene • Explain the importance of the carbon atom in the chemistry of biological systems • Explain isomers • Become familiar with hydroxyl groups, carbonyl groups, carboxyl groups and amino groups • Explain macromolecules, polymers and monomers • Explain how cells link monomers together to form polymers by dehydration synthesis • Explain how your body uses hydrolysis to break down the macromolecules contained in the food you eat. • Describe the four major classes of biologically important molecules (Carbohydrates, Lipids, Proteins, Nucleic acids). • Understanding these molecules will become an important part of your human biology studies. • Provide an example of a monosaccharide, disaccharide, and polysaccharide. • Explain the role of starch, cellulose and glycogen in plants and animals. • Explain the structure of lipids and their roles in energy storage. • Explain why lipids are hydrophobic. • Explain the difference between saturated and unsaturated fats • Explain trans fats

3. Learning Objectives • Describe the four major classes of biologically important molecules (Carbohydrates, Lipids, Proteins, Nucleic acids). • Understanding these molecules will become an important part of your human biology studies. • Provide an example of a monosaccharide, disaccharide, and polysaccharide. • Explain the role of starch, cellulose and glycogen in plants and animals. • Explain the structure of lipids and their roles in energy storage. • Explain why lipids are hydrophobic. • Explain the difference between saturated and unsaturated fats • Explain trans fats • Provide a brief explanation of the role and structure of phospholipids, waxes and steroids in plants and animals. • Explain the structure of proteins and how this structure contributes to their diversity of form and function in a living organism • Explain the importance of shape in proteins. What is meant by denaturation of a protein? • In terms of proteins, provide a brief explanation of each of the following: primary structure, secondary structure, tertiary structure, and quaternary structure. Please note that you are not responsible for understanding these in detail at this point. You will be covering protein synthesis in greater depth in the genetics section

4. Organic Compounds • Organic compounds are chemical compounds with one or more carbon atom covalently linked to other atoms • Carbon atoms are commonly linked to oxygen, hydrogen, and nitrogen • Eg: sugars, fats, proteins, nucleic acids Video: Difference between organic and inorganic compounds (1:45 min) https://www.youtube.com/watch?v=lC57cJzM8OA

5. Hydrocarbons • Compounds with Carbon linked only to Hydrogen are called hydrocarbons Methane (CH4) Propane (C3H8) Butane (C4H10) Video: Carbon the element of life (2:57 min) https://www.youtube.com/watch?v=ULiLt2rtpAg

6. Isomers • Isomers are compounds with the same chemical formula but with different arrangement of atoms and different chemical properties (eg. butane and isobutane)

7. Organic Functional Groups • Functional groups are a specific group of atoms within a molecule that have a characteristic arrangement of atoms • Functional groups have characteristic chemical properties regardless of other atoms present in the molecule

8. Common Organic Functional Groups Hydroxyl group Amino group Carboxyl group Carbonyl group

9. Macromolecules • A Monomer is the smallest chemical unit needed to be a building block for larger molecules (eg. glucose) • A molecule made of more than one monomer is called a polymer (eg. maltose) • Macromolecules are very large compounds, often consisting of thousands of atoms, made of repeating monomers (eg. starch)

10. Dehydration Synthesis • Dehydration synthesis is the chemical process where monomers are linked together to form polymers through the removal of water to form bonds • The formation of larger compounds is called anabolism

11. Hydrolysis • Hydrolysis is the chemical process where macromolecules are broken down into smaller molecules through the addition of water to break bonds • The breakdown of larger compounds to smaller compounds is called catabolism (or chemical digestion)

12. Carbohydrates • Contain Carbon, Hydrogen, Oxygen [C(H2O)]n • Also known as sugars or saccharides (chemical name often ends in –ose) • Dietary sources come from plants • Burning of carbohydrates provides fuel for energy • Carbohydrates form structural components

13. Carbohydrates • Monosaccharides are monomers of carbohydrates (eg. glucose) • Two monomers joined by an glycosidic bond form a disaccharide (eg. sucrose) • Many monomers joined by glycosidic bonds form a polysaccharide (eg. starch)

14. Carbohydrates • Starch is a storage form of energy in plant cells. Animals ingest starch as a source of carbohydrates • Glycogen is a storage form of energy in the liver and muscle cells of vertebrate animals when there is an excess of glucose • When an animal needs energy, glycogen is broken down into glucose

15. Carbohydrates • Cellulose is a structural component of plant cell walls to provide rigidity • Because of its alternating glycosidic bonds, cellulose (unlike starch) is indigestible for animals • When animals ingest plants, the cellulose in the cell walls is a source of dietary fiber

