Biology Chapter 2 Part 2 Fall 2024-2025

1. Chapter 2 Basic Chemistry Part 2

2. Chapter 2Basic Chemistry Organic molecules: • In biology, there are 4 major types of organic molecules (macromolecules): lipids, carbohydrates, proteins, and nucleic acids (RNA & DNA) • Macromolecules such as proteins and carbohydrates are polymers (chain) that are made of many similar or repeating units called monomers.

3. The polymers form by adding monomers in what is called the dehydration (loss of a water molecule) reaction. • Break down by removing monomers by what is called as hydrolysis(addition of a water molecule) reaction • Sugars, proteins and nucleic acids are true polymers while lipids are not true polymers; they are just large molecule

4. (a) Dehydration synthesis Monomers are joined by removal of OH from one monomer and removal of H from the other at the site of bond formation. H2O Figure 2.13a Dehydration synthesis and hydrolysis of biological molecules. Monomers linked by covalent bond Monomer 1 Monomer 2 (b) Hydrolysis Monomers are released by the addition of a water molecule, adding OH to one monomer and H to the other. H2O Monomers linked by covalent bond

5. Carbohydrates

6. Carbohydrates (cont.) • Sugars, starch, cellulose, glycogen, chitin: all consist of carbon, hydrogen and oxygen. • Carbohydrates means: hydrated carbon (C + H2O) • All consist of basic building blocks called simple sugar (monosaccharide) Types of Carbohydrates a. Monosaccharides • Monosaccharides generally have molecular formulas that are multiples of nCH2O (n number of carbon atoms) • n = 3 (trioses); 4 (tetroses); 5 (pentoses) or 6 (hexoses like C6H12O6 = glucose).

7. Carbohydrates (cont.) Monosaccharides (cont) Examples on Pentoses: Ribose and Deoxyribose (nucleic acids) Examples on Hexoses: Glucose, fructose, galactose Monosaccharides are classified either Ketoses or Aldoses. Ketoses: Contain ketone group (Fructose) Aldoses: Contain aldehyde group (glucose, galactose, ribose) Structure of Monosaccharides

8. b. Disaccharides: consists of two monosaccharides joined with each others through a dehydration reaction. The bond that is formed is called glycosidic linkage (bond). Carbohydrates Dehydration synthesis H2O Hydrolysis Glucose Fructose Water Sucrose (d) Dehydration synthesis and hydrolysis of a molecule of sucrose • Glucose + glucose = maltose (malt sugar) • Glucose + galactose = lactose (milk sugar) • Glucose + fructose = sucrose (table sugar, cane sugar)

9. C. Polysaccharides: Polymers of glucose; very large (1000s of linked monomers), insoluble  good for storage, lack sweetness; store high levels of energy Carbohydrates. • 2 types: • Starch: storage form of polysaccharide in plants (we consume); consists entirely of glucose monomers • Glycogen: storage form of polysaccharide in animals (liver and muscles); also made of glucose monomers; more extensively branched than starch.

10. Carbohydrates Q: Why the body needs carbohydrates? I. Provide easy -ready to use- source of energy • When we eat, most of our food is carbohydrate  digested in small intestine absorbed as monomers (glucose) in small intestine  goes to blood: • Part of it then go to cells  where it is broken down into H2O + CO2 +ATP (energy to power cell/body metabolism). • Another part goes to liver (and muscles) for storage in the form of glycogen • If we do not eat for few hours or if glucose content in food is low  glycogen from liver is degraded into glucose  blood  cells  ATP production II. Small amount of carbohydrates is used for structural/ functional purposes in our cells and tissues; 1-2% of cell mass is sugar.

