Basic Cell Chemistry

Chapter Goals After studying this chapter, students should be able to describe the structure of an atom and define the terms atomic mass, atomic number, and ion. explain how covalent bonds are formed and distinguish between nonpolar and polar covalent bonds. describe the structure of an ion and explain how ionic bonds are formed. describe the nature of hydrogen bonds and explain their significance. describe the structure of a water molecule and explain why some compounds are hydrophilic and others are hydrophobic. define the terms acid and base and explain the meaning of the pH scale. explain how the pH of the blood is stabilized by bicarbonate buffer, and define the terms acidosis and alkalosis. describe the different types of carbohydrates and give examples of each type.

Chapter Goals (cont’d) After studying this chapter, students should be able to describe the mechanisms and significance of dehydration synthesis and hydrolysis reactions and explain their significance. state the common characteristics of lipids and describe the different categories of lipids. describe how peptide bonds are formed and the different orders of protein structure. list some of the functions of proteins and explain why proteins provide specificity in their functions. tell what enzymes are and how they work. understand the concept of optima understand basic enzyme kinetics

Basic Cell Chemistry Matter and elements Atomic structure Ions

Atomic Structure B-1

B-2 Ionic Bond Atomic # = 11 Atomic Mass = 23 Atomic # = 17 Atomic Mass = 34

B-3 Crystalline Lattice

B-4 Covalent Bond

2.8

2.9

B-5 Polar Molecule

B-6 Hydrogen Bond

2.6

Acids, Bases and Salts Acid - proton donor –pH = -log[H + ] –Scale , with 7 being neutral Base - proton acceptor Salts - crystalline solids produced by neutralization reactions. Buffers resist change in pH

Biomolecules Functional Groups Carbohydrates Lipids Nucleic Acids Proteins

2.10

2.11

Carbohydrates (CH 2 O) Monosaccharides –Triose –Tetrose –Pentose –Hexose Disaccharides Oligosaccharides Polysaccharides

B-7 Hexose Monosaccharide (glucose)

2.16

B-8 Polysaccharide (glycogen)

Lipids Glycerides (Mono, Di, Tri) Phospholipids Steroids Prostaglandins

B-9 Triglyceride

2.19 Phospholipid and Sphingolipids

B-11 Steroid

B-12 Steroid Examples

2.22

Proteins Basic building blocks (amino acids) Primary Structure Secondary Structure Tertiary Structure Quaternary Structure

Amino Acid B-13

Peptide Bond B-14

Primary Structure B-15

Levels of Structure B-16

Side Chain Interactions B-17

Nucleic Acids Building Blocks (Nucleotides) DNA RNA

Structure of Nucleotide Triphosphate B-18

Enzymes Specific organic catalysts Cannot drive reactions Direction determined by LeChatlier Principle. E + S ES E + P E = enzyme; S = substrate; P = product

4.1a

4.1b

4.2

Induced Fit Model Binding of substrate causes the enzyme to change shape such that the enzyme fits around the substrate.

4.3

4.4

4.5

4.6

4.8

4.9

4.10

Chapter Summary Atoms, Ions, and Chemical Bonds Carbohydrates and Lipids Proteins

Atoms, Ions, and Chemical Bonds I. Covalent bonds are formed by atoms that share electrons. They are the strongest type of chemical bond. A. Electrons are equally shared in nonpolar covalent bonds and unequally shared in polar covalent bonds. B. Atoms of oxygen, nitrogen, and phosphorus strongly attract electrons and become electrically negative compared to the other atoms sharing electrons with them.

Atoms, Ions, and Chemical Bonds II. Ionic bonds are formed by atoms that transfer electrons; these weak bonds join atoms together in an ionic compound. A. If one atom in this compound takes the electron from another atom, it gains a net negative charge and the other atom becomes positively charged. B. Ionic bonds easily break when the ionic compound is dissolved in water. Dissociation of the ionic compound yields charged atoms called ions.

Atoms, Ions, and Chemical Bonds III. When hydrogen is bonded to an electronegative atom, it gains a slight positive charge and is weakly attracted to another electronegative atom. This weak attraction is a hydrogen bond.

Atoms, Ions, and Chemical Bonds IV. Acids donate hydrogen ions to solution, whereas bases lower the hydrogen ion concentration on a solution. A. The pH scale is a negative function of the logarithm of the hydrogen ion concentration. B. In a neutral solution the concentration of H + is equal to the concentration of OH -, and the pH is 7. C. Acids raise the H + concentration and thus lower the pH below 7; bases lower the H + concentration and thus raise the pH above 7.

Atoms, Ions, and Chemical Bonds V. Organic molecules contain atoms of carbon joined together by covalent bonds; atoms of nitrogen, oxygen, phosphorus, or sulfur may be present as specific functional groups in the organic molecule.

Carbohydrates and Lipids I. Carbohydrates contain carbon, hydrogen, and oxygen, usually in a ratio of 1:2:1. A. Carbohydrates consist of simple sugars (monosaccharides), disaccharides, and polysaccharides (such as glycogen). B. Covalent bonds between monosaccharides are formed by dehydration synthesis, or condensation. Bonds are broken by hydrolysis reactions.

Carbohydrates and Lipids II. Lipids are organic molecules that are insoluble in polar solvents such as water. A. Triglycerides (fat and oil) consist of three fatty acid molecules joined to a molecule of glycerol. B. Ketone bodies are smaller derivations of fatty acids. C. Phospholipids (such as lecithin) are phosphate- containing lipids that have a hydrophilic polar group. The rest of the molecule is hydrophobic. D. Steroids (including the hormones of the adrenal cortex and gonads) are lipids with a characteristic five-ring structure. E. Prostaglandins are a family of cyclic fatty acids, which serve a variety of regulatory functions

Proteins I. Proteins are composed of long chains of amino acids bound together by covalent peptide bonds. A. Each amino acid contains an amino group, a carboxyl group, and a functional group. Differences in the functional groups give each of the more than twenty different amino acids an individual identity. B. The polypeptide chain may be twisted into a helix (secondary structure) and bent and folded to form the tertiary structure of the protein. C. Proteins that are composed of two or more polypeptide chains are said to have a quaternary structure. D. Proteins may be combined with carbohydrates, lipids, or other molecules. E. Because of their great variety of possible structures, proteins serve a wider variety of specific functions than any other type of molecule.

Enzymes I. Enzymes are specific organic catalysts A. Most enzymes are proteins. B. Enzymes have a unique 3-D structure that enables them to bind to a specific substrate. C. Enzymes speed up chemical reactions by lowering activation energy. D. Since enzymes physically join to their substrate, they can become saturated. E. The structure of enzymes is encoded in DNA, so a mutation can affect enzyme structure.