2.1 Basic Chemistry Matter is anything that takes up space and has mass. The three states of matter are solid, liquid, and gas. All matter, living or nonliving, is made up of elements. Elements are substances that cannot be broken down into simpler substances by ordinary chemical means.

© Tom Mareschal/Alamy RF Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 60 Earth’s crust organisms 40 Percent by Weight 20 Fe Ca K S P Si Al Mg Na O N C H Element © Tom Mareschal/Alamy RF 92 naturally-occurring elements serve as building blocks of all matter. Other elements have been “human-made” and are not biologically important.

Elements That Make up 95% of Organisms (by weight) C Carbon H Hydrogen N Nitrogen O Oxygen P Phosphorus S Sulfur

2.4 Organic Molecules Organic molecules always include: carbon (C) and hydrogen (H) Those with only (H) and (C) are called hydrocarbons Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H H H H C C C C C C C C H H H H H H H H H

2.4 Organic Molecules The chemistry of carbon accounts for the formation of great variety of organic molecules. Carbon atoms contain four valence electrons. A carbon atom may share electrons with another carbon atom or other atoms in order to achieve eight electrons. Satisfying the octet rule

2.4 Organic Molecules Functional groups are a specific combination of bonded atoms that always react in the same way. The more common functional groups are listed in Table 2.1.

2.4 Organic Molecules Macromolecules contain many molecules joined together. Monomers: Simple organic molecules that exist individually Polymers: Large organic molecules form by combining monomers

2.4 Organic Molecules Polymers in cells and their monomers Polymer Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Polymer Monomer carbohydrate (e.g., starch) monosaccharide protein amino acid nucleic acid nucleotide

2.4 Organic Molecules Cells use common reactions to join monomers. In a dehydration reaction an -OH and -H are removed as a water molecule. In a hydrolysis reaction, components of water are added.

Figure 2.13 monomer OH H monomer dehydration reaction H2O monomer Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. monomer OH H monomer dehydration reaction H2O monomer monomer a. monomer monomer hydrolysis reaction H2O monomer OH H monomer Figure 2.13 b.

2.5 Carbohydrates Carbohydrates function for quick fuel and short-term energy storage in organisms. Play a structural role in woody plants, bacteria and insects On cell surfaces, involved in cell-to-cell recognition

Simple Carbohydrates Monosaccharides are sugars with 3 - 7 carbon atoms. Pentose refers to a 5-carbon sugar Hexose refers to a 6-carbon sugar Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH 6 5 C O O O H H H H H C C 4 1 OH H OH H HO OH HO OH C C 3 2 H OH H OH C6H12O6 Figure 2.14

Simple Carbohydrates Disaccharides contain two monosaccharides joined by the dehydration reaction. Examples – maltose, sucrose, lactose Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH CH2OH CH2OH O O O O H H dehydration reaction + + O H2O hydrolysis reaction OH HO glucose C6H12O6 glucose C6H12O6 maltose C12H22O11 water + + monosaccharide monosaccharide disaccharide water Figure 2.15

Polysaccharides Polysaccharides such as starch, glycogen, and cellulose are long polymers that contain many glucose subunits.

Starch and Glycogen Starch is the storage form of glucose in plants. May contain up to 4,000 glucose units Fewer side branches than glycogen Glycogen is the storage form of glucose in animals. Liver stores glucose as glycogen In between meals, the liver releases glucose stored in glycogen

© Jeremy Burgess/SPL/Photo Researchers, Inc. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH CH2OH CH2OH H O H H O H H O H H O H H H H H OH H OH H OH H OH H O O O O O H OH H OH H OH H OH branched nonbranched starch granule cell wall potato cells Figure 2.16 © Jeremy Burgess/SPL/Photo Researchers, Inc.

© Don W. Fawcett/Photo Researchers, Inc. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. CH2OH CH2OH CH2OH CH2OH O O O O H H H H H H H H H H H H OH H OH H OH H OH H O O O O O H OH H OH H OH H OH glycogen granule Figure 2.17 liver cells © Don W. Fawcett/Photo Researchers, Inc.

