Chapter 2: The Chemical Level of Organization

Introduction to Chemistry Matter is made up of atoms Atoms join together to form chemicals with different characteristics Chemical characteristics determine physiology at the molecular and cellular level

Atomic Particles Proton: Neutron: Electron: positive, 1 mass unit neutral, 1 mass unit Electron: negative, low mass

Particles and Mass Atomic number: Mass number: Atomic weight: number of protons Mass number: number of protons plus neutrons Atomic weight: exact mass of all particles (daltons)

Isotopes 2 or more elements with equal numbers of protons but different numbers of neutrons Electron shell p+ p + n e Hydrogen-1 (electron-shell model) (b) Hydrogen-2 deuterium (c) Hydrogen-3, tritium

Elements in the Human Body Table 2–1

How do atoms form molecules and compounds?

Molecules and Compounds atoms joined by strong bonds Compounds: atoms joined by strong or weak bonds

Chemical Bonds Ionic bonds: Covalent bonds: Hydrogen bonds: attraction between cations (+) and anions (-) Covalent bonds: strong electron bonds Non polar covalent bonds: equal sharing of electrons Polar covalent bonds: unequal sharing of electrons Hydrogen bonds: weak polar bonds

Ionic Bonds Are atoms with positive or negative charge Figure 2–3a

Electron-Shell Model and Covalent Bond Formed between atoms that share electrons Hydrogen (H2) Oxygen (O2) Carbon Dioxide (CO2) Nitric Oxide (NO) Molecule Electron-Shell Model and Structural Formula H–H O=O N=O O=C=O Free Radicals: Ion or molecule that contain unpaired electrons in the outermost shell. - Extremely Reactive -Typically enter into destructive reactions -Damage/destroy vital compounds

Hydrogen Bonds Attractive force between polar covalent molecules Weak force that holds molecules together Hydrogen bonds between H2O molecules cause surface tension Figure 2–6

How is it possible for two samples of hydrogen to contain the same number of atoms, yet have different weights? A. One sample has more bonds. B. One sample contains fewer electrons, decreasing weight. C. One sample contains more of hydrogen’s heavier isotope(s). D. One sample includes more protons, increasing weight.

Both oxygen and neon are gases at room temperature Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why? A. Neon has 8 electrons in its valence shell, oxygen has only 6. B. Neon cannot undergo bonding due to its polarity. C. Neon is exergonic. D. Neon’s molecular weight is too low to allow bonding.

Both oxygen and neon are gases at room temperature Both oxygen and neon are gases at room temperature. Oxygen combines readily with other elements, but neon does not. Why? A. Neon has 8 electrons in its valence shell, oxygen has only 6. B. Neon cannot undergo bonding due to its polarity. C. Neon is exergonic. D. Neon’s molecular weight is too low to allow bonding.

Which kind of bond holds atoms in a water molecule together Which kind of bond holds atoms in a water molecule together? What attracts water molecules to one another? A. polar covalent bonds; hydrogen bonds B. ionic bonds; charge interactions C. hydrogen bonds; charge interactions D. covalent bonds; hydrogen bonds

Why are chemical reactions important to physiology?

Energy Energy: Work: the capacity to do work a change in mass or distance

Forms of Energy Kinetic energy: Potential energy: Chemical energy: energy of motion Potential energy: stored energy Chemical energy: potential energy stored in chemical bonds When energy is exchanged, heat is produced - cells cannot capture it or use it for work

Break Down, Build Up Decomposition reaction (catabolism): AB A + B Synthesis reaction (anabolism): A + B AB Exchange reaction (reversible): AB + CD AD + CB If Water is Involved: Hydrolysis: A—B—C—D—E + H2O A—B—C—H + HO—D—E Dehydration synthesis (condensation): A—B—C—H + HO—D—E A—B—C—D—E + H2O

KEY CONCEPT Reversible reactions seek equilibrium, balancing opposing reaction rates Add or remove reactants: reaction rates adjust to reach a new equilibrium

How do enzymes control metabolism?