11. Lipids • Represent a unique group of hydrophobic molecules with diverse structures and functions both in plants and animals. • Consist mostly of hydrocarbons (hydrogen & carbon atoms; few oxygen atoms = i.e., less oxidized than sugars, therefore, have lots of chemical energy. • Example: tristearin C57H110O6. • Most lipids are insoluble in water (hydrophobic); dissolve in organic solvents like alcohol and acetone. Types of lipids: • Triglycerides (most abundant in the body) • Phospholipids • Steroid

12. Table 2.5 Representative Lipids Found in the Body (1 of 2).

13. Table 2.5 Representative Lipids Found in the Body (2 of 2).

14. Triglycerides Phospholipids Steroid

15. Lipids (cont.) Triglycerides (neutral fats) • Includes fat (in animals) and oil (in plants). • Large molecules (not polymers) constructed from two kinds of molecules 1glycerol(3 carbon alcohol with 3 OH groups) + 3 fatty acid(long hydrocarbon chain with carboxyl group)

16. Lipids (cont.) Fatty Acids Fatty acids are long hydrocarbon chain molecules that contain a polar carboxyl head group attached to a nonpolar hydrocarbon Tail (Head – hydrophilic; Tail – hydrophobic) Saturated: no double bonds between carbons, solid at room temperature, in animal fat. Unsaturated: contain one or more double bonds within chain, liquid at room temperature, in plants.

17. Lipids (cont.) • Functions of triglycerides • Compact energy storage • Insulation (subcutaneous fat) • Cushions internal organs Trans Fat: are oils that have been solidified by addition of hydrogen atom at the sites of double bonds (margarines). Omega-3 fatty acids: found in cold-water fish, decrease risk of heart disease.

18. Lipids (cont.) Phospholipids Polar “head” Figure 2.15b Lipids. Nonpolar “tail” (schematic phospholipid) 2 fatty acid chains (nonpolar tail) Phosphorus-containing group (polar head) Glycerol backbone (b) Typical structure of a phospholipid molecule (phosphatidylcholine). Two fatty acid chains and a phosphorous-containing group are attached to a glycerol backbone. Important structural component of cell membrane

19. Lipids (cont.) • Phospholipids in water spontaneously assemble into micelles and phospholipid bilayers (and liposomes). • In these structures, the nonpolar, hydrophobic tails are tucked away from contact with water, and the polar, hydrophilic heads of the phospholipids are facing the aqueous environment. Cell membranes are made of phospholipids and are also bilayers

20. Lipids (cont.) Steroids Characterized by the presence of a carbon skeleton consisting of 4 interconnected rings Cholesterol is a precursor of all steroid hormones (e.g. sex hormones). Also present in cell membranes, where they regulate membrane fluidity. Different steroids differ in functional groups attached Examples: Cholesterol Estradiol Progesterone Progesterone

21. Proteins Types and Functions of proteins • Structural proteins (support: e.g. silk, collagen, keratin... etc.) • storage proteins (ovalbumin in eggs, zeins in corn seeds, casein in milk, etc...) • transport proteins (O2 by hemoglobin, ion transporters in cell membrane) • hormonal proteins (coordination of organism's activities: e.g. insulin, glucagon, etc...) • receptor proteins (response of cell to chemical stimuli: e.g. neurotransmitter receptors, hormone receptors, etc...) • contractile proteins (involved in movement, e.g. actin and myosin.) • defense proteins (protection against disease, e.g. antibodies) • Enzymatic proteins (most crucial of functions; selective acceleration of chemical reactions)

22. Proteins (cont.) • Proteins are polymers formed by monomers called amino acids. • Amino acids consist of an asymmetric carbon bonded to 4 different covalent partners: Amino group: basic part Carboxyl group: Acidic part Hydrogen atom R (side chain group) All amino acids are identical except for the R group. Accordingly, there are 20 amino acids in proteins

24. Amino Acids Amine group Acid group Figure 2.17 Amino acid structures. (a) Generalized structure of all amino acids. (b) Glycine is the simplest amino acid. (e) Cysteine (a basic amino acid) has a sulfhydryl (—SH) group in the R group, which suggests that this amino acid is likely to participate in intramolecular bonding. (c) Aspartic acid (an acidic amino acid) has an acid group (—COOH) in the R group. (d) Lysine (a basic amino acid) has an amine group (—NH2) in the R group.

