Biochemistry

1. Biochemistry • Biochemistry is the study of the chemistry of living organisms • Much of biochemistry deals with the large, complex molecules necessary for life as we know it • However, most of these complex molecules are actually made of smaller, simpler units – they are biopolymers • There are four main classes of biopolymers – lipids, proteins, carbohydrates, and nucleic acids Tro: Chemistry: A Molecular Approach, 2/e

2. Lipids • Lipids are a family of compounds that are generally insoluble in water (ie. Non-polar). • Classes of Lipids: • Waxes = fatty acid and long chain alcohol (ester) • Fats & Oils = glycerol + three fatty acids • Phospholipids = glycerol + 2 fatty acids + phosphate + an amino alcohol • Sphingolipids = fatty acid + sphingosine + phosphate + an amino alcohol • Glycolipids = fatty acid + glycerol or sphingosine + one monosaccharide. • Steroids = a fused ring structure of three cyclohexanes and one cyclopentane.

3. Fatty Acids • Long chain carboxylic acids. • 12 – 18 Carbon’s are the most common. • Stearic acid is most often found in animal fat. CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2COOH And it can also be represented like this:

4. Fatty Acids • Can be saturated – all C-C single bonds. • Can be mono-unsaturated – one C-C double bond. • Ex) Oleic Acid found in olives and corn. • CH3(CH2)7CH=CH(CH2)7COOH • Can be poly-unsaturated – more than one C-C double bond. • Ex) Linoleic Acid found in soybeans and sunflowers. • CH3(CH2)4CH=CHCH2CH=CH(CH2)4COOH • In the Unsaturated acids, the cis isomer is usually found.

5. Physical Properties of Fats and Oils • The repeating zigzag shape of saturated fatty acids found in fats allows them to fit close together leading to strong attractions. As a result, a fat is solid at room temperature. • The unsaturated fatty acids found in oils do not stack together because of the double bonds. As a result, an oil is a liquid at room temperature.

6. Fats and Oils • Fats and oils are the most common lipids. • Often called triglycerides because they are a tri-ester of glycerol and three fatty acids. • Tristearin consists of three stearic acid molecules reacting with glycerol.

7. Reaction to Produce a Fat or Oil + 3 H2O

8. Steroids and Cholesterol • Steroids are any compounds containing the steroid nucleus (Pictured at right). • Cholesterol is the most important and abundant steroid in the body. • You cannot exist without this substance! • The sex hormones and the adrenocortical hormones depend on cholesterol for their synthesis.

9. Cholesterol and Hormones Cholesterol, Estrogen, and Testosterone

10. Carbohydrates • Simple Sugars have the formula Cn(H2O)n and were once thought to be “hydrates” of Carbon. • The Carbon cycle. ___________ • 6CO2 + 6H2O + energy  C6H12O6 + 6O2 _____________

11. Types of Carbohydrates • Monosaccharides – do not hydrolyze into smaller units. • Disaccharides – consist of two mono units joined together – these will hydrolyze. • Polysaccharides – consist of many mono units and are sometimes called “complex carbohydrates.”

12. Monosaccharides • Have between three and eight C atoms. • Number of C’s determines whether it is a triose (3), tetrose (4), pentose (5), hexose (6), etc. • All have at least two –OH groups and the term polyhydroxy- is sometimes used. • Will also have either an aldehyde or ketone group. • Aldehyde = aldose and ketone = ketose. • Molecules are written with the C backbone in a vertical direction.

13. Monosaccharides • Ketose or Aldose? • How many chiral carbons?

14. Monosaccharides and Chirality • Large monosaccharides have several chiral C’s. • If the lowest chiral C has the OH group on the left, then it is called the L isomer. If it is on the right, then it is called the D isomer. • Hint: C’s with double to the O are not chiral and the -CH2OH groups are also not chiral.

15. Glucose • How many chiral carbons? • Is this the D or L isomer? • Note: D-glucose is oxidized in the body to produce energy and L-glucose cannot be oxidized.

16. Cyclic Structure • In solution, glucose and other mono-saccharides become cyclic.

17. Disaccharides • Composed of two mono units. • Some common ones are: • Sucrose = Glucose + Fructose • Lactose (Milk sugar) = glucose + galactose • Maltose = glucose + glucose • In the presence of water and an acid catalyst, these linked molecules will split apart back into their mono units.

18. Sucrose

19. Polysaccharides • This is essentially a polymer of glucose units (usually). • Plant Starch exists in two forms: Amylose and Amylopectin. • Amylose is a long,continuous chain of glucose molecules. Typically has 250 – 4000 units. • Amylopectin is a branched chain of glucose molecules. Branches are about every 25 units.