Activation Energy Chemical reactions in cells cannot start without help Activation energy gets a reaction started Figure 2–7

Materials in Reactions Reactants: materials going into a reaction Products: materials coming out of a reaction Enzymes: proteins that lower the activation energy of a reaction

Energy In, Energy Out Exergonic reactions: Endergonic reactions: produce more energy than they use Heat will be the by-product Endergonic reactions: use more energy than they produce Most chemical reactions that sustain life cannot occur unless the right enzymes are present

How would you classify this reaction? In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy. How would you classify this reaction? A. endergonic B. exergonic C. decomposition D. B and C

How would you classify this reaction? In cells, glucose, a six-carbon molecule, is converted into two three-carbon molecules by a reaction that releases energy. How would you classify this reaction? A. endergonic B. exergonic C. decomposition D. B and C

Why are enzymes needed in our cells? A. to promote chemical reactions B. for chemical reactions to proceed under conditions compatible with life C. to lower activation energy requirements D. all of the above

What is the difference between organic and inorganic compounds?

Organic and Inorganic Molecules molecules based on carbon and hydrogen Inorganic: molecules not based on carbon and hydrogen

Essential Molecules Nutrients: Metabolites: essential molecules obtained from food Metabolites: molecules made or broken down in the body

Why is water so important to life?

Properties of Water Solubility: Reactivity: High heat capacity: water’s ability to dissolve a solute in a solvent to make a solution Reactivity: most body chemistry uses or occurs in water High heat capacity: water’s ability to absorb and retain heat Lubrication: to moisten and reduce friction Water is the key structural and functional component of cells and their control mechanisms, the nucleic acids

Aqueous Solutions Polar water molecules form hydration spheres around ions and small polar molecules to keep them in solution Figure 2–8

Electrolytes Inorganic ions: conduct electricity in solution Electrolyte imbalance seriously disturbs vital body functions

Molecules and Water Hydrophilic: Hydrophobic: hydro = water, philos = loving reacts with water Hydrophobic: phobos = fear does not react with water

Solutions Suspension: Concentration: a solution in which particles settle (sediment) Concentration: the amount of solute in a solvent (mol/L, mg/mL)

What is pH and why do we need buffers?

pH: Neutral, Acid, or Base? the concentration of hydrogen ions (H+) in a solution Neutral pH: a balance of H+ and OH— pure water = 7.0 Acid (acidic): pH lower than 7.0 high H+ concentration, low OH— concentration Base (basic): pH higher than 7.0 low H+ concentration, high OH— concentration

pH Scale Has an inverse relationship with H+ concentration: more H+ ions mean lower pH, less H+ ions mean higher pH Figure 2–9

KEY CONCEPT pH of body fluids measures free H+ ions in solution Excess H+ ions (low pH): Acidosis damages cells and tissues alters proteins interferes with normal physiological functions Excess OH— ions (high pH): Alkalosis Uncontrollable and sustained skeletal muscle contractions

Controlling pH Salts: Buffers: positive or negative ions in solution contain no H+ or OH— (NaCl) Buffers: weak acid/salt compounds neutralizes either strong acid or strong base

Why does a solution of table salt conduct electricity, but a sugar solution does not? A. Electrical conductivity requires ions. B. Sugar forms a colloid, salt forms a suspension. C. Electricity is absorbed by glucose molecules. D. Table salt is hydrophobic, sugar is hydrophilic.

How does an antacid help decrease stomach discomfort? A. by reducing buffering capacity of the stomach B. by decreasing pH of stomach contents C. by reacting a weak acid with a stronger one D. by neutralizing acid using a weak base

What kinds of organic compounds are there, and how do they work?

Functional Groups of Organic Compounds Molecular groups which allow molecules to interact with other molecules Table 2–4

Carbohydrates Consist of C:H:O in 1:2:1 ratio 1. Monosaccharides: simple sugars with 3 to 7 carbon atoms (glucose) Glucose: important metabolic fuel 2. Disaccharides: 2 simple sugars condensed by dehydration synthesis (sucrose)

Simple Sugars Structural Formula: Straight-chain form Ring from 3-D Isomers: Glucose vs. Fructose: - Same chemical formula but different shape Figure 2–10

Polysaccharides Chains of many simple sugars (glycogen) Formation: Dehydration synthesis Breakdown: Hydrolysis synthesis Glycogen: made and stored in muscle cells Figure 2–12

Carbohydrate Functions Polysaccharides Glycogen: made and stored in muscle cells Cellulose: structural component of plants -Ruminant Animals: Cattle, sheep, and deer Table 2–5

The Ruminant Stomach Ruminant stomach is polygastric: four compartments -Rumen -Reticulum -Abomasum -Omasum