25. Structural levels of proteins • Primary structure • Secondary structure • Alpha helix • Beta-pleated sheet • Tertiary structure • Quaternary structure

26. Primary structure Figure 2.18a The four levels of protein structure. Ala Ala Leu Glu Ala Ala Cys Aps Met Leu Lys Arg Gly His Amino acids (a) Primary structure. A protein’s primary structure is the unique sequence of amino acids in the polypeptide chain. Amino acids are linked with each other by covalent bond known as Peptide Bond.

27. Secondary structure Hydrogen bonds Figure 2.18b The four levels of protein structure. 𝛃-pleated sheet Alpha-helix • Secondary structure (b) Secondary structure. Two types of secondary structure are the alpha-helix and beta-pleated sheet. Secondary structure is reinforced by hydrogen bonds, represented by dashed lines in the figure.

28. Tertiary structure Polypeptide (single subunit) Figure 2.18c The four levels of protein structure. (c) Tertiary structure. The overall three-dimensional shape of the polypeptide or protein is called tertiary structure. It is reinforced by chemical bonds between the R-groups of amino acids in different regions of the polypeptide chain.

29. Quaternary structure Complete protein, with four polypeptide subunits Figure 2.18d The four levels of protein structure. (d) Quaternary structure. Some proteins consist of two or more polypeptide chains. For example, four polypeptides construct hemoglobin, the blood protein. Such proteins have quaternary structure.

31. A tertiary structure of protein showing alpha-helix and Beta sheet segments.

32. Types of proteins based on shape / function • Fibrous proteins: mostly known as structural proteins appearing in different body tissues. Could be secondary, tertiary or quaternary. Examples include collagen (in bone, tendons), keratin (skin, hair and nails). • Globular proteins (Functional Proteins): compact spherical molecules, water soluble, carry out different functions (enzymes, hemoglobin, antibodies, hormones, signaling receptors etc.) • The protein conformation is stabilized by hydrogen bonds, covalent bonds, ionic bonds, etc. However, changes in temp, pH, and salt concentration may lead to lose of three-dimensional structure. In this case the protein is said to be denatured (denaturation : unfolding of protein with resultant loss of function). • Examples: Hemoglobin loses function when pH is acidic • Pepsin become inactivated when the pH become alkaline.

33. Types of proteins based on shape / function Heme group Globin protein Fibrous proteins Triple helix of collagen (a fibrous or structural protein Globular proteins Hemoglobin molecule composed of the protein globin and attached heme groups. (Globin is a globular or functional protein.)

34. Table 2.6 Representative Classes of Functional Proteins.

35. Enzymes Enzymes are globular protein that function as biological catalysts in biochemical reactions. A catalyst is a substance that increase the rate of reaction without being affected by reactants or product and are: • Highly specific • Highly efficient • Not consumed in the reaction The catalytic activity is based on presence of active site to which a substrate (that needs to react or be changed) binds. Enzymes are named according to the type of reaction they catalyze: • hydrolase hydrolysis reaction • polymerase  polymerization reactions • phosphatase removes a phosphate group ……………. etc. • Enzymes in our bodies stay inactive except when needed  can be activated or inactivated by complex mechanisms

36. Enzyme-Substrate Reactions 1 2 3 Product (P) e.g., dipeptide Energy is absorbed; bond is formed. Substrates (S) e.g., amino acids Water is released. Peptide bond Figure 2.20 A simplified view of enzyme action. H2O Active site Enzyme-substrate complex (E-S) Enzyme (E) Enzyme (E) • Substrates bind at active • site, temporarily forming an • enzyme-substrate complex. • The E-S complex • undergoes internal • rearrangements that • form the product. • The enzyme • releases the product • of the reaction.