20. Polysaccharides • Animal Starch is also called ___________. This is essentially a branched chain as well. • Branches are about every 10 – 15 units. • ____________, found in cell walls of plants and animals, is also a long chain of glucose units much like amylose.

21. Polysaccharides • The linkage between each unit in cellulose is different (b linkage) and is resistant to hydrolysis. • Human’s do not possess the enzymes to break this material down for energy as some animals do. • We often refer to this material in our diet as “fiber.”

22. Amino Acids and Proteins

23. The Amino Acids • Are the building blocks of all proteins. • Twenty different versions of these. • All contain the carb. acid and amine functional groups. • Center C is called the alpha Carbon and it is chiral (except in Glycine) • Abbreviated by three letter designations.

24. Amino Acids • The R groups can be non-polar, polar, acidic, or basic. Serine Alanine Non-polar R group Acidic R Group

25. The Peptide Bond • Amino acids link together by the reaction of a carboxylic acid on one with the amine of another. • The linkage between the two is called a peptide bond.

26. Peptide Formation • Reaction to form peptide bond between any two amino acids is a condensation type:

27. Primary Structure • Chains of 3 – 50 amino acids are called polypeptides. • When more than 50 amino acids are joined, we usually call it a protein. • The specific sequence of amino acids in a protein is called the primary structure. • Our DNA codes for only a limited number of specific sequences for making proteins. • Approximately 100,000 different proteins found in humans.

28. Secondary Structure • This refers to how the amino acids along the polypeptide are arranged in space. • The three most common types are: • Alpha Helix - which is a corkscrew shape of the chain that results from Hydrogen bonding between every fourth amino acid. All of the R groups then are pointed outward. • Beta-Pleated Sheet – rows of amino acids are held flat with HB keeping them rigid. • Triple Helix – is three peptide chains woven together like a braid. HB is also a powerful force that holds this together.

29. Alpha Helix & Beta-Pleated Sheet

30. Tertiary Structure • This is the overall 3D shape of the protein. • The types and interactions of the R groups are important in this area. • Globular proteins, like hemoglobin and insulin, have a very compact and round shape. The non-polar R groups point inward and the polar R groups point outward and this makes these proteins soluble in water. • Fibrous proteins, like keratin (hair, skin), consist of long, thin, fibrous shapes. Cross-linking is an important aspect and determines whether you have curly or straight hair.

31. Tertiary Structure

32. Overview of Protein Structures

33. Albumin

34. Lysozyme

35. Nucleic Acids • Basic structure is a polymer of four different bases. • Each nucleotide consists of three parts: a sugar, a base, and a phosphate group.

36. Nucleotide Structure • Each nucleotide has three parts – a cyclic pentose, a phosphate group, and an organic aromatic base • The pentoses are the central backbone of the nucleotide • The pentose is attached to the organic base at C1 and to the phosphate group at C5 • The phosphate groups then link to each other to form a polymer

37. DNA and RNA • Deoxyribonucleic Acid is found primarily in the nucleus of the cell. • Ribonucleic Acid is found throughout the cell. • The sugar molecule Ribose differs by a single oxygen atom.

38. Bases • In DNA, the four cyclic bases are Adenine, Guanine, Cytosine, and Thymine. In RNA, Thymine is replaced by Uracil.

39. Base Pairing in DNA

40. Base Pairing in DNA • The bases in nucleic acids are complementary – they precisely pair with another base. • Adenine pairs with Thymine via two hydrogen bonds • Guanine pairs with Cytosine via three hydrogen bonds

41. Linking Nucleotides

42. Linking Nucleotides

43. Genetic Structure • Each sequence of three nucleotides is called a codon • A codon codes for one amino acid • AGT = Serine • ACC = Threonine • This is universal for all living things!

44. DNA Double Helix

45. DNA Double Helix • Base pairing generates the helical structure • In DNA, the complementary bases hold strands together by H-bonding • allow replication of strand

46. DNA Replication

47. Protein Synthesis • Transcription → translation • In nucleus, DNA strand at gene separates and a complementary copy of the gene is made in RNA • messenger RNA = mRNA • The mRNA travels into the cytoplasm where it links with a ribosome • At the ribosome, each codon on the RNA codes for a single amino acid, and these are joined together to form the polypeptide chain Tro: Chemistry: A Molecular Approach, 2/e

48. Protein Synthesis Tro: Chemistry: A Molecular Approach, 2/e