Rumen Occupies 80% of the stomach Muscular Pillar Contract to mix feed Digest starch and fibers Microbes produce VFA’s Lined with Papillae pH of 5.8-7.0 Provide a suitable environment for bacteria and protozoa

KEY CONCEPT Carbohydrates are quick energy sources and components of membranes Lipids have many functions, including membrane structure and energy storage Provides 2x more energy then carbohydrates

Lipids Mainly hydrophobic molecules such as fats, oils, and waxes Made mostly of carbon and hydrogen atoms (1:2), and some oxygen Less oxygen then carbon

Classes of Lipids Fatty acids Eicosanoids Glycerides Steroids Phospholipids and glycolipids

Fatty Acids Carboxyl group -COOH Hydrocarbon tail: Hydrophilic Hydrocarbon tail: Hydrophobic Longer tail = lower solubility Saturated vs. Unsaturated Saturated: solid at room temp. Cause solid plaques in arteries Unsaturated: liquid at room temp. Healthier Figure 2–13

Eicosanoids Used for cellular communication Never burned for energy 1. Leukotrienes: active in immune system Used by cells to signal injury 2. Prostaglandins: local hormones Used for cell-to-cell signaling to coordinate events

Steroids 4 carbon ring with attached carbon chains Not burned for energy Figure 2–16

Types of Steroids Cholesterol: Estrogens and testosterone: cell membrane formation and maintenance, cell division, and osmotic stability Estrogens and testosterone: Regulation of sexual function Corticosteroids and calcitrol: Tissue metabolism and mineral balance Bile salts: Processing of dietary fats

Glycerides Glycerides: are the fatty acids attached to a glycerol molecule Triglyceride: are the 3 fatty-acid tails, fat storage molecule Fat Deposits are Important Energy Storage Insulation Mechanical Protection -Knees and Eye Sockets Figure 2–15

Phospholipids Vs. Glycolipids Combination Lipids Cell Membranes are Composed of these lipids Hydrophilic Diglyceride Hydrophobic Figure 2–17a, b

Phospholipids Vs. Glycolipids Combination Lipids Spontaneous formation of Micelle Figure 2–17c

5 Lipid Types Table 2–6

A food contains organic molecules with the elements C, H, and O in a ratio of 1:2:1. What class of compounds do these molecules belong to, and what are their major functions in the body? A. lipids; energy source B. proteins; support and movement C. nucleic acids; determining inherited characteristics D. carbohydrates; energy source

When two monosaccharides undergo a dehydration synthesis reaction, which type of molecule is formed? A. polypeptide B. disaccharide C. eichosanoid D. polysaccharide

Which kind of lipid would be found in a sample of fatty tissue taken from beneath the skin? A. eichosanoid B. steroid C. triglyceride D. phospholipid

Which lipids would you find in human cell membranes? A. cholesterol B. glycolipids C. phospholipids D. all of the above

Protein Structure Proteins are the most abundant and important organic molecules Basic elements: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) Basic building blocks: 20 amino acids

Protein Functions 7 major protein functions: support: structural proteins movement: contractile proteins transport: transport proteins buffering: regulation of pH metabolic regulation: enzymes coordination and control: hormones defense: antibodies

Proteins Proteins: control anatomical structure and physiological function determine cell shape and tissue properties perform almost all cell functions

Amino Acid Structure central carbon hydrogen amino group (—NH2) carboxylic acid group (—COOH) variable side chain or R group Figure 2-18

Peptide Bond A dehydration synthesis between: amino group of 1 amino acid and the carboxylic acid group of another amino acid producing a peptide

Primary Structure Polypeptide: Linear sequence of amino acids How many amino acids were bound together What order they are bound Figure 2–20a

Secondary Structure Hydrogen bonds form spirals or pleats Figure 2–20b

Tertiary Structure Secondary structure folds into a unique shape Global coiling or folding due to R group interaction Figure 2–20c

Quaternary Structure Final protein shape: Fibrous proteins: several tertiary structures together Fibrous proteins: - structural sheets Globular proteins: - soluble spheres with active functions Figure 2–20d

Shape and Function Protein function is based on shape Shape is based on sequence of amino acids Denaturation: loss of shape and function due to heat or pH

Enzymes Enzymes are catalysts: proteins that lower the activation energy of a chemical reaction are not changed or used up in the reaction