16. Lipids • Triglycerides are neutral fats that function as long-term energy, emulsifiers, cushioning, and insulation • Triglycerides are composed of a glycerol connected to three fatty acid chains

17. Lipids • Fatty acids with single bonds between the carbons are saturated fatty acids • Fatty acids with one or more double bonds between the carbons are unsaturated fatty acids • Trans fats raise your bad cholesterol (LDL) while lowering your good cholesterol (HDL) levels, increasing risk of heart disease

18. Lipids • Lipids are also known as fats, waxes, steroids, or soaps • Lipids function as energy storage, water-proofing, insulation and cushioning, cell membrane components, chemical signals, and emulsifiers

19. Lipids • Phospholipids are cell membrane components that provide fluidity to the membrane • Phospholipids are composed of glycerol, two fatty acids, and a hydrocarbon chain attached to phosphate and nitrogen • Phospholipids have a polar, hydrophilic head and two neutral,hydrophobic tails

20. Lipids • Lipids are hydrophobic (does not react with water) due to its neutrally charged, non-polar, hydrocarbon chains • Waxes are hydrophobic lipids that provide water-proofing to prevent cells from losing water (eg. waxy cuticle in plant leaves and mammalian hair)

21. Lipids • Steroids act as intra-cellular chemical signalers to activate genes • Steroids are made of four interconnected carbon rings • The conversion of cholesterol gives rise to other forms of steroids (eg. testosterone, estrogen, cortisol, progesterone) Testosterone Video: lipids (6:28 min) https://www.youtube.com/watch?v=5BBYBRWzsLA

22. Proteins • The building block (monomer) of proteins is the amino acid • An amino acid is made of an amino group, a central Carbon and a carboxylic acid • There are 20 different amino acids, with a specific functional (R) group attached to the central Carbon • Our body produces 9* essential amino acids, the other 11 amino acids come from our diet

23. Proteins • Proteins are formed when peptide bonds join amino acids in a chain called a polypeptide • The folding of the polypeptide into a 3-D shape determines the structure and function of a protein

24. A protein’s shape determines its function as • structural components (eg. keratin in hair) • metabolic regulators (eg. insulin) • enzymes (eg. lactase) • blood components for transportation (eg. hemoglobin), clotting (eg. fibrin), and immunity (eg. antibodies)

25. Proteins • Proteins have different levels of folding • A primary protein (1°) is a polypeptide chain of amino acids joined by peptide bonds • A secondary protein (2°) is a 1° polypeptide chain folded into a spiral (alpha helix) or pleats (beta sheet) due to the formation of H-bonds between the R-groups

26. Proteins • A tertiary protein (3°) is a 2° polypeptide further folded due to ionic and covalent bonds between R-groups (eg. enzymes) • A quaternary protein (4°) is two or more 3° polypeptides held together by ionic and covalent bonds (eg. hemoglobin)

28. Proteins • Denaturation is when the 3-D shape of a protein has changed and the protein is no longer functional • Environmental factors such as changes in pH, extreme heat or the presence of heavy metals can cause a protein to denature Video: protein shape (2:05 min) https://www.youtube.com/watch?v=YhTpnRzp-eQ

29. Nucleic Acids • Nucleic Acids are DNA, RNA, and ATP • The monomer is a nucleotide containing phosphate, pentose sugar, nitrogenous base

30. Nucleic Acids • There are four types of nitrogenous bases in DNA and RNA (two purines and two pyrimidines) • ATP contains the purine base, Adenine

31. Nucleic Acids • Complementary bases pair up (purines with pyrimidines) by forming hydrogen bonds

32. DNA • DeoxyriboNucleicAcid is the carrier of genetic information • DNA nucleotides are joined into two polynucleotide strands • DNA is a double helix, with phosphate-sugar backbone and complementary base pairs in the rungs Video: What is DNA? (1:47 min) https://www.youtube.com/watch?v=uXdzuz5Q-hs

33. RNA • RiboNucleicAcid is the code for protein formation • There are three types of RNA that work together during protein synthesis: messenger RNA, transfer RNA, and ribosomal RNA) Video: What is RNA? (2:55 min) https://www.youtube.com/watch?v=Y4p6jhFaru4

34. What is the difference between DNA and RNA?

35. ATP • Adenosine TriPhosphate is the cell’s energy currency • ATP is composed of 3 phosphates, ribose sugar, adenine base • The bonds between phosphate molecules in ATP release energy when they are broken Video: ATP (1:55 min) https://www.youtube.com/watch?v=NN5Y57NbnrU