Cellulose Cellulose is found in the cell walls of plants. Some polysaccharides function as structural components of cells. Cellulose is found in the cell walls of plants. Accounts for the strong nature of the cell walls Has different chemical linkage than starch or glycogen Prevents us from digesting foods with cellulose Chiton, found in the exoskeleton of crabs, is another structural polysaccharide.

© Science Source/J.D. Litvay/Visuals Unlimited Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. plant cell wall cellulose fiber cellulose fibers microfibrils CH2OH H OH CH2OH H OH H O H H O H O OH H H O OH H O OH H H O OH H H O H H H H O O H OH CH2OH H OH CH2OH CH2OH H OH CH2OH H OH H O H H O H O OH H H O OH H O OH H H O OH H H O H H O H H O H OH CH2OH H OH CH2OH glucose molecules CH2OH H OH CH2OH H OH H O H H O H O OH H H O OH H O OH H H O OH H H O H H H H O O H OH CH2OH H OH CH2OH Figure 2.18 © Science Source/J.D. Litvay/Visuals Unlimited

2.6 Lipids Lipids contain more energy per gram than other biological molecules. Types Fats and oils used for energy storage Phospholipds from membranes Steroids include sex hormones

2.6 Lipids Lipids are diverse in structure and function. Lipids have one common characteristic – they do not dissolve in water (hydrophobic).

Fats and Oils Fats Oils Usually of animal origin Solid at room temperature Store energy, insulate against heat loss, form protective cushion Oils Usually of plant origin Liquid at room temperature

Fats and Oils A fat molecule is also known as a triglyceride or neutral fat. A triglyceride consists of One glycerol backbone Three fatty acids

Fats and Oils Figure 2.19 + + H H H H H H O H H H H O C C C C C H H C Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H O H H H H O C C C C C H H C O C C C C C H H C OH HO H H H H H H H H H H H H H H dehydration reaction O H H H H H H O + C C C C C C C H H C O C C C C C C C H + H C OH 3 H2O HO hydrolysis reaction H H H H H H H H H H H H H H H H H O H H H H H O C C C C C C H H C O C C C C C C H H C OH HO H H H H H H H H glycerol 3 fatty acids fat molecule 3 water molecules Figure 2.19

Emulsification Fat droplets disperse in water. Emulsifiers contain molecules with a polar and nonpolar end.

Saturated, Unsaturated, and Trans-Fatty Acids A fatty acid is a hydrocarbon chain that ends with the acidic group —COOH. Saturated fatty acids have no double bonds between carbon atoms. Unsaturated fatty acids have one or more double bonds between carbon atoms.

Comparison of Saturated, Unsaturated and Trans-Fats Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H C C C C C C H H H Unsaturated cis fats (oils) Saturated (butter) Unsaturated trans-fats (hydrogenated oils)

Phospholipids Phospholipids are comprised of two fatty acids and a phosphate group The phosphate group is polar so the molecules are not electrically neutral. The phosphate group forms a polar head (hydrophilic) while the rest of the molecule is a nonpolar (hydrophobic) tail.

Phsopholipids Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Polar Head R – O – O – phosphate – P O O – 1CH2 2CH 3CH2 Spontaneously form a bilayer in which the hydrophilic heads face outward toward watery solutions and the tails form the hydrophobic interior glycerol – – O O C O O C CH2 CH2 CH2 CH2 Fatty acids CH2 CH2 inside cell CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH CH CH CH CH2 outside cell CH2 CH2 CH2 a. Plasma membrane of a cell CH2 CH2 CH2 CH2 CH2 Nonpolar Tails CH2 CH2 CH2 CH2 CH2 CH2 CH3 CH2 Figure 2.21 CH3 b. Phospholipid structure

Steroids Steroids have a backbone of four fused carbon rings Examples: Cholesterol, Testosterone, Estrogen Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. OH OH CH3 CH3 CH3 O HO Figure 2.22 a. Testosterone b. Estrogen