How Enzymes Work Substrates: reactants in enzymatic reactions Active site: location on an enzyme that fits a particular substrate Figure 2–21

Enzyme Helpers Cofactor: Coenzyme: Isozymes: an ion or molecule that binds to an enzyme before substrates can bind Coenzyme: nonprotein organic cofactors (vitamins) Isozymes: 2 enzymes that can catalyze the same reaction

Enzyme Characteristics Specificity: one enzyme catalyzes one reaction Saturation limits: an enzyme’s maximum work rate Regulation: the ability to turn off and on

Conjugated Protein Glycoproteins: Proteoglycans: large protein + small carbohydrate includes enzymes, antibodies, hormones, and mucus production Proteoglycans: large polysaccharides + polypeptides promote viscosity

Proteins are chains of which small organic molecules? A. saccharides B. fatty acids C. amino acids D. nucleic acids

Which level of protein structure would be affected by an agent that breaks hydrogen bonds? A. the primary level of protein structure B. the secondary level of protein structure C. the tertiary level of protein structure D. the protein structure would NOT be affected by this agent

Why does boiling a protein affect its structural and functional properties? A. Heat denatures the protein, causing unfolding. B. Heat causes the formation of additional quaternary structure. C. Heating rearranges the primary structure of the protein. D. Heat alters the radical groups on the amino acids.

Why does boiling a protein affect its structural and functional properties? A. Heat denatures the protein, causing unfolding. B. Heat causes the formation of additional quaternary structure. C. Heating rearranges the primary structure of the protein. D. Heat alters the radical groups on the amino acids.

How might a change in an enzyme’s active site affect its functions? A. increased activity due to a better fit with the substrate B. decreased activity due to a poor substrate fit C. inhibited activity due to no substrate fit D. all of the above

Nucleic Acids C, H, O, N, and P Large organic molecules, found in the nucleus, which store and process information at the molecular level DNA – deoxyribonucleic acid RNA – ribonucleic acid

DNA and RNA DNA Determines inherited characteristics Directs protein synthesis Controls enzyme production Controls metabolism RNA Codes intermediate steps in protein synthesis

KEY CONCEPT DNA in the cell nucleus contains the information needed to construct all of the proteins in the body

Nucleotides Are the building blocks of DNA Have 3 molecular parts: sugar (deoxyribose) phosphate group nitrogenous base (A, G, T, C)

The Bases Figure 2–22b, c

Complementary Bases Purines pair with pyrimidines: DNA: RNA: adenine (A) and thymine (T) cytosine (C) and guanine (G) RNA: uracil (U) replaces thymine (T)

RNA and DNA RNA: DNA: a single strand a double helix joined at bases by hydrogen bonds

Protein Synthesis: Three forms of RNA messenger RNA (mRNA) Protein blueprint or instructions transfer RNA (tRNA) Carry amino acids to the place where proteins are being synthesized ribosomal RNA (rRNA) Forms the site of protein synthesis in the cell Factory = ribosomes

High-Energy Compounds: ADP and ATP - Assembled using RNA Nucleotides - Bonds are broken easily by cells to release energy as needed During digestion and cellular respiration: energy from food is transferred to high energy compounds for quick and easy access.

ADP to ATP: Phosphorylation ADP vs. ATP: adenosine diphosphate (ADP): 2 phosphate groups (di = 2) adenosine triphosphate (ATP): 3 phosphate groups (tri = 3) Adding a phosphate group to ADP with a high-energy bound to form the high-energy compound ATP ATPase: the enzyme that catalyzes phophorylation

The Energy Molecule Chemical energy stored in phosphate bonds Figure 2–24

A large organic molecule composed of the sugar ribose, nitrogenous bases, and phosphate groups is which kind of nucleic acid? A. DNA B. ATP C. tRNA D. RNA

What molecule is produced by the phosphorylation of ADP? A. ATPase B. ATP C. Adenosine Diphosphate D. Uridine Triphosphate

Compounds Important to Physiology Table 2–8

SUMMARY Atoms, molecules, and chemical bonds control cellular physiology Metabolism and energy work within the cell Importance of organic and inorganic nutrients and metabolites

SUMMARY Role of water and solubility in metabolism and cell structure Chemistry of acids and bases, pH and buffers Structure and function of carbohydrates, lipids, proteins, and nucleic acids AnnMarie Armenti, MS SCCC BIO 130