37. Nucleic acids (genetic material) • Nucleic acids encode the genetic information (i.e. primary structure of proteins). • Information flow proceeds from DNA to RNA to protein. This is called "central dogma". 2 types of nucleic acids1. Deoxyribonucleic acid (DNA)- deoxyribose sugar- double stranded (helix)- have thymine rather than uracil2. Ribonucleic acid (RNA)- ribose sugar- single stranded- uracil instead of thymine - three varieties: mRNA, rRNA, tRNA.

38. Structure of nucleic acids • The building blocks of nucleic acid, whether DNA or RNA, are called nucleotides • A nucleotide consists of: (1)pentose sugar (2)nitrogen base (3)phosphate group (PO4-) 1. The sugar (ribose or deoxyribose) 2. The nitrogen base: Come in two types either a: purine (2 ring structure) or pyrimidine (1 ring structure)

39. Nucleotide Structure Deoxyribose sugar Phosphate Adenine (A) Figure 2.21a Structure of DNA. (a) Adenine nucleotide (Chemical structure)

40. 21.1 DNA and RNA structure and function DNA structure The phosphate-sugar backbones are oriented in different directions. The strands are antiparallel: the carbons are numbered as 3’-5’ and 5’-3’ directions

41. Base-pairing and the double-stranded helix: • In DNA, a purine can only bases pairs with a pyrimidine • T base pairs with A (Complementary bases) => A=T note the 2 hydrogen bonds between the 2 bases • C base pairs with G (Complementary bases)=> C≡G note the 3 hydrogen bonds between the 2 bases • Note • A base sequence of ATGA on one chain is bonded to a complementary base sequence TACT on the other strand.

42. Hydrogen bond Deoxyribose sugar Figure 2.21d Structure of DNA. KEY: Phosphate Thymine (T) Adenine (A) Cytosine (C) Guanine (G) (d) Diagram of a DNA molecule

43. 21.1 DNA and RNA structure and function RNA structure and function • Single-stranded • Composed of repeating nucleotides • Sugar-phosphate backbone (Ribose-phosphate) • Bases are A, C, G and uracil (U) • Three types of RNA • Ribosomal (rRNA): Produced in nucleolus by DNA, joins with proteins to form ribosomes • Messenger (mRNA): Produced from DNA in nucleus, carries genetic information from DNA to the ribosomes in cytosol • Transfer (tRNA): Produced in nucleus, transfers amino acids to a ribosome where they are added to a forming protein. • Each tRNA binds with one amino acid (at least 20 different types of tRNA)

44. 21.1 DNA and RNA structure and function RNA structure

45. DNA vs. RNA structural differences • Functional differences: • DNA is the genetic material, genes consist of DNA • RNA mainly serves as an intermediate language during the translating of DNA (genetic) language into protein

46. Similarities: Are nucleic acids Are made of nucleotides Have sugar-phosphate backbones Are found in the nucleus Differences: DNA is double stranded while RNA is single stranded DNA has T while RNA has U RNA is also found in the cytoplasm as well as the nucleus while DNA is not Deoxyribose in DNA and Ribose in RNA 21.1 DNA and RNA structure and function Comparing DNA and RNA

47. Adenosine Triphosphate (ATP) We consume glucose Glucose metabolism (C6H12O6) (cellular respiration) 6 CO2 (g) + 6 H2O + ATP

48. ATP: structure and hydrolysis

49. Pi P A ADP ATP B A B Pi (a) Chemical work. ATP provides the energy needed to drive energy-absorbing chemical reactions. Figure 2.23 Three examples of how ATP drives cellular work. Solute Three examples of how ATP drives cellular work ADP ATP Pi P Membrane protein Pi (b) Transport work. ATP drives the transport of certain solutes (amino acids, for example) across cell membranes. ADP ATP Pi Relaxed smooth muscle cell Contracted smooth muscle cell (c) Mechanical work. ATP activates contractile proteins in muscle cells so that the cells can shorten and perform mechanical work.