2.7 Proteins Proteins are polymers composed of amino acid monomers Amino acids Amino group (-NH2) Acidic group (-COOH) R group varies Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group acidic group H H H R O OH H N C C N C C OH H O R H Figure 2.24 amino acid amino acid

Figure 2.23 H O H3N+ C C CH3 O– H O H3N+ C C O– CH H3C CH3 H O H3N+ C Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H O H3N+ C C CH3 O– H O H3N+ C C O– CH H3C CH3 H O H3N+ C C CH2 O– SH H O H3N+ C C O– CH2 Figure 2.23

2.7 Proteins Proteins perform many functions Structural proteins give support (keratin, collagen) Enzymes speed up chemical reactions Hormones are chemical messengers Actin and myosin move cells and muscles Some proteins transport molecules in blood Antibodies protect cells Channels allow substances to cross membranes

Peptides Peptides A polypeptide is a single chain of amino acids. A peptide bond joins two amino acids. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. amino group acidic group peptide bond H H H H O O H R R OH OH dehydration reaction H N C C N C C H N C C N C C H2O OH H O O R H hydrolysis reaction R H H amino acid amino acid water dipeptide Figure 2.24

Figure 2.25 H3N+ amino acid peptide bond COO– C CH hydrogen bond C N R Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H3N+ amino acid peptide bond COO– C CH hydrogen bond C N R CH C N hydrogen bond CH R R C N CH C N CH R N R C CH C N CH R C N R CH  (alpha) helix (beta) pleated sheet Figure 2.25

Figure 2.25  (alpha) helix (beta) pleated sheet disulfide bond Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  (alpha) helix (beta) pleated sheet disulfide bond Figure 2.25

Copyright © The McGraw-Hill Companies, Inc Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H3N+ amino acid peptide bond COO– C CH C hydrogen bond N CH R C N CH R hydrogen bond R C N CH C N CH R N R C C CH CH N R C N R CH  (alpha) helix (beta) pleated sheet disulfide bond Figure 2.25

2.8 Nucleic Acids The two types of nucleic acids are DNA (deoxyribonucleic acid) Stores genetic information in the cell and in the organism DNA replicates to transmit its information when a cell divides or organism reproduces RNA (ribonucleic acid)

Structure of DNA and RNA Both DNA and RNA are polymers of nucleotides Every nucleotide is a molecular complex of Phosphate Pentose sugar (ribose or deoxyribose) Nitrogen-containing base DNA contains: Adenine (A), Thymine (T), Guanine (G) and Cytosine (C) In RNA, uracil (U) replaces thymine

O nitrogen- containing base phosphate C –O P O C O– 5' O 4' S 1' 3' 2' Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. O nitrogen- containing base phosphate C –O P O C O– 5' O 4' S 1' 3' 2' pentose sugar Figure 2.26 Nucleotide structure

Structure of DNA and RNA The nucleotides form a linear molecule called a strand. DNA is a double helix of two strands. The two strands are held together by hydrogen bonds. Rungs of the ladder are formed by complementary paired bases. Adenine (A) always pairs with thymine (T) Cytosine (C) always pairs with guanine (G)

a: © Radius Images/Alamy RF Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. S S A T P P S C S G P P A G T T T A C S C one nucleotide S A G P P C G S S P P S S A T P P a. b. c. a: © Radius Images/Alamy RF

Structure of DNA and RNA RNA is single-stranded. Several types are involved in carrying information from DNA to make proteins. ATP (Adenosine Triphosphate) ATP is a high-energy molecule. ATP undergoes hydrolysis and energy is released. ATP is the energy “currency” of the cell.

Last two phosphate bonds are unstable and easily broken. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O + + P P P P P P energy Last two phosphate bonds are unstable and easily broken. Hydrolization forms ADP (adenosine diphosphate). ATP can be rebuilt. Add P to ADP to make ATP Figure 2.28